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Sample records for optimal basis set

  1. 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.

  2. Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets

    SciTech Connect

    Rossi, Tuomas P. Sakko, Arto; Puska, Martti J.; Lehtola, Susi; Nieminen, Risto M.

    2015-03-07

    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 that 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.

  3. Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets.

    PubMed

    Rossi, Tuomas P; Lehtola, Susi; Sakko, Arto; Puska, Martti J; Nieminen, Risto M

    2015-03-07

    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 that 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.

  4. Segmented contracted basis sets optimized for nuclear magnetic shielding.

    PubMed

    Jensen, Frank

    2015-01-13

    A family of segmented contracted basis sets is proposed, denoted pcSseg-n, which are optimized for calculating nuclear magnetic shielding constants. For the elements H-Ar, these are computationally more efficient than the previously proposed general contracted pcS-n basis sets, and the new basis sets are extended to also include the elements K-Kr. The pcSseg-n basis sets are optimized at the density functional level of theory, but it has been shown previously that these property-optimized basis sets are also suitable for calculating shielding constants with correlated wave function methods. The pcSseg-n basis sets are available in qualities ranging from (unpolarized) double-ζ to pentuple-ζ quality and should be suitable for both routine and benchmark calculations of nuclear magnetic shielding constants. The ability to rigorously separate basis set and method errors should aid in developing more accurate methods.

  5. Property-optimized gaussian basis sets for molecular response calculations.

    PubMed

    Rappoport, Dmitrij; Furche, Filipp

    2010-10-07

    With recent advances in electronic structure methods, first-principles calculations of electronic response properties, such as linear and nonlinear polarizabilities, have become possible for molecules with more than 100 atoms. Basis set incompleteness is typically the main source of error in such calculations since traditional diffuse augmented basis sets are too costly to use or suffer from near linear dependence. To address this problem, we construct the first comprehensive set of property-optimized augmented basis sets for elements H-Rn except lanthanides. The new basis sets build on the Karlsruhe segmented contracted basis sets of split-valence to quadruple-zeta valence quality and add a small number of moderately diffuse basis functions. The exponents are determined variationally by maximization of atomic Hartree-Fock polarizabilities using analytical derivative methods. The performance of the resulting basis sets is assessed using a set of 313 molecular static Hartree-Fock polarizabilities. The mean absolute basis set errors are 3.6%, 1.1%, and 0.3% for property-optimized basis sets of split-valence, triple-zeta, and quadruple-zeta valence quality, respectively. Density functional and second-order Møller-Plesset polarizabilities show similar basis set convergence. We demonstrate the efficiency of our basis sets by computing static polarizabilities of icosahedral fullerenes up to C(720) using hybrid density functional theory.

  6. Optimized Basis Sets for the Environment in the Domain-Specific Basis Set Approach of the Incremental Scheme.

    PubMed

    Anacker, Tony; Hill, J Grant; Friedrich, Joachim

    2016-04-21

    Minimal basis sets, denoted DSBSenv, based on the segmented basis sets of Ahlrichs and co-workers have been developed for use as environmental basis sets for the domain-specific basis set (DSBS) incremental scheme with the aim of decreasing the CPU requirements of the incremental scheme. The use of these minimal basis sets within explicitly correlated (F12) methods has been enabled by the optimization of matching auxiliary basis sets for use in density fitting of two-electron integrals and resolution of the identity. The accuracy of these auxiliary sets has been validated by calculations on a test set containing small- to medium-sized molecules. The errors due to density fitting are about 2-4 orders of magnitude smaller than the basis set incompleteness error of the DSBSenv orbital basis sets. Additional reductions in computational cost have been tested with the reduced DSBSenv basis sets, in which the highest angular momentum functions of the DSBSenv auxiliary basis sets have been removed. The optimized and reduced basis sets are used in the framework of the domain-specific basis set of the incremental scheme to decrease the computation time without significant loss of accuracy. The computation times and accuracy of the previously used environmental basis and that optimized in this work have been validated with a test set of medium- to large-sized systems. The optimized and reduced DSBSenv basis sets decrease the CPU time by about 15.4% and 19.4% compared with the old environmental basis and retain the accuracy in the absolute energy with standard deviations of 0.99 and 1.06 kJ/mol, respectively.

  7. Density functional theory optimized basis sets for gradient corrected functionals: 3d transition metal systems.

    PubMed

    Calaminici, Patrizia; Janetzko, Florian; Köster, Andreas M; Mejia-Olvera, Roberto; Zuniga-Gutierrez, Bernardo

    2007-01-28

    Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.

  8. Contraction of completeness-optimized basis sets: application to ground-state electron momentum densities.

    PubMed

    Lehtola, Susi; Manninen, Pekka; Hakala, Mikko; Hämäläinen, Keijo

    2013-01-28

    Completeness-optimization is a novel method for the formation of one-electron basis sets. Contrary to conventional methods of basis set generation that optimize the basis set with respect to ground-state energy, completeness-optimization is a completely general, black-box method that can be used to form cost-effective basis sets for any wanted property at any level of theory. In our recent work [J. Lehtola, P. Manninen, M. Hakala, and K. Hämäläinen, J. Chem. Phys. 137, 104105 (2012)] we applied the completeness-optimization approach to forming primitive basis sets tuned for calculations of the electron momentum density at the Hartree-Fock (HF) level of theory. The current work extends the discussion to contracted basis sets and to the post-HF level of theory. Contractions are found to yield significant reductions in the amount of functions without compromising the accuracy. We suggest polarization-consistent and correlation-consistent basis sets for the first three rows of the periodic table, which are completeness-optimized for electron momentum density calculations.

  9. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

    SciTech Connect

    Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.

    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 wave 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.

  10. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

    NASA Astrophysics Data System (ADS)

    Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.

    2015-12-01

    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 wave 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.

  11. Optimal composition of atomic orbital basis sets for recovering static correlation energies.

    PubMed

    Wallace, Andrew J; Crittenden, Deborah L

    2014-03-20

    Static correlation energies (Estat) are calculated in a range of basis sets for a chemically diverse collection of atoms and molecules. The reliability of a basis set in capturing Estat is assessed according to the following: mean and maximum absolute deviations from near-exact Estat estimates, monotonic convergence to the complete basis set limit, and ability to capture Estat accurately independent of changes in geometry, molecular size, and electronic configuration. Within the polarization and correlation-consistent basis set series, triple-ζ basis sets are the smallest that can reliably capture Estat. The cc-pVTZ basis set performs particularly well, recovering Estat to chemical accuracy for all atoms and molecules in our data set. A series of customized basis sets are constructed by stripping polarization functions from, and swapping polarization functions among, existing basis sets. Basis sets without polarization functions are incapable of accurately recovering Estat. Basis sets with a near-complete set of s, p, and d functions can approach chemical accuracy in maximum absolute error. However, this may be achieved at lower computational cost by using a well balanced triple-ζ basis set including f functions, along with a smaller number of s, p, and d functions. Recommended basis sets for calculating Estat with increasing accuracy at increasing computational cost are 6-311G(2d,2p), cc-pVTZ, and cc-pVQZ stripped of g functions.

  12. Complete Basis Set Model Chemistries

    NASA Astrophysics Data System (ADS)

    Ochterski, Joseph Wallace

    1994-01-01

    The major source of error in most ab initio calculations of molecular energies is the truncation of the one-electron basis set. Extrapolation to the complete basis set second -order (CBS2) limit using the N^{-1 } asymptotic convergence of N-configuration pair natural orbital (PNO) expansions can be combined with the use of relatively small basis sets for the higher-order correlation energy to develop cost effective computational models. Following this strategy, four new computational models denoted CBS-4, CBS-q, CBS-Q, and CBS-QCI/APNO are introduced. The mean absolute deviations (MAD) from experiment for the 125 energies of the G2 test set are 2.0, 1.7, 1.0 and 0.5 kcal/mol, respectively. The error distributions for all six models are indistinguishable from Gaussian distribution functions. Calculations on the cyclopropenyl radical and cyclopropenylidene provide new dissociation energies which are in accord with an interpretation of the thermochemistry emphasizing aromaticity. Several levels of theory are examined as candidates for the routine calculation of molecular geometries. The very simple UHF/3-21G* model gives bond lengths to an accuracy of +/-0.027 A compared with experiment for a test set of 69 small molecules. The commonly used MP2/6-31G* model (RMS error 0.025 A) offers virtually no improvement and use of the considerably more expensive QCISD calculations with the same basis set provides only a modest reduction to 0.020 A. However, spin projected MP3 calculations with a modified basis set including f -functions on Si, P, S, and Cl, reduce the RMS error to 0.010 A. This PMP3/6-31Gdf* model is recommended as a general scheme of geometry optimization for small molecules. The equilibrium structure and binding energy of the water dimer have been determined for several levels of ab initio theory. The basis set convergence of the SCF energy, the intramolecular and intermolecular MP2 energy, and higher-order effects, are examined separately and realistic error

  13. Assessment of density functional theory optimized basis sets for gradient corrected functionals to transition metal systems: the case of small Nin (n

    PubMed

    López Arvizu, Gregorio; Calaminici, Patrizia

    2007-05-21

    Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (nbasis sets optimized for generalized gradient approximation (GGA) as well as an all-electron basis set optimized for the local density approximation were employed. For both neutral and charged systems, several isomers and different multiplicities were studied in order to determine the lowest energy structures. A vibrational analysis was performed in order to characterize these isomers. Structural parameters, harmonic frequencies, binding energies, ionization potentials, and electron affinities are reported. This work shows that the employed GGA basis sets for the nickel atom are important for the correct prediction of the ground state structures of small nickel clusters and that the structural assignment of these systems can be performed, with a good resolution, over the ionization potential.

  14. Unifying General and Segmented Contracted Basis Sets. Segmented Polarization Consistent Basis Sets.

    PubMed

    Jensen, Frank

    2014-03-11

    We propose a method, denoted P-orthogonalization, for converting a general contracted basis set to a computationally more efficient segmented contracted basis set, while inheriting the full accuracy of the general contracted basis set. The procedure can be used for any general contracted basis set to remove the redundancies between general contracted functions in terms of primitive functions. The P-orthogonalization procedure is used to construct a segmented contracted version of the polarization consistent basis sets, which are optimized for density functional theory calculations. Benchmark calculations show that the new pcs-n basis sets provide uniform error control of the basis set incompleteness for molecular systems composed of atoms from the first three rows in the periodic table (H-Kr) and for different exchange-correlation functionals. The basis set errors at a given zeta quality level are lower than other existing basis sets, and the pcs-n basis sets are furthermore shown to be among the computationally most efficient. The pcs-n basis sets are available in qualities ranging from (unpolarized) double-zeta to pentuple zeta quality and should therefore be well suited for both routine and benchmark calculations using density functional theory methods in general.

  15. BASIS Set Exchange (BSE): Chemistry Basis Sets from the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Basis Set Library

    DOE Data Explorer

    Feller, D; Schuchardt, Karen L.; Didier, Brett T.; Elsethagen, Todd; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared; Li, Jun

    The Basis Set Exchange (BSE) provides a web-based user interface for downloading and uploading Gaussian-type (GTO) basis sets, including effective core potentials (ECPs), from the EMSL Basis Set Library. It provides an improved user interface and capabilities over its predecessor, the EMSL Basis Set Order Form, for exploring the contents of the EMSL Basis Set Library. The popular Basis Set Order Form and underlying Basis Set Library were originally developed by Dr. David Feller and have been available from the EMSL webpages since 1994. BSE not only allows downloading of the more than 500 Basis sets in various formats; it allows users to annotate existing sets and to upload new sets. (Specialized Interface)

  16. Random-phase approximation correlation energies from Lanczos chains and an optimal basis set: theory and applications to the benzene dimer.

    PubMed

    Rocca, Dario

    2014-05-14

    A new ab initio approach is introduced to compute the correlation energy within the adiabatic connection fluctuation dissipation theorem in the random phase approximation. First, an optimally small basis set to represent the response functions is obtained by diagonalizing an approximate dielectric matrix containing the kinetic energy contribution only. Then, the Lanczos algorithm is used to compute the full dynamical dielectric matrix and the correlation energy. The convergence issues with respect to the number of empty states or the dimension of the basis set are avoided and the dynamical effects are easily kept into account. To demonstrate the accuracy and efficiency of this approach the binding curves for three different configurations of the benzene dimer are computed: T-shaped, sandwich, and slipped parallel.

  17. Variationally optimized basis orbitals for biological molecules

    NASA Astrophysics Data System (ADS)

    Ozaki, T.; Kino, H.

    2004-12-01

    Numerical atomic basis orbitals are variationally optimized for biological molecules such as proteins, polysaccharides, and deoxyribonucleic acid within a density functional theory. Based on a statistical treatment of results of a fully variational optimization of basis orbitals ( full optimized basis orbitals) for 43 biological model molecules, simple sets of preoptimized basis orbitals classified under the local chemical environment (simple preoptimized basis orbitals) are constructed for hydrogen, carbon, nitrogen, oxygen, phosphorous, and sulfur atoms, each of which contains double valence plus polarization basis function. For a wide variety of molecules we show that the simple preoptimized orbitals provide well convergent energy and physical quantities comparable to those calculated by the full optimized orbitals, which demonstrates that the simple preoptimized orbitals possess substantial transferability for biological molecules.

  18. Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures.

    PubMed

    Goerigk, Lars; Collyer, Charles A; Reimers, Jeffrey R

    2014-12-18

    We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.

  19. Ballistocardiogram correction in simultaneous EEG/ fMRI recordings: a comparison of average artifact subtraction and optimal basis set methods using two popular software tools.

    PubMed

    Harrison, Amabilis H; Noseworthy, Michael D; Reilly, James P; Connolly, John F

    2014-01-01

    Electroencephalography data recorded during functional magnetic resonance imaging acquisition are subject to large cardiac-related artifacts that must be corrected during postprocessing. This study compared two widely used ballistocardiogram (BCG) correction algorithms as implemented in two software programs. Reduction of BCG amplitude, correlation of corrected data with electrocardiogram traces, correlation of independent components with electrocardiogram traces, and event-related potential signal-to-noise ratio from each algorithm were compared. Both algorithms effectively reduced the BCG artifact, with a slight advantage of average artifact subtraction over the optimal basis set method (0.1-2.2%) when the quality of the correction was examined at the individual subject level. This study provides users of these software tools with an important, practical, and previously unavailable comparison of the performance of these two methods.

  20. DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules.

    PubMed

    Wu, Anan; Xu, Xin

    2012-06-15

    We present a method, named DCMB, for the calculations of large molecules. It is a combination of a parallel divide-and-conquer (DC) method and a mixed-basis (MB) set scheme. In this approach, atomic forces, total energy and vibrational frequencies are obtained from a series of MB calculations, which are derived from the target system utilizing the DC concept. Unlike the fragmentation based methods, all DCMB calculations are performed over the whole target system and no artificial caps are introduced so that it is particularly useful for charged and/or delocalized systems. By comparing the DCMB results with those from the conventional method, we demonstrate that DCMB is capable of providing accurate prediction of molecular geometries, total energies, and vibrational frequencies of molecules of general interest. We also demonstrate that the high efficiency of the parallel DCMB code holds the promise for a routine geometry optimization of large complex systems.

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

    SciTech Connect

    Spackman, Peter R.; Karton, Amir

    2015-05-15

    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/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{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}.

  2. Basis set dependence of the doubly hybrid XYG3 functional

    NASA Astrophysics Data System (ADS)

    Zhang, Igor Ying; Luo, Yi; Xu, Xin

    2010-09-01

    In the present study, we investigated the basis set dependence of XYG3, a newly developed doubly hybrid functional [Y. Zhang, X. Xu, and W. A. Goddard III, Proc. Natl. Acad. Sci. U.S.A. 106, 4963 (2009)], in prediction of (1) heats of formation (HOFs), (2) bond dissociation enthalpies (BDEs), (3) reaction barrier heights (RBHs), and (4) nonbonded interactions (NBIs). We used basis sets of triple-zeta quality starting from 6-311+G(d,p) with increasing completeness of the polarization functions to the largest Pople-type basis set 6-311++G(3df,3pd) and found that there was a continued improvement with larger basis sets. We showed that while HOF predictions were prone to basis set deficiencies, the basis set dependences in calculating BDEs, RBHs, and NBIs were mild. All of them converged fast with the increase of basis set size. We extended XYG3 to propose the XYG3o functional which was specifically optimized for a particular basis set in order to enhance its performance when using basis set of moderate size. With the 6-311+G(2df,p) basis set, XYG3o led to MADs of 2.56 kcal/mol for HOFs of the G3/99 set, 1.17 kcal/mol for BDEs of the BDE92/07 set, 1.11 kcal/mol for RBHs of the NHTBH38/04 and HTBH38/04 sets, and 0.40 kcal/mol for NBIs of the NCIE31/05 set, being comparable to those obtained by using XYG3/6-311++G(3df,3pd).

  3. 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.

  4. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  5. Perspectives on Basis Sets Beautiful: Seasonal Plantings of Diffuse Basis Functions.

    PubMed

    Papajak, Ewa; Zheng, Jingjing; Xu, Xuefei; Leverentz, Hannah R; Truhlar, Donald G

    2011-10-11

    We present a perspective on the use of diffuse basis functions for electronic structure calculations by density functional theory and wave function theory. We especially emphasize minimally augmented basis sets and calendar basis sets. We base our conclusions on our previous experience with commonly computed quantities, such as bond energies, barrier heights, electron affinities, noncovalent (van der Waals and hydrogen bond) interaction energies, and ionization potentials, on Stephens et al.'s results for optical rotation and on our own new calculations (presented here) of polarizabilities and of potential energy curves of van der Waals complexes. We emphasize the benefits of partial augmentation of the higher-zeta basis sets in preference to full augmentation at a lower ζ level. Benefits and limitations of the use of fully, partially, and minimally augmented basis sets are reviewed for different electronic structure methods and molecular properties. We have found that minimal augmentation is almost always enough for density functional theory (DFT) when applied to ionization potentials, electron affinities, atomization energies, barrier heights, and hydrogen-bond energies. For electric dipole polarizabilities, we find that augmentation beyond minimal has an average effect of 8% at the polarized triple-ζ level and 5% at the polarized quadruple-ζ level. The effects are larger for potential energy curves of van der Waals complexes. The effects are also larger for wave function theory (WFT). Even for WFT though, full augmentation is not needed for most purposes, and a level of augmentation between minimal and full is optimal for most problems. The calendar basis sets named after the months provide a convergent sequence of partially augmented basis sets that can be used for such calculations. The jun-cc-pV(T+d)Z basis set is very useful for MP2-F12 calculations of barrier heights and hydrogen bond strengths.

  6. Approaching the Hartree-Fock Limit through the Complementary Auxiliary Basis Set Singles Correction and Auxiliary Basis Sets.

    PubMed

    Shaw, Robert A; Hill, J Grant

    2017-03-08

    Auxiliary basis sets for use in the resolution of the identity (RI) approximation in explicitly correlated methods are presented for the elements H-Ar. These extend the cc-pVnZ-F12/OptRI (n = D-Q) auxiliary basis sets of Peterson and co-workers by the addition of a small number of s- and p-functions, optimized so as to yield the greatest complementary auxiliary basis set (CABS) singles correction to the Hartree-Fock energy. The new sets, denoted OptRI+, also lead to a reduction in errors due to the RI approximation and hence an improvement in correlation energies. The atomization energies and heats of formation for a test set of small molecules, and spectroscopic constants for 27 diatomics, calculated at the CCSD(T)-F12b level, are shown to have improved error distributions for the new auxiliary basis sets with negligible additional effort. The OptRI+ sets retain all of the desirable properties of the original OptRI, including the production of smooth potential energy surfaces, while maintaining a compact nature.

  7. Chopped random-basis quantum optimization

    SciTech Connect

    Caneva, Tommaso; Calarco, Tommaso; Montangero, Simone

    2011-08-15

    In this work, we describe in detail the chopped random basis (CRAB) optimal control technique recently introduced to optimize time-dependent density matrix renormalization group simulations [P. Doria, T. Calarco, and S. Montangero, Phys. Rev. Lett. 106, 190501 (2011)]. Here, we study the efficiency of this control technique in optimizing different quantum processes and we show that in the considered cases we obtain results equivalent to those obtained via different optimal control methods while using less resources. We propose the CRAB optimization as a general and versatile optimal control technique.

  8. Entanglement patterns in mutually unbiased basis sets

    SciTech Connect

    Lawrence, Jay

    2011-08-15

    A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=p{sup N}), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (p{sup N}-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (p{sup N}-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.

  9. Atomic Natural Orbital Basis Sets for Transition Metals

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

    We show that atomic natural orbitals are an excellent way to contract transition-metal basis sets, even though the different low-lying electronic states may have very different basis set requirements.

  10. Correlation consistent basis sets for explicitly correlated wavefunctions: valence and core-valence basis sets for Li, Be, Na, and Mg.

    PubMed

    Hill, J Grant; Peterson, Kirk A

    2010-09-21

    Correlation consistent basis sets for the alkali and alkaline earth metals Li, Be, Na, and Mg have been optimized for use with explicitly correlated F12 methods. These include orbital basis sets for valence-only (denoted cc-pVnZ-F12) and core-valence (cc-pCVnZ-F12) correlation, along with compact complementary auxiliary basis sets for use in the resolution of the identity approximation. Additional auxiliary basis sets that can be employed in the density fitting of two-electron integrals in both explicitly correlated methods and in more conventional correlated methods, such as density fitted second-order Møller-Plesset perturbation theory (DF-MP2), have also been developed by adding additional diffuse or core-valence functions to the cc-pVnZ/MP2FIT sets of Hättig. Explicitly correlated calculations with the approximate CCSD(T)-F12b method have been carried out with these basis sets on a series of sixteen test molecules to demonstrate their accuracy for optimized geometries, harmonic vibrational frequencies, and atomization energies. Results comparable to conventional CCSD(T) quintuple-zeta, which are near the complete basis set limits for these molecules, are obtained using CCSD(T)-F12b with just triple-zeta quality basis sets. The effects on the spectroscopic constants from correlating the outer core electrons are accurately recovered with just the cc-pCVDZ-F12 basis sets.

  11. Basis Set Exchange: A Community Database for Computational Sciences

    SciTech Connect

    Schuchardt, Karen L.; Didier, Brett T.; Elsethagen, Todd O.; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared M.; Li, Jun; Windus, Theresa L.

    2007-05-01

    Basis sets are one of the most important input data for computational models in the chemistry, materials, biology and other science domains that utilize computational quantum mechanics methods. Providing a shared, web accessible environment where researchers can not only download basis sets in their required format, but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.

  12. Optimality for set-valued optimization in the sense of vector and set criteria.

    PubMed

    Kong, Xiangyu; Yu, GuoLin; Liu, Wei

    2017-01-01

    The vector criterion and set criterion are two defining approaches of solutions for the set-valued optimization problems. In this paper, the optimality conditions of both criteria of solutions are established for the set-valued optimization problems. By using Studniarski derivatives, the necessary and sufficient optimality conditions are derived in the sense of vector and set optimization.

  13. 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.

  14. Efficient Diffuse Basis Sets for Density Functional Theory.

    PubMed

    Papajak, Ewa; Truhlar, Donald G

    2010-03-09

    Eliminating all but the s and p diffuse functions on the non-hydrogenic atoms and all diffuse functions on the hydrogen atoms from the aug-cc-pV(x+d)Z basis sets of Dunning and co-workers, where x = D, T, Q, ..., yields the previously proposed "minimally augmented" basis sets, called maug-cc-pV(x+d)Z. Here, we present extensive and systematic tests of these basis sets for density functional calculations of chemical reaction barrier heights, hydrogen bond energies, electron affinities, ionization potentials, and atomization energies. The tests show that the maug-cc-pV(x+d)Z basis sets are as accurate as the aug-cc-pV(x+d)Z ones for density functional calculations, but the computational cost savings are a factor of about two to seven.

  15. Auxiliary basis sets for density fitting second-order Møller-Plesset perturbation theory: correlation consistent basis sets for the 5d elements Hf-Pt.

    PubMed

    Hill, J Grant

    2011-07-28

    Auxiliary basis sets specifically matched to the correlation consistent cc-pVnZ-PP, cc-pwCVnZ-PP, aug-cc-pVnZ-PP, and aug-cc-pwCVnZ-PP orbital basis sets (used in conjunction with pseudopotentials) for the 5d transition metal elements Hf-Pt have been optimized for use in density fitting second-order Møller-Plesset perturbation theory and other correlated ab initio methods. Calculations of the second-order Møller-Plesset perturbation theory correlation energy, for a test set of small to medium sized molecules, indicate that the density fitting error when utilizing these sets is negligible at three to four orders of magnitude smaller than the orbital basis set incompleteness error.

  16. LANL2DZ basis sets recontracted in the framework of density functional theory.

    PubMed

    Chiodo, S; Russo, N; Sicilia, E

    2006-09-14

    In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.

  17. Correlation consistent basis sets for explicitly correlated wavefunctions: pseudopotential-based basis sets for the post-d main group elements Ga-Rn.

    PubMed

    Hill, J Grant; Peterson, Kirk A

    2014-09-07

    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 the 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.

  18. Accurate universal Gaussian basis set for all atoms of the Periodic Table

    NASA Astrophysics Data System (ADS)

    de Castro, E. V. R.; Jorge, F. E.

    1998-04-01

    We have applied a discretized version of the generator coordinate Hartree-Fock method to generate a universal Gaussian basis set for the atoms from H through Lr. In general, for He to Rn the ground state Hartree-Fock total energy results obtained with our universal Gaussian basis set are lower than the corresponding ones obtained by Clementi et al. using larger atom-optimized geometrical Gaussian basis sets. For the atoms from H through Lr we have obtained ground state energy values with at least seven digits of accuracy (except for Pm, with six digits), in comparison with the corresponding ten digits of the numerical Hartree-Fock total energy results.

  19. Improved Segmented All-Electron Relativistically Contracted Basis Sets for the Lanthanides.

    PubMed

    Aravena, Daniel; Neese, Frank; Pantazis, Dimitrios A

    2016-03-08

    Improved versions of the segmented all-electron relativistically contracted (SARC) basis sets for the lanthanides are presented. The second-generation SARC2 basis sets maintain efficient construction of their predecessors and their individual adaptation to the DKH2 and ZORA Hamiltonians, but feature exponents optimized with a completely new orbital shape fitting procedure and a slightly expanded f space that results in sizable improvement in CASSCF energies and in significantly more accurate prediction of spin-orbit coupling parameters. Additionally, an extended set of polarization/correlation functions is constructed that is appropriate for multireference correlated calculations and new auxiliary basis sets for use in resolution-of-identity (density-fitting) approximations in combination with both DFT and wave function based treatments. Thus, the SARC2 basis sets extend the applicability of the first-generation DFT-oriented basis sets to routine all-electron wave function-based treatments of lanthanide complexes. The new basis sets are benchmarked with respect to excitation energies, radial distribution functions, optimized geometries, orbital eigenvalues, ionization potentials, and spin-orbit coupling parameters of lanthanide systems and are shown to be suitable for the description of magnetic and spectroscopic properties using both DFT and multireference wave function-based methods.

  20. Attenuated second order Møller-Plesset perturbation theory: correcting finite basis set errors and infinite basis set inaccuracies

    NASA Astrophysics Data System (ADS)

    Goldey, Matthew; Head-Gordon, Martin

    2015-03-01

    Second order Møller-Plesset perturbation theory (MP2) in finite basis sets describes several classes of noncovalent interactions poorly due to basis set superposition error (BSSE) and underlying inaccurate physics for dispersion interactions. Attenuation of the Coulomb operator provides a direct path toward improving MP2 for noncovalent interactions. In limited basis sets, we demonstrate improvements in accuracy for intermolecular interactions with a three to five-fold reduction in RMS errors. For a range of inter- and intermolecular test cases, attenuated MP2 even outperforms complete basis set estimates of MP2. Finite basis attenuated MP2 is useful for inter- and intramolecular interactions where higher cost approaches are intractable. Extending this approach, recent research pairs attenuated MP2 with long-range correction to describe potential energy landscapes, and further results for large systems with noncovalent interactions are shown. This work was supported by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We acknowledge computational resources obtained under NSF Award CHE-1048789.

  1. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-03-01

    The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

  2. Scar Functions, Barriers for Chemical Reactivity, and Vibrational Basis Sets.

    PubMed

    Revuelta, F; Vergini, E; Benito, R M; Borondo, F

    2016-07-14

    The performance of a recently proposed method to efficiently calculate scar functions is analyzed in problems of chemical interest. An application to the computation of wave functions associated with barriers relevant for the LiNC ⇄ LiCN isomerization reaction is presented as an illustration. These scar functions also constitute excellent elements for basis sets suitable for quantum calculation of vibrational energy levels. To illustrate their efficiency, a calculation of the LiNC/LiCN eigenfunctions is also presented.

  3. Basis set convergence of CCSD(T) equilibrium geometries using a large and diverse set of molecular structures.

    PubMed

    Spackman, Peter R; Jayatilaka, Dylan; Karton, Amir

    2016-09-14

    We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H-X, 49 X-Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ∼4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0.0019 (D

  4. The Neural Basis of Optimism and Pessimism

    PubMed Central

    2013-01-01

    Our survival and wellness require a balance between optimism and pessimism. Undue pessimism makes life miserable; however, excessive optimism can lead to dangerously risky behaviors. A review and synthesis of the literature on the neurophysiology subserving these two worldviews suggests that optimism and pessimism are differentially associated with the two cerebral hemispheres. High self-esteem, a cheerful attitude that tends to look at the positive aspects of a given situation, as well as an optimistic belief in a bright future are associated with physiological activity in the left-hemisphere (LH). In contrast, a gloomy viewpoint, an inclination to focus on the negative part and exaggerate its significance, low self-esteem as well as a pessimistic view on what the future holds are interlinked with neurophysiological processes in the right-hemisphere (RH). This hemispheric asymmetry in mediating optimistic and pessimistic outlooks is rooted in several biological and functional differences between the two hemispheres. The RH mediation of a watchful and inhibitive mode weaves a sense of insecurity that generates and supports pessimistic thought patterns. Conversely, the LH mediation of an active mode and the positive feedback it receives through its motor dexterity breed a sense of confidence in one's ability to manage life's challenges, and optimism about the future. PMID:24167413

  5. Auxiliary Basis Sets for Density Fitting in Explicitly Correlated Calculations: The Atoms H-Ar.

    PubMed

    Kritikou, Stella; Hill, J Grant

    2015-11-10

    Auxiliary basis sets specifically matched to the correlation consistent cc-pVnZ-F12 and cc-pCVnZ-F12 orbital basis sets for the elements H-Ar have been optimized at the density-fitted second-order Møller-Plesset perturbation theory level of theory for use in explicitly correlated (F12) methods, which utilize density fitting for the evaluation of two-electron integrals. Calculations of the correlation energy for a test set of small to medium sized molecules indicate that the density fitting error when using these auxiliary sets is 2 to 3 orders of magnitude smaller than the F12 orbital basis set incompleteness error. The error introduced by the use of these fitting sets within the resolution-of-the-identity approximation of the many-electron integrals arising in F12 theory has also been assessed and is demonstrated to be negligible and well-controlled. General guidelines are proposed for the optimization of density fitting auxiliary basis sets for use with F12 methods for other elements.

  6. 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).

  7. Optimal grids for generalized finite basis and discrete variable representations: definition and method of calculation.

    PubMed

    Szalay, Viktor

    2006-10-21

    The method of optimal generalized finite basis and discrete variable representations (FBR and DVR) generalizes the standard, Gaussian quadrature grid-classical orthonormal polynomial basis-based FBR/DVR method to general sets of grid points and to general, nondirect product, and/or nonpolynomial bases. Here, it is shown how an optimal set of grid points can be obtained for an optimal generalized FBR/DVR calculation with a given truncated basis. Basis set optimized and potential optimized grids are defined. The optimized grids are shown to minimize a function of grid points derived by relating the optimal generalized FBR of a Hamiltonian operator to a non-Hermitian effective Hamiltonian matrix. Locating the global minimum of this function can be reduced to finding the zeros of a function in the case of one dimensional problems and to solving a system of D nonlinear equations repeatedly in the case of D>1 dimensional problems when there is an equal number of grid points and basis functions. Gaussian quadrature grids are shown to be basis optimized grids. It is demonstrated by a numerical example that an optimal generalized FBR/DVR calculation of the eigenvalues of a Hamiltonian operator with potential optimized grids can have orders of magnitude higher accuracy than a variational calculation employing the same truncated basis. Nevertheless, for numerical integration with the optimal generalized FBR quadrature rule basis optimized grids are the best among grids of the same number of points. The notions of Gaussian quadrature and Gaussian quadrature accuracy are extended to general, multivariable basis functions.

  8. Large Atomic Natural Orbital Basis Sets for the First Transition Row Atoms

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    Large atomic natural orbital (ANO) basis sets are tabulated for the Sc to Cu. The primitive sets are taken from the large sets optimized by Partridge, namely (21s 13p 8d) for Sc and Ti and (20s 12p 9d) for V to Cu. These primitive sets are supplemented with three p, one d, six f, and four g functions. The ANO sets are derived from configuration interaction density matrices constructed as the average of the lowest states derived from the 3d(sup n)4s(sup 2) and 3d(sup n+1)4s(sup 1) occupations. For Ni, the 1S(3d(sup 10)) state is included in the averaging. The choice of basis sets for molecular calculations is discussed.

  9. Coupled-cluster based basis sets for valence correlation calculations

    NASA Astrophysics Data System (ADS)

    Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.

    2016-03-01

    Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.

  10. The local electron affinity for non-minimal basis sets.

    PubMed

    Clark, Timothy

    2010-07-01

    A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EA(L). Intensity filtering allows EA(L) to be calculated using semiempirical molecular orbital techniques that include polarisation functions. Without intensity filtering, such techniques yield spurious EA(L) values that are dominated by the polarisation functions. As intensity filtering should also be applicable for ab initio or density functional theory calculations with large basis sets, it also makes EA(L) available for these techniques.

  11. Semiclassical basis sets for the computation of molecular vibrational states.

    PubMed

    Revuelta, F; Vergini, E; Benito, R M; Borondo, F

    2017-01-07

    In this paper, we extend a method recently reported [F. Revuelta et al., Phys. Rev. E 87, 042921 (2013)] for the calculation of the eigenstates of classically highly chaotic systems to cases of mixed dynamics, i.e., those presenting regular and irregular motions at the same energy. The efficiency of the method, which is based on the use of a semiclassical basis set of localized wave functions, is demonstrated by applying it to the determination of the vibrational states of a realistic molecular system, namely, the LiCN molecule.

  12. Development of new auxiliary basis functions of the Karlsruhe segmented contracted basis sets including diffuse basis functions (def2-SVPD, def2-TZVPPD, and def2-QVPPD) for RI-MP2 and RI-CC calculations.

    PubMed

    Hellweg, Arnim; Rappoport, Dmitrij

    2015-01-14

    We report optimized auxiliary basis sets for use with the Karlsruhe segmented contracted basis sets including moderately diffuse basis functions (Rappoport and Furche, J. Chem. Phys., 2010, 133, 134105) in resolution-of-the-identity (RI) post-self-consistent field (post-SCF) computations for the elements H-Rn (except lanthanides). The errors of the RI approximation using optimized auxiliary basis sets are analyzed on a comprehensive test set of molecules containing the most common oxidation states of each element and do not exceed those of the corresponding unaugmented basis sets. During these studies an unsatisfying performance of the def2-SVP and def2-QZVPP auxiliary basis sets for Barium was found and improved sets are provided. We establish the versatility of the def2-SVPD, def2-TZVPPD, and def2-QZVPPD basis sets for RI-MP2 and RI-CC (coupled-cluster) energy and property calculations. The influence of diffuse basis functions on correlation energy, basis set superposition error, atomic electron affinity, dipole moments, and computational timings is evaluated at different levels of theory using benchmark sets and showcase examples.

  13. Near Hartree-Fock quality Gaussian type orbital basis sets for the first- and third-row atoms

    NASA Technical Reports Server (NTRS)

    Partridge, Harry

    1989-01-01

    Energy-optimized, near Hartree-Fock (NHF) quality Gaussian type orbital (GTO) basis sets are reported for the second-row (Li to Ne) and fourth-row (K to Kr) atoms. The most accurate basis sets reported for the second row are (18s 13p) sets which are with 4 micro E(H) of the numerical Hartree-Fock (NHF) results. For B to Ne basis sets with more than 15s functions are quadruple zeta in the valence space. For the second-row transition metal atoms the (20s 12p 9d) basis sets are triple zeta in the valence space and are approximately equivalent to Clementi and Roetti's accurate Slater type orbital sets. Supplementing the (20s 12p 9d) basis sets optimized for the lowest state with the 4s(2)3d(n) occupation with a diffuse d function gives self-consistent-field energy separations to the 4s(1)3d(n+1) and 3d(n+2) states which are within 100 micro E(H) of the NHF results. The most accurate basis sets for the transition metal atoms are with 30 micro E(H) of the NHF results. In addition, energy optimized sets are reported for He(3P), Li(2P) and Be(3P).

  14. Basis set limit geometries for ammonia at the SCF and MP2 levels of theory

    NASA Technical Reports Server (NTRS)

    Defrees, D. J.; Mclean, A. D.

    1984-01-01

    The controversy over the Hartree-Fock bond angle of NH3 is resolved and the convergence of the geometry for the molecule as the basis set is systematically improved with both SCF and correlated MP2 wave functions. The results of the geometrical optimizations, carried out in four stages with a series of uncontracted bases sets, are shown. The obtained structure for NH3 supports the results of Radom and Rodwell (1980) that the Hartree-Fock limit angle is significantly greater than was previously believed.

  15. Optimal Piecewise Linear Basis Functions in Two Dimensions

    SciTech Connect

    Brooks III, E D; Szoke, A

    2009-01-26

    We use a variational approach to optimize the center point coefficients associated with the piecewise linear basis functions introduced by Stone and Adams [1], for polygonal zones in two Cartesian dimensions. Our strategy provides optimal center point coefficients, as a function of the location of the center point, by minimizing the error induced when the basis function interpolation is used for the solution of the time independent diffusion equation within the polygonal zone. By using optimal center point coefficients, one expects to minimize the errors that occur when these basis functions are used to discretize diffusion equations, or transport equations in optically thick zones (where they approach the solution of the diffusion equation). Our optimal center point coefficients satisfy the requirements placed upon the basis functions for any location of the center point. We also find that the location of the center point can be optimized, but this requires numerical calculations. Curiously, the optimum center point location is independent of the values of the dependent variable on the corners only for quadrilaterals.

  16. Auxiliary basis sets for density-fitted correlated wavefunction calculations: weighted core-valence and ECP basis sets for post-d elements.

    PubMed

    Hättig, Christof; Schmitz, Gunnar; Kossmann, Jörg

    2012-05-14

    We report optimised auxiliary basis sets for the resolution-of-the-identity (or density-fitting) approximation of two-electron integrals in second-order Møller-Plesset perturbation theory (MP2) and similar electronic structure calculations with correlation-consistent basis sets for the post-d elements Ga-Kr, In-Xe, and Tl-Rn. The auxiliary basis sets are optimised such that the density-fitting error is negligible compared to the one-electron basis set error. To check to which extent this criterion is fulfilled we estimated for a test set of 80 molecules the basis set limit of the correlation energy at the MP2 level and evaluated the remaining density-fitting and the one-electron basis set errors. The resulting auxiliary basis sets are only 2-6 times larger than the corresponding one-electron basis sets and lead in MP2 calculations to speed-ups of the integral evaluation by one to three orders of magnitude. The density-fitting errors in the correlation energy are at least hundred times smaller than the one-electron basis set error, i.e. in the order of only 1-100 μH per atom.

  17. 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.

    PubMed

    Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    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 produces <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.

  18. 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

    NASA Astrophysics Data System (ADS)

    Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin

    2016-07-01

    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 produces <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.

  19. Basis set expansion for inverse problems in plasma diagnostic analysis

    SciTech Connect

    Jones, B.; Ruiz, C. L.

    2013-07-15

    A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)] is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20–25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.

  20. Basis set expansion for inverse problems in plasma diagnostic analysis

    NASA Astrophysics Data System (ADS)

    Jones, B.; Ruiz, C. L.

    2013-07-01

    A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)], 10.1063/1.1482156 is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20-25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.

  1. Basis Set Requirements for Sulfur Compounds in Density Functional Theory:  a Comparison between Correlation-Consistent, Polarized-Consistent, and Pople-Type Basis Sets.

    PubMed

    Denis, Pablo A

    2005-09-01

    We have investigated the SX (X = first- or second-row atom), SO2, and SO3 molecules employing the correlation-consistent (cc), the recently developed polarization-consistent (pc), and three Pople-type basis sets, in conjunction with the B3LYP functional. The results confirmed that the aug-pc basis sets represent a great contribution in terms of cost-benefits. In the case of the B3LYP functional, when employing the aug-pc-3 and aug-pc-4 basis sets, it is possible to obtain results that are of aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z quality, respectively, at a much lower cost. The estimations obtained employing smaller members of the family are of nearly double-ζ quality and do not provide reliable results. There is no basis set of quadruple-ζ quality among the polarized-consistent basis sets, although in terms of composition, the aug-pc-3 basis set is a QZ basis set. A precise estimation of the Kohn-Sham complete basis set (CBS) limit with the aug-pc-X basis sets is too difficult for the B3LYP functional because the ∞(aug-pc-4, aug-pc-3, aug-pc-2) extrapolation gives the same results as those of the aug-pc-4 basis set. This is in contrast with the results observed for ab initio methodologies for which the largest basis sets provided the best estimation of the CBS limit. In our opinion, the closest results to the B3LYP/CBS limit are expected to be those obtained with a two-point extrapolation employing the aug-cc-pV(X+d)Z (X = 5, 6) basis sets. The results obtained with this extrapolation are very close to those predicted by the ∞(aug-pc-3, aug-pc-2, aug-pc-1) extrapolation, and that provides a cheaper but more inaccurate alternative to estimate the CBS limit. Minor problems were found for the aug-pc-X basis sets and the B3LYP functional for molecules in which sulfur is bound to a very electronegative element, such as SO, SF, SO2, and SO3. For these molecules, the cc basis sets were demonstrated to be more useful. The importance of tight d functions was observed

  2. 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.

  3. Evaluation of Density Functionals and Basis Sets for Carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...

  4. Accurate Electron Densities at Nuclei Using Small Ramp-Gaussian Basis Sets.

    PubMed

    McKemmish, Laura K; Gilbert, Andrew T B

    2015-08-11

    Electron densities at nuclei are difficult to calculate accurately with all-Gaussian basis sets because they lack an electron-nuclear cusp. The newly developed mixed ramp-Gaussian basis sets, such as R-31G, possess electron-nuclear cusps due to the presence of ramp functions in the basis. The R-31G basis set is a general-purpose mixed ramp-Gaussian basis set modeled on the 6-31G basis set. The prediction of electron densities at nuclei using R-31G basis sets for Li-F outperforms Dunning, Pople, and Jensen general purpose all-Gaussian basis sets of triple-ζ quality or lower and the cc-pVQZ basis set. It is of similar quality to the specialized pcJ-0 basis set which was developed with partial decontraction of core functions and extra high exponent s-Gaussians to predict electron density at the nucleus. These results show significant advantages in the properties of mixed ramp-Gaussian basis sets compared to all-Gaussian basis sets.

  5. Basis set convergence of electric properties in HF and DFT calculations of nucleic acid bases

    NASA Astrophysics Data System (ADS)

    Campos, C. T.; Jorge, F. E.

    Recently, a hierarchical sequence of augmented basis sets of double, triple, and quadruple zeta valence quality plus polarization functions (AXZP, X = D, T, and Q) for the atoms from H to Ar were presented by Jorge et al. We report a systematic study of basis sets required to obtain accurate values of several electric properties for benzene, pyridine, the five common nucleic acid bases (uracil, cytosine, thymine, guanine, and adenine), and three related bases (fluorouracil, 5-methylcytosine, and hypoxanthine) at their full optimized geometries. Two methods were examined: Hartree-Fock (HF) and density functional theory (DFT). Including electron correlation decreases the magnitude of the dipole moment and increases the mean polarizability and also the polarizability anisotropy for every molecule. Calculated B3LYP/ADZP dipole moments and dipole polarizabilities show good agreement with both experimental and ab initio results based on second-order Møller-Plesset perturbation theory calculations. We have also showed that a basis set of double zeta quality is enough to obtain reliable and accurate electric property results for this kind of compounds.

  6. Time-domain semi-parametric estimation based on a metabolite basis set.

    PubMed

    Ratiney, H; Sdika, M; Coenradie, Y; Cavassila, S; van Ormondt, D; Graveron-Demilly, D

    2005-02-01

    A novel and fast time-domain quantitation algorithm--quantitation based on semi-parametric quantum estimation (QUEST)--invoking optimal prior knowledge is proposed and tested. This nonlinear least-squares algorithm fits a time-domain model function, made up from a basis set of quantum-mechanically simulated whole-metabolite signals, to low-SNR in vivo data. A basis set of in vitro measured signals can be used too. The simulated basis set was created with the software package NMR-SCOPE which can invoke various experimental protocols. Quantitation of 1H short echo-time signals is often hampered by a background signal originating mainly from macromolecules and lipids. Here, we propose and compare three novel semi-parametric approaches to handle such signals in terms of bias-variance trade-off. The performances of our methods are evaluated through extensive Monte-Carlo studies. Uncertainty caused by the background is accounted for in the Cramér-Rao lower bounds calculation. Valuable insight about quantitation precision is obtained from the correlation matrices. Quantitation with QUEST of 1H in vitro data, 1H in vivo short echo-time and 31P human brain signals at 1.5 T, as well as 1H spectroscopic imaging data of human brain at 1.5 T, is demonstrated.

  7. Is there an optimal basis to maximise optical information transfer?

    PubMed Central

    Chen, Mingzhou; Dholakia, Kishan; Mazilu, Michael

    2016-01-01

    We establish the concept of the density of the optical degrees of freedom that may be applied to any photonics based system. As a key example of this versatile approach we explore information transfer using optical communication. We demonstrate both experimentally, theoretically and numerically that the use of a basis set with fields containing optical vortices does not increase the telecommunication capacity of an optical system. PMID:26976626

  8. Sensory irritation as a basis for setting occupational exposure limits.

    PubMed

    Brüning, Thomas; Bartsch, Rüdiger; Bolt, Hermann Maximillian; Desel, Herbert; Drexler, Hans; Gundert-Remy, Ursula; Hartwig, Andrea; Jäckh, Rudolf; Leibold, Edgar; Pallapies, Dirk; Rettenmeier, Albert W; Schlüter, Gerhard; Stropp, Gisela; Sucker, Kirsten; Triebig, Gerhard; Westphal, Götz; van Thriel, Christoph

    2014-10-01

    There is a need of guidance on how local irritancy data should be incorporated into risk assessment procedures, particularly with respect to the derivation of occupational exposure limits (OELs). Therefore, a board of experts from German committees in charge of the derivation of OELs discussed the major challenges of this particular end point for regulatory toxicology. As a result, this overview deals with the question of integrating results of local toxicity at the eyes and the upper respiratory tract (URT). Part 1 describes the morphology and physiology of the relevant target sites, i.e., the outer eye, nasal cavity, and larynx/pharynx in humans. Special emphasis is placed on sensory innervation, species differences between humans and rodents, and possible effects of obnoxious odor in humans. Based on this physiological basis, Part 2 describes a conceptual model for the causation of adverse health effects at these targets that is composed of two pathways. The first, "sensory irritation" pathway is initiated by the interaction of local irritants with receptors of the nervous system (e.g., trigeminal nerve endings) and a downstream cascade of reflexes and defense mechanisms (e.g., eyeblinks, coughing). While the first stages of this pathway are thought to be completely reversible, high or prolonged exposure can lead to neurogenic inflammation and subsequently tissue damage. The second, "tissue irritation" pathway starts with the interaction of the local irritant with the epithelial cell layers of the eyes and the URT. Adaptive changes are the first response on that pathway followed by inflammation and irreversible damages. Regardless of these initial steps, at high concentrations and prolonged exposures, the two pathways converge to the adverse effect of morphologically and biochemically ascertainable changes. Experimental exposure studies with human volunteers provide the empirical basis for effects along the sensory irritation pathway and thus, "sensory

  9. Benchmarks of improved complete basis set extrapolation schemes designed for standard CCSD(T) atomization energies.

    PubMed

    Feller, David

    2013-02-21

    Simple modifications of complete basis set extrapolation formulas chosen from the literature are examined with respect to their abilities to reproduce a diverse set of 183 reference atomization energies derived primarily from very large basis set standard, frozen core coupled-cluster singles, doubles plus perturbative triples (CCSD(T)) with the aug-cc-pVnZ basis sets. This reference set was augmented with a few larger chemical systems treated with explicitly correlated CCSD(T)-F12b using a quadruple zeta quality basis set followed by extrapolation to complete basis set limit. Tuning the extrapolation formula parameters for the present reference set resulted in substantial reductions in the error metrics. In the case of the best performing approach, the aVnZ extrapolated results are equivalent to or better than results obtained from raw aV(n + 3)Z basis set calculations. To the extent this behavior holds for molecules outside the reference set, it represents an improvement of at least one basis set level over the original formulations and a further significant reduction in the amount of computer time needed to accurately approximate the basis set limit.

  10. New Slater-type orbital basis sets for first row transition elements

    NASA Astrophysics Data System (ADS)

    Bernardo, L. A. G.; Sordo, J. A.

    1986-08-01

    A comparative study, at the atomic level, of the quality of eight Slater-type orbitals (STO) basis sets has been carried out for the first row transition elements. Two new basis sets are proposed for these elements: the β1 basis set (small-size-type) and the α2 basis set (intermediate-size-type). Both basis sets have been developed according to the so-called δ test [J. A. Sordo and L. Pueyo, Int. J. Quantum Chem. XXVIII, 687 (1985)]. The results suggest that the errors detected by means of the δ test could be responsible for the wrong ordering predicted by 2-ζ (and lower quality basis sets) for the 4s13d10 (2S) and 4s23d9(2D) states in Cu. All the quality tests used indicated that β1 basis sets would be very appropriate for performing economical molecular calculations and that α2 basis sets, with only one STO more than 2-ζ basis sets, would provide atomic results near the Hartree-Fock limit.

  11. Basis set effects on the geometry of C96H24

    NASA Astrophysics Data System (ADS)

    Bauschlicher, Charles W.

    2016-11-01

    C96H24 has D6h symmetry using the 4-31G, 6-31G, cc-pVDZ, or cc-pVTZ basis sets, but has lower symmetry if the 6-31G∗∗ or 6-311G∗∗ basis sets are used. Changing the carbon 3d exponent in the 6-31G∗∗ basis set can restore the D6h symmetry, but raises the total energy. The question of geometry vs basis set is discussed.

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

    SciTech Connect

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-03-07

    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 D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.

  13. The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex

    SciTech Connect

    Shirkov, Leonid; Makarewicz, Jan

    2015-05-28

    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 allowed 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.

  14. Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.

    PubMed

    Siiskonen, Antti; Priimagi, Arri

    2017-02-01

    In recent years, halogen bonding has become an important design tool in crystal engineering, supramolecular chemistry and biosciences. The fundamentals of halogen bonding have been studied extensively with high-accuracy computational methods. Due to its non-covalency, the use of triple-zeta (or larger) basis sets is often recommended when studying halogen bonding. However, in the large systems often encountered in supramolecular chemistry and biosciences, large basis sets can make the calculations far too slow. Therefore, small basis sets, which would combine high computational speed and high accuracy, are in great demand. This study focuses on comparing how well density functional theory (DFT) methods employing small, double-zeta basis sets can estimate halogen-bond strengths. Several methods with triple-zeta basis sets are included for comparison. Altogether, 46 DFT methods were tested using two data sets of 18 and 33 halogen-bonded complexes for which the complexation energies have been previously calculated with the high-accuracy CCSD(T)/CBS method. The DGDZVP basis set performed far better than other double-zeta basis sets, and it even outperformed the triple-zeta basis sets. Due to its small size, it is well-suited to studying halogen bonding in large systems.

  15. 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.

  16. Method/basis set dependence of NICS values among metallic nano-clusters and hydrocarbons.

    PubMed

    Badri, Zahra; Foroutan-Nejad, Cina; Rashidi-Ranjbar, Parviz

    2012-03-14

    The influence of various all-electron basis sets and effective core potentials employed along with several DFT functionals (B3LYP, B3PW91, BLYP, BP86 and M06) on the magnitude of nucleus independent chemical shift (NICS) values in different metallic nano-clusters and hydrocarbons is studied. In general, it is demonstrated that the NICS values are very sensitive to the applied method/basis set; however, the method/basis set dependence is more prominent for computed NICS values in transition metal clusters. In hydrocarbons, medium-size basis sets perform roughly similar to large basis sets in most cases. It is also found that NICS(0) values are more sensitive to the method/basis set variation compared to the NICS values computed at 1 or 2 Å above the ring plane. However, in many cases, no broad-spectrum regulation is found for the effect of basis set/method on the magnitude of NICS values. A detailed study showed that bond length alternation in a molecule has an insignificant effect on the magnitude of NICS values so the influence of method/basis sets on the magnitude of NICS values mostly arises from the different predicted ring current intensities at various computational levels.

  17. Generation of basis sets with high degree of fulfillment of the Hellmann-Feynman theorem.

    PubMed

    Rico, J Fernández; López, R; Ema, I; Ramírez, G

    2007-03-01

    A direct relationship is established between the degree of fulfillment of the Hellman-Feynman (electrostatic) theorem, measured as the difference between energy derivatives and electrostatic forces, and the stability of the basis set, measured from the indices that characterize the distance of the space generated by the basis functions to the space of their derivatives with respect to the nuclear coordinates. On the basis of this relationship, a criterion for obtaining basis sets of moderate size with a high degree of fulfillment of the theorem is proposed. As an illustrative application, previously reported Slater basis sets are extended by using this criterion. The resulting augmented basis sets are tested on several molecules finding that the differences between energy gradient and electrostatic forces are reduced by at least one order of magnitude.

  18. Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies.

    PubMed

    Boström, Jonas; Delcey, Mickaël G; Aquilante, Francesco; Serrano-Andrés, Luis; Pedersen, Thomas Bondo; Lindh, Roland

    2010-03-09

    The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.

  19. Compression of biomedical signals with mother wavelet optimization and best-basis wavelet packet selection.

    PubMed

    Brechet, Laurent; Lucas, Marie-Françoise; Doncarli, Christian; Farina, Dario

    2007-12-01

    We propose a novel scheme for signal compression based on the discrete wavelet packet transform (DWPT) decompositon. The mother wavelet and the basis of wavelet packets were optimized and the wavelet coefficients were encoded with a modified version of the embedded zerotree algorithm. This signal dependant compression scheme was designed by a two-step process. The first (internal optimization) was the best basis selection that was performed for a given mother wavelet. For this purpose, three additive cost functions were applied and compared. The second (external optimization) was the selection of the mother wavelet based on the minimal distortion of the decoded signal given a fixed compression ratio. The mother wavelet was parameterized in the multiresolution analysis framework by the scaling filter, which is sufficient to define the entire decomposition in the orthogonal case. The method was tested on two sets of ten electromyographic (EMG) and ten electrocardiographic (ECG) signals that were compressed with compression ratios in the range of 50%-90%. For 90% compression ratio of EMG (ECG) signals, the percent residual difference after compression decreased from (mean +/- SD) 48.6 +/- 9.9% (21.5 +/- 8.4%) with discrete wavelet transform (DWT) using the wavelet leading to poorest performance to 28.4 +/- 3.0% (6.7 +/- 1.9%) with DWPT, with optimal basis selection and wavelet optimization. In conclusion, best basis selection and optimization of the mother wavelet through parameterization led to substantial improvement of performance in signal compression with respect to DWT and randon selection of the mother wavelet. The method provides an adaptive approach for optimal signal representation for compression and can thus be applied to any type of biomedical signal.

  20. 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

  1. Efficient basis sets for non-covalent interactions in XDM-corrected density-functional theory.

    PubMed

    Johnson, Erin R; Otero-de-la-Roza, Alberto; Dale, Stephen G; DiLabio, Gino A

    2013-12-07

    In the development and application of dispersion-corrected density-functional theory, the effects of basis set incompleteness have been largely mitigated through the use of very large, nearly-complete basis sets. However, the use of such large basis sets makes application of these methods inefficient for large systems. In this work, we examine a series of basis sets, including Pople-style, correlation-consistent, and polarization-consistent bases, for their ability to efficiently and accurately predict non-covalent interactions when used in conjunction with the exchange-hole dipole moment (XDM) dispersion model. We find that the polarization-consistent 2 (pc-2) basis sets, and two modifications thereof with some diffuse functions removed, give performance of comparable quality to that obtained with aug-cc-pVTZ basis sets, while being roughly 12 to 23 times faster computationally. The behavior is explained, in part, by the role of diffuse functions in recovering small density changes in the intermolecular region. The general performance of the modified basis sets is tested by application of XDM to standard intermolecular benchmark sets at, and away from, equilibrium.

  2. Confidence sets for optimal factor levels of a response surface.

    PubMed

    Wan, Fang; Liu, Wei; Bretz, Frank; Han, Yang

    2016-12-01

    Construction of confidence sets for the optimal factor levels is an important topic in response surfaces methodology. In Wan et al. (2015), an exact (1-α) confidence set has been provided for a maximum or minimum point (i.e., an optimal factor level) of a univariate polynomial function in a given interval. In this article, the method has been extended to construct an exact (1-α) confidence set for the optimal factor levels of response surfaces. The construction method is readily applied to many parametric and semiparametric regression models involving a quadratic function. A conservative confidence set has been provided as an intermediate step in the construction of the exact confidence set. Two examples are given to illustrate the application of the confidence sets. The comparison between confidence sets indicates that our exact confidence set is better than the only other confidence set available in the statistical literature that guarantees the (1-α) confidence level.

  3. Basis set generation for quantum dynamics simulations using simple trajectory-based methods.

    PubMed

    Saller, Maximilian A C; Habershon, Scott

    2015-01-13

    Methods for solving the time-dependent Schrödinger equation generally employ either a global static basis set, which is fixed at the outset, or a dynamic basis set, which evolves according to classical-like or variational equations of motion; the former approach results in the well-known exponential scaling with system size, while the latter can suffer from challenging numerical problems, such as singular matrices, as well as violation of energy conservation. Here, we suggest a middle road: building a basis set using trajectories to place time-independent basis functions in the regions of phase space relevant to wave function propagation. This simple approach, which potentially circumvents many of the problems traditionally associated with global or dynamic basis sets, is successfully demonstrated for two challenging benchmark problems in quantum dynamics, namely, relaxation dynamics following photoexcitation in pyrazine, and the spin Boson model.

  4. Vicinal proton—proton coupling constants. Basis set dependence in SCF ab initio calculations

    NASA Astrophysics Data System (ADS)

    San-Fabián, Jesús; Guilleme, Joaquín; Díez, Ernesto; Lazzeretti, Paolo; Malagoli, Massimo; Zanasi, Riccardo

    1993-04-01

    An SCF ab initio study of the angular dependence and substituent effects upon the vicinal coupling constants has been carried out for the molecules CH 3CH 3, CH 2FCH 3 and CHF 2CH 3. The four contributions to 3JHH ( JFC, JSD, JOD and JOP) have been computed using the STO-3G, 6-31G, 6-31G * and 6-31G ** basis sets. The major contributions arise from the FC term. The magnitude of the SD contributions is very small and near independent of the size of the basis set. The magnitude of the orbital contributions OR (=OD+OP) decreases as the size of the basis set increases. The FC term slightly overestimates both the individual and the interaction substituent effects for basis sets larger than the STO-3G one. For this basis such effects are underestimated.

  5. Bi-directional evolutionary level set method for topology optimization

    NASA Astrophysics Data System (ADS)

    Zhu, Benliang; Zhang, Xianmin; Fatikow, Sergej; Wang, Nianfeng

    2015-03-01

    A bi-directional evolutionary level set method for solving topology optimization problems is presented in this article. The proposed method has three main advantages over the standard level set method. First, new holes can be automatically generated in the design domain during the optimization process. Second, the dependency of the obtained optimized configurations upon the initial configurations is eliminated. Optimized configurations can be obtained even being started from a minimum possible initial guess. Third, the method can be easily implemented and is computationally more efficient. The validity of the proposed method is tested on the mean compliance minimization problem and the compliant mechanisms topology optimization problem.

  6. Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: weighted core-valence correlation consistent basis sets for the 4d elements Y-Pd.

    PubMed

    Hill, J Grant

    2013-09-30

    Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit.

  7. 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.

  8. Achieving the Complete-Basis Limit in Large Molecular Clusters: Computationally Efficient Procedures to Eliminate Basis-Set Superposition Error

    NASA Astrophysics Data System (ADS)

    Richard, Ryan M.; Herbert, John M.

    2013-06-01

    Previous electronic structure studies that have relied on fragmentation have been primarily interested in those methods' abilities to replicate the supersystem energy (or a related energy difference) without recourse to the ability of those supersystem results to replicate experiment or high accuracy benchmarks. Here we focus on replicating accurate ab initio benchmarks, that are suitable for comparison to experimental data. In doing this it becomes imperative that we correct our methods for basis-set superposition errors (BSSE) in a computationally feasible way. This criterion leads us to develop a new method for BSSE correction, which we term the many-body counterpoise correction, or MBn for short. MBn is truncated at order n, in much the same manner as a normal many-body expansion leading to a decrease in computational time. Furthermore, its formulation in terms of fragments makes it especially suitable for use with pre-existing fragment codes. A secondary focus of this study is directed at assessing fragment methods' abilities to extrapolate to the complete basis set (CBS) limit as well as compute approximate triples corrections. Ultimately, by analysis of (H_2O)_6 and (H_2O)_{10}F^- systems, it is concluded that with large enough basis-sets (triple or quad zeta) fragment based methods can replicate high level benchmarks in a fraction of the time.

  9. Comparison of Property-Oriented Basis Sets for the Computation of Electronic and Nuclear Relaxation Hyperpolarizabilities.

    PubMed

    Zaleśny, Robert; Baranowska-Łączkowska, Angelika; Medveď, Miroslav; Luis, Josep M

    2015-09-08

    In the present work, we perform an assessment of several property-oriented atomic basis sets in computing (hyper)polarizabilities with a focus on the vibrational contributions. Our analysis encompasses the Pol and LPol-ds basis sets of Sadlej and co-workers, the def2-SVPD and def2-TZVPD basis sets of Rappoport and Furche, and the ORP basis set of Baranowska-Łączkowska and Łączkowski. Additionally, we use the d-aug-cc-pVQZ and aug-cc-pVTZ basis sets of Dunning and co-workers to determine the reference estimates of the investigated electric properties for small- and medium-sized molecules, respectively. We combine these basis sets with ab initio post-Hartree-Fock quantum-chemistry approaches (including the coupled cluster method) to calculate electronic and nuclear relaxation (hyper)polarizabilities of carbon dioxide, formaldehyde, cis-diazene, and a medium-sized Schiff base. The primary finding of our study is that, among all studied property-oriented basis sets, only the def2-TZVPD and ORP basis sets yield nuclear relaxation (hyper)polarizabilities of small molecules with average absolute errors less than 5.5%. A similar accuracy for the nuclear relaxation (hyper)polarizabilites of the studied systems can also be reached using the aug-cc-pVDZ basis set (5.3%), although for more accurate calculations of vibrational contributions, i.e., average absolute errors less than 1%, the aug-cc-pVTZ basis set is recommended. It was also demonstrated that anharmonic contributions to first and second hyperpolarizabilities of a medium-sized Schiff base are particularly difficult to accurately predict at the correlated level using property-oriented basis sets. For instance, the value of the nuclear relaxation first hyperpolarizability computed at the MP2/def2-TZVPD level of theory is roughly 3 times larger than that determined using the aug-cc-pVTZ basis set. We link the failure of the def2-TZVPD basis set with the difficulties in predicting the first-order field

  10. Pseudospectral sampling of Gaussian basis sets as a new avenue to high-dimensional quantum dynamics

    NASA Astrophysics Data System (ADS)

    Heaps, Charles

    This thesis presents a novel approach to modeling quantum molecular dynamics (QMD). Theoretical approaches to QMD are essential to understanding and predicting chemical reactivity and spectroscopy. We implement a method based on a trajectory-guided basis set. In this case, the nuclei are propagated in time using classical mechanics. Each nuclear configuration corresponds to a basis function in the quantum mechanical expansion. Using the time-dependent configurations as a basis set, we are able to evolve in time using relatively little information at each time step. We use a basis set of moving frozen (time-independent width) Gaussian functions that are well-known to provide a simple and efficient basis set for nuclear dynamics. We introduce a new perspective to trajectory-guided Gaussian basis sets based on existing numerical methods. The distinction is based on the Galerkin and collocation methods. In the former, the basis set is tested using basis functions, projecting the solution onto the functional space of the problem and requiring integration over all space. In the collocation method, the Dirac delta function tests the basis set, projecting the solution onto discrete points in space. This effectively reduces the integral evaluation to function evaluation, a fundamental characteristic of pseudospectral methods. We adopt this idea for independent trajectory-guided Gaussian basis functions. We investigate a series of anharmonic vibrational models describing dynamics in up to six dimensions. The pseudospectral sampling is found to be as accurate as full integral evaluation, while the former method is fully general and integration is only possible on very particular model potential energy surfaces. Nonadiabatic dynamics are also investigated in models of photodissociation and collinear triatomic vibronic coupling. Using Ehrenfest trajectories to guide the basis set on multiple surfaces, we observe convergence to exact results using hundreds of basis functions

  11. Trail-Needs pseudopotentials in quantum Monte Carlo calculations with plane-wave/blip basis sets

    NASA Astrophysics Data System (ADS)

    Drummond, N. D.; Trail, J. R.; Needs, R. J.

    2016-10-01

    We report a systematic analysis of the performance of a widely used set of Dirac-Fock pseudopotentials for quantum Monte Carlo (QMC) calculations. We study each atom in the periodic table from hydrogen (Z =1 ) to mercury (Z =80 ), with the exception of the 4 f elements (57 ≤Z ≤70 ). We demonstrate that ghost states are a potentially serious problem when plane-wave basis sets are used in density functional theory (DFT) orbital-generation calculations, but that this problem can be almost entirely eliminated by choosing the s channel to be local in the DFT calculation; the d channel can then be chosen to be local in subsequent QMC calculations, which generally leads to more accurate results. We investigate the achievable energy variance per electron with different levels of trial wave function and we determine appropriate plane-wave cutoff energies for DFT calculations for each pseudopotential. We demonstrate that the so-called "T-move" scheme in diffusion Monte Carlo is essential for many elements. We investigate the optimal choice of spherical integration rule for pseudopotential projectors in QMC calculations. The information reported here will prove crucial in the planning and execution of QMC projects involving beyond-first-row elements.

  12. Computational study of influence of diffuse basis functions on geometry optimization and spectroscopic properties of losartan potassium

    NASA Astrophysics Data System (ADS)

    Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta

    2015-02-01

    The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91 kJ/mol and 114.32 kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99 kJ/mol and 117.08 kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29 Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22 Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions

  13. Computational study of influence of diffuse basis functions on geometry optimization and spectroscopic properties of losartan potassium.

    PubMed

    Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta

    2015-02-25

    The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91kJ/mol and 114.32kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99kJ/mol and 117.08kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions when

  14. Basis set limit coupled-cluster studies of hydrogen-bonded systems

    NASA Astrophysics Data System (ADS)

    Boese, A. Daniel

    2015-07-01

    As hydrogen-bonded systems are of utmost importance in especially biological and chemical systems, a new set of highly accurate reference dissociation energies, denoted HB49, is devised. For the molecules in this set, the basis set convergence of post-Hartree-Fock methods, including F12 methods, is investigated. Using combined Møller-Plesset perturbation theory (MP2) and CCSD(T) approaches for energies and MP2 and QCISD(T) for gradients, we achieve CCSD(T) accuracy, which has been determined before to yield an accuracy of 0.2 kJ/mol for a subset of HB49. Both conventional extrapolation techniques and F12 techniques are competitive with each other. By using MP2+ΔCCSD(T), a rather fast basis set convergence is obtained when both basis sets are carefully chosen. In memory of a great supervisor Prof. Nicholas C. Handy

  15. Systematically convergent basis sets with relativistic pseudopotentials. II. Small-core pseudopotentials and correlation consistent basis sets for the post-d group 16-18 elements

    SciTech Connect

    Peterson, Kirk A.; Figgen, Detlev; Goll, Erich; Stoll, Hermann; Dolg, Michael F.

    2003-12-01

    Series of correlation consistent basis sets have been developed for the post-d group 16-18 elements in conjunction with small-core relativistic pseudopotentials (PPs) of the energy-consistent variety. The latter were adjusted to multiconfiguration Dirac-Hartree-Fock data based on the Dirac-Coulomb-Breit Hamiltonian. The outer-core (n-1)spd shells are explicitly treated together with the nsp valence shell with these PPs. The accompanying cc-pVnZ-PP and aug-cc-pVnZ-PP basis sets range in size from DZ to 5Z quality and yield systematic convergence of both Hartree-Fock and correlated total energies. In addition to the calculation of atomic electron affinities and dipole polarizabilities of the rare gas atoms, numerous molecular benchmark calculations (HBr, HI, HAt, Br2, I2, At2, SiSe, SiTe, SiPo, KrH+, XeH+, and RnH+) are also reported at the coupled cluster level of theory. For the purposes of comparison, all-electron calculations using the Douglas-Kroll-Hess Hamiltonian have also been carried out for the halogen-containing molecules using basis sets of 5Z quality.

  16. The static response function in Kohn-Sham theory: an appropriate basis for its matrix representation in case of finite AO basis sets.

    PubMed

    Kollmar, Christian; Neese, Frank

    2014-10-07

    The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.

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

    SciTech Connect

    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 definable 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.

  18. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.

    PubMed

    Steele, Ryan P

    2015-12-17

    This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

  19. Magnetic properties with multiwavelets and DFT: the complete basis set limit achieved.

    PubMed

    Jensen, Stig Rune; Flå, Tor; Jonsson, Dan; Monstad, Rune Sørland; Ruud, Kenneth; Frediani, Luca

    2016-08-03

    Multiwavelets are emerging as an attractive alternative to traditional basis sets such as Gaussian-type orbitals and plane waves. One of their distinctive properties is the ability to reach the basis set limit (often a chimera for traditional approaches) reliably and consistently by fixing the desired precision ε. We present our multiwavelet implementation of the linear response formalism, applied to static magnetic properties, at the self-consistent field level of theory (both for Hartree-Fock and density functional theories). We demonstrate that the multiwavelets consistently improve the accuracy of the results when increasing the desired precision, yielding results that have four to five digits precision, thus providing a very useful benchmark which could otherwise only be estimated by extrapolation methods. Our results show that magnetizabilities obtained with the augmented quadruple-ζ basis (aug-cc-pCVQZ) are practically at the basis set limit, whereas absolute nuclear magnetic resonance shielding tensors are more challenging: even by making use of a standard extrapolation method, the accuracy is not substantially improved. In contrast, our results provide a benchmark that: (1) confirms the validity of the extrapolation ansatz; (2) can be used as a reference to achieve a property-specific extrapolation scheme, thus providing a means to obtain much better extrapolated results; (3) allows us to separate functional-specific errors from basis-set ones and thus to assess the level of cancellation between basis set and functional errors often exploited in density functional theory.

  20. Systematic Study of Locally Dense Basis Sets for NMR Shielding Constants.

    PubMed

    Reid, David M; Kobayashi, Rika; Collins, Michael A

    2014-01-14

    This paper presents a systematic study of partitioning schemes for locally dense basis sets in the context of NMR shielding calculations. The partitionings explored were based exclusively on connectivity and utilized the basis sets from the pcS-n series. Deviations from pcS-4 shieldings were calculated for a set of 28 organic molecules at the HF, B3LYP, and KT3 levels of theory, with the primary goal being the determination of an efficient scheme that achieves maximal deviations of 0.1 ppm for (1)H and 1 ppm for (13)C. Both atom based and group based divisions of basis sets were examined, with the latter providing the most promising results. It is demonstrated that for the systems studied, at least pcS-1 is required for all parts of the molecule. This, coupled with pcS-3 on the group of interest and pcS-2 on the adjacent groups, is sufficient to achieve the desired level of accuracy at a minimal computational expense. In addition, the suitability of the pcS-n basis sets for post-SCF methods was confirmed through a comparison with other standard basis sets at the MP2 level.

  1. Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Arnold, James (Technical Monitor)

    1998-01-01

    The addition of tight functions to sulphur and extrapolation to the complete basis set limit are required to obtain accurate atomization energies. Six different extrapolation procedures are tried. The best atomization energies come from the series of basis sets that yield the most consistent results for all extrapolation techniques. In the variable alpha approach, alpha values larger than 4.5 or smaller than 3, appear to suggest that the extrapolation may not be reliable. It does not appear possible to determine a reliable basis set series using only the triple and quadruple zeta based sets. The scalar relativistic effects reduce the atomization of SO and SO2 by 0.34 and 0.81 kcal/mol, respectively, and clearly must be accounted for if a highly accurate atomization energy is to be computed. The magnitude of the core-valence (CV) contribution to the atomization is affected by missing diffuse valence functions. The CV contribution is much more stable if basis set superposition errors are accounted for. A similar study of SF, SF(+), and SF6 shows that the best family of basis sets varies with the nature of the S bonding.

  2. Effects of Chemical Aging on Global Secondary Organic Aerosol using the Volatility Basis Set Approach

    NASA Astrophysics Data System (ADS)

    Park, R.; Jo, D.; Kim, M.; Spracklen, D. V.; Hodzic, A.

    2014-12-01

    Organic aerosol (OA) constitutes significant mass fractions (20-90%) of total dry fine aerosols in the atmosphere. However, global models of OA have shown large discrepancies when compared to the observations because of the limited capability to simulate secondary OA (SOA). For reducing the discrepancies between observations and models, recent studies have shown that chemical aging reactions in the atmosphere are important because they can lead to decreases in organic volatility, resulting in increase of SOA mass yields. To efficiently simulate chemical aging of SOA in the atmosphere, we implemented the volatility basis set approach in a global 3-D chemical transport model (GEOS-Chem). We present full-year simulations and their comparisons with multiple observations - global aerosol mass spectrometer dataset, the Interagency Monitoring of Protected Visual Environments from the United States, the European Monitoring and Evaluation Programme dataset and water-soluble organic carbon observation data collected over East Asia. Using different input parameters in the model, we also explore the uncertainty of the SOA simulation for which we use an observational constraint to find the optimized values with which the model reduces the discrepancy from the observations. Finally, we estimate the effect of OA on climate using our best simulation results.

  3. Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets

    SciTech Connect

    Holden, Zachary C.; Richard, Ryan M.; Herbert, John M.

    2013-12-28

    An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.

  4. Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Barclay, V. J.

    "Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations

  5. Efficient calculation of integrals in mixed ramp-Gaussian basis sets.

    PubMed

    McKemmish, Laura K

    2015-04-07

    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 very 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.

  6. Representability of Bloch states on Projector-augmented-wave (PAW) basis sets

    NASA Astrophysics Data System (ADS)

    Agapito, Luis; Ferretti, Andrea; Curtarolo, Stefano; Buongiorno Nardelli, Marco

    2015-03-01

    Design of small, yet `complete', localized basis sets is necessary for an efficient dual representation of Bloch states on both plane-wave and localized basis. Such simultaneous dual representation permits the development of faster more accurate (beyond DFT) electronic-structure methods for atomistic materials (e.g. the ACBN0 method.) by benefiting from algorithms (real and reciprocal space) and hardware acceleration (e.g. GPUs) used in the quantum-chemistry and solid-state communities. Finding a `complete' atomic-orbital basis (partial waves) is also a requirement in the generation of robust and transferable PAW pseudopotentials. We have employed the atomic-orbital basis from available PAW data sets, which extends through most of the periodic table, and tested the representability of Bloch states on such basis. Our results show that PAW data sets allow systematic and accurate representability of the PAW Bloch states, better than with traditional quantum-chemistry double-zeta- and double-zeta-polarized-quality basis sets.

  7. Efficient calculation of integrals in mixed ramp-Gaussian basis sets

    SciTech Connect

    McKemmish, Laura K.

    2015-04-07

    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 very 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.

  8. Obtaining Good Performance With Triple-ζ-Type Basis Sets in Double-Hybrid Density Functional Theory Procedures.

    PubMed

    Chan, Bun; Radom, Leo

    2011-09-13

    A variety of combinations of B-LYP-based double-hybrid density functional theory (DHDFT) procedures and basis sets have been examined. A general observation is that the optimal combination of exchange contributions is in the proximity of 30% Becke 1988 (B88) exchange and 70% Hartree-Fock (HF) exchange, while for the correlation contributions, the use of independently optimized spin-component-scaled Møller-Plesset second-order perturbation theory (SCS-MP2) parameters (MP2OS and MP2SS) is beneficial. The triple-ζ Dunning aug'-cc-pVTZ+d and Pople 6-311+G(3df,2p)+d basis sets are found to be cost-effective for DHDFT methods. As a result, we have formulated the DuT-D3 DHDFT procedure, which employs the aug'-cc-pVTZ+d basis set and includes 30% B88 and 70% HF exchange energies, 59% LYP, 47% MP2OS, and 36% MP2SS correlation energies, and a D3 dispersion correction with the parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.35. Likewise, the PoT-D3 DHDFT procedure was formulated with the 6-311+G(3df,2p)+d basis set and has 32% B88 and 68% HF exchange energies, 63% LYP, 46% MP2OS, and 27% MP2SS correlation energies, and the D3 parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.30. Testing using the large E3 set of 740 energies demonstrates the robustness of these methods. Further comparisons show that the performance of these methods, particularly DuT-D3, compares favorably with the previously reported DSD-B-LYP and DSD-B-LYP-D3 methods used in conjunction with quadruple-ζ aug'-pc3+d and aug'-def2-QZVP basis sets but at lower computational expense. The previously reported ωB97X-(LP)/6-311++G(3df,3pd) procedure also performs very well. Our findings highlight the cost-effectiveness of appropriate- and moderate-sized triple-ζ basis sets in the application of DHDFT procedures.

  9. Basis set effects on the Hartree-Fock description of confined many-electron atoms

    NASA Astrophysics Data System (ADS)

    Garza, Jorge; Hernández-Pérez, Julio M.; Ramírez, José-Zeferino; Vargas, Rubicelia

    2012-01-01

    In this work, the basis sets designed by Clementi, Bunge and Thakkar, for atomic systems, have been used to obtain the electronic structure of confined many-electron atoms by using Roothaan's approach in the Hartree-Fock context with a new code written in C, which uses the message-passing interface library. The confinement was imposed as Ludeña suggested to simulate walls with infinity potential. For closed-shell atoms, the Thakkar basis set functions give the best total energies (TE) as a function of the confinement radius, obtaining the following ordering: TE(Thakkar) < TE(Bunge) < TE(Clementi). However, for few open-shell atoms this ordering is not preserved and a trend, for the basis sets, is not observed. Although there are differences between the TE predicted by these basis set functions, the corresponding pressures are similar to each other; it means that changes in the total energy are described almost in the same way by using any of these basis sets. By analysing the total energy as a function of the inverse of the volume we propose an equation of state; for regions of small volumes, this equation predicts that the pressure is inversely proportional to the square of the volume.

  10. Prolapse-free relativistic Gaussian basis sets for the superheavy elements up to Uuo (Z = 118) and Lr (Z = 103)

    SciTech Connect

    Macedo, Luiz Guilherme M de Borin, Antonio Carlos; Silva, Alberico B.F. da

    2007-11-15

    Prolapse-free basis sets suitable for four-component relativistic quantum chemical calculations are presented for the superheavy elements up to {sub 118}Uuo ({sub 104}Rf, {sub 105}Db, {sub 106}Sg, {sub 107}Bh, {sub 108}Hs, {sub 109}Mt, {sub 110}Ds, {sub 111}Rg, {sub 112}Uub, {sub 113}Uut, {sub 114}Uuq, {sub 115}Uup, {sub 116}Uuh, {sub 117}Uus, {sub 118}Uuo) and {sub 103}Lr. These basis sets were optimized by minimizing the absolute values of the energy difference between the Dirac-Fock-Roothaan total energy and the corresponding numerical value at a milli-Hartree order of magnitude, resulting in a good balance between cost and accuracy. Parameters for generating exponents and new numerical data for some superheavy elements are also presented.

  11. Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties

    SciTech Connect

    Woon, D.E.; Dunning, T.H. Jr. )

    1994-02-15

    An accurate description of the electrical properties of atoms and molecules is critical for quantitative predictions of the nonlinear properties of molecules and of long-range atomic and molecular interactions between both neutral and charged species. We report a systematic study of the basis sets required to obtain accurate correlated values for the static dipole ([alpha][sub 1]), quadrupole ([alpha][sub 2]), and octopole ([alpha][sub 3]) polarizabilities and the hyperpolarizability ([gamma]) of the rare gas atoms He, Ne, and Ar. Several methods of correlation treatment were examined, including various orders of Moller--Plesset perturbation theory (MP2, MP3, MP4), coupled-cluster theory with and without perturbative treatment of triple excitations [CCSD, CCSD(T)], and singles and doubles configuration interaction (CISD). All of the basis sets considered here were constructed by adding even-tempered sets of diffuse functions to the correlation consistent basis sets of Dunning and co-workers. With multiply-augmented sets we find that the electrical properties of the rare gas atoms converge smoothly to values that are in excellent agreement with the available experimental data and/or previously computed results. As a further test of the basis sets presented here, the dipole polarizabilities of the F[sup [minus

  12. Influence of basis sets and electron correlation on theoretically predicted infrared intensities

    SciTech Connect

    Miller, M.D. ); Jensen, F. ); Chapman, O.L.; Houk, K.N. )

    1989-06-01

    A systematic study of the effects of basis sets and electron correlation on calculated infrared intensities has been performed with ab initio molecular orbital calculations and Moeller-Plesset perturbation theory. Absolute IR intensities of hydrogen fluoride, hydroxy radical, carbon monoxide, hydrogen cyanide, and formaldehyde have been calculated with basis sets ranging from 3-21G to 6-311++G(2dd{prime},2pp{prime}) and with electron correlation corrections up through MP4(SDTQ). A basis set with polarization and diffuse functions is necessary to obtain reasonably accurate intensities. Electron correlation significantly improves the agreement between experimental and calculated values. Except for carbon monoxide, the intensities calculated at the MP4 level compare favorably with experimental intensities, the errors being less than the measured difference between those obtained from inert-gas matrices at low temperature and those reported for the gas phase.

  13. 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

  14. A basis set convergence study of conventional and HSF electron densities in the Li 2 molecule

    NASA Astrophysics Data System (ADS)

    Challacombe, Matt; Cioslowski, Jerzy

    1994-07-01

    Calculations of nonnuclear, Hartree-Fock HSF and CHSF electron densities are reported for the first time. The positions of critical points in the conventional, HSF, and CHSF electron densities of the Li 2 molecule (including the nonnuclear maximum) and corresponding values of the electron density are computed for a sequence of systematically improved basis sets. The basis set convergence of these topological properties, as well as that of the densities at nuclei, are examined. Quantities derived from HSF and CHSF electron densities are found to converge more rapidly than their conventional counterparts.

  15. Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.

    PubMed

    Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F

    2016-10-05

    Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.

  16. Convergent Partially Augmented Basis Sets for Post-Hartree-Fock Calculations of Molecular Properties and Reaction Barrier Heights.

    PubMed

    Papajak, Ewa; Truhlar, Donald G

    2011-01-11

    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", "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.

  17. Convergent Partially Augmented Basis Sets for Post-Hartree-Fock Calculations of Molecular Properties and Reaction Barrier Heights

    SciTech Connect

    Papajak, Ewa; Truhlar, Donald G.

    2011-01-11

    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”, “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.

  18. MRD-CI potential surfaces using balanced basis sets. IV. The H/sub 2/ molecule and the H/sub 3/ surface

    SciTech Connect

    Wright, J.S.; Kruus, E.

    1986-12-15

    The utility of midbond functions in molecular calculations was tested in two cases where the correct results are known: the H/sub 2/ potential curve and the collinear H/sub 3/ potential surface. For H/sub 2/, a variety of basis sets both with and without bond functions was compared to the exact nonrelativistic potential curve of Kolos and Wolniewicz (J. Chem. Phys. 43, 2429 (1965)). It was found that optimally balanced basis sets at two levels of quality were the double zeta single polarization plus sp bond function basis (BF1) and the triple zeta double polarization plus two sets of sp bond function basis (BF2). These gave bond dissociation energies D/sub e/ = 4.7341 and 4.7368 eV, respectively (expt. 4.7477 eV). Four basis sets were tested for basis set superposition errors, which were found to be small relative to basis set incompleteness and therefore did not affect any conclusions regarding basis set balance. Basis sets BF1 and BF2 were used to construct potential surfaces for collinear H/sub 3/, along with the corresponding basis sets DZ*P and TZ*PP which contain no bond functions. Barrier heights of 12.52, 10.37, 10.06, and 9.96 kcal/mol were obtained for basis sets DZ*P, TZ*PP, BF1, and BF2, respectively, compared to an estimated limiting value of 9.60 kcal/mol. Difference maps, force constants, and relative rms deviations show that the bond functions improve the surface shape as well as the barrier height.

  19. An extended basis set {ital ab} {ital initio} study of alkali metal cation--water clusters

    SciTech Connect

    Feller, D.; Glendening, E.D.; Woon, D.E.; Feyereisen, M.W.

    1995-09-01

    Ionic clusters comprised of a single alkali metal cation and up to eight water molecules were studied at the Hartree--Fock and correlated levels of theory using the correlation consistent sequence of basis sets. Estimates of the degree of convergence in the computed properties with respect to the complete basis set limit were facilitated by the underlying systematic manner in which the correlation consistent sets approach completeness. In favorable cases, improved property values could be obtained by fitting finite basis set results with a simple analytical expression in order to extrapolate to the complete basis set limit. The sensitivity of structures and binding energies were analyzed with regard to the inclusion of valence and core-valence correlation recovery at the MP2, MP4, and CCSD(T) levels of theory. The replacement of metal core electrons and the introduction of relativistic contributions via effective core potentials was compared to corresponding all-electron results. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  20. How to spoil a good basis set for Rayleigh-Ritz calculations

    SciTech Connect

    Pupyshev, Vladimir I.; Montgomery, H. E. Jr.

    2013-08-15

    For model quantum mechanical systems such as the harmonic oscillator and a particle in an impenetrable box, we consider the set of exact discrete spectrum functions and define the modified basis set by subtraction of the ground state wavefunction from all the other wavefunctions with some real weights. It is demonstrated that the modified set of functions is complete in the space of square integrable functions if and only if the series of the squared weights diverges. A similar, but nonequivalent criterion is derived for convergence of Rayleigh-Ritz ground state energy calculations to the exact ground state energy value with the basis set extension. Some numerical illustrations are provided which demonstrate a wide variety of possible situations for model systems.

  1. A minimization method on the basis of embedding the feasible set and the epigraph

    NASA Astrophysics Data System (ADS)

    Zabotin, I. Ya; Shulgina, O. N.; Yarullin, R. S.

    2016-11-01

    We propose a conditional minimization method of the convex nonsmooth function which belongs to the class of cutting-plane methods. During constructing iteration points a feasible set and an epigraph of the objective function are approximated by the polyhedral sets. In this connection, auxiliary problems of constructing iteration points are linear programming problems. In optimization process there is some opportunity of updating sets which approximate the epigraph. These updates are performed by periodically dropping of cutting planes which form embedding sets. Convergence of the proposed method is proved, some realizations of the method are discussed.

  2. Energy-optimal path planning by stochastic dynamically orthogonal level-set optimization

    NASA Astrophysics Data System (ADS)

    Subramani, Deepak N.; Lermusiaux, Pierre F. J.

    2016-04-01

    A stochastic optimization methodology is formulated for computing energy-optimal paths from among time-optimal paths of autonomous vehicles navigating in a dynamic flow field. Based on partial differential equations, the methodology rigorously leverages the level-set equation that governs time-optimal reachability fronts for a given relative vehicle-speed function. To set up the energy optimization, the relative vehicle-speed and headings are considered to be stochastic and new stochastic Dynamically Orthogonal (DO) level-set equations are derived. Their solution provides the distribution of time-optimal reachability fronts and corresponding distribution of time-optimal paths. An optimization is then performed on the vehicle's energy-time joint distribution to select the energy-optimal paths for each arrival time, among all stochastic time-optimal paths for that arrival time. Numerical schemes to solve the reduced stochastic DO level-set equations are obtained, and accuracy and efficiency considerations are discussed. These reduced equations are first shown to be efficient at solving the governing stochastic level-sets, in part by comparisons with direct Monte Carlo simulations. To validate the methodology and illustrate its accuracy, comparisons with semi-analytical energy-optimal path solutions are then completed. In particular, we consider the energy-optimal crossing of a canonical steady front and set up its semi-analytical solution using a energy-time nested nonlinear double-optimization scheme. We then showcase the inner workings and nuances of the energy-optimal path planning, considering different mission scenarios. Finally, we study and discuss results of energy-optimal missions in a wind-driven barotropic quasi-geostrophic double-gyre ocean circulation.

  3. Correlation consistent basis sets for actinides. I. The Th and U atoms.

    PubMed

    Peterson, Kirk A

    2015-02-21

    New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc - pV nZ - PP and cc - pV nZ - DK3, as well as outer-core correlation (valence + 5s5p5d), cc - pwCV nZ - PP and cc - pwCV nZ - DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThFn (n = 2 - 4), ThO2, and UFn (n = 4 - 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF4, ThF3, ThF2, and ThO2 are all within their experimental uncertainties. Bond dissociation energies of ThF4 and ThF3, as well as UF6 and UF5, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF4 and ThO2. The DKH3 atomization energy of ThO2 was calculated to be smaller than the DKH2 value by ∼1 kcal/mol.

  4. Correlation consistent basis sets for actinides. I. The Th and U atoms

    SciTech Connect

    Peterson, Kirk A.

    2015-02-21

    New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than the DKH2

  5. An approach to develop chemical intuition for atomistic electron transport calculations using basis set rotations

    NASA Astrophysics Data System (ADS)

    Borges, A.; Solomon, G. C.

    2016-05-01

    Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and -π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems.

  6. Evolutionary optimization of radial basis function classifiers for data mining applications.

    PubMed

    Buchtala, Oliver; Klimek, Manuel; Sick, Bernhard

    2005-10-01

    In many data mining applications that address classification problems, feature and model selection are considered as key tasks. That is, appropriate input features of the classifier must be selected from a given (and often large) set of possible features and structure parameters of the classifier must be adapted with respect to these features and a given data set. This paper describes an evolutionary algorithm (EA) that performs feature and model selection simultaneously for radial basis function (RBF) classifiers. In order to reduce the optimization effort, various techniques are integrated that accelerate and improve the EA significantly: hybrid training of RBF networks, lazy evaluation, consideration of soft constraints by means of penalty terms, and temperature-based adaptive control of the EA. The feasibility and the benefits of the approach are demonstrated by means of four data mining problems: intrusion detection in computer networks, biometric signature verification, customer acquisition with direct marketing methods, and optimization of chemical production processes. It is shown that, compared to earlier EA-based RBF optimization techniques, the runtime is reduced by up to 99% while error rates are lowered by up to 86%, depending on the application. The algorithm is independent of specific applications so that many ideas and solutions can be transferred to other classifier paradigms.

  7. Vibrational frequency scale factors for density functional theory and the polarization consistent basis sets.

    PubMed

    Laury, Marie L; Carlson, Matthew J; Wilson, Angela K

    2012-11-15

    Calculated harmonic vibrational frequencies systematically deviate from experimental vibrational frequencies. The observed deviation can be corrected by applying a scale factor. Scale factors for: (i) harmonic vibrational frequencies [categorized into low (<1000 cm(-1)) and high (>1000 cm(-1))], (ii) vibrational contributions to enthalpy and entropy, and (iii) zero-point vibrational energies (ZPVEs) have been determined for widely used density functionals in combination with polarization consistent basis sets (pc-n, n = 0,1,2,3,4). The density functionals include pure functionals (BP86, BPW91, BLYP, HCTH93, PBEPBE), hybrid functionals with Hartree-Fock exchange (B3LYP, B3P86, B3PW91, PBE1PBE, mPW1K, BH&HLYP), hybrid meta functionals with the kinetic energy density gradient (M05, M06, M05-2X, M06-2X), a double hybrid functional with Møller-Plesset correlation (B2GP-PLYP), and a dispersion corrected functional (B97-D). The experimental frequencies for calibration were from 41 organic molecules and the ZPVEs for comparison were from 24 small molecules (diatomics, triatomics). For this family of basis sets, the scale factors for each property are more dependent on the functional selection than on basis set level, and thus allow for a suggested scale factor for each density functional when employing polarization consistent basis sets (pc-n, n = 1,2,3,4). A separate scale factor is recommended when the un-polarized basis set, pc-0, is used in combination with the density functionals.

  8. Accurate calculation of the intensity dependence of the refractive index using polarized basis sets.

    PubMed

    Baranowska-Łączkowska, Angelika; Łączkowski, Krzysztof Z; Fernández, Berta

    2012-01-14

    Using the single and double excitation coupled cluster level of theory (CCSD) and the density functional theory/Becke 3-parameter Lee-Yang and Parr (DFT/B3LYP) methods, we test the performance of the Pol, ZPol, and LPol-n (n = ds, dl, fs, fl) basis sets in the accurate description of the intensity dependence of the refractive index in the Ne atom, and the N(2) and the CO molecules. Additionally, we test the aug-pc-n (n = 1, 2) basis sets of Jensen, and the SVPD, TZVPD, and QZVPD bases by Rappoport and Furche. Tests involve calculations of dynamic polarizabilities and frequency dependent second hyperpolarizabilities. The results are interpreted in terms of the medium constants entering the expressions for optically induced birefringences. In all achiral systems, the performance of the LPol-n sets is very good. Also the aug-pc-2 set yields promising results. Accurate CCSD results available in the literature allow us to select the best basis sets in order to carry out DFT/B3LYP calculations of medium constants in larger molecules. As applications, we show results for (R)-fluoro-oxirane and (R)-methyloxirane.

  9. Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets.

    PubMed

    Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost

    2009-11-10

    Hartree-Fock exchange with a truncated Coulomb operator has recently been discussed in the context of periodic plane-waves calculations [Spencer, J.; Alavi, A. Phys. Rev. B: Solid State, 2008, 77, 193110]. In this work, this approach is extended to Gaussian basis sets, leading to a stable and accurate procedure for evaluating Hartree-Fock exchange at the Γ-point. Furthermore, it has been found that standard hybrid functionals can be transformed into short-range functionals without loss of accuracy. The well-defined short-range nature of the truncated exchange operator can naturally be exploited in integral screening procedures and makes this approach interesting for both condensed phase and gas phase systems. The presented Hartree-Fock implementation is massively parallel and scales up to ten thousands of cores. This makes it feasible to perform highly accurate calculations on systems containing thousands of atoms or ten thousands of basis functions. The applicability of this scheme is demonstrated by calculating the cohesive energy of a LiH crystal close to the Hartree-Fock basis set limit and by performing an electronic structure calculation of a complete protein (rubredoxin) in solution with a large and flexible basis set.

  10. Training set optimization under population structure in genomic selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The optimization of the training set (TRS) in genomic selection (GS) has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the Coefficient of D...

  11. Heats of formation for third-period hydrides: test of an extended basis set

    SciTech Connect

    Gordon, M.S.; Heitzinger, J.

    1987-04-23

    The extended basis set developed by McLean and Chandler for third-period atoms is combined with the -311G hydrogen basis and augmented by polarization functions to predict the heats of formation of third-period hydrides at the full MP4 computational level. The calculated heats of formation are at least as accurate as those predicted for second-row hydrides by using MP4/6-311G(d,p) wave functions, with a root mean square error of approximately 4 kcal/mol.

  12. Level-Set Topology Optimization with Aeroelastic Constraints

    NASA Technical Reports Server (NTRS)

    Dunning, Peter D.; Stanford, Bret K.; Kim, H. Alicia

    2015-01-01

    Level-set topology optimization is used to design a wing considering skin buckling under static aeroelastic trim loading, as well as dynamic aeroelastic stability (flutter). The level-set function is defined over the entire 3D volume of a transport aircraft wing box. Therefore, the approach is not limited by any predefined structure and can explore novel configurations. The Sequential Linear Programming (SLP) level-set method is used to solve the constrained optimization problems. The proposed method is demonstrated using three problems with mass, linear buckling and flutter objective and/or constraints. A constraint aggregation method is used to handle multiple buckling constraints in the wing skins. A continuous flutter constraint formulation is used to handle difficulties arising from discontinuities in the design space caused by a switching of the critical flutter mode.

  13. Constructing DNA Barcode Sets based on Particle Swarm Optimization.

    PubMed

    Waang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi

    2017-03-07

    Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

  14. 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.

  15. S H bond dissociation enthalpies: The importance of a complete basis set approach

    NASA Astrophysics Data System (ADS)

    Cabral do Couto, P.; Costa Cabral, Benedito J.; Martinho Simões, José A.

    2006-04-01

    The S-H homolytic bond dissociation enthalpies (BDEs) for several compounds of reference were estimated by different theoretical methods including CCSD(T), CBS-QB3, and the multi-coefficient extrapolated density functional theory multi-level approaches, MCG3-MPWB and MCG3-TS. Emphasis was placed on the importance of extrapolating theoretical BDEs to complete basis set. A very good agreement between S-H BDEs from CCSD(T) calculations and experiment is observed when a simple dual extrapolation scheme to complete basis set proposed by Truhlar is adopted. For thiophenol, our CCSD(T) estimate for the S-H BDE (347.2 kJ mol -1) supports a recent experimental value obtained from time-resolved photoacoustic calorimetry (349 ± 5 kJ mol -1).

  16. Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets.

    PubMed

    Jacobsen, Ruth L; Johnson, Russell D; Irikura, Karl K; Kacker, Raghu N

    2013-02-12

    Anharmonic calculations using vibrational perturbation theory are known to provide near-spectroscopic accuracy when combined with high-level ab initio potential energy functions. However, performance with economical, popular electronic structure methods is less well characterized. We compare the accuracy of harmonic and anharmonic predictions from Hartree-Fock, second-order perturbation, and density functional theories combined with 6-31G(d) and 6-31+G(d,p) basis sets. As expected, anharmonic frequencies are closer than harmonic frequencies to experimental fundamentals. However, common practice is to correct harmonic predictions using multiplicative scaling. The surprising conclusion is that scaled anharmonic calculations are no more accurate than scaled harmonic calculations for the basis sets we used. The data used are from the Computational Chemistry Comparison and Benchmark Database (CCCBDB), maintained by the National Institute of Standards and Technology, which includes more than 3939 independent vibrations for 358 molecules.

  17. Basis-set expansion and truncation approach to interacting Bose particles problem

    NASA Astrophysics Data System (ADS)

    Sze, Michelle Wynne; Sykes, Andrew; Corson, John; Bohn, John

    2014-05-01

    As ultracold gases push into regimes beyond mean-field physics, alternative approaches are required to follow their behavior. To this end, we investigate a basis set expansion and truncation scheme based on perturbation theory to obtain approximate ground state energies as a function of interaction parameter. We explore the ability of this approach to describe interacting Bose particles in 1D and 3D. AFOSR MURI, US DoD through the NDSEG Fellowship Program, and JILA PFC.

  18. Parameterization of Model Validating Sets for Uncertainty Bound Optimizations. Revised

    NASA Technical Reports Server (NTRS)

    Lim, K. B.; Giesy, D. P.

    2000-01-01

    Given measurement data, a nominal model and a linear fractional transformation uncertainty structure with an allowance on unknown but bounded exogenous disturbances, easily computable tests for the existence of a model validating uncertainty set are given. Under mild conditions, these tests are necessary and sufficient for the case of complex, nonrepeated, block-diagonal structure. For the more general case which includes repeated and/or real scalar uncertainties, the tests are only necessary but become sufficient if a collinearity condition is also satisfied. With the satisfaction of these tests, it is shown that a parameterization of all model validating sets of plant models is possible. The new parameterization is used as a basis for a systematic way to construct or perform uncertainty tradeoff with model validating uncertainty sets which have specific linear fractional transformation structure for use in robust control design and analysis. An illustrative example which includes a comparison of candidate model validating sets is given.

  19. Accuracy of Lagrange-sinc functions as a basis set for electronic structure calculations of atoms and molecules

    SciTech Connect

    Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook; Kim, Woo Youn

    2015-03-07

    We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal to 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.

  20. Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting

    PubMed Central

    Das Sarma, Akash; Parameswaran, Aditya; Widom, Jennifer

    2017-01-01

    We study crowdsourcing quality management, that is, given worker responses to a set of tasks, our goal is to jointly estimate the true answers for the tasks, as well as the quality of the workers. Prior work on this problem relies primarily on applying Expectation-Maximization (EM) on the underlying maximum likelihood problem to estimate true answers as well as worker quality. Unfortunately, EM only provides a locally optimal solution rather than a globally optimal one. Other solutions to the problem (that do not leverage EM) fail to provide global optimality guarantees as well. In this paper, we focus on filtering, where tasks require the evaluation of a yes/no predicate, and rating, where tasks elicit integer scores from a finite domain. We design algorithms for finding the global optimal estimates of correct task answers and worker quality for the underlying maximum likelihood problem, and characterize the complexity of these algorithms. Our algorithms conceptually consider all mappings from tasks to true answers (typically a very large number), leveraging two key ideas to reduce, by several orders of magnitude, the number of mappings under consideration, while preserving optimality. We also demonstrate that these algorithms often find more accurate estimates than EM-based algorithms. This paper makes an important contribution towards understanding the inherent complexity of globally optimal crowdsourcing quality management. PMID:28149000

  1. Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting.

    PubMed

    Das Sarma, Akash; Parameswaran, Aditya; Widom, Jennifer

    2016-01-01

    We study crowdsourcing quality management, that is, given worker responses to a set of tasks, our goal is to jointly estimate the true answers for the tasks, as well as the quality of the workers. Prior work on this problem relies primarily on applying Expectation-Maximization (EM) on the underlying maximum likelihood problem to estimate true answers as well as worker quality. Unfortunately, EM only provides a locally optimal solution rather than a globally optimal one. Other solutions to the problem (that do not leverage EM) fail to provide global optimality guarantees as well. In this paper, we focus on filtering, where tasks require the evaluation of a yes/no predicate, and rating, where tasks elicit integer scores from a finite domain. We design algorithms for finding the global optimal estimates of correct task answers and worker quality for the underlying maximum likelihood problem, and characterize the complexity of these algorithms. Our algorithms conceptually consider all mappings from tasks to true answers (typically a very large number), leveraging two key ideas to reduce, by several orders of magnitude, the number of mappings under consideration, while preserving optimality. We also demonstrate that these algorithms often find more accurate estimates than EM-based algorithms. This paper makes an important contribution towards understanding the inherent complexity of globally optimal crowdsourcing quality management.

  2. Relativistic correlating basis sets for actinide atoms from 90Th to 103Lr.

    PubMed

    Noro, Takeshi; Sekiya, Masahiro; Osanai, You; Koga, Toshikatsu; Matsuyama, Hisashi

    2007-12-01

    For 14 actinide atoms from (90)Th to (103)Lr, contracted Gaussian-type function sets are developed for the description of correlations of the 5f, 6d, and 7s electrons. Basis sets for the 6d orbitals are also prepared, since the orbitals are important in molecular environments despite their vacancy in the ground state of some actinides. A segmented contraction scheme is employed for the compactness and efficiency. Contraction coefficients and exponents are so determined as to minimize the deviation from accurate natural orbitals of the lowest term arising from the 5f(n-1)6d(1)7s(2) configuration. The spin-free relativistic effects are considered through the third-order Douglas-Kroll approximation. To test the present correlating sets, all-electron calculations are performed on the ground state of (90)ThO molecule. The calculated spectroscopic constants are in excellent agreement with experimental values.

  3. Ghost transmission: How large basis sets can make electron transport calculations worse

    SciTech Connect

    Herrmann, Carmen; Solomon, Gemma C.; Subotnik, Joseph E.; Mujica, Vladimiro; Ratner, Mark A.

    2010-01-01

    The Landauer approach has proven to be an invaluable tool for calculating the electron transport properties of single molecules, especially when combined with a nonequilibrium Green’s function approach and Kohn–Sham density functional theory. However, when using large nonorthogonal atom-centered basis sets, such as those common in quantum chemistry, one can find erroneous results if the Landauer approach is applied blindly. In fact, basis sets of triple-zeta quality or higher sometimes result in an artificially high transmission and possibly even qualitatively wrong conclusions regarding chemical trends. In these cases, transport persists when molecular atoms are replaced by basis functions alone (“ghost atoms”). The occurrence of such ghost transmission is correlated with low-energy virtual molecular orbitals of the central subsystem and may be interpreted as a biased and thus inaccurate description of vacuum transmission. An approximate practical correction scheme is to calculate the ghost transmission and subtract it from the full transmission. As a further consequence of this study, it is recommended that sensitive molecules be used for parameter studies, in particular those whose transmission functions show antiresonance features such as benzene-based systems connected to the electrodes in meta positions and other low-conducting systems such as alkanes and silanes.

  4. Kinetically balanced Gaussian basis-set approach to relativistic Compton profiles of atoms

    SciTech Connect

    Jaiswal, Prerit; Shukla, Alok

    2007-02-15

    Atomic Compton profiles (CPs) are a very important property which provide us information about the momentum distribution of atomic electrons. Therefore, for CPs of heavy atoms, relativistic effects are expected to be important, warranting a relativistic treatment of the problem. In this paper, we present an efficient approach aimed at ab initio calculations of atomic CPs within a Dirac-Hartree-Fock (DHF) formalism, employing kinetically balanced Gaussian basis functions. The approach is used to compute the CPs of noble gases ranging from He to Rn, and the results have been compared to the experimental and other theoretical data, wherever possible. The influence of the quality of the basis set on the calculated CPs has also been systematically investigated.

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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

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

    SciTech Connect

    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

  8. Geometrically constrained isogeometric parameterized level-set based topology optimization via trimmed elements

    NASA Astrophysics Data System (ADS)

    Wang, Yingjun; Benson, David J.

    2016-12-01

    In this paper, an approach based on the fast point-in-polygon (PIP) algorithm and trimmed elements is proposed for isogeometric topology optimization (TO) with arbitrary geometric constraints. The isogeometric parameterized level-set-based TO method, which directly uses the non-uniform rational basis splines (NURBS) for both level set function (LSF) parameterization and objective function calculation, provides higher accuracy and efficiency than previous methods. The integration of trimmed elements is completed by the efficient quadrature rule that can design the quadrature points and weights for arbitrary geometric shape. Numerical examples demonstrate the efficiency and flexibility of the method.

  9. Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

    PubMed

    Gaspari, Roberto; Rapallo, Arnaldo

    2008-06-28

    In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum

  10. Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

    PubMed

    Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz

    2014-02-01

    Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

  11. Correlation consistent basis sets for lanthanides: The atoms La-Lu.

    PubMed

    Lu, Qing; Peterson, Kirk A

    2016-08-07

    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, 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 Gd2, GdF, and GdF3. 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 Gd2, 151.7 (-36.6) for GdF, and 447.1 (-295.2) for GdF3.

  12. An Efficient Radial Basis Function Mesh Deformation Scheme within an Adjoint-Based Aerodynamic Optimization Framework

    NASA Astrophysics Data System (ADS)

    Poirier, Vincent

    Mesh deformation schemes play an important role in numerical aerodynamic optimization. As the aerodynamic shape changes, the computational mesh must adapt to conform to the deformed geometry. In this work, an extension to an existing fast and robust Radial Basis Function (RBF) mesh movement scheme is presented. Using a reduced set of surface points to define the mesh deformation increases the efficiency of the RBF method; however, at the cost of introducing errors into the parameterization by not recovering the exact displacement of all surface points. A secondary mesh movement is implemented, within an adjoint-based optimization framework, to eliminate these errors. The proposed scheme is tested within a 3D Euler flow by reducing the pressure drag while maintaining lift of a wing-body configured Boeing-747 and an Onera-M6 wing. As well, an inverse pressure design is executed on the Onera-M6 wing and an inverse span loading case is presented for a wing-body configured DLR-F6 aircraft.

  13. FDR-FET: an optimizing gene set enrichment analysis method.

    PubMed

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher's exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications.

  14. Extrapolation of G0W0 energy levels from small basis sets for elements from H to Cl

    NASA Astrophysics Data System (ADS)

    Zhu, Tong; Blum, Volker

    G0W0 calculations based on orbitals from a density-functional theory reference are widely used to predict carrier levels in molecular and inorganic materials. Their computational feasibility, however, is limited by the need to evaluate slow-converging sums over unoccupied states, requiring large basis sets paired with unfavorable scaling exponents to evaluate the self-energy. In the quantum chemistry literature, complete basis set (CBS) extrapolation strategies have been used successfully to overcome this problem for total energies. We here apply the principle of basis set extrapolation to G0W0 energy levels. For a set of 49 small molecules and clusters containing the elements H, Li through F, and Na through Cl, we test established extrapolation strategies based on Dunning's correlation-consistent (cc) basis sets (aug)-cc-pVNZ (N=2-5), as well as numeric atom-centered NAO-VCC-nZ (n=2-5) basis sets in the FHI-aims all-electron code. For the occupied and lowest unoccupied levels, different extrapolation strategies agree within +/-50 meV based on large 4Z and 5Z basis sets. We show that extrapolation based on much smaller 2Z and 3Z basis sets with largest errors +/- 100 meV based on a refinement of the NAO-VCC-nZ basis sets.

  15. Variational Trajectory Optimization Tool Set: Technical description and user's manual

    NASA Technical Reports Server (NTRS)

    Bless, Robert R.; Queen, Eric M.; Cavanaugh, Michael D.; Wetzel, Todd A.; Moerder, Daniel D.

    1993-01-01

    The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included.

  16. An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification

    PubMed Central

    Samal, Ashok; Rong, Panying; Green, Jordan R.

    2016-01-01

    Purpose The authors sought to determine an optimal set of flesh points on the tongue and lips for classifying speech movements. Method The authors used electromagnetic articulographs (Carstens AG500 and NDI Wave) to record tongue and lip movements from 13 healthy talkers who articulated 8 vowels, 11 consonants, a phonetically balanced set of words, and a set of short phrases during the recording. We used a machine-learning classifier (support-vector machine) to classify the speech stimuli on the basis of articulatory movements. We then compared classification accuracies of the flesh-point combinations to determine an optimal set of sensors. Results When data from the 4 sensors (T1: the vicinity between the tongue tip and tongue blade; T4: the tongue-body back; UL: the upper lip; and LL: the lower lip) were combined, phoneme and word classifications were most accurate and were comparable with the full set (including T2: the tongue-body front; and T3: the tongue-body front). Conclusion We identified a 4-sensor set—that is, T1, T4, UL, LL—that yielded a classification accuracy (91%–95%) equivalent to that using all 6 sensors. These findings provide an empirical basis for selecting sensors and their locations for scientific and emerging clinical applications that incorporate articulatory movements. PMID:26564030

  17. Simulations of smog-chamber experiments using the two-dimensional volatility basis set: linear oxygenated precursors.

    PubMed

    Chacon-Madrid, Heber J; Murphy, Benjamin N; Pandis, Spyros N; Donahue, Neil M

    2012-10-16

    We use a two-dimensional volatility basis set (2D-VBS) box model to simulate secondary organic aerosol (SOA) mass yields of linear oxygenated molecules: n-tridecanal, 2- and 7-tridecanone, 2- and 7-tridecanol, and n-pentadecane. A hybrid model with explicit, a priori treatment of the first-generation products for each precursor molecule, followed by a generic 2D-VBS mechanism for later-generation chemistry, results in excellent model-measurement agreement. This strongly confirms that the 2D-VBS mechanism is a predictive tool for SOA modeling but also suggests that certain important first-generation products for major primary SOA precursors should be treated explicitly for optimal SOA predictions.

  18. Optimizing antibiotic therapy in the intensive care unit setting

    PubMed Central

    Kollef, Marin H

    2001-01-01

    Antibiotics are one of the most common therapies administered in the intensive care unit setting. In addition to treating infections, antibiotic use contributes to the emergence of resistance among pathogenic microorganisms. Therefore, avoiding unnecessary antibiotic use and optimizing the administration of antimicrobial agents will help to improve patient outcomes while minimizing further pressures for resistance. This review will present several strategies aimed at achieving optimal use of antimicrobial agents. It is important to note that each intensive care unit should have a program in place which monitors antibiotic utilization and its effectiveness. Only in this way can the impact of interventions aimed at improving antibiotic use (e.g. antibiotic rotation, de-escalation therapy) be evaluated at the local level. PMID:11511331

  19. Analytic basis set for high-Z atomic QED calculations: Heavy He-like ions

    NASA Astrophysics Data System (ADS)

    Hylton, D. J.; Snyderman, N. J.

    1997-04-01

    A relativistic Sturmian analytic basis set representation for the Coulomb-Dirac Green function, previously studied by Zapryagaev, Manakov, and Pal'chikov [Opt. Spectrosc. 52, 248 (1982)], is investigated for application to high-Z atomic QED calculations. This pseudoeigenfunction representation follows from exact identities starting from the Whittaker function representation. It eliminates the radial ordering problem of that representation, and so is particularly useful for numerical calculation of the perturbation theory Feynman diagrams with more than one electron Green function. While the Green function represents discrete bound states, and both positive and negative energy continuum states, the Sturmian (bound-state-like) form for the pseudoeigenfunctions makes it possible to more analytically calculate matrix elements for full photon exchange, reducing numerical problems for high photon frequency. For He-like Fm (Z=100) we calculate the perturbation theory equivalent of the Dirac-Fock-Breit ground-state energy, agreeing well with the Grant code and with the numerical B-spline basis set approach results of Blundell, Mohr, Johnson, and Sapirstein [Phys. Rev. A 48, 2615 (1993)]. Preliminary results on the relativistic and QED correlation are also reported.

  20. Analytic basis set for high-Z atomic QED calculations: Heavy He-like ions

    SciTech Connect

    Hylton, D.J.; Snyderman, N.J.

    1997-04-01

    A relativistic Sturmian analytic basis set representation for the Coulomb-Dirac Green function, previously studied by Zapryagaev, Manakov, and Pal{close_quote}chikov [Opt. Spectrosc. {bold 52}, 248 (1982)], is investigated for application to high-Z atomic QED calculations. This pseudoeigenfunction representation follows from exact identities starting from the Whittaker function representation. It eliminates the radial ordering problem of that representation, and so is particularly useful for numerical calculation of the perturbation theory Feynman diagrams with more than one electron Green function. While the Green function represents discrete bound states, and both positive and negative energy continuum states, the Sturmian (bound-state-like) form for the pseudoeigenfunctions makes it possible to more analytically calculate matrix elements for full photon exchange, reducing numerical problems for high photon frequency. For He-like Fm (Z=100) we calculate the perturbation theory equivalent of the Dirac-Fock-Breit ground-state energy, agreeing well with the Grant code and with the numerical B-spline basis set approach results of Blundell, Mohr, Johnson, and Sapirstein [Phys. Rev. A {bold 48}, 2615 (1993)]. Preliminary results on the relativistic and QED correlation are also reported. {copyright} {ital 1997} {ital The American Physical Society}

  1. FDR-FET: an optimizing gene set enrichment analysis method

    PubMed Central

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as “gene sets”. Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher’s exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications. PMID:21918636

  2. Using symmetry-adapted optimized sum-of-products basis functions to calculate vibrational spectra

    NASA Astrophysics Data System (ADS)

    Leclerc, Arnaud; Carrington, Tucker

    2016-01-01

    Vibrational spectra can be computed without storing full-dimensional vectors by using low-rank sum-of-products (SOP) basis functions. We introduce symmetry constraints in the SOP basis functions to make it possible to separately calculate states in different symmetry subgroups. This is done using a power method to compute eigenvalues and an alternating least squares method to optimize basis functions. Owing to the fact that the power method favours the convergence of the lowest states, one must be careful not to exclude basis functions of some symmetries. Exploiting symmetry facilitates making assignments and improves the accuracy. The method is applied to the acetonitrile molecule.

  3. Asynchronous parallel generating set search for linearly-constrained optimization.

    SciTech Connect

    Lewis, Robert Michael; Griffin, Joshua D.; Kolda, Tamara Gibson

    2006-08-01

    Generating set search (GSS) is a family of direct search methods that encompasses generalized pattern search and related methods. We describe an algorithm for asynchronous linearly-constrained GSS, which has some complexities that make it different from both the asynchronous bound-constrained case as well as the synchronous linearly-constrained case. The algorithm has been implemented in the APPSPACK software framework and we present results from an extensive numerical study using CUTEr test problems. We discuss the results, both positive and negative, and conclude that GSS is a reliable method for solving small-to-medium sized linearly-constrained optimization problems without derivatives.

  4. 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.

  5. An active set algorithm for treatment planning optimization.

    PubMed

    Hristov, D H; Fallone, B G

    1997-09-01

    An active set algorithm for optimization of radiation therapy dose planning by intensity modulated beams has been developed. The algorithm employs a conjugate-gradient routine for subspace minimization in order to achieve a higher rate of convergence than the widely used constrained steepest-descent method at the expense of a negligible amount of overhead calculations. The performance of the new algorithm has been compared to that of the constrained steepest-descent method for various treatment geometries and two different objectives. The active set algorithm is found to be superior to the constrained steepest descent, both in terms of its convergence properties and the residual value of the cost functions at termination. Its use can significantly accelerate the design of conformal plans with intensity modulated beams by decreasing the number of time-consuming dose calculations.

  6. Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.

    2014-11-01

    The Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an efficient site-centered, electronic-structure technique for addressing an assembly of N scatterers. Wave functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax=(l,mmax), while scattering matrices, which determine spectral properties, are truncated at Lt r=(l,mt r) where phase shifts δl >ltr are negligible. Historically, Lmax is set equal to Lt r, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax>Lt r with δl >ltr set to zero [X.-G. Zhang and W. H. Butler, Phys. Rev. B 46, 7433 (1992), 10.1103/PhysRevB.46.7433]. We present a numerically efficient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N (ltr+1 ) 2 ] and includes higher-L contributions via linear algebra [R2 process with rank N (lmax+1) 2 ]. The augmented-KKR approach yields properly normalized wave functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe, and L 1 0 CoPt and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Lt r.

  7. Accurate dispersion interactions from standard density-functional theory methods with small basis sets.

    PubMed

    Mackie, Iain D; Dilabio, Gino A

    2010-06-21

    B971, PBE and PBE1 density functionals with 6-31G(d) basis sets are shown to accurately describe the binding in dispersion bound dimers. This is achieved through the use of dispersion-correcting potentials (DCPs) in conjunction with counterpoise corrections. DCPs resemble and are applied like conventional effective core potentials that can be used with most computational chemistry programs without code modification. Rather, DCPs are implemented by simple appendage to the input files for these types of programs. Binding energies are predicted to within ca. 11% and monomer separations to within ca. 0.06 A of high-level wavefunction data using B971/6-31G(d)-DCP. Similar results are obtained for PBE and PBE1 with the 6-31G(d) basis sets and DCPs. Although results found using the 3-21G(d) are not as impressive, they never-the-less show promise as a means of initial study for a wide variety of dimers, including those dominated by dispersion, hydrogen-bonding and a mixture of interactions. Notable improvement is found in comparison to M06-2X/6-31G(d) data, e.g., mean absolute deviations for the S22-set of dimers of ca. 13.6 and 16.5% for B971/6-31G(d)-DCP and M06-2X, respectively. However, it should be pointed out that the latter data were obtained using a larger integration grid size since a smaller grid results in different binding energies and geometries for simple dispersion-bound dimers such as methane and ethene.

  8. Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

    SciTech Connect

    Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.

    2014-11-04

    Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax = (l,m)max, while scattering matrices, which determine spectral properties, are truncated at Ltr = (l,m)tr where phase shifts δl>ltr are negligible. Historically, Lmax is set equal to Ltr, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax > Ltr with δl>ltr set to zero [Zhang and Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N(ltr + 1)2] and includes higher-L contributions via linear algebra [R2 process with rank N(lmax +1)2]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L10 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Ltr.

  9. Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism

    DOE PAGES

    Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; ...

    2014-11-04

    Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax = (l,m)max, while scattering matrices, which determine spectral properties, are truncated at Ltr = (l,m)tr where phase shifts δl>ltr are negligible. Historically, Lmax is set equal to Ltr, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax > Ltr with δl>ltr set to zero [Zhang andmore » Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N(ltr + 1)2] and includes higher-L contributions via linear algebra [R2 process with rank N(lmax +1)2]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L10 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Ltr.« less

  10. 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.

  11. A restricted-open-shell complete-basis-set model chemistry

    NASA Astrophysics Data System (ADS)

    Wood, Geoffrey P. F.; Radom, Leo; Petersson, George A.; Barnes, Ericka C.; Frisch, Michael J.; Montgomery, John A.

    2006-09-01

    A restricted-open-shell model chemistry based on the complete basis set-quadratic Becke3 (CBS-QB3) model is formulated and denoted ROCBS-QB3. As the name implies, this method uses spin-restricted wave functions, both for the direct calculations of the various components of the electronic energy and for extrapolating the correlation energy to the complete-basis-set limit. These modifications eliminate the need for empirical corrections that are incorporated in standard CBS-QB3 to compensate for spin contamination when spin-unrestricted wave functions are used. We employ an initial test set of 19 severely spin-contaminated species including doublet radicals and both singlet and triplet biradicals. The mean absolute deviation (MAD) from experiment for the new ROCBS-QB3 model (3.6±1.5kJmol-1) is slightly smaller than that of the standard unrestricted CBS-QB3 version (4.8±1.5kJmol-1) and substantially smaller than the MAD for the unrestricted CBS-QB3 before inclusion of the spin correction (16.1±1.5kJmol-1). However, when applied to calculate the heats of formation at 298K for the moderately spin-contaminated radicals in the G2/97 test set, ROCBS-QB3 does not perform quite as well as the standard unrestricted CBS-QB3, with a MAD from experiment of 3.8±1.6kJmol-1 (compared with 2.9±1.6kJmol-1 for standard CBS-QB3). ROCBS-QB3 performs marginally better than standard CBS-QB3 for the G2/97 set of ionization energies with a MAD of 4.1±0.1kJmol-1 (compared with 4.4±0.1kJmol-1) and electron affinities with a MAD of 3.9±0.2kJmol-1 (compared with 4.3±0.2kJmol-1), but the differences in MAD values are comparable to the experimental uncertainties. Our overall conclusion is that ROCBS-QB3 eliminates the spin correction in standard CBS-QB3 with no loss in accuracy.

  12. A restricted-open-shell complete-basis-set model chemistry.

    PubMed

    Wood, Geoffrey P F; Radom, Leo; Petersson, George A; Barnes, Ericka C; Frisch, Michael J; Montgomery, John A

    2006-09-07

    A restricted-open-shell model chemistry based on the complete basis set-quadratic Becke3 (CBS-QB3) model is formulated and denoted ROCBS-QB3. As the name implies, this method uses spin-restricted wave functions, both for the direct calculations of the various components of the electronic energy and for extrapolating the correlation energy to the complete-basis-set limit. These modifications eliminate the need for empirical corrections that are incorporated in standard CBS-QB3 to compensate for spin contamination when spin-unrestricted wave functions are used. We employ an initial test set of 19 severely spin-contaminated species including doublet radicals and both singlet and triplet biradicals. The mean absolute deviation (MAD) from experiment for the new ROCBS-QB3 model (3.6+/-1.5 kJ mol(-1)) is slightly smaller than that of the standard unrestricted CBS-QB3 version (4.8+/-1.5 kJ mol(-1)) and substantially smaller than the MAD for the unrestricted CBS-QB3 before inclusion of the spin correction (16.1+/-1.5 kJ mol(-1)). However, when applied to calculate the heats of formation at 298 K for the moderately spin-contaminated radicals in the G2/97 test set, ROCBS-QB3 does not perform quite as well as the standard unrestricted CBS-QB3, with a MAD from experiment of 3.8+/-1.6 kJ mol(-1) (compared with 2.9+/-1.6 kJ mol(-1) for standard CBS-QB3). ROCBS-QB3 performs marginally better than standard CBS-QB3 for the G2/97 set of ionization energies with a MAD of 4.1+/-0.1 kJ mol(-1) (compared with 4.4+/-0.1 kJ mol(-1)) and electron affinities with a MAD of 3.9+/-0.2 kJ mol(-1) (compared with 4.3+/-0.2 kJ mol(-1)), but the differences in MAD values are comparable to the experimental uncertainties. Our overall conclusion is that ROCBS-QB3 eliminates the spin correction in standard CBS-QB3 with no loss in accuracy.

  13. Optimal sets of measurement data for profile reconstruction in scatterometry

    NASA Astrophysics Data System (ADS)

    Gross, H.; Rathsfeld, A.; Scholze, F.; Bär, M.; Dersch, U.

    2007-06-01

    We discuss numerical algorithms for the determination of periodic surface structures from light diffraction patterns. With decreasing feature sizes of lithography masks, increasing demands on metrology techniques arise. Scatterometry as a non-imaging indirect optical method is applied to simple periodic line structures in order to determine parameters like side-wall angles, heights, top and bottom widths and to evaluate the quality of the manufacturing process. The numerical simulation of diffraction is based on the finite element solution of the Helmholtz equation. The inverse problem seeks to reconstruct the grating geometry from measured diffraction patterns. Restricting the class of gratings and the set of measurements, this inverse problem can be reformulated as a non-linear operator equation in Euclidean spaces. The operator maps the grating parameters to special efficiencies of diffracted plane wave modes. We employ a Gauss-Newton type iterative method to solve this operator equation. The reconstruction properties and the convergence of the algorithm, however, is controlled by the local conditioning of the non-linear mapping. To improve reconstruction and convergence, we determine optimal sets of efficiencies optimizing the condition numbers of the corresponding Jacobians. Numerical examples are presented for "chrome on glass" masks under the wavelength 632.8 nm and for EUV masks.

  14. Singularity Correction for Long-Range-Corrected Density Functional Theory with Plane-Wave Basis Sets.

    PubMed

    Kawashima, Yukio; Hirao, Kimihiko

    2017-03-09

    We introduced two methods to correct the singularity in the calculation of long-range Hartree-Fock (HF) exchange for long-range-corrected density functional theory (LC-DFT) calculations in plane-wave basis sets. The first method introduces an auxiliary function to cancel out the singularity. The second method introduces a truncated long-range Coulomb potential, which has no singularity. We assessed the introduced methods using the LC-BLYP functional by applying it to isolated systems of naphthalene and pyridine. We first compared the total energies and the HOMO energies of the singularity-corrected and uncorrected calculations and confirmed that singularity correction is essential for LC-DFT calculations using plane-wave basis sets. The LC-DFT calculation results converged rapidly with respect to the cell size as the other functionals, and their results were in good agreement with the calculated results obtained using Gaussian basis sets. LC-DFT succeeded in obtaining accurate orbital energies and excitation energies. We next applied LC-DFT with singularity correction methods to the electronic structure calculations of the extended systems, Si and SiC. We confirmed that singularity correction is important for calculations of extended systems as well. The calculation results of the valence and conduction bands by LC-BLYP showed good convergence with respect to the number of k points sampled. The introduced methods succeeded in overcoming the singularity problem in HF exchange calculation. We investigated the effect of the singularity correction on the excitation state calculation and found that careful treatment of the singularities is required compared to ground-state calculations. We finally examined the excitonic effect on the band gap of the extended systems. We calculated the excitation energies to the first excited state of the extended systems using a supercell model at the Γ point and found that the excitonic binding energy, supposed to be small for

  15. Basis sets for ab initio periodic Hartree-Fock studies of zeolite/adsorbate interactions: He, Ne, and Ar in silica sodalite

    SciTech Connect

    Nada, R.; Nicholas, J.B.; McCarthy, M.I.; Hess, A.C.

    1996-11-15

    Silica sodalite is an ideal model system to establish base-line computer requirements of ab initio periodic Hartree-Fock (PHF) calculations of zeolites. In this article, the authors investigate the effect of various basis sets on the structural and electronic properties of bulk silica sodalite. They also study the interaction of He, Ne, and Ar with the sodalite cage. This work shows that basis-set superposition errors (BSSE) in calculations using STO-3G and 6-21G(*) basis sets are as large as the interaction energies, leading to poor confidence in the results. To cure this problem, the authors present high-quality basis sets for si, O, He, Ne, and Ar, optimized for use with PHF methods, and demonstrate that the new basis set greatly reduces BSSE. The theoretical barriers for transfer of the rare gases between sodalite cages are 5.6, 13.2, and 62.1 kcal/mol for He, Ne, and Ar. 27 refs., 6 figs., 8 tabs.

  16. TiCl, TiH and TiH+ Bond Energies, a Test of a Correlation Consistent Ti Basis Set

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1999-01-01

    Correlation consistent basis sets are developed for Ti atom. The polarization functions are optimized for the average of the 3F and 5F states. One series of correlation consistent basis sets is for 3d and 4s correlation, while the second series includes 3s and 3p correlation as well as 3d and 4s correlation. These basis sets are tested using the Ti 3F-5F separation and the dissociation energies of TiCl X4Phi, TiH X4Phi, and TiH(+) X3Phi. The CCSD(T) complete basis set limit values are determined by extrapolation. The Douglas Kroll approach is used to compute the scalar relativistic effect. Spin-orbit effects are taken from experiment and/or computed at the CASSCF level. The Ti 3F-5F separation is in excellent agreement with experiment, while the TiCl, TiH, and TiH(+) bond energies are in good agreement with experiment. Extrapolation with the valence basis set is consistent with other atoms, while including 3s and 3p correlation appears to make extrapolation.

  17. Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets

    NASA Astrophysics Data System (ADS)

    Paier, Joachim; Diaconu, Cristian V.; Scuseria, Gustavo E.; Guidon, Manuel; Vandevondele, Joost; Hutter, Jürg

    2009-11-01

    Calculating highly accurate thermochemical properties of condensed matter via wave-function-based approaches (such as, e.g., Hartree-Fock or hybrid functionals) has recently attracted much interest. We here present two strategies providing accurate Hartree-Fock energies for solid LiH in a large Gaussian basis set and applying periodic boundary conditions. The total energies were obtained using two different approaches, namely, a supercell evaluation of Hartree-Fock exchange using a truncated Coulomb operator and an extrapolation toward the full-range Hartree-Fock limit of a Padé fit to a series of short-range screened Hartree-Fock calculations. These two techniques agreed to significant precision. We also present the Hartree-Fock cohesive energy of LiH (converged to within sub-millielectron volt) at the experimental equilibrium volume as well as the Hartree-Fock equilibrium lattice constant and bulk modulus.

  18. Calculation of bond dissociation energies of diatomic molecules using bond function basis sets with counterpoise corrections

    SciTech Connect

    Li, Z.; Pan, Y.K.; Tao, F.M.

    1996-01-15

    Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.

  19. AgH, Ag/sub 2/, and AgO revisited: Basis set extensions

    SciTech Connect

    Martin, R.L.

    1987-05-01

    An extended basis set has been developed for Ag which significantly improves the agreement between theoretical and experimental spectroscopic parameters for AgH, AgO, and Ag/sub 2/. The major improvement comes about as a result of the improved treatment of electron correlation in the Ag d shell upon the introduction of f functions. Their inclusion produces very slight differences at the SCF level, but significant reductions in r/sub e/ and increases in ..omega../sub e/ and D/sub e/ in the Mo-dash-barller--Plesset perturbation theory expansion. At the MP4(SDTQ) level, typical results are 0.02 A too long for r/sub e/, 4% too low for ..omega../sub e/, and 10 kcal too small for D/sub e/. From a pragmatic standpoint, MP2 give results very similar to this at a much reduced level of effort.

  20. Dynamic sensitivity analysis of long running landslide models through basis set expansion and meta-modelling

    NASA Astrophysics Data System (ADS)

    Rohmer, Jeremy

    2016-04-01

    Predicting the temporal evolution of landslides is typically supported by numerical modelling. Dynamic sensitivity analysis aims at assessing the influence of the landslide properties on the time-dependent predictions (e.g., time series of landslide displacements). Yet two major difficulties arise: 1. Global sensitivity analysis require running the landslide model a high number of times (> 1000), which may become impracticable when the landslide model has a high computation time cost (> several hours); 2. Landslide model outputs are not scalar, but function of time, i.e. they are n-dimensional vectors with n usually ranging from 100 to 1000. In this article, I explore the use of a basis set expansion, such as principal component analysis, to reduce the output dimensionality to a few components, each of them being interpreted as a dominant mode of variation in the overall structure of the temporal evolution. The computationally intensive calculation of the Sobol' indices for each of these components are then achieved through meta-modelling, i.e. by replacing the landslide model by a "costless-to-evaluate" approximation (e.g., a projection pursuit regression model). The methodology combining "basis set expansion - meta-model - Sobol' indices" is then applied to the La Frasse landslide to investigate the dynamic sensitivity analysis of the surface horizontal displacements to the slip surface properties during the pore pressure changes. I show how to extract information on the sensitivity of each main modes of temporal behaviour using a limited number (a few tens) of long running simulations. In particular, I identify the parameters, which trigger the occurrence of a turning point marking a shift between a regime of low values of landslide displacements and one of high values.

  1. A complete basis set model chemistry. V. Extensions to six or more heavy atoms

    NASA Astrophysics Data System (ADS)

    Ochterski, Joseph W.; Petersson, G. A.; Montgomery, J. A., Jr.

    1996-02-01

    The major source of error in most ab initio calculations of molecular energies is the truncation of the one-electron basis set. Extrapolation to the complete basis set second-order (CBS2) limit using the N-1 asymptotic convergence of N-configuration pair natural orbital (PNO) expansions can be combined with the use of relatively small basis sets for the higher-order (i.e., MP3, MP4, and QCI) correlation energy to develop cost effective computational models. Following this strategy, three new computational models denoted CBS-4, CBS-q, and CBS-Q, are introduced. The mean absolute deviations (MAD) from experiment for the 125 energies of the G2 test set are 2.0, 1.7, and 1.0 kcal/mol, respectively. These results compare favorably with the MAD for the more costly G2(MP2), G2, and CBS-QCI/APNO models (1.6, 1.2, and 0.5 kcal/mol, respectively). The error distributions over the G2 test set are indistinguishable from Gaussian distribution functions for all six models, indicating that the rms errors can be interpreted in the same way that experimental uncertainties are used to assess reliability. However, a broader range of examples reveals special difficulties presented by spin contamination, high molecular symmetry, and localization problems in molecules with multiple lone pairs on the same atom. These characteristics can occasionally result in errors several times the size expected from the Gaussian distributions. Each of the CBS models has a range of molecular size for which it is the most accurate computational model currently available. The largest calculations reported for these models include: The CBS-4 heat of formation of tetranitrohydrazine (91.5±5 kcal/mol), the CBS-4 and CBS-q isomerization energies for the conversion of azulene to naphthalene (ΔHcalc=-35.2±1.0 kcal/mol, ΔHexp=-35.3±2.2 kcal/mol), and the CBS-Q heat of formation of SF6 (ΔHcalc=-286.6±1.3 kcal/mol, ΔHexp=-288.3±0.2 kcal/mol). The CBS-Q value for the dissociation energy of a C-H bond in

  2. Basis set effects on the intermolecular interaction energies of methane dimers obtained by the Moeller-Plesset perturbation theory calculation

    SciTech Connect

    Tsuzuki, Seiji; Tanabe, Kazutoshi )

    1991-03-21

    Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.

  3. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    NASA Astrophysics Data System (ADS)

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-01

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  4. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    SciTech Connect

    Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  5. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

    PubMed

    Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit

  6. Practical aspects of variable reduction formulations and reduced basis algorithms in multidisciplinary design optimization

    NASA Technical Reports Server (NTRS)

    Lewis, Robert Michael

    1995-01-01

    This paper discusses certain connections between nonlinear programming algorithms and the formulation of optimization problems for systems governed by state constraints. The major points of this paper are the detailed calculation of the sensitivities associated with different formulations of optimization problems and the identification of some useful relationships between different formulations. These relationships have practical consequences; if one uses a reduced basis nonlinear programming algorithm, then the implementations for the different formulations need only differ in a single step.

  7. 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.

  8. Optimal gate-width setting for passive neutrons multiplicity counting

    SciTech Connect

    Croft, Stephen; Evans, Louise G; Schear, Melissa A

    2010-01-01

    When setting up a passive neutron coincidence counter it is natural to ask what coincidence gate settings should be used to optimize the counting precision. If the gate width is too short then signal is lost and the precision is compromised because in a given period only a few coincidence events will be observed. On the other hand if the gate is too large the signal will be maximized but it will also be compromised by the high level of random pile-up or Accidental coincidence events which must be subtracted. In the case of shift register electronics connected to an assay chamber with an exponential dieaway profile operating in the regime where the Accidentals rate dominates the Reals coincidence rate but where dead-time is not a concern, simple arguments allow one to show that the relative precision on the net Reals rate is minimized when the coincidence gate is set to about 1.2 times the lie dieaway time of the system. In this work we show that making the same assumptions it is easy to show that the relative precision on the Triples rates is also at a minimum when the relative precision of the Doubles (or Reals) is at a minimum. Although the analysis is straightforward to our knowledge such a discussion has not been documented in the literature before. Actual measurement systems do not always behave in the ideal we choose to model them. Fortunately however the variation in the relative precision as a function of gate width is rather flat for traditional safeguards counters and so the performance is somewhat forgiving of the exact choice. The derivation further serves to delineate the important parameters which determine the relative counting precision of the Doubles and Triples rates under the regime considered. To illustrate the similarities and differences we consider the relative standard deviation that might be anticipated for a passive correlation count of an axial section of a spent nuclear fuel assembly under practically achievable conditions.

  9. European air quality modelled by CAMx including the volatility basis set scheme

    NASA Astrophysics Data System (ADS)

    Ciarelli, G.; Aksoyoglu, S.; Crippa, M.; Jimenez, J. L.; Nemitz, E.; Sellegri, K.; Äijälä, M.; Carbone, S.; Mohr, C.; O'Dowd, C.; Poulain, L.; Baltensperger, U.; Prévôt, A. S. H.

    2015-12-01

    Four periods of EMEP (European Monitoring and Evaluation Programme) intensive measurement campaigns (June 2006, January 2007, September-October 2008 and February-March 2009) were modelled using the regional air quality model CAMx with VBS (Volatility Basis Set) approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February-March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosols (OA). Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database Airbase. Sulfur dioxide (SO2) and ozone (O3) were found to be overestimated for all the four periods with O3 having the largest mean bias during June 2006 and January-February 2007 periods (8.93 and 12.30 ppb mean biases, respectively). In contrast, nitrogen dioxide (NO2) and carbon monoxide (CO) were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 very well for all the four periods with average biases ranging from -2.13 to 1.04 μg m-3. Comparisons with AMS (Aerosol Mass Spectrometer) measurements at different sites in Europe during February-March 2009, showed that in general the model over-predicts the inorganic aerosol fraction and under-predicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of volatility basis set scheme (VBS) on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February-March 2009 the chamber-case reduced the total OA concentrations by about 43 % on average. On the other hand, a test based on ambient measurement data increased OA concentrations by about 47 % for the same period bringing model

  10. Optimization of head movement recognition using Augmented Radial Basis Function Neural Network.

    PubMed

    Yuwono, Mitchell; Handojoseno, A M Ardi; Nguyen, H T

    2011-01-01

    For people with severe spine injury, head movement recognition control has been proven to be one of the most convenient and intuitive ways to control a power wheelchair. While substantial research has been done in this area, the challenge to improve system reliability and accuracy remains due to the diversity in movement tendencies and the presence of movement artifacts. We propose a Neural-Network Configuration which we call Augmented Radial Basis Function Neural-Network (ARBF-NN). This network is constructed as a Radial Basis Function Neural-Network (RBF-NN) with a Multilayer Perceptron (MLP) augmentation layer to negate optimization limitation posed by linear classifiers in conventional RBF-NN. The RBF centroid is optimized through Regrouping Particle Swarm Optimization (RegPSO) seeded with K-Means. The trial results of ARBF-NN on Head-movement show a significant improvement on recognition accuracy up to 98.1% in sensitivity.

  11. Numerical Aspects of Atomic Physics: Helium Basis Sets and Matrix Diagonalization

    NASA Astrophysics Data System (ADS)

    Jentschura, Ulrich; Noble, Jonathan

    2014-03-01

    We present a matrix diagonalization algorithm for complex symmetric matrices, which can be used in order to determine the resonance energies of auto-ionizing states of comparatively simple quantum many-body systems such as helium. The algorithm is based in multi-precision arithmetic and proceeds via a tridiagonalization of the complex symmetric (not necessarily Hermitian) input matrix using generalized Householder transformations. Example calculations involving so-called PT-symmetric quantum systems lead to reference values which pertain to the imaginary cubic perturbation (the imaginary cubic anharmonic oscillator). We then proceed to novel basis sets for the helium atom and present results for Bethe logarithms in hydrogen and helium, obtained using the enhanced numerical techniques. Some intricacies of ``canned'' algorithms such as those used in LAPACK will be discussed. Our algorithm, for complex symmetric matrices such as those describing cubic resonances after complex scaling, is faster than LAPACK's built-in routines, for specific classes of input matrices. It also offer flexibility in terms of the calculation of the so-called implicit shift, which is used in order to ``pivot'' the system toward the convergence to diagonal form. We conclude with a wider overview.

  12. The Scientific Basis of Uncertainty Factors Used in Setting Occupational Exposure Limits

    PubMed Central

    Dankovic, D. A.; Naumann, B. D.; Maier, A.; Dourson, M. L.; Levy, L. S.

    2015-01-01

    The uncertainty factor concept is integrated into health risk assessments for all aspects of public health practice, including by most organizations that derive occupational exposure limits. The use of uncertainty factors is predicated on the assumption that a sufficient reduction in exposure from those at the boundary for the onset of adverse effects will yield a safe exposure level for at least the great majority of the exposed population, including vulnerable subgroups. There are differences in the application of the uncertainty factor approach among groups that conduct occupational assessments; however, there are common areas of uncertainty which are considered by all or nearly all occupational exposure limit-setting organizations. Five key uncertainties that are often examined include interspecies variability in response when extrapolating from animal studies to humans, response variability in humans, uncertainty in estimating a no-effect level from a dose where effects were observed, extrapolation from shorter duration studies to a full life-time exposure, and other insufficiencies in the overall health effects database indicating that the most sensitive adverse effect may not have been evaluated. In addition, a modifying factor is used by some organizations to account for other remaining uncertainties—typically related to exposure scenarios or accounting for the interplay among the five areas noted above. Consideration of uncertainties in occupational exposure limit derivation is a systematic process whereby the factors applied are not arbitrary, although they are mathematically imprecise. As the scientific basis for uncertainty factor application has improved, default uncertainty factors are now used only in the absence of chemical-specific data, and the trend is to replace them with chemical-specific adjustment factors whenever possible. The increased application of scientific data in the development of uncertainty factors for individual chemicals also

  13. The Scientific Basis of Uncertainty Factors Used in Setting Occupational Exposure Limits.

    PubMed

    Dankovic, D A; Naumann, B D; Maier, A; Dourson, M L; Levy, L S

    2015-01-01

    The uncertainty factor concept is integrated into health risk assessments for all aspects of public health practice, including by most organizations that derive occupational exposure limits. The use of uncertainty factors is predicated on the assumption that a sufficient reduction in exposure from those at the boundary for the onset of adverse effects will yield a safe exposure level for at least the great majority of the exposed population, including vulnerable subgroups. There are differences in the application of the uncertainty factor approach among groups that conduct occupational assessments; however, there are common areas of uncertainty which are considered by all or nearly all occupational exposure limit-setting organizations. Five key uncertainties that are often examined include interspecies variability in response when extrapolating from animal studies to humans, response variability in humans, uncertainty in estimating a no-effect level from a dose where effects were observed, extrapolation from shorter duration studies to a full life-time exposure, and other insufficiencies in the overall health effects database indicating that the most sensitive adverse effect may not have been evaluated. In addition, a modifying factor is used by some organizations to account for other remaining uncertainties-typically related to exposure scenarios or accounting for the interplay among the five areas noted above. Consideration of uncertainties in occupational exposure limit derivation is a systematic process whereby the factors applied are not arbitrary, although they are mathematically imprecise. As the scientific basis for uncertainty factor application has improved, default uncertainty factors are now used only in the absence of chemical-specific data, and the trend is to replace them with chemical-specific adjustment factors whenever possible. The increased application of scientific data in the development of uncertainty factors for individual chemicals also has

  14. Parallel axes gear set optimization in two-parameter space

    NASA Astrophysics Data System (ADS)

    Theberge, Y.; Cardou, A.; Cloutier, L.

    1991-05-01

    This paper presents a method for optimal spur and helical gear transmission design that may be used in a computer aided design (CAD) approach. The design objective is generally taken as obtaining the most compact set for a given power input and gear ratio. A mixed design procedure is employed which relies both on heuristic considerations and computer capabilities. Strength and kinematic constraints are considered in order to define the domain of feasible designs. Constraints allowed include: pinion tooth bending strength, gear tooth bending strength, surface stress (resistance to pitting), scoring resistance, pinion involute interference, gear involute interference, minimum pinion tooth thickness, minimum gear tooth thickness, and profile or transverse contact ratio. A computer program was developed which allows the user to input the problem parameters, to select the calculation procedure, to see constraint curves in graphic display, to have an objective function level curve drawn through the design space, to point at a feasible design point and to have constraint values calculated at that point. The user can also modify some of the parameters during the design process.

  15. Multivariate Parameter Sets for Optimal Synthesis of Compliant Mechanisms

    NASA Technical Reports Server (NTRS)

    Shibakov, Alex; Hull, Patrick V.; Canfield, Stephen L.; Tinker, Mike

    2005-01-01

    This paper will propose the use of control maps along with discretized elements or meshes in the design parameter set for optimizing compliant mechanisms. The use of control maps will be demonstrated to encode the motion of groups of nodes or control points within a compliant mechanism design with simple mapping rules. The technique will serve as an alternative to increased mesh size or node wandering techniques that have been proposed to increase the number of alternative design shapes that may be considered. As an alternative approach, the proposed control map parameterization has the significant benefit that it minimizes the number of design parameters necessary (parameters increase linearly with the mesh size) in describing a given design making it computationally efficient. A limited number of tiles can produce a map that has a significant effect on the final shape. If the tiles are chosen appropriately, the problems such as material overlap and non-convex mesh elements are avoided automatically. This paper will describe the implementation of these control maps and provide several examples showing their implementation in the compliant mechanism topology synthesis process.

  16. Optimality Conditions in Differentiable Vector Optimization via Second-Order Tangent Sets

    SciTech Connect

    Jimenez, Bienvenido Novo, Vicente

    2004-03-15

    We provide second-order necessary and sufficient conditions for a point to be an efficient element of a set with respect to a cone in a normed space, so that there is only a small gap between necessary and sufficient conditions. To this aim, we use the common second-order tangent set and the asymptotic second-order cone utilized by Penot. As an application we establish second-order necessary conditions for a point to be a solution of a vector optimization problem with an arbitrary feasible set and a twice Frechet differentiable objective function between two normed spaces. We also establish second-order sufficient conditions when the initial space is finite-dimensional so that there is no gap with necessary conditions. Lagrange multiplier rules are also given.

  17. Operationalizing the concept of the optimal healing environment in clinical settings: the importance of "readiness".

    PubMed

    Findlay, Barbara; Verhoef, Marja

    2004-01-01

    Creation of an optimal healing environment (OHE) in a clinical setting is a multifaceted undertaking and subject to a wide variety of developmental influences. While comprehensive definitions for OHE might provide sufficient guidance for communicating philosophy and values and developing patient-practitioner processes, direction for creating a supportive administrative structure or establishing an evaluation/research strategy is less defined. Operationalizing the concept of OHE by breaking it down into components such as values, structure, process, and measurement of outcomes, proved to be a useful framework for analyzing the evolution of our integrated care program. Future OHE initiatives may benefit from using this type of framework to assess readiness among cocreators prior to development and implementation, as a guide for ongoing evaluation of an OHE postimplementation and as a basis for comparing OHEs across a variety of clinical settings.

  18. Effects of chemical aging on global secondary organic aerosol using the volatility basis set approach

    NASA Astrophysics Data System (ADS)

    Jo, D. S.; Park, R. J.; Kim, M. J.; Spracklen, D. V.

    2013-12-01

    A global 3-D chemical transport model (GEOS-Chem) is used with the volatility basis set (VBS) approach to examine the effects of chemical aging on global secondary organic aerosol (SOA) concentrations and budgets. We present full-year simulations and their comparisons with the global aerosol mass spectrometer (AMS) dataset, the Interagency Monitoring of Protected Visual Environments (IMPROVE) dataset from the United States, the European Monitoring and Evaluation Programme (EMEP) dataset from Europe, and water-soluble organic carbon observation data collected over East Asia. Using different chemical aging constants, we find that the model results with 4 × 10-11 cm3 molecule-1 s-1 are in better agreement with all observations relative to the model results with other aging constants, without aging, and with the two-product approach. The model simulations are improved when chemical aging is considered, especially for rural regions. However, the simulations still underestimate observed oxygenated organic aerosol (OOA) in urban areas. Two sensitivity simulations including semi-volatile primary organic aerosol (POA) were conducted. We find that including semi-volatile POA improves the model in terms of the hydrogen-like organic aerosol (HOA) to OOA ratio. However, the total OA concentrations are not improved. The total SOA production is considerably increased by 53%, from 26.0 to 39.9 Tg yr-1, after considering chemical aging, remaining lower than top-down estimates of SOA production. Direct radiative forcing (DRF) increases by -0.07 W m-2 due to the chemical aging of SOA, which is comparable to the mean DRF (-0.13 W m-2) of OA from the AeroCom multi-model study. This result indicates considerable global and, more importantly, regional climate implications. For example, the regional DRF change due to chemical aging of SOA in the eastern US is -0.29 W m-2, which is 4 times greater in magnitude than the global mean value.

  19. Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors

    SciTech Connect

    Kamiya, Muneaki; Hirata, So; Valiev, Marat

    2008-02-19

    Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of the cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.

  20. Molecular structure, IR spectra, and chemical reactivity of cisplatin and transplatin: DFT studies, basis set effect and solvent effect.

    PubMed

    Wang, Yang; Liu, Qingzhu; Qiu, Ling; Wang, Tengfei; Yuan, Haoliang; Lin, Jianguo; Luo, Shineng

    2015-01-01

    Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N-H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.

  1. Optimization of global model composed of radial basis functions using the term-ranking approach

    SciTech Connect

    Cai, Peng; Tao, Chao Liu, Xiao-Jun

    2014-03-15

    A term-ranking method is put forward to optimize the global model composed of radial basis functions to improve the predictability of the model. The effectiveness of the proposed method is examined by numerical simulation and experimental data. Numerical simulations indicate that this method can significantly lengthen the prediction time and decrease the Bayesian information criterion of the model. The application to real voice signal shows that the optimized global model can capture more predictable component in chaos-like voice data and simultaneously reduce the predictable component (periodic pitch) in the residual signal.

  2. Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.

    PubMed

    Bielecki, Jakub; Lipiec, Ewelina

    2016-02-01

    Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

  3. Correction of the basis set superposition error in SCF and MP2 interaction energies. The water dimer

    NASA Astrophysics Data System (ADS)

    Szcześniak, M. M.; Scheiner, Steve

    1986-06-01

    There has been some discussion concerning whether basis set superposition error is more correctly evaluated using the full set of ghost orbitals of the partner molecule or some subset thereof. A formal treatment is presented, arguing that the full set is required at the Møller-Plesset level. Numerical support for this position is provided by calculation of the interaction energy between a pair of water molecules, using a series of moderate sized basis sets ranging from 6-31G** to the [432/21] contraction suggested by Clementi and Habitz. These energies, at both the SCF and MP2 levels, behave erratically with respect to changes in details of the basis set, e.g., H p-function exponent. On the other hand, after counterpoise correction using the full set of partner ghost orbitals, the interaction energies are rather insensitive to basis set and behave in a manner consistent with calculated monomer properties. For long intersystem separations, the contribution of correlation to the interaction is repulsive despite the attractive influence of dispersion. This effect is attributed to partial account of intrasystem correlation and can be approximated at long distances via electrostatic terms linear in MP2-induced changes in the monomer moments.

  4. Optimization of massive countermeasure design in complex rockfall settings

    NASA Astrophysics Data System (ADS)

    Agliardi, Federico; Crosta, Giovanni B.

    2015-04-01

    Rockfall protection is a major need in areas impended by subvertical rockwalls with complex 3D morphology and little or no talus to provide natural rockfall attenuation. The design of massive embankments, usually required to ensure such protection, is particularly difficult in complex rockfall settings, due to: widespread occurrence of rockfall sources; difficult characterization of size distribution and location of unstable volumes; variability of failure mechanisms; spatial scattering of rockfall trajectories; high expected kinetic energies. Moreover, rockwalls in complex lithological and structural settings are often prone to mass falls related to rock mass sector collapses. All these issues may hamper a safe application of classic embankment analysis approaches, using empirical rules or 2D-based height/energy statistics, and point to the need of integrated analyses of rock slope instability and rockfall runout in 3D. We explore the potential of combining advanced rock mass characterisation techniques and 3D rockfall modelling to support challenging countermeasure design at a site near Lecco (Southern Alps, Italy). Here subvertical cliffs up to 600 m high impend on a narrow (< 150 m) strip of flat land along the Como Lake shore. Rock is thickly bedded limestone (Dolomia Principale Fm) involved in a ENE-trending, S-verging kilometre-scale anticline fold. The spatial variability of bedding attitude and fracture intensity is strongly controlled by the geological structure, with individual block sizes varying in the range 0.2-15 m3. This results in spatially variable rockfall susceptibility and mechanisms, from single block falls to mass falls. Several rockfall events occurred between 1981 and 2010 motivated the design of slope benching and a massive embankment. To support reliable design verification and optimization we performed a 3D assessment of both rock slope instability and rockfall runout. We characterised fracture patterns and rock mass quality associated

  5. Evaluation of European air quality modelled by CAMx including the volatility basis set scheme

    NASA Astrophysics Data System (ADS)

    Ciarelli, Giancarlo; Aksoyoglu, Sebnem; Crippa, Monica; Jimenez, Jose-Luis; Nemitz, Eriko; Sellegri, Karine; Äijälä, Mikko; Carbone, Samara; Mohr, Claudia; O'Dowd, Colin; Poulain, Laurent; Baltensperger, Urs; Prévôt, André S. H.

    2016-08-01

    Four periods of EMEP (European Monitoring and Evaluation Programme) intensive measurement campaigns (June 2006, January 2007, September-October 2008 and February-March 2009) were modelled using the regional air quality model CAMx with VBS (volatility basis set) approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February-March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosol (OA). Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database AirBase. Sulfur dioxide (SO2) and ozone (O3) were found to be overestimated for all the four periods, with O3 having the largest mean bias during June 2006 and January-February 2007 periods (8.9 pbb and 12.3 ppb mean biases respectively). In contrast, nitrogen dioxide (NO2) and carbon monoxide (CO) were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 for all the four periods with average biases ranging from -2.1 to 1.0 µg m-3. Comparisons with AMS (aerosol mass spectrometer) measurements at different sites in Europe during February-March 2009 showed that in general the model overpredicts the inorganic aerosol fraction and underpredicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of VBS scheme on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February-March 2009 the chamber case reduced the total OA concentrations by about 42 % on average. In contrast, a test based on ambient measurement data increased OA concentrations by about 42 % for the same period bringing model and observations into better agreement

  6. Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

    PubMed

    Saravanan, Chandra; Shao, Yihan; Baer, Roi; Ross, Philip N; Head-Gordon, Martin

    2003-04-15

    A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package.

  7. On the optimal parameter and noise identification on the basis of three parameter probability distributions

    NASA Astrophysics Data System (ADS)

    Jakšić, Nikola

    2015-03-01

    The optimality of the procedure of parameter identification is scrutinized in this paper. It was shown, with the relations between the mathematical theory of function approximation, three parameter probability distributions, which can adjust their shape, and the maximum-likelihood method, that the optimal expression of the distance between measured data and model fitting it can be established by using the three parameter probability distributions on the basis of iteration procedure, where the noise contained in the measured signal is extracted as well. The iterative method for optimal system/model parameter identification is presented and tested by the numerical experimentation. Four types of noise added to the simple single-degree-of-freedom system response are considered: Gauss, Cauchy, Laplace and Uniform. The method performs well for the noise types at relatively high noise content in the signal.

  8. 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.

  9. Optimal control of the sweeping process over polyhedral controlled sets

    NASA Astrophysics Data System (ADS)

    Colombo, G.; Henrion, R.; Nguyen, D. Hoang; Mordukhovich, B. S.

    2016-02-01

    The paper addresses a new class of optimal control problems governed by the dissipative and discontinuous differential inclusion of the sweeping/Moreau process while using controls to determine the best shape of moving convex polyhedra in order to optimize the given Bolza-type functional, which depends on control and state variables as well as their velocities. Besides the highly non-Lipschitzian nature of the unbounded differential inclusion of the controlled sweeping process, the optimal control problems under consideration contain intrinsic state constraints of the inequality and equality types. All of this creates serious challenges for deriving necessary optimality conditions. We develop here the method of discrete approximations and combine it with advanced tools of first-order and second-order variational analysis and generalized differentiation. This approach allows us to establish constructive necessary optimality conditions for local minimizers of the controlled sweeping process expressed entirely in terms of the problem data under fairly unrestrictive assumptions. As a by-product of the developed approach, we prove the strong W 1 , 2-convergence of optimal solutions of discrete approximations to a given local minimizer of the continuous-time system and derive necessary optimality conditions for the discrete counterparts. The established necessary optimality conditions for the sweeping process are illustrated by several examples.

  10. Identifying the optimal gene and gene set in hepatocellular carcinoma based on differential expression and differential co-expression algorithm.

    PubMed

    Dong, Li-Yang; Zhou, Wei-Zhong; Ni, Jun-Wei; Xiang, Wei; Hu, Wen-Hao; Yu, Chang; Li, Hai-Yan

    2017-02-01

    The objective of this study was to identify the optimal gene and gene set for hepatocellular carcinoma (HCC) utilizing differential expression and differential co-expression (DEDC) algorithm. The DEDC algorithm consisted of four parts: calculating differential expression (DE) by absolute t-value in t-statistics; computing differential co-expression (DC) based on Z-test; determining optimal thresholds on the basis of Chi-squared (χ2) maximization and the corresponding gene was the optimal gene; and evaluating functional relevance of genes categorized into different partitions to determine the optimal gene set with highest mean minimum functional information (FI) gain (Δ*G). The optimal thresholds divided genes into four partitions, high DE and high DC (HDE-HDC), high DE and low DC (HDE-LDC), low DE and high DC (LDE‑HDC), and low DE and low DC (LDE-LDC). In addition, the optimal gene was validated by conducting reverse transcription-polymerase chain reaction (RT-PCR) assay. The optimal threshold for DC and DE were 1.032 and 1.911, respectively. Using the optimal gene, the genes were divided into four partitions including: HDE-HDC (2,053 genes), HED-LDC (2,822 genes), LDE-HDC (2,622 genes), and LDE-LDC (6,169 genes). The optimal gene was microtubule‑associated protein RP/EB family member 1 (MAPRE1), and RT-PCR assay validated the significant difference between the HCC and normal state. The optimal gene set was nucleoside metabolic process (GO\\GO:0009116) with Δ*G = 18.681 and 24 HDE-HDC partitions in total. In conclusion, we successfully investigated the optimal gene, MAPRE1, and gene set, nucleoside metabolic process, which may be potential biomarkers for targeted therapy and provide significant insight for revealing the pathological mechanism underlying HCC.

  11. 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 (basis set for each atom belonging to our studied model compounds depends on its location with respect to the coupled fluorine atoms and on the cis/trans or synperiplanar/antiperiplanar conformation of the molecule. Carbon atoms in the bonding path connecting the coupled fluorine atoms have to be described with better basis sets than the carbon atoms outside this path. For the hydrogen atoms directly connected to the coupling pathway in molecules with trans or antiperiplanar conformations and for all hydrogen atoms not directly connected to the coupling pathway one can employ a minimal basis set with only one s-function. Employing these type of LDBSs we can reduce the number of necessary basis functions by about 30% without losing more than about 1 Hz in accuracy. The analysis of the four contributions to the vicinal fluorine-fluorine coupling constants shows that the non-contact orbital paramagnetic term is the most important contribution followed by the also non-contact spin-dipolar term. The Fermi contact term is the largest contribution only in the synperiplanar conformations of 1,2-difluoroethane and -propane.

  12. Nuclear-electronic orbital reduced explicitly correlated Hartree-Fock approach: Restricted basis sets and open-shell systems

    SciTech Connect

    Brorsen, Kurt R.; Sirjoosingh, Andrew; Pak, Michael V.; Hammes-Schiffer, Sharon

    2015-06-07

    The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF{sup −} and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN{sup +}, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.

  13. Nuclear-electronic orbital reduced explicitly correlated Hartree-Fock approach: Restricted basis sets and open-shell systems

    NASA Astrophysics Data System (ADS)

    Brorsen, Kurt R.; Sirjoosingh, Andrew; Pak, Michael V.; Hammes-Schiffer, Sharon

    2015-06-01

    The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF- and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN+, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.

  14. Perturbative correction for the basis set incompleteness error of complete-active-space self-consistent field.

    PubMed

    Kong, Liguo; Valeev, Edward F

    2010-11-07

    To reduce the basis set incompleteness of the complete-active-space self-consistent field (CASSCF) wave function and energy we develop a second-order perturbation correction due to single excitations to complete set of unoccupied states. Other than the one- and two-electron integrals, only one- and two-particle reduced density matrices are required to compute the correction, denoted as [2](S). Benchmark calculations on prototypical ground-state bond-breaking problems show that only the aug-cc-pVXZ basis is needed with the [2](S) correction to match the accuracy of CASSCF energies of the aug-cc-pV(X+1)Z quality.

  15. Density functional theory and the correlation consistent basis sets: the tight d effect on HSO and HOS.

    PubMed

    Wang, Nick X; Wilson, Angela K

    2005-08-18

    The HSO and HOS isomers have been revisited using the DFT functionals, B3LYP, B3PW91, and PBE, in combination with tight d-augmented correlation consistent basis sets, cc-pV(x+d)Z and aug-cc-pV(x+d)Z for second-row atoms. Structures, vibrationally averaged structures, relative energies, harmonic and anharmonic frequencies, enthalpies of formation of HSO and HOS, and the barrier for the HSO/HOS isomerization have been determined. These results were compared with results from previous DFT and ab initio studies in which the standard correlation consistent basis sets were used. The relative energies of the two isomers converge more rapidly and smoothly with respect to increasing basis set size for the tight d-augmented sets than for the standard basis sets. Our best calculations, B3PW91/aug-cc-pV(5+d)Z, for the relative energy of the isomers are in excellent agreement with previous CCSD(T) results given by Wilson and Dunning.

  16. A set of f-polarization functions for pseudo-potential basis sets of the transition metals ScCu, YAg and LaAu

    NASA Astrophysics Data System (ADS)

    Ehlers, A. W.; Böhme, M.; Dapprich, S.; Gobbi, A.; Höllwarth, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Frenking, G.

    1993-06-01

    A Set of seven-component f-type polarization functions has been optimized for use with the pseudo-potentials of Hay and Wadt at the CISD level of theory for the transition metals ScCu, YAg, LaAu in the energetically lowest-lying s 1 d n electronic state.

  17. Optimization of wavelengths sets for multispectral reflectance imaging of rat olfactory bulb activation in vivo

    NASA Astrophysics Data System (ADS)

    Renaud, Rémi; Bendahmane, Mounir; Chery, Romain; Martin, Claire; Gurden, Hirac; Pain, Frederic

    2012-06-01

    Wide field multispectral imaging of light backscattered by brain tissues provides maps of hemodynamics changes (total blood volume and oxygenation) following activation. This technique relies on the fit of the reflectance images obtain at two or more wavelengths using a modified Beer-Lambert law1,2. It has been successfully applied to study the activation of several sensory cortices in the anesthetized rodent using visible light1-5. We have carried out recently the first multispectral imaging in the olfactory bulb6 (OB) of anesthetized rats. However, the optimization of wavelengths choice has not been discussed in terms of cross talk and uniqueness of the estimated parameters (blood volume and saturation maps) although this point was shown to be crucial for similar studies in Diffuse Optical Imaging in humans7-10. We have studied theoretically and experimentally the optimal sets of wavelength for multispectral imaging of rodent brain activation in the visible. Sets of optimal wavelengths have been identified and validated in vivo for multispectral imaging of the OB of rats following odor stimulus. We studied the influence of the wavelengths sets on the magnitude and time courses of the oxy- and deoxyhemoglobin concentration variations as well as on the spatial extent of activated brain areas following stimulation. Beyond the estimation of hemodynamic parameters from multispectral reflectance data, we observed repeatedly and for all wavelengths a decrease of light reflectance. For wavelengths longer than 590 nm, these observations differ from those observed in the somatosensory and barrel cortex and question the basis of the reflectance changes during activation in the OB. To solve this issue, Monte Carlo simulations (MCS) have been carried out to assess the relative contribution of absorption, scattering and anisotropy changes to the intrinsic optical imaging signals in somatosensory cortex (SsC) and OB model.

  18. Optimizing Design Parameters for Sets of Concentric Tube Robots using Sampling-based Motion Planning.

    PubMed

    Baykal, Cenk; Torres, Luis G; Alterovitz, Ron

    2015-09-28

    Concentric tube robots are tentacle-like medical robots that can bend around anatomical obstacles to access hard-to-reach clinical targets. The component tubes of these robots can be swapped prior to performing a task in order to customize the robot's behavior and reachable workspace. Optimizing a robot's design by appropriately selecting tube parameters can improve the robot's effectiveness on a procedure-and patient-specific basis. In this paper, we present an algorithm that generates sets of concentric tube robot designs that can collectively maximize the reachable percentage of a given goal region in the human body. Our algorithm combines a search in the design space of a concentric tube robot using a global optimization method with a sampling-based motion planner in the robot's configuration space in order to find sets of designs that enable motions to goal regions while avoiding contact with anatomical obstacles. We demonstrate the effectiveness of our algorithm in a simulated scenario based on lung anatomy.

  19. Optimizing Design Parameters for Sets of Concentric Tube Robots using Sampling-based Motion Planning

    PubMed Central

    Baykal, Cenk; Torres, Luis G.; Alterovitz, Ron

    2015-01-01

    Concentric tube robots are tentacle-like medical robots that can bend around anatomical obstacles to access hard-to-reach clinical targets. The component tubes of these robots can be swapped prior to performing a task in order to customize the robot’s behavior and reachable workspace. Optimizing a robot’s design by appropriately selecting tube parameters can improve the robot’s effectiveness on a procedure-and patient-specific basis. In this paper, we present an algorithm that generates sets of concentric tube robot designs that can collectively maximize the reachable percentage of a given goal region in the human body. Our algorithm combines a search in the design space of a concentric tube robot using a global optimization method with a sampling-based motion planner in the robot’s configuration space in order to find sets of designs that enable motions to goal regions while avoiding contact with anatomical obstacles. We demonstrate the effectiveness of our algorithm in a simulated scenario based on lung anatomy. PMID:26951790

  20. Highly accurate relativistic universal Gaussian basis set: Dirac-Fock-Coulomb calculations for atomic systems up to nobelium

    NASA Astrophysics Data System (ADS)

    Malli, G. L.; Da Silva, A. B. F.; Ishikawa, Yasuyuki

    1994-10-01

    A universal Gaussian basis set is developed that leads to relativistic Dirac-Fock SCF energies of comparable accuracy as that obtained by the accurate numerical finite-difference method (GRASP2 package) [J. Phys. B 25, 1 (1992)]. The Gaussian-type functions of our universal basis set satisfy the relativistic boundary conditions associated with the finite nuclear model for a finite speed of light and conform to the so-called kinetic balance at the nonrelativistic limit. We attribute the exceptionally high accuracy obtained in our calculations to the fact that the representation of the relativistic dynamics of an electron in a spherical ball finite nucleus near the origin in terms of our universal Gaussian basis set is as accurate as that provided by the numerical finite-difference method. Results of the Dirac-Fock-Coulomb energies for a number of atoms up to No (Z=102) and some negative ions are presented and compared with the recent results obtained with the numerical finite-difference method and geometrical Gaussian basis sets by Parpia, Mohanty, and Clementi [J. Phys. B 25, 1 (1992)]. The accuracy of our calculations is estimated to be within a few parts in 109 for all the atomic systems studied.

  1. Accurate Gaussian basis sets for atomic and molecular calculations obtained from the generator coordinate method with polynomial discretization.

    PubMed

    Celeste, Ricardo; Maringolo, Milena P; Comar, Moacyr; Viana, Rommel B; Guimarães, Amanda R; Haiduke, Roberto L A; da Silva, Albérico B F

    2015-10-01

    Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.

  2. Particle swarm optimization-based radial basis function network for estimation of reference evapotranspiration

    NASA Astrophysics Data System (ADS)

    Petković, Dalibor; Gocic, Milan; Shamshirband, Shahaboddin; Qasem, Sultan Noman; Trajkovic, Slavisa

    2016-08-01

    Accurate estimation of the reference evapotranspiration (ET0) is important for the water resource planning and scheduling of irrigation systems. For this purpose, the radial basis function network with particle swarm optimization (RBFN-PSO) and radial basis function network with back propagation (RBFN-BP) were used in this investigation. The FAO-56 Penman-Monteith equation was used as reference equation to estimate ET0 for Serbia during the period of 1980-2010. The obtained simulation results confirmed the proposed models and were analyzed using the root mean-square error (RMSE), the mean absolute error (MAE), and the coefficient of determination ( R 2). The analysis showed that the RBFN-PSO had better statistical characteristics than RBFN-BP and can be helpful for the ET0 estimation.

  3. Holocene sea level variations on the basis of integration of independent data sets

    SciTech Connect

    Sahagian, D.; Berkman, P. . Dept. of Geological Sciences and Byrd Polar Research Center)

    1992-01-01

    Variations in sea level through earth history have occurred at a wide variety of time scales. Sea level researchers have attacked the problem of measuring these sea level changes through a variety of approaches, each relevant only to the time scale in question, and usually only relevant to the specific locality from which a specific type of data are derived. There is a plethora of different data types that can and have been used (locally) for the measurement of Holocene sea level variations. The problem of merging different data sets for the purpose of constructing a global eustatic sea level curve for the Holocene has not previously been adequately addressed. The authors direct the efforts to that end. Numerous studies have been published regarding Holocene sea level changes. These have involved exposed fossil reef elevations, elevation of tidal deltas, elevation of depth of intertidal peat deposits, caves, tree rings, ice cores, moraines, eolian dune ridges, marine-cut terrace elevations, marine carbonate species, tide gauges, and lake level variations. Each of these data sets is based on particular set of assumptions, and is valid for a specific set of environments. In order to obtain the most accurate possible sea level curve for the Holocene, these data sets must be merged so that local and other influences can be filtered out of each data set. Since each data set involves very different measurements, each is scaled in order to define the sensitivity of the proxy measurement parameter to sea level, including error bounds. This effectively determines the temporal and spatial resolution of each data set. The level of independence of data sets is also quantified, in order to rule out the possibility of a common non-eustatic factor affecting more than one variety of data. The Holocene sea level curve is considered to be independent of other factors affecting the proxy data, and is taken to represent the relation between global ocean water and basin volumes.

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

    PubMed

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

    2016-05-21

    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.

  5. Geometrical correction for the inter- and intramolecular basis set superposition error in periodic density functional theory calculations.

    PubMed

    Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan

    2013-09-26

    We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.

  6. Joint multiregion segmentation and parametric estimation of image motion by basis function representation and level set evolution.

    PubMed

    Vázquez, Carlos; Mitiche, Amar; Laganière, Robert

    2006-05-01

    The purpose of this study is to investigate a variational method for joint segmentation and parametric estimation of image motion by basis function representation of motion and level set evolution. The functional contains three terms. One term is of classic regularization to bias the solution toward a segmentation with smooth boundaries. A second term biases the solution toward a segmentation with boundaries which coincide with motion discontinuities, following a description of motion discontinuities by a function of the image spatio-temporal variations. The third term refers to region information and measures conformity of the parametric representation of the motion of each region of segmentation to the image spatio-temporal variations. The components of motion in each region of segmentation are represented as functions in a space generated by a set of basis functions. The coefficients of the motion components considered combinations of the basis functions are the parameters of representation. The necessary conditions for a minimum of the functional, which are derived taking into consideration the dependence of the motion parameters on segmentation, lead to an algorithm which condenses to concurrent curve evolution, implemented via level sets, and estimation of the parameters by least squares within each region of segmentation. The algorithm and its implementation are verified on synthetic and real images using a basis of cosine transforms.

  7. Optimized virtual orbital subspace for faster GW calculations in localized basis

    NASA Astrophysics Data System (ADS)

    Bruneval, Fabien

    2016-12-01

    The popularity of the GW approximation to the self-energy to access the quasiparticle energies of molecules is constantly increasing. As the other methods addressing the electronic correlation, the GW self-energy unfortunately shows a very slow convergence with respect to the basis complexity, which precludes the calculation of accurate quasiparticle energies for large molecules. Here we propose a method to mitigate this issue that relies on two steps: (i) the definition of a reduced virtual orbital subspace, thanks to a much smaller basis set; (ii) the account of the remainder through the simpler one-ring approximation to the self-energy. We assess the quality of the corrected quasiparticle energies for simple molecules, and finally we show an application to large graphene chunks to demonstrate the numerical efficiency of the scheme.

  8. Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set

    NASA Astrophysics Data System (ADS)

    Bennie, Simon J.; Stella, Martina; Miller, Thomas F.; Manby, Frederick R.

    2015-07-01

    Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O ( N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.

  9. Optimal tooth numbers for compact standard spur gear sets

    NASA Technical Reports Server (NTRS)

    Savage, M.; Coy, J. J.; Townsend, D. P.

    1981-01-01

    The design of a standard gear mesh is treated with the objective of minimizing the gear size for a given ratio, pinion torque, and allowable tooth strength. Scoring, pitting fatigue, bending fatigue, and the kinematic limits of contact ratio and interference are considered. A design space is defined in terms of the number of teeth on the pinion and the diametral pitch. This space is then combined with the objective function of minimum center distance to obtain an optimal design region. This region defines the number of pinion teeth for the most compact design. The number is a function of the gear ratio only. A design example illustrating this procedure is also given.

  10. An optimal period for setting sustained variability levels.

    PubMed

    Stokes, P D; Balsam, P

    2001-03-01

    In two experiments, we investigated how explicit reinforcement of highly variable behavior at different points in training affected performance after the requirement was eliminated. Two versions of a computer game, differing in the number of possible solution paths, were used. In each, an optimal period of training for producing sustained high variability was found. Exposure to a high lag requirement shortly after acquisition sustained variability. Rewarding variability at other times did not have a sustained effect. The implications for learning and problem solving are discussed.

  11. On the Kohn-Sham density response in a localized basis set

    NASA Astrophysics Data System (ADS)

    Foerster, Dietrich; Koval, Peter

    2009-07-01

    We construct the Kohn-Sham density response function χ0 in a previously described basis of the space of orbital products. The calculational complexity of our construction is O(N2Nω) for a molecule of N atoms and in a spectroscopic window of Nω frequency points. As a first application, we use χ0 to calculate the molecular spectra from the Petersilka-Gossmann-Gross equation. With χ0 as input, we obtain the correct spectra with an extra computational effort that grows also as O(N2Nω) and, therefore, less steeply in N than the O(N3) complexity of solving Casida's equations. Our construction should be useful for the study of excitons in molecular physics and in related areas where χ0 is a crucial ingredient.

  12. [Psychophysiologic pattern of pilot's activity during flight as a basis for setting up his workplace].

    PubMed

    Frolov, N I

    1997-01-01

    The psychophysiological pattern of a pilot is considered on the basis of experiments made during flights. Five components of his activity, which may be estimated, are identified. These include sensory, motor, autonomic, occupational, and psychological components. The "reserves of attention" are singled out as an objective independent parameter that characterizes the activity of a pilot. Five determinants of the level of physiological responses are identified in a pilot during flight. Their mechanisms are most efficiently analyzed in terms of the basic concepts developed by P.K. Anokhin, P.V. Simonov, K.V. Sudakov. The objective activity estimates make it possible to assess the adequacy of a working place to the problems to be solved, to apply the anthrocentric principle in working out the pilot's working place by taking into account his psychophysiological capacities.

  13. Possible calcium centers for hydrogen storage applications: An accurate many-body study by AFQMC calculations with large basis sets

    NASA Astrophysics Data System (ADS)

    Purwanto, Wirawan; Krakauer, Henry; Zhang, Shiwei; Virgus, Yudistira

    2011-03-01

    Weak H2 physisorption energies present a significant challenge to first-principle theoretical modeling and prediction of materials for H storage. There has been controversy regarding the accuracy of DFT on systems involving Ca cations. We use the auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca + , - 4{H}2 . AFQMC scales as Nbasis3and has demonstrated accuracy similar to or better than the gold-standard coupled cluster CCSD(T) method. We apply a modified Cholesky decomposition to achieve efficient Hubbard-Stratonovich transformation in AFQMC at large basis sizes. We employ the largest correlation consistent basis sets available, up to Ca/cc-pCV5Z, to extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure. Supported by DOE and NSF. Calculations were performed at OLCF Jaguar and CPD.

  14. Optimizing distance-based methods for large data sets

    NASA Astrophysics Data System (ADS)

    Scholl, Tobias; Brenner, Thomas

    2015-10-01

    Distance-based methods for measuring spatial concentration of industries have received an increasing popularity in the spatial econometrics community. However, a limiting factor for using these methods is their computational complexity since both their memory requirements and running times are in {{O}}(n^2). In this paper, we present an algorithm with constant memory requirements and shorter running time, enabling distance-based methods to deal with large data sets. We discuss three recent distance-based methods in spatial econometrics: the D&O-Index by Duranton and Overman (Rev Econ Stud 72(4):1077-1106, 2005), the M-function by Marcon and Puech (J Econ Geogr 10(5):745-762, 2010) and the Cluster-Index by Scholl and Brenner (Reg Stud (ahead-of-print):1-15, 2014). Finally, we present an alternative calculation for the latter index that allows the use of data sets with millions of firms.

  15. Electric field gradients of transition metal complexes from density functional theory: assessment of functionals, geometries and basis sets.

    PubMed

    Bjornsson, Ragnar; Bühl, Michael

    2010-06-14

    Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C(6)H(6))(CO)(3), MnO(3)F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omegaPBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.

  16. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets.

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-09

    We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.

  17. 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.

  18. 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.

  19. Perturbing engine performance measurements to determine optimal engine control settings

    DOEpatents

    Jiang, Li; Lee, Donghoon; Yilmaz, Hakan; Stefanopoulou, Anna

    2014-12-30

    Methods and systems for optimizing a performance of a vehicle engine are provided. The method includes determining an initial value for a first engine control parameter based on one or more detected operating conditions of the vehicle engine, determining a value of an engine performance variable, and artificially perturbing the determined value of the engine performance variable. The initial value for the first engine control parameter is then adjusted based on the perturbed engine performance variable causing the engine performance variable to approach a target engine performance variable. Operation of the vehicle engine is controlled based on the adjusted initial value for the first engine control parameter. These acts are repeated until the engine performance variable approaches the target engine performance variable.

  20. 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.

  1. A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines.

    PubMed

    Chitwood, Daniel H; Kumar, Ravi; Headland, Lauren R; Ranjan, Aashish; Covington, Michael F; Ichihashi, Yasunori; Fulop, Daniel; Jiménez-Gómez, José M; Peng, Jie; Maloof, Julin N; Sinha, Neelima R

    2013-07-01

    Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations.

  2. Three-body problem in quantum mechanics: hyperspherical elliptic coordinates and harmonic basis sets.

    PubMed

    Aquilanti, Vincenzo; Tonzani, Stefano

    2004-03-01

    Elliptic coordinates within the hyperspherical formalism for three-body problems were proposed some time ago [V. Aquilanti, S. Cavalli, and G. Grossi, J. Chem. Phys. 85, 1362 (1986)] and recently have also found application, for example, in chemical reaction theory [see O. I. Tolstikhin and H. Nakamura, J. Chem. Phys. 108, 8899 (1998)]. Here we consider their role in providing a smooth transition between the known "symmetric" and "asymmetric" parametrizations, and focus on the corresponding hyperspherical harmonics. These harmonics, which will be called hyperspherical elliptic, involve products of two associated Lame polynomials. We will provide an expansion of these new sets in a finite series of standard hyperspherical harmonics, producing a powerful tool for future applications in the field of scattering and bound-state quantum-mechanical three-body problems.

  3. Multi-stage approach for structural damage detection problem using basis pursuit and particle swarm optimization

    NASA Astrophysics Data System (ADS)

    Gerist, Saleheh; Maheri, Mahmoud R.

    2016-12-01

    In order to solve structural damage detection problem, a multi-stage method using particle swarm optimization is presented. First, a new spars recovery method, named Basis Pursuit (BP), is utilized to preliminarily identify structural damage locations. The BP method solves a system of equations which relates the damage parameters to the structural modal responses using the sensitivity matrix. Then, the results of this stage are subsequently enhanced to the exact damage locations and extents using the PSO search engine. Finally, the search space is reduced by elimination of some low damage variables using micro search (MS) operator embedded in the PSO algorithm. To overcome the noise present in structural responses, a method known as Basis Pursuit De-Noising (BPDN) is also used. The efficiency of the proposed method is investigated by three numerical examples: a cantilever beam, a plane truss and a portal plane frame. The frequency response is used to detect damage in the examples. The simulation results demonstrate the accuracy and efficiency of the proposed method in detecting multiple damage cases and exhibit its robustness regarding noise and its advantages compared to other reported solution algorithms.

  4. [The BASYS observation system for the analysis of aggressive behavior in classroom-settings].

    PubMed

    Wettstein, Alexander

    2012-01-01

    Educational or therapeutic measures of aggressive student behavior are often based on the judgments of teachers. However, empirical studies show that the objectivity of these judgments is generally low. In order to assess aggressive behavior in classroom settings, we developed a context-sensitive observational system. The observation system exists in a version for teachers in action as well as a version for the uninvolved observer. The teacher version allows categorizing aggressive behavior while teaching. The aim is to differentiate the perception and the judgments of teachers, so that the judgments can serve as trustable diagnostic information. The version for an independent observer, in addition, contains categories to collect information about the context in which aggressions take place. The behavior observation system was tested in four field-studies in regular and special classes. The empirical results show that, after training, teachers were able to make objective observations, and that aggressive behavior depends to a large extent on situational factors. The system allows identification of problematic people-environment relationships and the derivation of intervention measures.

  5. Reduced Design Load Basis for Ultimate Blade Loads Estimation in Multidisciplinary Design Optimization Frameworks

    NASA Astrophysics Data System (ADS)

    Pavese, Christian; Tibaldi, Carlo; Larsen, Torben J.; Kim, Taeseong; Thomsen, Kenneth

    2016-09-01

    The aim is to provide a fast and reliable approach to estimate ultimate blade loads for a multidisciplinary design optimization (MDO) framework. For blade design purposes, the standards require a large amount of computationally expensive simulations, which cannot be efficiently run each cost function evaluation of an MDO process. This work describes a method that allows integrating the calculation of the blade load envelopes inside an MDO loop. Ultimate blade load envelopes are calculated for a baseline design and a design obtained after an iteration of an MDO. These envelopes are computed for a full standard design load basis (DLB) and a deterministic reduced DLB. Ultimate loads extracted from the two DLBs with the two blade designs each are compared and analyzed. Although the reduced DLB supplies ultimate loads of different magnitude, the shape of the estimated envelopes are similar to the one computed using the full DLB. This observation is used to propose a scheme that is computationally cheap, and that can be integrated inside an MDO framework, providing a sufficiently reliable estimation of the blade ultimate loading. The latter aspect is of key importance when design variables implementing passive control methodologies are included in the formulation of the optimization problem. An MDO of a 10 MW wind turbine blade is presented as an applied case study to show the efficacy of the reduced DLB concept.

  6. Basis set convergence and performance of density functional theory including exact exchange contributions for geometries and harmonic frequencies

    NASA Astrophysics Data System (ADS)

    Martin, Jan M. L.; El-Yazal, Jamal; François, Jean-Pierre

    1995-12-01

    The performance of the Becke three-parameter Lee-Yang-Parr (B3LYP) method for geometries and harmonic frequencies has been compared with other density functional methods and accurate coupled cluster calculations, and its basis set convergence investigated. In a basis of [3s2p1d] quality, B3LYP geometries are more accurate than CCSD(T) due to an error compensation. Using simple additivity corrections, B3LYP/[4s3p2d1f] calculations allow the prediction of geometries to within 0·002 Å, on average. Except for certain special cases where frequencies are especially sensitive to the basis set, B3LYP/[4s3p2d1f] frequencies do not represent a clear improvement over B3LYP/[3s2p1d], while the latter are of nearly the same quality as CCSD(T)/[3s2p1d]. Applications to ethylene, benzene, furan and pyrrole are presented. For the latter three molecules, our best structures and harmonic frequencies are believed to be the most accurate computed values available.

  7. Using Optimal Control to Disambiguate the Effect of Depression on Sensorimotor, Motivational and Goal-Setting Functions

    PubMed Central

    Huang, He; Harlé, Katia; Movellan, Javier; Paulus, Martin

    2016-01-01

    Differentiating the ability from the motivation to act is of central importance to psychiatric disorders in general and depression in particular. However, it has been difficult to develop quantitative approaches to relate depression to poor motor performance in goal-directed tasks. Here, we use an inverse optimal control approach to provide a computational framework that can be used to infer and factorize performance deficits into three components: sensorimotor speed, goal setting and motivation. Using a novel computer-simulated driving experiment, we found that (1) severity of depression is associated with both altered sensorimotor speed and motivational function; (2) moderately to severely depressed individuals show an increased distance from the stop sign indicating aversive learning affecting goal setting functions. Taken together, the inverse optimal control framework can disambiguate on an individual basis the sensorimotor from the motivational dysfunctions in depression, which may help to develop more precisely targeted interventions. PMID:27973592

  8. 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

    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.

  9. Small Al clusters. I - The effect of basis set and correlation on the geometry of small Al clusters

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Pettersson, Lars G. M.

    1987-01-01

    A detailed study is presented of the basis set requirements and effects of correlation on the geometry and structure of small Al(n) clusters n = 2, 4, and 13. An effective core potential (ECP) is developed from the Huzinaga basis which accurately reproduces the all-electron results. It is found that depolarization functions are very important in computing the bond length, and that the bond contraction obtained is about as large for a 13-atom cluster as for the Al(4) rhombus structure. With d functions on each center in Al(13), a bond distance shorter than the bulk is obtained, as expected. The inclusion of correlation in Al(4) is found to be less important than the addition of polarization functions for determining the bond length, but increases substantially the calculated atomization energy. These calibration calculations allow an accurate treatment for Al(n) clusters to be designed.

  10. A matrix representation of the translation operator with respect to a basis set of exponentially declining functions

    NASA Astrophysics Data System (ADS)

    Filter, Eckhard; Steinborn, E. Otto

    1980-12-01

    The matrix elements of the translation operator with respect to a complete orthonormal basis set of the Hilbert space L2(R3) are given in closed form as functions of the displacement vector. The basis functions are composed of an exponential, a Laguerre polynomial, and a regular solid spherical harmonic. With this formalism, a function which is defined with respect to a certain origin, can be ''shifted'', i.e., expressed in terms of given functions which are defined with respect to another origin. In this paper we also demonstrate the feasibility of this method by applying it to problems that are of special interest in the theory of the electronic structure of molecules and solids. We present new one-center expansions for some exponential-type functions (ETF's), and a closed-form expression for a multicenter integral over ETF's is given and numerically tested.

  11. Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c.

    PubMed

    González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A

    2015-08-11

    Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin's transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ's histone chaperone activity.

  12. Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c

    PubMed Central

    González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A.

    2015-01-01

    Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin’s transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ’s histone chaperone activity. PMID:26216969

  13. Performance of density functional theory for 3d transition metal-containing complexes: utilization of the correlation consistent basis sets.

    PubMed

    Tekarli, Sammer M; Drummond, Michael L; Williams, T Gavin; Cundari, Thomas R; Wilson, Angela K

    2009-07-30

    The performance of 44 density functionals used in conjunction with the correlation consistent basis sets (cc-pVnZ where n = T and Q) has been assessed for the gas-phase enthalpies of formation at 298.15 K of 3d transition metal (TM) containing systems. Nineteen molecules were examined: ScS, VO, VO(2), Cr(CO)(6), MnS, MnCl(2), Mn(CO)(5)Cl, FeCl(3), Fe(CO)(5), CoH(CO)(4), NiCl(2), Ni(CO)(4), CuH, CuF, CuCl, ZnH, ZnO, ZnCl, and Zn(CH(3))(2). Of the functionals examined, the functionals that resulted in the smallest mean absolute deviation (MAD, in parentheses, kcal mol(-1)) from experiment were B97-1 (6.9), PBE1KCIS (8.1), TPSS1KCIS (9.6), B97-2 (9.7), and B98 (10.7). All five of these functionals include some degree of Hartree-Fock (HF) exchange. The impact of increasing the basis set from cc-pVTZ to cc-pVQZ was found to be slight for the generalized gradient approximation (GGA) and meta-GGA (MGGA) functionals studied, indicating basis set saturation at the triple-zeta level. By contrast, for most of the generalized gradient exchange (GGE), hybrid GGA (HGGA), and hybrid meta-GGA (HMGGA) functionals considered, improvements in the average MAD of 2-3 kcal mol(-1) were seen upon progressing to a quadruple-zeta level basis set. Overall, it was found that the functionals that include Hartree-Fock exchange performed best overall, but those with greater than 40% HF exchange exhibit significantly poor performance for the prediction of enthalpies of formation for 3d TM complexes. Carbonyl-containing complexes, a mainstay in organometallic TM chemistry, are demonstrated to be exceedingly difficult to describe accurately with all but 2 of the 44 functionals considered. The most accurate functional, for both CO-containing and CO-free compounds, is B97-1/cc-pVQZ, which is shown to be capable of yielding results within 1 kcal mol(-1) of high-level ab initio composite methodologies.

  14. A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

    NASA Astrophysics Data System (ADS)

    Simon, Sílvia; Duran, Miquel

    1997-08-01

    Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

  15. The Study of the Optimal Parameter Settings in a Hospital Supply Chain System in Taiwan

    PubMed Central

    Liao, Hung-Chang; Chen, Meng-Hao; Wang, Ya-huei

    2014-01-01

    This study proposed the optimal parameter settings for the hospital supply chain system (HSCS) when either the total system cost (TSC) or patient safety level (PSL) (or both simultaneously) was considered as the measure of the HSCS's performance. Four parameters were considered in the HSCS: safety stock, maximum inventory level, transportation capacity, and the reliability of the HSCS. A full-factor experimental design was used to simulate an HSCS for the purpose of collecting data. The response surface method (RSM) was used to construct the regression model, and a genetic algorithm (GA) was applied to obtain the optimal parameter settings for the HSCS. The results show that the best method of obtaining the optimal parameter settings for the HSCS is the simultaneous consideration of both the TSC and the PSL to measure performance. Also, the results of sensitivity analysis based on the optimal parameter settings were used to derive adjustable strategies for the decision-makers. PMID:25250397

  16. Evaluation of one-dimensional and two-dimensional volatility basis sets in simulating the aging of secondary organic aerosol with smog-chamber experiments.

    PubMed

    Zhao, Bin; Wang, Shuxiao; Donahue, Neil M; Chuang, Wayne; Hildebrandt Ruiz, Lea; Ng, Nga L; Wang, Yangjun; Hao, Jiming

    2015-02-17

    We evaluate the one-dimensional volatility basis set (1D-VBS) and two-dimensional volatility basis set (2D-VBS) in simulating the aging of SOA derived from toluene and α-pinene against smog-chamber experiments. If we simulate the first-generation products with empirical chamber fits and the subsequent aging chemistry with a 1D-VBS or a 2D-VBS, the models mostly overestimate the SOA concentrations in the toluene oxidation experiments. This is because the empirical chamber fits include both first-generation oxidation and aging; simulating aging in addition to this results in double counting of the initial aging effects. If the first-generation oxidation is treated explicitly, the base-case 2D-VBS underestimates the SOA concentrations and O:C increase of the toluene oxidation experiments; it generally underestimates the SOA concentrations and overestimates the O:C increase of the α-pinene experiments. With the first-generation oxidation treated explicitly, we could modify the 2D-VBS configuration individually for toluene and α-pinene to achieve good model-measurement agreement. However, we are unable to simulate the oxidation of both toluene and α-pinene with the same 2D-VBS configuration. We suggest that future models should implement parallel layers for anthropogenic (aromatic) and biogenic precursors, and that more modeling studies and laboratory research be done to optimize the "best-guess" parameters for each layer.

  17. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells.

    PubMed

    Masoli, Stefano; Rizza, Martina F; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio

    2017-01-01

    In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models.

  18. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells

    PubMed Central

    Masoli, Stefano; Rizza, Martina F.; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio

    2017-01-01

    In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models. PMID:28360841

  19. Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties.

    PubMed

    Browning, Nicholas J; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole; Roethlisberger, Ursula

    2017-04-06

    The training of molecular models of quantum mechanical properties based on statistical machine learning requires large data sets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of training examples is often difficult or impossible to achieve, as prior knowledge may be unavailable. Ordinarily representative selection of training molecules from such data sets is achieved through random sampling. We use genetic algorithms for the optimization of training set composition consisting of tens of thousands of small organic molecules. The resulting machine learning models are considerably more accurate: in the limit of small training sets, mean absolute errors for out-of-sample predictions are reduced by up to ∼75%. We discuss and present optimized training sets consisting of 10 molecular classes for all molecular properties studied. We show that these classes can be used to design improved training sets for the generation of machine learning models of the same properties in similar but unrelated molecular sets.

  20. Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: Application to methanol

    NASA Astrophysics Data System (ADS)

    Van Houteghem, Marc; Verstraelen, Toon; Ghysels, An; Vanduyfhuys, Louis; Waroquier, Michel; Van Speybroeck, Veronique

    2012-09-01

    An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

  1. 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 .

  2. An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification

    ERIC Educational Resources Information Center

    Wang, Jun; Samal, Ashok; Rong, Panying; Green, Jordan R.

    2016-01-01

    Purpose: The authors sought to determine an optimal set of flesh points on the tongue and lips for classifying speech movements. Method: The authors used electromagnetic articulographs (Carstens AG500 and NDI Wave) to record tongue and lip movements from 13 healthy talkers who articulated 8 vowels, 11 consonants, a phonetically balanced set of…

  3. Aerostructural Level Set Topology Optimization for a Common Research Model Wing

    NASA Technical Reports Server (NTRS)

    Dunning, Peter D.; Stanford, Bret K.; Kim, H. Alicia

    2014-01-01

    The purpose of this work is to use level set topology optimization to improve the design of a representative wing box structure for the NASA common research model. The objective is to minimize the total compliance of the structure under aerodynamic and body force loading, where the aerodynamic loading is coupled to the structural deformation. A taxi bump case was also considered, where only body force loads were applied. The trim condition that aerodynamic lift must balance the total weight of the aircraft is enforced by allowing the root angle of attack to change. The level set optimization method is implemented on an unstructured three-dimensional grid, so that the method can optimize a wing box with arbitrary geometry. Fast matching and upwind schemes are developed for an unstructured grid, which make the level set method robust and efficient. The adjoint method is used to obtain the coupled shape sensitivities required to perform aerostructural optimization of the wing box structure.

  4. Approximate approach for optimization space flights with a low thrust on the basis of sufficient optimality conditions

    NASA Astrophysics Data System (ADS)

    Salmin, Vadim V.

    2017-01-01

    Flight mechanics with a low-thrust is a new chapter of mechanics of space flight, considered plurality of all problems trajectory optimization and movement control laws and the design parameters of spacecraft. Thus tasks associated with taking into account the additional factors in mathematical models of the motion of spacecraft becomes increasingly important, as well as additional restrictions on the possibilities of the thrust vector control. The complication of the mathematical models of controlled motion leads to difficulties in solving optimization problems. Author proposed methods of finding approximate optimal control and evaluating their optimality based on analytical solutions. These methods are based on the principle of extending the class of admissible states and controls and sufficient conditions for the absolute minimum. Developed procedures of the estimation enabling to determine how close to the optimal founded solution, and indicate ways to improve them. Authors describes procedures of estimate for approximately optimal control laws for space flight mechanics problems, in particular for optimization flight low-thrust between the circular non-coplanar orbits, optimization the control angle and trajectory movement of the spacecraft during interorbital flights, optimization flights with low-thrust between arbitrary elliptical orbits Earth satellites.

  5. Explicitly correlated Gaussian basis set expansion approach for few-body systems with spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Guan, Qingze; Blume, Doerte

    2016-05-01

    The explicit correlated Gaussian (ECG) basis set expansion approach is a variational approach that has been used in various areas, including molecular, nuclear, atomic, and chemical physics. In the world of cold atoms, e.g., the ECG approach has been used to calculate the eigenenergies and eigenstates of few-body systems governed by Efimov physics. Since the first experimental realization of synthesized gauge fields, few-body systems with spin-orbit coupling have attracted a great deal of attention. Here, the ECG approach is customized to few-body systems with both short-range interactions and spin-orbit couplings. Benchmark tests and a performance analysis will be presented. Support by the NSF is gratefully acknowledged.

  6. The enthalpy of formation of the pentane-2,4-dionate radical: A complete basis set approach

    NASA Astrophysics Data System (ADS)

    Cabral do Couto, P.; Costa Cabral, Benedito J.; Martinho Simões, José A.

    2006-02-01

    Thermochemical properties of pentane-2,4-dione (acetylacetone, Hacac) and its radical (acac) were investigated by DFT and ab initio calculations based on complete basis set (CBS) extrapolation procedures, including CBS-QB3 and a modified CBS procedure that we named CBS-QB3-tz. We provide evidence that the most stable acac radical conformer is generated by C-H bond homolysis. The enthalpy of formation of gaseous acac, Δ fH∘(acac,g), was estimated as -228.3 kJ/mol (CBS-QB3) and -226.7 kJ/mol (CBS-QB3-tz). Based on these results, our recommended value for Δ fH∘(acac,g) is -227 ± 8 kJ/mol, implying that many literature values reported for metal-acac bond dissociation enthalpies in coordination complexes should be revised.

  7. Density functional theory analysis of Raman frequency modes of monoclinic zirconium oxide using Gaussian basis sets and isotopic substitution.

    PubMed

    Daramola, Damilola A; Muthuvel, Madhivanan; Botte, Gerardine G

    2010-07-29

    Geometry and vibration properties for monoclinic zirconium oxide were studied using Gaussian basis sets and LDA, GGA, and B3LYP functionals. Bond angles, bond lengths, lattice parameters, and Raman frequencies were calculated and compared to experimental values. Bond angles and lengths were found to agree within experimental standard deviations. The B3LYP gave the best performance of all three functionals with a percent error of 1.35% for the lattice parameters while the average difference between experimental and calculated Raman frequency values was -3 cm(-1). The B3LYP functional was then used to assign the atomic vibrations causing each frequency mode using isotopic substitution of (93.40)Zr for (91.22)Zr and (18.00)O for (16.00)O. This resulted in seven modes assigned to the Zr atom, ten modes to the O atom, and one mode being a mixture of both.

  8. 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.

  9. Pros and Cons of Using the Informed Basis Set to Account for Hemodynamic Response Variability with Developmental Data.

    PubMed

    Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine

    2016-01-01

    Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4-6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data.

  10. Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

    NASA Astrophysics Data System (ADS)

    Oberhofer, Harald; Blumberger, Jochen

    2010-12-01

    We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

  11. Pros and Cons of Using the Informed Basis Set to Account for Hemodynamic Response Variability with Developmental Data

    PubMed Central

    Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine

    2016-01-01

    Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4–6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data. PMID:27471441

  12. Dressing the chopped-random-basis optimization: A bandwidth-limited access to the trap-free landscape

    NASA Astrophysics Data System (ADS)

    Rach, N.; Müller, M. M.; Calarco, T.; Montangero, S.

    2015-12-01

    In quantum optimal control theory the success of an optimization algorithm is highly influenced by how the figure of merit to be optimized behaves as a function of the control field, i.e., by the control landscape. Constraints on the control field introduce local minima in the landscape—false traps—which might prevent an efficient solution of the optimal control problem. Rabitz et al. [Science 303, 1998 (2004), 10.1126/science.1093649] showed that local minima occur only rarely for unconstrained optimization. Here, we extend this result to the case of bandwidth-limited control pulses showing that in this case one can eliminate the false traps arising from the constraint. Based on this theoretical understanding, we modify the chopped-random-basis (CRAB) optimal control algorithm and show that this development exploits the advantages of both (unconstrained) gradient algorithms and of truncated basis methods, allowing one to always follow the gradient of the unconstrained landscape by bandwidth-limited control functions. We study the effects of additional constraints and show that for reasonable constraints the convergence properties are still maintained. Finally, we numerically show that this approach saturates the theoretical bound on the minimal bandwidth of the control needed to optimally drive the system.

  13. 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

  14. Cost optimization for series-parallel execution of a collection of intersecting operation sets

    NASA Astrophysics Data System (ADS)

    Dolgui, Alexandre; Levin, Genrikh; Rozin, Boris; Kasabutski, Igor

    2016-05-01

    A collection of intersecting sets of operations is considered. These sets of operations are performed successively. The operations of each set are activated simultaneously. Operation durations can be modified. The cost of each operation decreases with the increase in operation duration. In contrast, the additional expenses for each set of operations are proportional to its time. The problem of selecting the durations of all operations that minimize the total cost under constraint on completion time for the whole collection of operation sets is studied. The mathematical model and method to solve this problem are presented. The proposed method is based on a combination of Lagrangian relaxation and dynamic programming. The results of numerical experiments that illustrate the performance of the proposed method are presented. This approach was used for optimization multi-spindle machines and machining lines, but the problem is common in engineering optimization and thus the techniques developed could be useful for other applications.

  15. 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.

  16. Optimal testing input sets for reduced diagnosis time of nuclear power plant digital electronic circuits

    SciTech Connect

    Kim, D.S.; Seong, P.H. . Dept. of Nuclear Engineering)

    1994-02-01

    This paper describes the optimal testing input sets required for the fault diagnosis of the nuclear power plant digital electronic circuits. With the complicated systems such as very large scale integration (VLSI), nuclear power plant (NPP), and aircraft, testing is the major factor of the maintenance of the system. Particularly, diagnosis time grows quickly with the complexity of the component. In this research, for reduce diagnosis time the authors derived the optimal testing sets that are the minimal testing sets required for detecting the failure and for locating of the failed component. For reduced diagnosis time, the technique presented by Hayes fits best for the approach to testing sets generation among many conventional methods. However, this method has the following disadvantages: (a) it considers only the simple network (b) it concerns only whether the system is in failed state or not and does not provide the way to locate the failed component. Therefore the authors have derived the optimal testing input sets that resolve these problems by Hayes while preserving its advantages. When they applied the optimal testing sets to the automatic fault diagnosis system (AFDS) which incorporates the advanced fault diagnosis method of artificial intelligence technique, they found that the fault diagnosis using the optimal testing sets makes testing the digital electronic circuits much faster than that using exhaustive testing input sets; when they applied them to test the Universal (UV) Card which is a nuclear power plant digital input/output solid state protection system card, they reduced the testing time up to about 100 times.

  17. Optimization of Training Sets for Neural-Net Processing of Characteristic Patterns from Vibrating Solids

    NASA Technical Reports Server (NTRS)

    Decker, Arthur J.

    2001-01-01

    Artificial neural networks have been used for a number of years to process holography-generated characteristic patterns of vibrating structures. This technology depends critically on the selection and the conditioning of the training sets. A scaling operation called folding is discussed for conditioning training sets optimally for training feed-forward neural networks to process characteristic fringe patterns. Folding allows feed-forward nets to be trained easily to detect damage-induced vibration-displacement-distribution changes as small as 10 nm. A specific application to aerospace of neural-net processing of characteristic patterns is presented to motivate the conditioning and optimization effort.

  18. Stacking sequence and shape optimization of laminated composite plates via a level-set method

    NASA Astrophysics Data System (ADS)

    Allaire, G.; Delgado, G.

    2016-12-01

    We consider the optimal design of composite laminates by allowing a variable stacking sequence and in-plane shape of each ply. In order to optimize both variables we rely on a decomposition technique which aggregates the constraints into one unique constraint margin function. Thanks to this approach, an exactly equivalent bi-level optimization problem is established. This problem is made up of an inner level represented by the combinatorial optimization of the stacking sequence and an outer level represented by the topology and geometry optimization of each ply. We propose for the stacking sequence optimization an outer approximation method which iteratively solves a set of mixed integer linear problems associated to the evaluation of the constraint margin function. For the topology optimization of each ply, we lean on the level set method for the description of the interfaces and the Hadamard method for boundary variations by means of the computation of the shape gradient. Numerical experiments are performed on an aeronautic test case where the weight is minimized subject to different mechanical constraints, namely compliance, reserve factor and buckling load.

  19. Second-order lower radial tangent derivatives and applications to set-valued optimization.

    PubMed

    Xu, Bihang; Peng, Zhenhua; Xu, Yihong

    2017-01-01

    We introduce the concepts of second-order radial composed tangent derivative, second-order radial tangent derivative, second-order lower radial composed tangent derivative, and second-order lower radial tangent derivative for set-valued maps by means of a radial tangent cone, second-order radial tangent set, lower radial tangent cone, and second-order lower radial tangent set, respectively. Some properties of second-order tangent derivatives are discussed, using which second-order necessary optimality conditions are established for a point pair to be a Henig efficient element of a set-valued optimization problem, and in the expressions the second-order tangent derivatives of the objective function and the constraint function are separated.

  20. Thermodynamics of forming water clusters at various temperatures and pressures by Gaussian-2, Gaussian-3, complete basis set-QB3, and complete basis set-APNO model chemistries; implications for atmospheric chemistry.

    PubMed

    Dunn, Meghan E; Pokon, Emma K; Shields, George C

    2004-03-03

    The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate Delta H degrees and Delta G degrees values for neutral clusters of water, (H(2)O)(n), where n = 2-6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 x 10(14) molecules/cm(3), water trimer concentrations of 2.6 x 10(12) molecules/cm(3), tetramer concentrations of approximately 5.8 x 10(11) molecules/cm(3), and pentamer concentrations of approximately 3.5 x 10(10) molecules/cm(3) in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.

  1. Topology Optimization using the Level Set and eXtended Finite Element Methods: Theory and Applications

    NASA Astrophysics Data System (ADS)

    Villanueva Perez, Carlos Hernan

    Computational design optimization provides designers with automated techniques to develop novel and non-intuitive optimal designs. Topology optimization is a design optimization technique that allows for the evolution of a broad variety of geometries in the optimization process. Traditional density-based topology optimization methods often lack a sufficient resolution of the geometry and physical response, which prevents direct use of the optimized design in manufacturing and the accurate modeling of the physical response of boundary conditions. The goal of this thesis is to introduce a unified topology optimization framework that uses the Level Set Method (LSM) to describe the design geometry and the eXtended Finite Element Method (XFEM) to solve the governing equations and measure the performance of the design. The methodology is presented as an alternative to density-based optimization approaches, and is able to accommodate a broad range of engineering design problems. The framework presents state-of-the-art methods for immersed boundary techniques to stabilize the systems of equations and enforce the boundary conditions, and is studied with applications in 2D and 3D linear elastic structures, incompressible flow, and energy and species transport problems to test the robustness and the characteristics of the method. A comparison of the framework against density-based topology optimization approaches is studied with regards to convergence, performance, and the capability to manufacture the designs. Furthermore, the ability to control the shape of the design to operate within manufacturing constraints is developed and studied. The analysis capability of the framework is validated quantitatively through comparison against previous benchmark studies, and qualitatively through its application to topology optimization problems. The design optimization problems converge to intuitive designs and resembled well the results from previous 2D or density-based studies.

  2. A mathematical basis for the design optimization of adaptive trusses in precision control

    NASA Technical Reports Server (NTRS)

    Das, S. K.; Utku, S.; Chen, G. S.; Wada, B. K.

    1991-01-01

    Optimal actuator placement schemes are presently studied for cases of adaptive truss precision control and prestressing control, with a view to the maximization of actuator efficiencies. In statically indeterminate truss structures, the optimal placement criteria and techniques differ, depending on whether the primary determinate structure is known. A suboptimal actuator-placement solution to the global optimization problem which combines displacement control and prestressing control is suggested, by combining the separate displacement control and prestressing control optimization results. Attention is given to the results obtained for the illustrative case of a two-bay, three-dimensional precision truss structure.

  3. Predictions of Optical Excitations in Transition-Metal Complexes with Time Dependent-Density Functional Theory:  Influence of Basis Sets.

    PubMed

    Petit, Laurence; Maldivi, Pascale; Adamo, Carlo

    2005-09-01

    The calculation of the absorption spectra of four families of transition-metal complexes (Ni(CO)4, MnO4(-), MF6 (M = Cr, Mo, W) and CpM(CO)2 (M = Rh, Ir)) has been undertaken to unravel the influence of basis sets onto excitation energies, oscillator strengths, and assignments. Three among the most common pseudopotentials, with the corresponding valence basis sets, and two all-electron basis sets have been used for the metal center description in the framework of the time dependent Density Functional Theory (TD-DFT). Our results show that this approach does not particularly depend on the basis set used on the metal atoms. Furthermore, the chosen functional PBE0 provides transitions in good agreement with experiments, and it provides an accuracy of about 0.3 eV, comparable to that of refined post-Hartree-Fock methods.

  4. The FERMI @ Elettra Technical Optimization Study: PreliminaryParameter Set and Initial Studies

    SciTech Connect

    Byrd, John; Corlett, John; Doolittle, Larry; Fawley, William; Lidia, Steven; Penn, Gregory; Ratti, Alex; Staples, John; Wilcox,Russell; Wurtele, Jonathan; Zholents, Alexander

    2005-08-01

    The goal of the FERMI {at} Elettra Technical Optimization Study is to produce a machine design and layout consistent with user needs for radiation in the approximate ranges 100 nm to 40 nm, and 40 nm to 10 nm, using seeded FEL's. The Study will involve collaboration between Italian and US physicists and engineers, and will form the basis for the engineering design and the cost estimation.

  5. Benchmark Calculations with Correlated Molecular Wave Functions. XIII. Potential Energy Curves for He-2, Ne-2, and Ar-2 Using Correlation Consistent Basis Sets Through Augmented Sextuple Zeta.

    SciTech Connect

    Mourik, Van Tonja; Wilson, Angela K.; Dunning, Thomas H.

    1999-02-20

    The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)].

  6. A Computationally Inexpensive Optimal Guidance via Radial-Basis-Function Neural Network for Autonomous Soft Landing on Asteroids.

    PubMed

    Zhang, Peng; Liu, Keping; Zhao, Bo; Li, Yuanchun

    2015-01-01

    Optimal guidance is essential for the soft landing task. However, due to its high computational complexities, it is hardly applied to the autonomous guidance. In this paper, a computationally inexpensive optimal guidance algorithm based on the radial basis function neural network (RBFNN) is proposed. The optimization problem of the trajectory for soft landing on asteroids is formulated and transformed into a two-point boundary value problem (TPBVP). Combining the database of initial states with the relative initial co-states, an RBFNN is trained offline. The optimal trajectory of the soft landing is determined rapidly by applying the trained network in the online guidance. The Monte Carlo simulations of soft landing on the Eros433 are performed to demonstrate the effectiveness of the proposed guidance algorithm.

  7. A Computationally Inexpensive Optimal Guidance via Radial-Basis-Function Neural Network for Autonomous Soft Landing on Asteroids

    PubMed Central

    Zhang, Peng; Liu, Keping; Zhao, Bo; Li, Yuanchun

    2015-01-01

    Optimal guidance is essential for the soft landing task. However, due to its high computational complexities, it is hardly applied to the autonomous guidance. In this paper, a computationally inexpensive optimal guidance algorithm based on the radial basis function neural network (RBFNN) is proposed. The optimization problem of the trajectory for soft landing on asteroids is formulated and transformed into a two-point boundary value problem (TPBVP). Combining the database of initial states with the relative initial co-states, an RBFNN is trained offline. The optimal trajectory of the soft landing is determined rapidly by applying the trained network in the online guidance. The Monte Carlo simulations of soft landing on the Eros433 are performed to demonstrate the effectiveness of the proposed guidance algorithm. PMID:26367382

  8. Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn-Sham complete basis set limit.

    PubMed

    Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A; Żyła, Adriana

    2016-01-01

    In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies. Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit.

  9. Optimization of structures on the basis of fracture mechanics and reliability criteria

    NASA Technical Reports Server (NTRS)

    Heer, E.; Yang, J. N.

    1973-01-01

    Systematic summary of factors which are involved in optimization of given structural configuration is part of report resulting from study of analysis of objective function. Predicted reliability of performance of finished structure is sharply dependent upon results of coupon tests. Optimization analysis developed by study also involves expected cost of proof testing.

  10. Internal combustion engine report: Spark ignited ICE GenSet optimization and novel concept development

    SciTech Connect

    Keller, J.; Blarigan, P. Van

    1998-08-01

    In this manuscript the authors report on two projects each of which the goal is to produce cost effective hydrogen utilization technologies. These projects are: (1) the development of an electrical generation system using a conventional four-stroke spark-ignited internal combustion engine generator combination (SI-GenSet) optimized for maximum efficiency and minimum emissions, and (2) the development of a novel internal combustion engine concept. The SI-GenSet will be optimized to run on either hydrogen or hydrogen-blends. The novel concept seeks to develop an engine that optimizes the Otto cycle in a free piston configuration while minimizing all emissions. To this end the authors are developing a rapid combustion homogeneous charge compression ignition (HCCI) engine using a linear alternator for both power take-off and engine control. Targeted applications include stationary electrical power generation, stationary shaft power generation, hybrid vehicles, and nearly any other application now being accomplished with internal combustion engines.

  11. A level set-based shape optimization method for periodic sound barriers composed of elastic scatterers

    NASA Astrophysics Data System (ADS)

    Hashimoto, Hiroshi; Kim, Min-Geun; Abe, Kazuhisa; Cho, Seonho

    2013-10-01

    This paper presents a level set-based topology optimization method for noise barriers formed from an assembly of scatterers. The scattering obstacles are modeled by elastic bodies arranged periodically along the wall. Due to the periodicity, the problem can be reduced to that in a unit cell. The interaction between the elastic scatterers and the acoustic field is described in the context of the level set analysis. The semi-infinite acoustic wave regions located on the both sides of the barrier are represented by impedance matrices. The objective function is defined by the energy transmission passing the barrier. The design sensitivity is evaluated analytically by the aid of adjoint equations. The dependency of the optimal profile on the stiffness of scatterers and on the target frequency band is examined. The feasibility of the developed optimization method is proved through numerical examples.

  12. Image segmentation using globally optimal growth in three dimensions with an adaptive feature set

    NASA Astrophysics Data System (ADS)

    Taylor, David C.; Barrett, William A.

    1994-09-01

    A globally optimal region growing algorithm for 3D segmentation of anatomical objects is developed. The notion of simple 3D connected component labelling is extended to enable the combination of arbitrary features in the segmentation process. This algorithm uses a hybrid octree-btree structure to segment an object of interest in an ordered fashion. This tree structure overcomes the computational complexity of global optimality in three dimensions. The segmentation process is controlled by a set of active features, which work in concert to extract the object of interest. The cost function used to enforce the order is based on the combination of active features. The characteristics of the data throughout the volume dynamically influences which features are active. A foundation for applying user interaction with the object directly to the feature set is established. The result is a system which analyzes user input and neighborhood data and optimizes the tools used in the segmentation process accordingly.

  13. An Approach to Feature Selection Based on Ant Colony Optimization and Rough Set

    NASA Astrophysics Data System (ADS)

    Wu, Junyun; Qiu, Taorong; Wang, Lu; Huang, Haiquan

    Feature selection plays an important role in many fields. This paper proposes a method for feature selection which combined the rough set method and ant colony optimization algorithm. The algorithm used the attribute dependence and the attribute importance as the inspiration factor which applied to the transfer rules. For further, the quality of classification based on rough set method and the length of the feature subset were used to build the pheromone update strategy. Through the test of data set, results show that the proposed method is feasible.

  14. Unbiased QM/MM approach using accurate multipoles from a linear scaling DFT calculation with a systematic basis set

    NASA Astrophysics Data System (ADS)

    Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel

    The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.

  15. Design of cognitive engine for cognitive radio based on the rough sets and radial basis function neural network

    NASA Astrophysics Data System (ADS)

    Yang, Yanchao; Jiang, Hong; Liu, Congbin; Lan, Zhongli

    2013-03-01

    Cognitive radio (CR) is an intelligent wireless communication system which can dynamically adjust the parameters to improve system performance depending on the environmental change and quality of service. The core technology for CR is the design of cognitive engine, which introduces reasoning and learning methods in the field of artificial intelligence, to achieve the perception, adaptation and learning capability. Considering the dynamical wireless environment and demands, this paper proposes a design of cognitive engine based on the rough sets (RS) and radial basis function neural network (RBF_NN). The method uses experienced knowledge and environment information processed by RS module to train the RBF_NN, and then the learning model is used to reconfigure communication parameters to allocate resources rationally and improve system performance. After training learning model, the performance is evaluated according to two benchmark functions. The simulation results demonstrate the effectiveness of the model and the proposed cognitive engine can effectively achieve the goal of learning and reconfiguration in cognitive radio.

  16. Wide-range photoabsorption cross-sections of simple metals: large basis-set OPW calculations for sodium

    NASA Astrophysics Data System (ADS)

    Kitamura, Hikaru

    2013-02-01

    Photoabsorption cross-sections of simple metals are formulated through a solid-state band theory based on the orthogonalized-plane-wave (OPW) method in Slater’s local-exchange approximation, where interband transitions of core and conduction electrons are evaluated up to the soft x-ray regime by using large basis sets. The photoabsorption cross-sections of a sodium crystal are computed for a wide photon energy range from 3 to 1800 eV. It is found that the numerical results reproduce the existing x-ray databases fairly well for energies above the L2,3-edge (31 eV), verifying a consistency between solid-state and atomic models for inner-shell photoabsorption; additional oscillatory structures in the present spectra manifest solid-state effects. Our computed results in the vacuum ultraviolet regime (6-30 eV) are also in better agreement with experimental data compared to earlier theories, although some discrepancies remain in the range of 20-30 eV. The influence of the core eigenvalues on the absorption spectra is examined.

  17. Coupled Cluster and Møller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Pitoňák, Michal; Aquilante, Francesco; Neogrády, Pavel; Pedersen, Thomas Bondo; Lindh, Roland

    2012-06-12

    We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys.2006, 8, 1985-1993] of molecules at the Møller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)Eh for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)Eh is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-ζ AO basis sets, they provide results 1-2 orders of magnitude more accurate.

  18. Optimal Sensor Selection for Classifying a Set of Ginsengs Using Metal-Oxide Sensors

    PubMed Central

    Miao, Jiacheng; Zhang, Tinglin; Wang, You; Li, Guang

    2015-01-01

    The sensor selection problem was investigated for the application of classification of a set of ginsengs using a metal-oxide sensor-based homemade electronic nose with linear discriminant analysis. Samples (315) were measured for nine kinds of ginsengs using 12 sensors. We investigated the classification performances of combinations of 12 sensors for the overall discrimination of combinations of nine ginsengs. The minimum numbers of sensors for discriminating each sample set to obtain an optimal classification performance were defined. The relation of the minimum numbers of sensors with number of samples in the sample set was revealed. The results showed that as the number of samples increased, the average minimum number of sensors increased, while the increment decreased gradually and the average optimal classification rate decreased gradually. Moreover, a new approach of sensor selection was proposed to estimate and compare the effective information capacity of each sensor. PMID:26151212

  19. Development of optimization models for the set behavior and compressive strength of sodium activated geopolymer pastes

    NASA Astrophysics Data System (ADS)

    Fillenwarth, Brian Albert

    As large countries such as China begin to industrialize and concerns about global warming continue to grow, there is an increasing need for more environmentally friendly building materials. One promising material known as a geopolymer can be used as a portland cement replacement and in this capacity emits around 67% less carbon dioxide. In addition to potentially reducing carbon emissions, geopolymers can be synthesized with many industrial waste products such as fly ash. Although the benefits of geopolymers are substantial, there are a few difficulties with designing geopolymer mixes which have hindered widespread commercialization of the material. One such difficulty is the high variability of the materials used for their synthesis. In addition to this, interrelationships between mix design variables and how these interrelationships impact the set behavior and compressive strength are not well understood. A third complicating factor with designing geopolymer mixes is that the role of calcium in these systems is not well understood. In order to overcome these barriers, this study developed predictive optimization models through the use of genetic programming with experimentally collected set times and compressive strengths of several geopolymer paste mixes. The developed set behavior models were shown to predict the correct set behavior from the mix design over 85% of the time. The strength optimization model was shown to be capable of predicting compressive strengths of geopolymer pastes from their mix design to within about 1 ksi of their actual strength. In addition to this the optimization models give valuable insight into the key factors influencing strength development as well as the key factors responsible for flash set and long set behaviors in geopolymer pastes. A method for designing geopolymer paste mixes was developed from the generated optimization models. This design method provides an invaluable tool for use in future geopolymer research as well as

  20. Modeling and optimization of microbial hyaluronic acid production by Streptococcus zooepidemicus using radial basis function neural network coupling quantum-behaved particle swarm optimization algorithm.

    PubMed

    Liu, Long; Sun, Jun; Xu, Wenbo; Du, Guocheng; Chen, Jian

    2009-01-01

    Hyaluronic acid (HA) is a natural biopolymer with unique physiochemical and biological properties and finds a wide range of applications in biomedical and cosmetic fields. It is important to increase HA production to meet the increasing HA market demand. This work is aimed to model and optimize the amino acids addition to enhance HA production of Streptococcus zooepidemicus with radial basis function (RBF) neural network coupling quantum-behaved particle swarm optimization (QPSO) algorithm. In the RBF-QPSO approach, RBF neural network is used as a bioprocess modeling tool and QPSO algorithm is applied to conduct the optimization with the established RBF neural network black model as the objective function. The predicted maximum HA yield was 6.92 g/L under the following conditions: arginine 0.062 g/L, cysteine 0.036 g/L, and lysine 0.043 g/L. The optimal amino acids addition allowed HA yield increased from 5.0 g/L of the control to 6.7 g/L in the validation experiments. Moreover, the modeling and optimization capacity of the RBF-QPSO approach was compared with that of response surface methodology (RSM). It was indicated that the RBF-QPSO approach gave a slightly better modeling and optimization result compared with RSM. The developed RBF-QPSO approach in this work may be helpful for the modeling and optimization of the other multivariable, nonlinear, time-variant bioprocesses.

  1. 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)

    NASA Astrophysics Data System (ADS)

    Brandbyge, Mads

    2014-05-01

    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, and 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.

  2. The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin.

    PubMed

    Paschoal, Diego; Marcial, Bruna L; Lopes, Juliana Fedoce; De Almeida, Wagner B; Dos Santos, Hélio F

    2012-11-05

    In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis-diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all-electron basis sets (ABS). In addition, a modified all-electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6-31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol(-1), which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol(-1). For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol(-1), respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree-Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6-31+G(d) or B3PW91/mDZP/6-31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP-DNA complex), the lower levels B3LYP/LANL2DZ/6-31+G(d) and B3LYP/SBKJC-VDZ/6-31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol(-1), respectively, which is only 13% higher than the actual value.

  3. Optimizing Geographic Allotment of Photovoltaic Capacity in a Distributed Generation Setting: Preprint

    SciTech Connect

    Urquhart, B.; Sengupta, M.; Keller, J.

    2012-09-01

    A multi-objective optimization was performed to allocate 2MW of PV among four candidate sites on the island of Lanai such that energy was maximized and variability in the form of ramp rates was minimized. This resulted in an optimal solution set which provides a range of geographic allotment alternatives for the fixed PV capacity. Within the optimal set, a tradeoff between energy produced and variability experienced was found, whereby a decrease in variability always necessitates a simultaneous decrease in energy. A design point within the optimal set was selected for study which decreased extreme ramp rates by over 50% while only decreasing annual energy generation by 3% over the maximum generation allocation. To quantify the allotment mix selected, a metric was developed, called the ramp ratio, which compares ramping magnitude when all capacity is allotted to a single location to the aggregate ramping magnitude in a distributed scenario. The ramp ratio quantifies simultaneously how much smoothing a distributed scenario would experience over single site allotment and how much a single site is being under-utilized for its ability to reduce aggregate variability. This paper creates a framework for use by cities and municipal utilities to reduce variability impacts while planning for high penetration of PV on the distribution grid.

  4. Go-ICP: A Globally Optimal Solution to 3D ICP Point-Set Registration.

    PubMed

    Yang, Jiaolong; Li, Hongdong; Campbell, Dylan; Jia, Yunde

    2016-11-01

    The Iterative Closest Point (ICP) algorithm is one of the most widely used methods for point-set registration. However, being based on local iterative optimization, ICP is known to be susceptible to local minima. Its performance critically relies on the quality of the initialization and only local optimality is guaranteed. This paper presents the first globally optimal algorithm, named Go-ICP, for Euclidean (rigid) registration of two 3D point-sets under the L2 error metric defined in ICP. The Go-ICP method is based on a branch-and-bound scheme that searches the entire 3D motion space SE(3). By exploiting the special structure of SE(3) geometry, we derive novel upper and lower bounds for the registration error function. Local ICP is integrated into the BnB scheme, which speeds up the new method while guaranteeing global optimality. We also discuss extensions, addressing the issue of outlier robustness. The evaluation demonstrates that the proposed method is able to produce reliable registration results regardless of the initialization. Go-ICP can be applied in scenarios where an optimal solution is desirable or where a good initialization is not always available.

  5. Estimation of isotropic nuclear magnetic shieldings in the CCSD(T) and MP2 complete basis set limit using affordable correlation calculations.

    PubMed

    Kupka, Teobald; Stachów, Michał; Kaminsky, Jakub; Sauer, Stephan P A

    2013-08-01

    A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2 O, H2 O, HF, F2 , HCN, SiH4 and H2 S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T)), with affordable pcS-2 basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and shieldings obtained with the significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS-2, MP2/pcS-2 and DFT/CBS calculations with pcS-n basis sets. The proposed method leads to a fairly accurate estimation of nuclear magnetic shieldings and considerable saving of computational efforts.

  6. Calibration and comparison of the Gaussian-2, complete basis set, and density functional methods for computational thermochemistry

    NASA Astrophysics Data System (ADS)

    Petersson, G. A.; Malick, David K.; Wilson, William G.; Ochterski, Joseph W.; Montgomery, J. A.; Frisch, M. J.

    1998-12-01

    We have reexamined several high-accuracy Gaussian-2, complete basis set and density functional methods for computational thermochemistry (in order of increasing speed): G2, G2(MP2), CBS-Q, G2(MP2,SVP), CBS-q, CBS-4, and B3LYP/6-311+G(3df,2p). We have employed ΔfH2980 for the "extended G2 neutral test set" for this comparison. Several errors in previous studies have been corrected and experimental spin-orbit interactions have been included in all calculated atomic energies. The mean absolute deviations from experiment are 1.43, 1.76, 1.19, 1.64, 2.34, 2.66, and 3.43 kcal/mol, respectively. The maximum deviations from experiment are 10.6, 8.8, 8.1, 9.4, 11.4, 12.9, and 24.1 kcal/mol respectively. The species responsible for these maximum errors are in order: SiF4, SiF4, Cl2C=CCl2, F2C=CF2, ClF3, ClF3, and SiCl4. All seven methods have relatively large errors for bonds to halogens, but these errors are sufficiently systematic to benefit from empirical corrections. After a discussion of ill conditioning in the "bond separation reaction" implementation of isodesmic reactions, we determine "isodesmic bond additivity corrections" (BACs) for several types of bonds by least-squares fits to the heats of formation for 76 organic species with up to ten carbons and a variety of heteroatoms. The mean absolute deviations are reduced from 1.49, 1.93, 1.22, 1.53, 2.28, 3.09, and 3.45 kcal/mol to 0.55, 0.57, 0.77, 0.63, 1.03, 0.98, and 1.16 kcal/mol. The maximum errors are reduced to about 3 kcal/mol for all but the DFT method (4.2 kcal/mol). The BACs are especially useful for larger molecules with many similar bonds. For example, the CBS-Q error for Cl2C=CCl2 is reduced from 8.1 to 3.0 kcal/mol and the CBS-4 errors for benzene and naphthalene are reduced from 10.5 and 17.5 to 2.1 and 1.6 kcal/mol, respectively.

  7. The route to MBxNyCz molecular wheels: II. Results using accurate functionals and basis sets

    NASA Astrophysics Data System (ADS)

    Güthler, A.; Mukhopadhyay, S.; Pandey, R.; Boustani, I.

    2014-04-01

    Applying ab initio quantum chemical methods, molecular wheels composed of metal and light atoms were investigated. High quality basis sets 6-31G*, TZPV, and cc-pVTZ as well as exchange and non-local correlation functionals B3LYP, BP86 and B3P86 were used. The ground-state energy and structures of cyclic planar and pyramidal clusters TiBn (for n = 3-10) were computed. In addition, the relative stability and electronic structures of molecular wheels TiBxNyCz (for x, y, z = 0-10) and MBnC10-n (for n = 2 to 5 and M = Sc to Zn) were determined. This paper sustains a follow-up study to the previous one of Boustani and Pandey [Solid State Sci. 14 (2012) 1591], in which the calculations were carried out at the HF-SCF/STO3G/6-31G level of theory to determine the initial stability and properties. The results show that there is a competition between the 2D planar and the 3D pyramidal TiBn clusters (for n = 3-8). Different isomers of TiB10 clusters were also studied and a structural transition of 3D-isomer into 2D-wheel is presented. Substitution boron in TiB10 by carbon or/and nitrogen atoms enhances the stability and leads toward the most stable wheel TiB3C7. Furthermore, the computations show that Sc, Ti and V at the center of the molecular wheels are energetically favored over other transition metal atoms of the first row.

  8. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.

    PubMed

    Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf

    2013-03-12

    The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.

  9. Antiferromagnetic vs. non-magnetic ε phase of solid oxygen. Periodic density functional theory studies using a localized atomic basis set and the role of exact exchange.

    PubMed

    Ramírez-Solís, A; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ochoa-Calle, A J

    2017-01-25

    The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε1 phase and a higher pressure NM ε0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O2 molecules in the (O2)4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O2)4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O2)4 unit cell for the low-pressure regime of the ε phase.

  10. A Sequential Optimization Sampling Method for Metamodels with Radial Basis Functions

    PubMed Central

    Pan, Guang; Ye, Pengcheng; Yang, Zhidong

    2014-01-01

    Metamodels have been widely used in engineering design to facilitate analysis and optimization of complex systems that involve computationally expensive simulation programs. The accuracy of metamodels is strongly affected by the sampling methods. In this paper, a new sequential optimization sampling method is proposed. Based on the new sampling method, metamodels can be constructed repeatedly through the addition of sampling points, namely, extrema points of metamodels and minimum points of density function. Afterwards, the more accurate metamodels would be constructed by the procedure above. The validity and effectiveness of proposed sampling method are examined by studying typical numerical examples. PMID:25133206

  11. 42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED 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...

  12. 42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED 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...

  13. 42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED 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...

  14. 42 CFR 415.170 - Conditions for payment on a fee schedule basis for physician services in a teaching setting.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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...

  15. 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...

  16. Ant Colony Optimization Analysis on Overall Stability of High Arch Dam Basis of Field Monitoring

    PubMed Central

    Liu, Xiaoli; Chen, Hong-Xin; Kim, Jinxie

    2014-01-01

    A dam ant colony optimization (D-ACO) analysis of the overall stability of high arch dams on complicated foundations is presented in this paper. A modified ant colony optimization (ACO) model is proposed for obtaining dam concrete and rock mechanical parameters. A typical dam parameter feedback problem is proposed for nonlinear back-analysis numerical model based on field monitoring deformation and ACO. The basic principle of the proposed model is the establishment of the objective function of optimizing real concrete and rock mechanical parameter. The feedback analysis is then implemented with a modified ant colony algorithm. The algorithm performance is satisfactory, and the accuracy is verified. The m groups of feedback parameters, used to run a nonlinear FEM code, and the displacement and stress distribution are discussed. A feedback analysis of the deformation of the Lijiaxia arch dam and based on the modified ant colony optimization method is also conducted. By considering various material parameters obtained using different analysis methods, comparative analyses were conducted on dam displacements, stress distribution characteristics, and overall dam stability. The comparison results show that the proposal model can effectively solve for feedback multiple parameters of dam concrete and rock material and basically satisfy assessment requirements for geotechnical structural engineering discipline. PMID:25025089

  17. Ant colony optimization analysis on overall stability of high arch dam basis of field monitoring.

    PubMed

    Lin, Peng; Liu, Xiaoli; Chen, Hong-Xin; Kim, Jinxie

    2014-01-01

    A dam ant colony optimization (D-ACO) analysis of the overall stability of high arch dams on complicated foundations is presented in this paper. A modified ant colony optimization (ACO) model is proposed for obtaining dam concrete and rock mechanical parameters. A typical dam parameter feedback problem is proposed for nonlinear back-analysis numerical model based on field monitoring deformation and ACO. The basic principle of the proposed model is the establishment of the objective function of optimizing real concrete and rock mechanical parameter. The feedback analysis is then implemented with a modified ant colony algorithm. The algorithm performance is satisfactory, and the accuracy is verified. The m groups of feedback parameters, used to run a nonlinear FEM code, and the displacement and stress distribution are discussed. A feedback analysis of the deformation of the Lijiaxia arch dam and based on the modified ant colony optimization method is also conducted. By considering various material parameters obtained using different analysis methods, comparative analyses were conducted on dam displacements, stress distribution characteristics, and overall dam stability. The comparison results show that the proposal model can effectively solve for feedback multiple parameters of dam concrete and rock material and basically satisfy assessment requirements for geotechnical structural engineering discipline.

  18. Optimal Space Station solar array gimbal angle determination via radial basis function neural networks

    NASA Technical Reports Server (NTRS)

    Clancy, Daniel J.; Oezguener, Uemit; Graham, Ronald E.

    1994-01-01

    The potential for excessive plume impingement loads on Space Station Freedom solar arrays, caused by jet firings from an approaching Space Shuttle, is addressed. An artificial neural network is designed to determine commanded solar array beta gimbal angle for minimum plume loads. The commanded angle would be determined dynamically. The network design proposed involves radial basis functions as activation functions. Design, development, and simulation of this network design are discussed.

  19. Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets.

    PubMed

    Echenique, Pablo; Alonso, José Luis

    2008-07-15

    We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH(2). The model chemistries (MCs) investigated are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the most accurate PES in the literature. All data sets have been analyzed according to a general framework, which can be extended to other complex problems and which captures the nearness concept in the space of MCs. The great number of MCs evaluated has allowed us to significantly explore this space and show that the correlation between accuracy and computational cost of the methods is imperfect, thus justifying a systematic search for the combination of features in a MC that is optimal to deal with peptides. Regarding the particular MCs studied, the most important conclusion is that the potentially very cost-saving heterolevel approximation is a very efficient one to describe the whole PES of HCO-L-Ala-NH(2). Finally, we show that, although RHF may be used to calculate the geometry if a MP2 single-point energy calculation follows, pure RHF//RHF homolevels are not recommendable for this problem.

  20. Generated spiral bevel gears: Optimal machine-tool settings and tooth contact analysis

    NASA Technical Reports Server (NTRS)

    Litvin, F. L.; Tsung, W. J.; Coy, J. J.; Heine, C.

    1985-01-01

    Geometry and kinematic errors were studied for Gleason generated spiral bevel gears. A new method was devised for choosing optimal machine settings. These settings provide zero kinematic errors and an improved bearing contact. The kinematic errors are a major source of noise and vibration in spiral bevel gears. The improved bearing contact gives improved conditions for lubrication. A computer program for tooth contact analysis was developed, and thereby the new generation process was confirmed. The new process is governed by the requirement that during the generation process there is directional constancy of the common normal of the contacting surfaces for generator and generated surfaces of pinion and gear.

  1. Generated spiral bevel gears - Optimal machine-tool settings and tooth contact analysis

    NASA Technical Reports Server (NTRS)

    Litvin, F. L.; Tsung, W.-J.; Coy, J. J.; Heine, C.

    1985-01-01

    Geometry and kinematic errors were studied for Gleason generated spiral bevel gears. A new method was devised for choosing optimal machine settings. These settings provide zero kinematic errors and an improved bearing contact. The kinematic errors are a major source of noise and vibration in spiral bevel gears. The improved bearing contact gives improved conditions for lubrication. A computer program for tooth contact analysis was developed, and thereby the new generation process was confirmed. The new process is governed by the requirement that during the generation process there is directional constancy of the common normal of the contacting surfaces for generator and generated surfaces of pinion and gear.

  2. Classification improvement by optimal dimensionality reduction when training sets are of small size

    NASA Technical Reports Server (NTRS)

    Starks, S. A.; Defigueiredo, R. J. P.; Vanrooy, D. L.

    1976-01-01

    A computer simulation was performed to test the conjecture that, when the sizes of the training sets are small, classification in a subspace of the original data space may give rise to a smaller probability of error than the classification in the data space itself; this is because the gain in the accuracy of estimation of the likelihood functions used in classification in the lower dimensional space (subspace) offsets the loss of information associated with dimensionality reduction (feature extraction). A number of pseudo-random training and data vectors were generated from two four-dimensional Gaussian classes. A special algorithm was used to create an optimal one-dimensional feature space on which to project the data. When the sizes of the training sets are small, classification of the data in the optimal one-dimensional space is found to yield lower error rates than the one in the original four-dimensional space.

  3. A jazz-based approach for optimal setting of pressure reducing valves in water distribution networks

    NASA Astrophysics Data System (ADS)

    De Paola, Francesco; Galdiero, Enzo; Giugni, Maurizio

    2016-05-01

    This study presents a model for valve setting in water distribution networks (WDNs), with the aim of reducing the level of leakage. The approach is based on the harmony search (HS) optimization algorithm. The HS mimics a jazz improvisation process able to find the best solutions, in this case corresponding to valve settings in a WDN. The model also interfaces with the improved version of a popular hydraulic simulator, EPANET 2.0, to check the hydraulic constraints and to evaluate the performances of the solutions. Penalties are introduced in the objective function in case of violation of the hydraulic constraints. The model is applied to two case studies, and the obtained results in terms of pressure reductions are comparable with those of competitive metaheuristic algorithms (e.g. genetic algorithms). The results demonstrate the suitability of the HS algorithm for water network management and optimization.

  4. Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N2 intermolecular potential and microwave spectrum.

    PubMed

    Baranowska-Łączkowska, Angelika; Fernández, Berta

    2014-01-30

    In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto.

  5. Character Projection Mask Set Optimization for Enhancing Throughput of MCC Projection Systems

    NASA Astrophysics Data System (ADS)

    Sugihara, Makoto; Matsunaga, Yusuke; Murakami, Kazuaki

    Character projection (CP) lithography is utilized for maskless lithography and is a potential for the future photomask manufacture because it can project ICs much faster than point beam projection or variable-shaped beam (VSB) projection. In this paper, we first present a projection mask set development methodology for multi-column-cell (MCC) systems, in which column-cells can project patterns in parallel with the CP and VSB lithographies. Next, we present an INLP (integer nonlinear programming) model as well as an ILP (integer linear programming) model for optimizing a CP mask set of an MCC projection system so that projection time is reduced. The experimental results show that our optimization has achieved 33.4% less projection time in the best case than a naive CP mask development approach. The experimental results indicate that our CP mask set optimization method has virtually increased cell pattern objects on CP masks and has decreased VSB projection so that it has achieved higher projection throughput than just parallelizing two column-cells with conventional CP masks.

  6. Functionalization and fragmentation during ambient organic aerosol aging: application of the 2-D volatility basis set to field studies

    NASA Astrophysics Data System (ADS)

    Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Dall'Osto, M.; O'Dowd, C.; Kiendler-Scharr, A.; Pandis, S. N.

    2012-04-01

    Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS) in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1) heterogeneous oxidation via OH uptake to the particle-phase and (2) aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA) mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE) lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and aqueous

  7. Functionalization and fragmentation during ambient organic aerosol aging: application of the 2-D volatility basis set to field studies

    NASA Astrophysics Data System (ADS)

    Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Dall'Osto, M.; O'Dowd, C.; Kiendler-Scharr, A.; Pandis, S. N.

    2012-11-01

    Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS) in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1) heterogeneous oxidation via OH uptake to the particle-phase and (2) aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA) mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE) lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and aqueous

  8. Modeling organic aerosols in a megacity: comparison of simple and complex representations of the volatility basis set approach

    NASA Astrophysics Data System (ADS)

    Shrivastava, M.; Fast, J.; Easter, R.; Gustafson, W. I., Jr.; Zaveri, R. A.; Jimenez, J. L.; Saide, P.; Hodzic, A.

    2011-07-01

    The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25 %, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15 % oxygen mass per generation of oxidation; however, all modeling cases still under

  9. Modeling organic aerosols in a megacity: comparison of simple and complex representations of the volatility basis set approach

    NASA Astrophysics Data System (ADS)

    Shrivastava, M.; Fast, J.; Easter, R.; Gustafson, W. I., Jr.; Zaveri, R. A.; Jimenez, J. L.; Saide, P.; Hodzic, A.

    2010-12-01

    The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25%, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15% oxygen mass per generation of oxidation; however, all modeling cases still under

  10. Characterising Biomass Burning Aerosol in WRF-Chem using the Volatility Basis Set, with Evaluation against SAMBBA Flight Data

    NASA Astrophysics Data System (ADS)

    Lowe, D.; Topping, D. O.; Archer-Nicholls, S.; Darbyshire, E.; Morgan, W.; Liu, D.; Allan, J. D.; Coe, H.; McFiggans, G.

    2015-12-01

    The burning of forests in the Amazonia region is a globally significant source of carbonaceous aerosol, containing both absorbing and scattering components [1]. In addition biomass burning aerosol (BBA) are also efficient cloud condensation nuclei (CCN), modifying cloud properties and influencing atmospheric circulation and precipitation tendencies [2]. The impacts of BBA are highly dependent on their size distribution and composition. A bottom-up emissions inventory, the Brazilian Biomass Burning Emissions Model (3BEM) [3], utilising satellite products to generate daily fire emission maps is used. Injection of flaming emissions within the atmospheric column is simulated using both a sub-grid plume-rise parameterisation [4], and simpler schemes, within the Weather Research and Forecasting Model with Chemistry (WRF-Chem, v3.4.1) [5]. Aerosol dynamics are simulated using the sectional MOSAIC scheme [6], incorporating a volatility basis set (VBS) treatment of organic aerosol [7]. For this work we have modified the 9-bin VBS to use the biomass burning specific scheme developed by May et al. [8]. The model has been run for September 2012 over South America (at a 25km resolution). We will present model results evaluating the modelled aerosol vertical distribution, size distribution, and composition against measurements taken by the FAAM BAe-146 research aircraft during the SAMBBA campaign. The main focus will be on investigating the factors controlling the vertical gradient of the organic mass to black carbon ratio of the measured aerosol. This work is supported by the Nature Environment Research Council (NERC) as part of the SAMBBA project under grant NE/J010073/1. [1] D. G. Streets et al., 2004, J. Geophys. Res., 109, D24212. [2] M. O. Andreae et al., 2004, Science, 303, 1337-1342. [3] K. Longo et al., 2010, Atmos. Chem. Phys., 10, 5,785-5,795. [4] S. Freitas et al., 2007, Atmos. Chem. Phys., 7, 3,385-3,398. [5] S. Archer-Nicholls et al., 2015, Geosci. Model Dev., 8

  11. On the basis-set dependence of local and integrated electron density properties: Application of a new computer program for quantum-chemical density analysis.

    PubMed

    Volkov, Anatoliy; Koritsanszky, Tibor; Chodkiewicz, Michal; King, Harry F

    2009-07-15

    A new computer program for post-processing analysis of quantum-chemical electron densities is described. The code can work with Slater- and Gaussian-type basis functions of arbitrary angular momentum. It has been applied to explore the basis-set dependence of the electron density and its Laplacian in terms of local and integrated topological properties. Our analysis, including Gaussian/Slater basis sets up to sextuple/quadruple-zeta order, shows that these properties considerably depend on the choice of type and number of primitives utilized in the wavefunction expansion. Basis sets with high angular momentum (l = 5 or l = 6) are necessary to achieve convergence for local properties of the density and the Laplacian. In agreement with previous studies, atomic charges defined within Bader's Quantum Theory of Atoms in Molecules appear to be much more basis-set dependent than the Hirshfeld's stockholder charges. The former ones converge only at the quadruple-zeta/higher level with Gaussian/Slater functions.

  12. Accurate relativistic adapted Gaussian basis sets for francium through Ununoctium without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models.

    PubMed

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade

    2013-10-15

    Accurate relativistic adapted Gaussian basis sets (RAGBSs) for 87 Fr up to 118 Uuo atoms without variational prolapse were developed here with the use of a polynomial version of the Generator Coordinate Dirac-Fock method. Two finite nuclear models have been used, the Gaussian and uniform sphere models. The largest RAGBS error, with respect to numerical Dirac-Fock results, is 15.4 miliHartree for Ununoctium with a basis set size of 33s30p19d14f functions.

  13. Network Conduciveness with Application to the Graph-Coloring and Independent-Set Optimization Transitions

    PubMed Central

    Barbosa, Valmir C.

    2010-01-01

    Background Given an undirected graph, we consider the two problems of combinatorial optimization, which ask that its chromatic and independence numbers be found. Although both problems are NP-hard, when either one is solved on the incrementally denser graphs of a random sequence, at certain critical values of the number of edges, it happens that the transition to the next value causes optimal solutions to be obtainable substantially more easily than right before it. Methodology/Principal Findings We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another. We demonstrate that the performance jumps of graph coloring and independent sets at the critical-value transitions in the number of edges can be understood by resorting to the network that represents the solution space of the problems for each graph and examining its conduciveness between the non-optimal solutions and the optimal ones. Right past each transition, this network becomes strikingly more conducive in the direction of the optimal solutions than it was just before it, while at the same time becoming less conducive in the opposite direction. Conclusions/Significance Network conduciveness provides a useful conceptual framework for explaining the performance jumps associated with graph coloring and independent sets. We believe it may also become instrumental in helping clarify further issues related to NP-hardness that remain poorly understood. Additionally, it may become useful also in other areas in which network theory has a role to play. PMID:20628597

  14. Optimized tumor cryptic peptides: the basis for universal neo-antigen-like tumor vaccines

    PubMed Central

    Menez-Jamet, Jeanne; Gallou, Catherine; Rougeot, Aude

    2016-01-01

    The very impressive clinical results recently obtained in cancer patients treated with immune response checkpoint inhibitors boosted the interest in immunotherapy as a therapeutic choice in cancer treatment. However, these inhibitors require a pre-existing tumor specific immune response and the presence of tumor infiltrating T cells to be efficient. This immune response can be triggered by cancer vaccines. One of the main issues in tumor vaccination is the choice of the right antigen to target. All vaccines tested to date targeted tumor associated antigens (TAA) that are self-antigens and failed to show a clinical efficacy because of the immune self-tolerance to TAA. A new class of tumor antigens has recently been described, the neo-antigens that are created by point mutations of tumor expressing proteins and are recognized by the immune system as non-self. Neo-antigens exhibit two main properties: they are not involved in the immune self-tolerance process and are immunogenic. However, the majority of the neo-antigens are patient specific and their use as cancer vaccines requires their previous identification in each patient individualy that can be done only in highly specialized research centers. It is therefore evident that neo-antigens cannot be used for patient vaccination worldwide. This raises the question of whether we can find neo-antigen like vaccines, which would not be patient specific. In this review we show that optimized cryptic peptides from TAA are neo-antigen like peptides. Optimized cryptic peptides are recognized by the immune system as non-self because they target self-cryptic peptides that escape self-tolerance; in addition they are strongly immunogenic because their sequence is modified in order to enhance their affinity for the HLA molecule. The first vaccine based on the optimized cryptic peptide approach, Vx-001, which targets the widely expressed tumor antigen telomerase reverse transcriptase (TERT), has completed a large phase I clinical

  15. Optimal real-time Q-ball imaging using regularized Kalman filtering with incremental orientation sets.

    PubMed

    Deriche, Rachid; Calder, Jeff; Descoteaux, Maxime

    2009-08-01

    Diffusion MRI has become an established research tool for the investigation of tissue structure and orientation. Since its inception, Diffusion MRI has expanded considerably to include a number of variations such as diffusion tensor imaging (DTI), diffusion spectrum imaging (DSI) and Q-ball imaging (QBI). The acquisition and analysis of such data is very challenging due to its complexity. Recently, an exciting new Kalman filtering framework has been proposed for DTI and QBI reconstructions in real-time during the repetition time (TR) of the acquisition sequence. In this article, we first revisit and thoroughly analyze this approach and show it is actually sub-optimal and not recursively minimizing the intended criterion due to the Laplace-Beltrami regularization term. Then, we propose a new approach that implements the QBI reconstruction algorithm in real-time using a fast and robust Laplace-Beltrami regularization without sacrificing the optimality of the Kalman filter. We demonstrate that our method solves the correct minimization problem at each iteration and recursively provides the optimal QBI solution. We validate with real QBI data that our proposed real-time method is equivalent in terms of QBI estimation accuracy to the standard offline processing techniques and outperforms the existing solution. Last, we propose a fast algorithm to recursively compute gradient orientation sets whose partial subsets are almost uniform and show that it can also be applied to the problem of efficiently ordering an existing point-set of any size. This work enables a clinician to start an acquisition with just the minimum number of gradient directions and an initial estimate of the orientation distribution functions (ODF) and then the next gradient directions and ODF estimates can be recursively and optimally determined, allowing the acquisition to be stopped as soon as desired or at any iteration with the optimal ODF estimates. This opens new and interesting opportunities for

  16. Time-optimal path planning in dynamic flows using level set equations: theory and schemes

    NASA Astrophysics Data System (ADS)

    Lolla, Tapovan; Lermusiaux, Pierre F. J.; Ueckermann, Mattheus P.; Haley, Patrick J.

    2014-10-01

    We develop an accurate partial differential equation-based methodology that predicts the time-optimal paths of autonomous vehicles navigating in any continuous, strong, and dynamic ocean currents, obviating the need for heuristics. The goal is to predict a sequence of steering directions so that vehicles can best utilize or avoid currents to minimize their travel time. Inspired by the level set method, we derive and demonstrate that a modified level set equation governs the time-optimal path in any continuous flow. We show that our algorithm is computationally efficient and apply it to a number of experiments. First, we validate our approach through a simple benchmark application in a Rankine vortex flow for which an analytical solution is available. Next, we apply our methodology to more complex, simulated flow fields such as unsteady double-gyre flows driven by wind stress and flows behind a circular island. These examples show that time-optimal paths for multiple vehicles can be planned even in the presence of complex flows in domains with obstacles. Finally, we present and support through illustrations several remarks that describe specific features of our methodology.

  17. Extracellular voltage threshold settings can be tuned for optimal encoding of movement and stimulus parameters

    NASA Astrophysics Data System (ADS)

    Oby, Emily R.; Perel, Sagi; Sadtler, Patrick T.; Ruff, Douglas A.; Mischel, Jessica L.; Montez, David F.; Cohen, Marlene R.; Batista, Aaron P.; Chase, Steven M.

    2016-06-01

    Objective. A traditional goal of neural recording with extracellular electrodes is to isolate action potential waveforms of an individual neuron. Recently, in brain-computer interfaces (BCIs), it has been recognized that threshold crossing events of the voltage waveform also convey rich information. To date, the threshold for detecting threshold crossings has been selected to preserve single-neuron isolation. However, the optimal threshold for single-neuron identification is not necessarily the optimal threshold for information extraction. Here we introduce a procedure to determine the best threshold for extracting information from extracellular recordings. We apply this procedure in two distinct contexts: the encoding of kinematic parameters from neural activity in primary motor cortex (M1), and visual stimulus parameters from neural activity in primary visual cortex (V1). Approach. We record extracellularly from multi-electrode arrays implanted in M1 or V1 in monkeys. Then, we systematically sweep the voltage detection threshold and quantify the information conveyed by the corresponding threshold crossings. Main Results. The optimal threshold depends on the desired information. In M1, velocity is optimally encoded at higher thresholds than speed; in both cases the optimal thresholds are lower than are typically used in BCI applications. In V1, information about the orientation of a visual stimulus is optimally encoded at higher thresholds than is visual contrast. A conceptual model explains these results as a consequence of cortical topography. Significance. How neural signals are processed impacts the information that can be extracted from them. Both the type and quality of information contained in threshold crossings depend on the threshold setting. There is more information available in these signals than is typically extracted. Adjusting the detection threshold to the parameter of interest in a BCI context should improve our ability to decode motor intent

  18. A computerized traffic control algorithm to determine optimal traffic signal settings. Ph.D. Thesis - Toledo Univ.

    NASA Technical Reports Server (NTRS)

    Seldner, K.

    1977-01-01

    An algorithm was developed to optimally control the traffic signals at each intersection using a discrete time traffic model applicable to heavy or peak traffic. Off line optimization procedures were applied to compute the cycle splits required to minimize the lengths of the vehicle queues and delay at each intersection. The method was applied to an extensive traffic network in Toledo, Ohio. Results obtained with the derived optimal settings are compared with the control settings presently in use.

  19. Small and efficient basis sets for the evaluation of accurate interaction energies: aromatic molecule-argon ground-state intermolecular potentials and rovibrational states.

    PubMed

    Cybulski, Hubert; Baranowska-Łączkowska, Angelika; Henriksen, Christian; Fernández, Berta

    2014-11-06

    By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these

  20. A study of H+H2 and several H-bonded molecules by phaseless auxiliary-field quantum Monte Carlo with plane wave and Gaussian basis sets.

    PubMed

    Al-Saidi, W A; Krakauer, Henry; Zhang, Shiwei

    2007-05-21

    The authors present phaseless auxiliary-field (AF) quantum Monte Carlo (QMC) calculations of the ground states of some hydrogen-bonded systems. These systems were selected to test and benchmark different aspects of the new phaseless AF QMC method. They include the transition state of H+H(2) near the equilibrium geometry and in the van der Walls limit, as well as the H(2)O, OH, and H(2)O(2) molecules. Most of these systems present significant challenges for traditional independent-particle electronic structure approaches, and many also have exact results available. The phaseless AF QMC method is used either with a plane wave basis with pseudopotentials or with all-electron Gaussian basis sets. For some systems, calculations are done with both to compare and characterize the performance of AF QMC under different basis sets and different Hubbard-Stratonovich decompositions. Excellent results are obtained using as input single Slater determinant wave functions taken from independent-particle calculations. Comparisons of the Gaussian based AF QMC results with exact full configuration interaction show that the errors from controlling the phase problem with the phaseless approximation are small. At the large basis-size limit, the AF QMC results using both types of basis sets are in good agreement with each other and with experimental values.

  1. On the Optimal Identification of Tag Sets in Time-Constrained RFID Configurations

    PubMed Central

    Vales-Alonso, Javier; Bueno-Delgado, María Victoria; Egea-López, Esteban; Alcaraz, Juan José; Pérez-Mañogil, Juan Manuel

    2011-01-01

    In Radio Frequency Identification facilities the identification delay of a set of tags is mainly caused by the random access nature of the reading protocol, yielding a random identification time of the set of tags. In this paper, the cumulative distribution function of the identification time is evaluated using a discrete time Markov chain for single-set time-constrained passive RFID systems, namely those ones where a single group of tags is assumed to be in the reading area and only for a bounded time (sojourn time) before leaving. In these scenarios some tags in a set may leave the reader coverage area unidentified. The probability of this event is obtained from the cumulative distribution function of the identification time as a function of the sojourn time. This result provides a suitable criterion to minimize the probability of losing tags. Besides, an identification strategy based on splitting the set of tags in smaller subsets is also considered. Results demonstrate that there are optimal splitting configurations that reduce the overall identification time while keeping the same probability of losing tags. PMID:22163777

  2. On the optimal identification of tag sets in time-constrained RFID configurations.

    PubMed

    Vales-Alonso, Javier; Bueno-Delgado, María Victoria; Egea-López, Esteban; Alcaraz, Juan José; Pérez-Mañogil, Juan Manuel

    2011-01-01

    In Radio Frequency Identification facilities the identification delay of a set of tags is mainly caused by the random access nature of the reading protocol, yielding a random identification time of the set of tags. In this paper, the cumulative distribution function of the identification time is evaluated using a discrete time Markov chain for single-set time-constrained passive RFID systems, namely those ones where a single group of tags is assumed to be in the reading area and only for a bounded time (sojourn time) before leaving. In these scenarios some tags in a set may leave the reader coverage area unidentified. The probability of this event is obtained from the cumulative distribution function of the identification time as a function of the sojourn time. This result provides a suitable criterion to minimize the probability of losing tags. Besides, an identification strategy based on splitting the set of tags in smaller subsets is also considered. Results demonstrate that there are optimal splitting configurations that reduce the overall identification time while keeping the same probability of losing tags.

  3. Triaging multiple victims in an avalanche setting: the Avalanche Survival Optimizing Rescue Triage algorithmic approach.

    PubMed

    Bogle, Lee B; Boyd, Jeff J; McLaughlin, Kyle A

    2010-03-01

    As winter backcountry activity increases, so does exposure to avalanche danger. A complicated situation arises when multiple victims are caught in an avalanche and where medical and other rescue demands overwhelm resources in the field. These mass casualty incidents carry a high risk of morbidity and mortality, and there is no recommended approach to patient care specific to this setting other than basic first aid principles. The literature is limited with regard to triaging systems applicable to avalanche incidents. In conjunction with the development of an electronic avalanche rescue training module by the Canadian Avalanche Association, we have designed the Avalanche Survival Optimizing Rescue Triage algorithm to address the triaging of multiple avalanche victims to optimize survival and disposition decisions.

  4. Weighted Fuzzy Interpolative Reasoning Based on the Slopes of Fuzzy Sets and Particle Swarm Optimization Techniques.

    PubMed

    Chen, Shyi-Ming; Hsin, Wen-Chyuan

    2015-07-01

    In this paper, we propose a new weighted fuzzy interpolative reasoning method for sparse fuzzy rule-based systems based on the slopes of fuzzy sets. We also propose a particle swarm optimization (PSO)-based weights-learning algorithm to automatically learn the optimal weights of the antecedent variables of fuzzy rules for weighted fuzzy interpolative reasoning. We apply the proposed weighted fuzzy interpolative reasoning method using the proposed PSO-based weights-learning algorithm to deal with the computer activity prediction problem, the multivariate regression problems, and the time series prediction problems. The experimental results show that the proposed weighted fuzzy interpolative reasoning method using the proposed PSO-based weights-learning algorithm outperforms the existing methods for dealing with the computer activity prediction problem, the multivariate regression problems, and the time series prediction problems.

  5. Informed consent in the NICU setting: an ethically optimal model for research solicitation.

    PubMed

    Golec, Lisa; Gibbins, Sharyn; Dunn, Michael S; Hebert, Philip

    2004-12-01

    Recruiting patients for studies in the Neonatal Intensive Care Unit is a complex endeavour. Much discussion has occurred regarding the optimal recruitment "model" for this environment. This paper discusses current and suggested recruitment models for the NICU setting and presents a systematic approach to the consent process that focuses on the protection and promotion of parental autonomy. The proposed model incorporates several key considerations for an ethically optimal approach to the inclusion of neonates in research: informing parents about research and their rights prior to any solicitation, asking parents if they wish to be approached for research, approaching for one study at a time, assuring the study is relevant to the infants' current clinical status, minimising information overload, allowing parents appropriate time (which will vary from study to study) to consider their choice, and providing a waiting period between subsequent approaches. It is argued that parental ability to make a truly informed choice may be improved when following the proposed model.

  6. Accurate density-functional calculation of core-electron binding energies with a scaled polarized triple-zeta basis set. (III). Extension to open-shell molecules

    NASA Astrophysics Data System (ADS)

    Hu, Ching-Han; Chong, Delano P.

    1997-03-01

    Density functional theory and the unrestricted generalized transition state (uGTS) model were applied to study the core-electron binding energies (CEBEs) of open-shell molecules. Basis set scaling based on Clementi and Raimondi's rules for atomic screening was used along with the cc-pVTZ basis set. The scaled pVTZ basis set is almost as good as the cc-pV5Z and complete basis set limit in predicting CEBEs. For small molecules (O 2, NO, NF 2 and NO 2) the average absolute deviation (aad) of our prediction (scaled pVTZ) is only 0.29 eV. For the larger molecule (CF 3) 2NO the aad is 0.56 eV, compared with experimental uncertainty of 0.5 eV. Theoretical predicted multiplet splittings for the small molecules agree quite well with experiment: the average deviation is -0.33 eV. For (CF 3) 2NO the calculated multiplet splittings are much smaller than the experimental ones. We also predict the CEBEs of PO, SN and SO, which have not been observed experimentally.

  7. An improved generator coordinate Hartree-Fock method applied to the choice of contracted Gaussian basis sets for first-row diatomic molecules

    SciTech Connect

    Pinheiro, J.C.; Jorge, F.E.; Castro, E.V.R. de

    2000-05-15

    Accurate Gaussian basis sets (18s for Li and Be and 20s11p for the atoms from B to Ne) for the first-row atoms, generated with an improved generator coordinate Hartree-Fock method, were contracted and enriched with polarization functions. These basis sets were tested for B{sub 2}, C{sub 2}, BeO, Cn{sup {minus}}, LiF, N{sub 2}, CO, BF, NO{sup +}, O{sub 2}, and F{sub 2}. At the Hartree-Fock (HP), second-order Moeller-Plesset (MP2), fourth-order Moeller-Plesset (MP4), and density functional theory (DFT) levels, the dipole moments, bond lengths, and harmonic vibrational frequencies were studied, and at the MP2, MP4, and DFT levels, the dissociation energies were evaluated and compared with the corresponding experimental values and with values obtained using other contracted Gaussian basis sets and numerical HF calculations. For all diatomic molecules studied, the differences between the total energies, obtained with the largest contracted basis set [6s5p3d1f], and those calculated with the numerical HF methods were always less than 3.2 mhartree.

  8. Vibrational frequency scaling factors for correlation consistent basis sets and the methods CC2 and MP2 and their spin-scaled SCS and SOS variants

    SciTech Connect

    Friese, Daniel H.; Törk, Lisa; Hättig, Christof

    2014-11-21

    We present scaling factors for vibrational frequencies calculated within the harmonic approximation and the correlated wave-function methods coupled cluster singles and doubles model (CC2) and Møller-Plesset perturbation theory (MP2) with and without a spin-component scaling (SCS or spin-opposite scaling (SOS)). Frequency scaling factors and the remaining deviations from the reference data are evaluated for several non-augmented basis sets of the cc-pVXZ family of generally contracted correlation-consistent basis sets as well as for the segmented contracted TZVPP basis. We find that the SCS and SOS variants of CC2 and MP2 lead to a slightly better accuracy for the scaled vibrational frequencies. The determined frequency scaling factors can also be used for vibrational frequencies calculated for excited states through response theory with CC2 and the algebraic diagrammatic construction through second order and their spin-component scaled variants.

  9. Optimization of Training Sets For Neural-Net Processing of Characteristic Patterns From Vibrating Solids

    NASA Technical Reports Server (NTRS)

    Decker, Arthur J. (Inventor)

    2006-01-01

    An artificial neural network is disclosed that processes holography generated characteristic pattern of vibrating structures along with finite-element models. The present invention provides for a folding operation for conditioning training sets for optimally training forward-neural networks to process characteristic fringe pattern. The folding pattern increases the sensitivity of the feed-forward network for detecting changes in the characteristic pattern The folding routine manipulates input pixels so as to be scaled according to the location in an intensity range rather than the position in the characteristic pattern.

  10. An adaptive optimal bandwidth sensor for video imaging and sparsifying basis

    NASA Astrophysics Data System (ADS)

    Noor, Imama

    Many compressive sensing architectures have shown promise towards reducing the bandwidth for image acquisition significantly. In order to use these architectures for video acquisition we need a scheme that is able to effectively exploit temporal redundancies in a sequence. In this thesis we study a method to efficiently sample and reconstruct specific video sequences. The method is suitable for implementation using a single pixel detector along with a digital micromirror device (DMD) or other forms of spatial light modulators (SLMs). Conventional implementations of single pixel cameras are able to spatially compress the signal but the compressed measurements make it difficult to exploit temporal redundancies directly. Moreover a single pixel camera needs to make measurements in a sequential manner before the scene changes making it inefficient for video imaging. In this thesis we discuss a measurement scheme that exploits sparsity along the time axis for video imaging. After acquiring all measurements required for the first frame, measurements are only acquired from the areas which change in subsequent frames. We segment the first frame and detect magnitude and direction of change for each segment and acquire compressed measurements for the changing segments in the predicted direction. TV minimization is used to reconstruct the dynamic areas and PSNR variation is studied against different parameters of proposed scheme. We show the reconstruction results for a few test sequences commonly used for performance analysis and demonstrate the practical utility of the scheme. A comparison is made with existing algorithms to show the effectiveness of proposed method for specific video sequences. We also discuss use of customized transform to improve reconstruction of submillimeter wave single pixel imager. We use a sparseness inducing transformation on the measurements and optimize the result using l1 minimization algorithms. We demonstrate improvement in result of several

  11. Full CI calibration of model hamiltonian, large basis set studies of the H 2-H 2 van der Waals interaction.

    NASA Astrophysics Data System (ADS)

    Burton, P. G.

    1983-08-01

    The non-variational CEPA2 PNO ansatz, recently employed in detailed studies of the H 2-H 2 van der Waals interaction by Burton and Senff and the full CI extrapolation studies on the same system by Burton are discussed in relation to the explicit full CI study of Harrison and Handy for the planar T configuration of H 2-H 2 ( R = 6.5 ao) in a basis of 80 functions.

  12. A linear optimal transportation framework for quantifying and visualizing variations in sets of images

    PubMed Central

    Wang, Wei; Slepčev, Dejan; Basu, Saurav; Ozolek, John A.

    2012-01-01

    Transportation-based metrics for comparing images have long been applied to analyze images, especially where one can interpret the pixel intensities (or derived quantities) as a distribution of ‘mass’ that can be transported without strict geometric constraints. Here we describe a new transportation-based framework for analyzing sets of images. More specifically, we describe a new transportation-related distance between pairs of images, which we denote as linear optimal transportation (LOT). The LOT can be used directly on pixel intensities, and is based on a linearized version of the Kantorovich-Wasserstein metric (an optimal transportation distance, as is the earth mover’s distance). The new framework is especially well suited for computing all pairwise distances for a large database of images efficiently, and thus it can be used for pattern recognition in sets of images. In addition, the new LOT framework also allows for an isometric linear embedding, greatly facilitating the ability to visualize discriminant information in different classes of images. We demonstrate the application of the framework to several tasks such as discriminating nuclear chromatin patterns in cancer cells, decoding differences in facial expressions, galaxy morphologies, as well as sub cellular protein distributions. PMID:23729991

  13. A set of d-polarization functions for pseudo-potential basis sets of the main group elements AlBi and f-type polarization functions for Zn, Cd, Hg

    NASA Astrophysics Data System (ADS)

    Höllwarth, A.; Böhme, M.; Dapprich, S.; Ehlers, A. W.; Gobbi, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Frenking, G.

    1993-06-01

    A set of five-component d-type polarization functions has been optimized for the main group elements AlBi at the energetically lowest lying s 2p n electronic states for use with the effective core potentials of Hay and Wadt at the CISD level of theory. Also a set of f-type polarization functions is suggested for the elements Zn, Cd and Hg.

  14. Two-stage fan. 4: Performance data for stator setting angle optimization

    NASA Technical Reports Server (NTRS)

    Burger, G. D.; Keenan, M. J.

    1975-01-01

    Stator setting angle optimization tests were conducted on a two-stage fan to improve efficiency at overspeed, stall margin at design speed, and both efficiency and stall margin at partspeed. The fan has a design pressure ratio of 2.8, a flow rate of 184.2 lb/sec (83.55 kg/sec) and a 1st-stage rotor tip speed of 1450 ft/sec (441.96 in/sec). Performance was obtained at 70,100, and 105 percent of design speed with different combinations of 1st-stage and 2nd-stage stator settings. One combination of settings, other than design, was common to all three speeds. At design speed, a 2.0 percentage point increase in stall margin was obtained at the expense of a 1.3 percentage point efficiency decrease. At 105 percent speed, efficiency was improved by 1.8 percentage points but stall margin decreased 4.7 percentage points. At 70 percent speed, no change in stall margin or operating line efficiency was obtained with stator resets although considerable speed-flow requlation occurred.

  15. Differential optimal dopamine levels for set-shifting and working memory in Parkinson's disease.

    PubMed

    Fallon, Sean James; Smulders, Katrijn; Esselink, Rianne A; van de Warrenburg, Bart P; Bloem, Bastiaan R; Cools, Roshan

    2015-10-01

    Parkinson's disease (PD) is an important model for the role of dopamine in supporting human cognition. However, despite the uniformity of midbrain dopamine depletion only some patients experience cognitive impairment. The neurocognitive mechanisms of this heterogeneity remain unclear. A genetic polymorphism in the catechol O-methyltransferase (COMT) enzyme, predominantly thought to exert its cognitive effect through acting on prefrontal cortex (PFC) dopamine transmission, provides us with an experimental window onto dopamine's role in cognitive performance in PD. In a large cohort of PD patients (n=372), we examined the association between COMT genotype and two tasks known to implicate prefrontal dopamine (spatial working memory and attentional set-shifting) and on a task less sensitive to prefrontal dopamine (paired associates learning). Consistent with the known neuroanatomical locus of its effects, differences between the COMT genotype groups were observed on dopamine-dependant tasks, but not the paired associates learning task. However, COMT genotype had differential effects on the two prefrontal dopamine tasks. Putative prefrontal dopamine levels influenced spatial working memory in an 'Inverted-U'-shaped fashion, whereas a linear, dose-dependant pattern was observed for attentional set-shifting. Cumulatively, these results revise our understanding of when COMT genotype modulates cognitive functioning in PD patients by showing that the behavioural consequences of genetic variation vary according to task demands, presumably because set-shifting and working memory have different optimal dopamine levels.

  16. New relativistic atomic natural orbital basis sets for lanthanide atoms with applications to the Ce diatom and LuF3.

    PubMed

    Roos, Björn O; Lindh, Roland; Malmqvist, Per-Ake; Veryazov, Valera; Widmark, Per-Olof; Borin, Antonio Carlos

    2008-11-13

    New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.1 eV in most cases. Two molecular applications are included as illustration: the cerium diatom and the LuF3 molecule. In both cases it is shown that 4f orbitals are not involved in the chemical bond in contrast to an earlier claim for the latter molecule.

  17. 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

  18. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    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.

  19. Combining radial basis function surrogates and dynamic coordinate search in high-dimensional expensive black-box optimization

    NASA Astrophysics Data System (ADS)

    Regis, Rommel G.; Shoemaker, Christine A.

    2013-05-01

    This article presents the DYCORS (DYnamic COordinate search using Response Surface models) framework for surrogate-based optimization of HEB (High-dimensional, Expensive, and Black-box) functions that incorporates an idea from the DDS (Dynamically Dimensioned Search) algorithm. The iterate is selected from random trial solutions obtained by perturbing only a subset of the coordinates of the current best solution. Moreover, the probability of perturbing a coordinate decreases as the algorithm reaches the computational budget. Two DYCORS algorithms that use RBF (Radial Basis Function) surrogates are developed: DYCORS-LMSRBF is a modification of the LMSRBF algorithm while DYCORS-DDSRBF is an RBF-assisted DDS. Numerical results on a 14-D watershed calibration problem and on eleven 30-D and 200-D test problems show that DYCORS algorithms are generally better than EGO, DDS, LMSRBF, MADS with kriging, SQP, an RBF-assisted evolution strategy, and a genetic algorithm. Hence, DYCORS is a promising approach for watershed calibration and for HEB optimization.

  20. Synthetic enzyme mixtures for biomass deconstruction: production and optimization of a core set.

    PubMed

    Banerjee, Goutami; Car, Suzana; Scott-Craig, John S; Borrusch, Melissa S; Aslam, Nighat; Walton, Jonathan D

    2010-08-01

    The high cost of enzymes is a major bottleneck preventing the development of an economically viable lignocellulosic ethanol industry. Commercial enzyme cocktails for the conversion of plant biomass to fermentable sugars are complex mixtures containing more than 80 proteins of suboptimal activities and relative proportions. As a step toward the development of a more efficient enzyme cocktail for biomass conversion, we have developed a platform, called GENPLAT, that uses robotic liquid handling and statistically valid experimental design to analyze synthetic enzyme mixtures. Commercial enzymes (Accellerase 1000 +/- Multifect Xylanase, and Spezyme CP +/- Novozyme 188) were used to test the system and serve as comparative benchmarks. Using ammonia-fiber expansion (AFEX) pretreated corn stover ground to 0.5 mm and a glucan loading of 0.2%, an enzyme loading of 15 mg protein/g glucan, and 48 h digestion at 50 degrees C, commercial enzymes released 53% and 41% of the available glucose and xylose, respectively. Mixtures of three, five, and six pure enzymes of Trichoderma species, expressed in Pichia pastoris, were systematically optimized. Statistical models were developed for the optimization of glucose alone, xylose alone, and the average of glucose + xylose for two digestion durations, 24 and 48 h. The resulting models were statistically significant (P < 0.0001) and indicated an optimum composition for glucose release (values for optimized xylose release are in parentheses) of 29% (5%) cellobiohydrolase 1, 5% (14%) cellobiohydrolase 2, 25% (25%) endo-beta1,4-glucanase 1, 14% (5%) beta-glucosidase, 22% (34%) endo-beta1,4-xylanase 3, and 5% (17%) beta-xylosidase in 48 h at a protein loading of 15 mg/g glucan. Comparison of two AFEX-treated corn stover preparations ground to different particle sizes indicated that particle size (100 vs. 500 microm) makes a large difference in total digestibility. The assay platform and the optimized "core" set together provide a starting

  1. Locally Advanced Lung Cancer: An Optimal Setting for Vaccines and Other Immunotherapies

    PubMed Central

    Iyengar, Puneeth; Gerber, David E.

    2013-01-01

    Lung cancer has traditionally been considered relatively resistant to immunotherapies. However, recent advances in the understanding of tumor-associated antigens, anti-tumor immune responses, and tumor immunosuppression mechanisms have resulted in a number of promising immunomodulatory therapies such as vaccines and checkpoint inhibitors. Locally advanced non-small cell lung cancer (NSCLC) is an optimal setting for these treatments because standard therapies such as surgery, radiation, and chemotherapy may enhance anti-tumor immune effects by debulking the tumor, increasing tumor antigen presentation, and promoting T-cell response and trafficking. Clinical trials incorporating immunomodulatory agents into combined modality therapy of locally advanced NSCLC have shown promising results. Future challenges include identifying biomarkers to predict those patients most likely to benefit from this approach, radiographic assessment of treatment effects, the timing and dosing of combined modality treatment including immunotherapies, and avoidance of potentially overlapping toxicities. PMID:23708072

  2. Optimizing the Choice of Filter Sets for Space Based Imaging Instruments

    NASA Astrophysics Data System (ADS)

    Elliott, Rachel E.; Farrah, Duncan; Petty, Sara M.; Harris, Kathryn Amy

    2015-01-01

    We investigate the challenge of selecting a limited number of filters for space based imaging instruments such that they are able to address multiple heterogeneous science goals. The number of available filter slots for a mission is bounded by factors such as instrument size and cost. We explore methods used to extract the optimal group of filters such that they complement each other most effectively. We focus on three approaches; maximizing the separation of objects in two-dimensional color planes, SED fitting to select those filter sets that give the finest resolution in fitted physical parameters, and maximizing the orthogonality of physical parameter vectors in N-dimensional color-color space. These techniques are applied to a test-case, a UV/optical imager with space for five filters, with the goal of measuring the properties of local stars through to distant galaxies.

  3. Developing interpretable models with optimized set reduction for identifying high risk software components

    NASA Technical Reports Server (NTRS)

    Briand, Lionel C.; Basili, Victor R.; Hetmanski, Christopher J.

    1993-01-01

    Applying equal testing and verification effort to all parts of a software system is not very efficient, especially when resources are limited and scheduling is tight. Therefore, one needs to be able to differentiate low/high fault frequency components so that testing/verification effort can be concentrated where needed. Such a strategy is expected to detect more faults and thus improve the resulting reliability of the overall system. This paper presents the Optimized Set Reduction approach for constructing such models, intended to fulfill specific software engineering needs. Our approach to classification is to measure the software system and build multivariate stochastic models for predicting high risk system components. We present experimental results obtained by classifying Ada components into two classes: is or is not likely to generate faults during system and acceptance test. Also, we evaluate the accuracy of the model and the insights it provides into the error making process.

  4. Relativistic coupled-cluster calculations on XeF{sub 6}: Delicate interplay between electron-correlation and basis-set effects

    SciTech Connect

    Cheng, Lan Stanton, John F.; Gauss, Jürgen

    2015-06-14

    A systematic relativistic coupled-cluster study is reported on the harmonic vibrational frequencies of the O{sub h}, C{sub 3v}, and C{sub 2v} conformers of XeF{sub 6}, with scalar-relativistic effects efficiently treated using the spin-free exact two-component theory in its one-electron variant (SFX2C-1e). Atomic natural orbital type basis sets recontracted for the SFX2C-1e scheme have been shown to provide rapid basis-set convergence for the vibrational frequencies. SFX2C-1e as well as complementary pseudopotential based computations consistently predicts that both O{sub h} and C{sub 3v} structures are local minima on the potential energy surface, while the C{sub 2v} structure is a transition state. Qualitative disagreement between the present results for the O{sub h} structure and those from CCSD(T)-F12b calculations [Peterson et al., J. Phys. Chem. A 116, 9777 (2012)], which yielded a triply degenerate imaginary frequency for the O{sub h} structure, is attributed here to the high sensitivity of the computed harmonic frequencies of the t{sub 1u} bending modes to the basis-set effects of triples contributions.

  5. Enthalpy difference between conformations of normal alkanes: Intramolecular basis set superposition error (BSSE) in the case of n-butane and n-hexane

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2008-10-01

    In this paper, an extra error source for high-quality ab initio calculation of conformation equilibrium in normal alkanes—intramolecular basis set superposition error (BSSE)—is discussed. Normal butane (n-butane) and normal hexane (n-hexane) are used as representative examples. Single-point energy difference and BSSE values of trans and gauche conformations for n-butane (and trans-trans-trans and gauche-gauche-gauche conformations for n-hexane) were calculated using popular electron correlation methods: The second-order Moller-Plesset (MP2), the fourth-order Moller-Plesset (MP4), and coupled cluster with single and double substitutions with noniterative triple excitation [CCSD(T)] levels of theory. Extrapolation to the complete basis set is applied. The difference between BSSE-corrected and uncorrected relative energy values ranges from ˜100 cal/mol (in case of n-butane) to more than 1000 cal/mol (in case of n-hexane). The influence of basis set type (Pople or Dunning) and size [up to 6-311G(3df,3pd) and aug-cc-pVQZ] is discussed.

  6. Periodic local Møller-Plesset second order perturbation theory method applied to molecular crystals: study of solid NH3 and CO2 using extended basis sets.

    PubMed

    Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Civalleri, Bartolomeo

    2010-04-07

    We have calculated the equilibrium geometry, formation energy, and bulk modulus of two molecular bulk crystals, NH(3) and CO(2), at the periodic post-Hartree-Fock correlated level. The dependence of the results on the basis set has been analyzed, by employing basis sets up to aug-cc-pVQZ quality. In the calculations, we used the periodic local Møller-Plesset second order perturbation theory (LMP2), implemented in the CRYSCOR program. Multipolar expansion techniques, as well as density fitting, are employed in this code to reduce the number of and to factorize the required electron repulsion integrals; as a consequence of that, the computational cost for the correlation part of the calculations is comparable to that of the Hartree-Fock. Auxiliary calculations performed on molecular dimers are also reported to verify the accuracy of the LMP2 approach and of the basis sets used. Furthermore, the effect of spin-component scaling has been investigated for the two crystals. One intention of the present paper is also to lay out and specify the computational setup, which is generally applicable for accurate CRYSCOR calculations on molecular crystals.

  7. The electron affinity of gallium nitride (GaN) and digallium nitride (GaNGa): the importance of the basis set superposition error in strongly bound systems.

    PubMed

    Tzeli, Demeter; Tsekouras, Athanassios A

    2008-04-14

    The electron affinity of GaN and Ga2N as well as the geometries and the dissociation energies of the ground states of gallium nitrides GaN, GaN(-), Ga2N, and Ga2N(-) were systematically studied by employing the coupled cluster method, RCCSD(T), in conjunction with a series of basis sets, (aug-)cc-pVxZ(-PP), x=D, T, Q, and 5 and cc-pwCVxZ(-PP), x=D, T, and Q. The calculated dissociation energy and the electron affinity of GaN are 2.12 and 1.84 eV, respectively, and those of Ga2N are 6.31 and 2.53 eV. The last value is in excellent agreement with a recent experimental value for the electron affinity of Ga2N of 2.506+/-0.008 eV. For such quality in the results to be achieved, the Ga 3d electrons had to be included in the correlation space. Moreover, when a basis set is used, which has not been developed for the number of the electrons which are correlated in a calculation, the quantities calculated need to be corrected for the basis set superposition error.

  8. 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.

  9. Optimize Flue Gas Settings to Promote Microalgae Growth in Photobioreactors via Computer Simulations

    PubMed Central

    He, Lian; Chen, Amelia B; Yu, Yi; Kucera, Leah; Tang, Yinjie

    2013-01-01

    Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently than plants3, but also synthesize advanced biofuels2-4. Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth5. On the other hand, the high concentrations of CO2 in industrial exhaust gases have adverse effects on algal physiology. Consequently, both cultivation conditions (such as nutrients and light) and the control of the flue gas flow into the photo-bioreactors are important to develop an efficient “flue gas to algae” system. Researchers have proposed different photobioreactor configurations4,6 and cultivation strategies7,8 with flue gas. Here, we present a protocol that demonstrates how to use models to predict the microalgal growth in response to flue gas settings. We perform both experimental illustration and model simulations to determine the favorable conditions for algal growth with flue gas. We develop a Monod-based model coupled with mass transfer and light intensity equations to simulate the microalgal growth in a homogenous photo-bioreactor. The model simulation compares algal growth and flue gas consumptions under different flue-gas settings. The model illustrates: 1) how algal growth is influenced by different volumetric mass transfer coefficients of CO2; 2) how we can find optimal CO2 concentration for algal growth via the dynamic optimization approach (DOA); 3) how we can design a rectangular on-off flue gas pulse to promote algal biomass growth and to reduce the usage of flue gas. On the experimental side, we present a protocol for growing Chlorella under the flue gas (generated by natural gas combustion). The experimental results qualitatively validate the model predictions that the high frequency flue gas pulses can significantly improve algal cultivation. PMID:24121788

  10. Setting an Optimal α That Minimizes Errors in Null Hypothesis Significance Tests

    PubMed Central

    Mudge, Joseph F.; Baker, Leanne F.; Edge, Christopher B.; Houlahan, Jeff E.

    2012-01-01

    Null hypothesis significance testing has been under attack in recent years, partly owing to the arbitrary nature of setting α (the decision-making threshold and probability of Type I error) at a constant value, usually 0.05. If the goal of null hypothesis testing is to present conclusions in which we have the highest possible confidence, then the only logical decision-making threshold is the value that minimizes the probability (or occasionally, cost) of making errors. Setting α to minimize the combination of Type I and Type II error at a critical effect size can easily be accomplished for traditional statistical tests by calculating the α associated with the minimum average of α and β at the critical effect size. This technique also has the flexibility to incorporate prior probabilities of null and alternate hypotheses and/or relative costs of Type I and Type II errors, if known. Using an optimal α results in stronger scientific inferences because it estimates and minimizes both Type I errors and relevant Type II errors for a test. It also results in greater transparency concerning assumptions about relevant effect size(s) and the relative costs of Type I and II errors. By contrast, the use of α = 0.05 results in arbitrary decisions about what effect sizes will likely be considered significant, if real, and results in arbitrary amounts of Type II error for meaningful potential effect sizes. We cannot identify a rationale for continuing to arbitrarily use α = 0.05 for null hypothesis significance tests in any field, when it is possible to determine an optimal α. PMID:22389720

  11. A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines[C][W][OPEN

    PubMed Central

    Chitwood, Daniel H.; Kumar, Ravi; Headland, Lauren R.; Ranjan, Aashish; Covington, Michael F.; Ichihashi, Yasunori; Fulop, Daniel; Jiménez-Gómez, José M.; Peng, Jie; Maloof, Julin N.; Sinha, Neelima R.

    2013-01-01

    Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations. PMID:23872539

  12. Nonlocal games and optimal steering at the boundary of the quantum set

    NASA Astrophysics Data System (ADS)

    Zhen, Yi-Zheng; Goh, Koon Tong; Zheng, Yu-Lin; Cao, Wen-Fei; Wu, Xingyao; Chen, Kai; Scarani, Valerio

    2016-08-01

    The boundary between classical and quantum correlations is well characterized by linear constraints called Bell inequalities. It is much harder to characterize the boundary of the quantum set itself in the space of no-signaling correlations. For the points on the quantum boundary that violate maximally some Bell inequalities, J. Oppenheim and S. Wehner [Science 330, 1072 (2010), 10.1126/science.1192065] pointed out a complex property: Alice's optimal measurements steer Bob's local state to the eigenstate of an effective operator corresponding to its maximal eigenvalue. This effective operator is the linear combination of Bob's local operators induced by the coefficients of the Bell inequality, and it can be interpreted as defining a fine-grained uncertainty relation. It is natural to ask whether the same property holds for other points on the quantum boundary, using the Bell expression that defines the tangent hyperplane at each point. We prove that this is indeed the case for a large set of points, including some that were believed to provide counterexamples. The price to pay is to acknowledge that the Oppenheim-Wehner criterion does not respect equivalence under the no-signaling constraint: for each point, one has to look for specific forms of writing the Bell expressions.

  13. Optimal allocation of the limited oral cholera vaccine supply between endemic and epidemic settings

    PubMed Central

    Moore, Sean M.; Lessler, Justin

    2015-01-01

    The World Health Organization (WHO) recently established a global stockpile of oral cholera vaccine (OCV) to be preferentially used in epidemic response (reactive campaigns) with any vaccine remaining after 1 year allocated to endemic settings. Hence, the number of cholera cases or deaths prevented in an endemic setting represents the minimum utility of these doses, and the optimal risk-averse response to any reactive vaccination request (i.e. the minimax strategy) is one that allocates the remaining doses between the requested epidemic response and endemic use in order to ensure that at least this minimum utility is achieved. Using mathematical models, we find that the best minimax strategy is to allocate the majority of doses to reactive campaigns, unless the request came late in the targeted epidemic. As vaccine supplies dwindle, the case for reactive use of the remaining doses grows stronger. Our analysis provides a lower bound for the amount of OCV to keep in reserve when responding to any request. These results provide a strategic context for the fulfilment of requests to the stockpile, and define allocation strategies that minimize the number of OCV doses that are allocated to suboptimal situations. PMID:26423441

  14. Optimal allocation of the limited oral cholera vaccine supply between endemic and epidemic settings.

    PubMed

    Moore, Sean M; Lessler, Justin

    2015-10-06

    The World Health Organization (WHO) recently established a global stockpile of oral cholera vaccine (OCV) to be preferentially used in epidemic response (reactive campaigns) with any vaccine remaining after 1 year allocated to endemic settings. Hence, the number of cholera cases or deaths prevented in an endemic setting represents the minimum utility of these doses, and the optimal risk-averse response to any reactive vaccination request (i.e. the minimax strategy) is one that allocates the remaining doses between the requested epidemic response and endemic use in order to ensure that at least this minimum utility is achieved. Using mathematical models, we find that the best minimax strategy is to allocate the majority of doses to reactive campaigns, unless the request came late in the targeted epidemic. As vaccine supplies dwindle, the case for reactive use of the remaining doses grows stronger. Our analysis provides a lower bound for the amount of OCV to keep in reserve when responding to any request. These results provide a strategic context for the fulfilment of requests to the stockpile, and define allocation strategies that minimize the number of OCV doses that are allocated to suboptimal situations.

  15. Development of chicken meat caruncles on the basis of sensory attributes: process optimization using response surface methodology.

    PubMed

    Singh, Parminder; Sahoo, Jhari; Talwar, Gopika; Chatli, Manish K; Biswas, Ashim K

    2015-03-01

    A three factor Box-Behnken design of response surface methodology was employed to optimize spent hen meat level (600-700 g kg(-1)), oil level (25-75 g kg(-1)) and cooking time (3-5 min) for development of ready-to-eat chicken meat caruncles on the basis of sensory attributes - colour/appearance, flavour, crispiness, after-taste, meat flavour intensity and overall acceptability. The analysis of variance showed that meat and cooking time interaction showed significant effect (p < 0.01; p < 0.05; p < 0.1) on colour/appearance and crispiness of chicken meat caruncles. Quadratically meat level showed significantly higher effect (p < 0.01; p < 0.05; p < 0.1) on crispiness; and oil level and cooking time (p < 0.05; p < 0.1) on after-taste of chicken meat caruncles. Linearly meat level showed significantly higher (p < 0.05; p < 0.1) effect on colour/appearance, after-taste, meat flavour intensity and overall acceptability of chicken meat caruncles. The optimized conditions were: 650 g kg(-1) meat level, 50 g kg(-1) oil level and cooking time as 4 min. Among all sensory parameters, crispiness is one of the most important sensory parameters for meat snacks, which was highest (6.68) at the optimized conditions in the final product. The other sensory parameters ranged from 6.33 to 6.68 on an eight point scale. Box-Behnken design of RSM performed well in the optimization process of development of chicken meat caruncles to produce product with very high degree of acceptability. 650 g kg(-1) of spent hen meat level produced the most acceptable product in terms of sensory profile.

  16. Discovery and Molecular Basis of a Diverse Set of Polycomb Repressive Complex 2 Inhibitors Recognition by EED

    PubMed Central

    Zhang, Man; Zhao, Mengxi; Feng, Lijian; Luo, Xiao; Gao, Zhenting; Huang, Ying; Ardayfio, Ophelia; Zhang, Ji-Hu; Lin, Ying; Fan, Hong; Mi, Yuan; Li, Guobin; Liu, Lei; Feng, Leying; Luo, Fangjun; Teng, Lin; Qi, Wei; Ottl, Johannes; Lingel, Andreas; Bussiere, Dirksen E.; Yu, Zhengtian; Atadja, Peter; Lu, Chris; Li, En; Gu, Justin; Zhao, Kehao

    2017-01-01

    Polycomb repressive complex 2 (PRC2), a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. It binds to the tri-methylated lysine 27 of the histone H3 (H3K27me3), and through which stimulates the activity of PRC2 allosterically. Recently, we disclosed a novel PRC2 inhibitor EED226 which binds to the K27me3-pocket on EED and showed strong antitumor activity in xenograft mice model. Here, we further report the identification and validation of four other EED binders along with EED162, the parental compound of EED226. The crystal structures for all these five compounds in complex with EED revealed a common deep pocket induced by the binding of this diverse set of compounds. This pocket was created after significant conformational rearrangement of the aromatic cage residues (Y365, Y148 and F97) in the H3K27me3 binding pocket of EED, the width of which was delineated by the side chains of these rearranged residues. In addition, all five compounds interact with the Arg367 at the bottom of the pocket. Each compound also displays unique features in its interaction with EED, suggesting the dynamics of the H3K27me3 pocket in accommodating the binding of different compounds. Our results provide structural insights for rational design of novel EED binder for the inhibition of PRC2 complex activity. PMID:28072869

  17. Harmonic Vibrational Frequencies: Approximate Global Scaling Factors for TPSS, M06, and M11 Functional Families Using Several Common Basis Sets.

    PubMed

    Kashinski, D O; Chase, G M; Nelson, R G; Di Nallo, O E; Scales, A N; VanderLey, D L; Byrd, E F C

    2017-03-23

    We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.

  18. Application of fuzzy sets to optimal reactive power planning with security constraints

    SciTech Connect

    Abdul-Rahman, K.H.; Shahidehpour, S.M. . Dept. of Electrical and Computer Engineering)

    1994-05-01

    This paper presents a mathematical formulation for the optimal reactive power planning taking into account the static security constraints and the non-probabilistic uncertainty in load values. The planning process is decomposed into investment and operation problems via the generalized Benders decomposition (GBD). Fixed and variable costs are considered in the investment problem. Linguistic declarations of load values in the operation problem are translated into possibility distribution functions. The operation problem is decomposed into 4 subproblems via Dantzig-Wolfe decomposition (DWD), and the modeling of multi-area power systems is considered by applying a second DWD to each subproblem, leading to a significant reduction in its dimensions for personal computer applications. Voltage constraints within each area are modeled as fuzzy sets for the static security analysis by biasing the final solution towards desired values of variables within their given ranges. The overall solution is a compromise between economics (lower investment and operation costs) and security (tighter feasible region). Numerical examples for the applicability of the proposed approach to multi-area power systems are discussed.

  19. SCF DVM-Xα with basis set of numerical Hartree—Fock functions and its applications to MoF 6, WF 6, and UF 6

    NASA Astrophysics Data System (ADS)

    Gutsev, G. L.; Levin, A. A.

    1980-10-01

    A self-consistent version of the discrete variational method is described based on the use of numerical LCAO basis functions obtained as solutions of the Hartree—Fock equations for free atoms. Sets of single-zeta Slater functions are applied to approximate atomic densities further employed in the calculations of the Coulomb potential. The computer programs realizing this approach have been written and utilized to calculate electronic structures of molybdenum, tungsten and uranium hexafluorides. The ionization potentials calculated are in good quantitative agreement with experimental data. The deviations of the calculated valence state IP's from those determined by photoelectron spectroscopy do not exceed 1 eV.

  20. Second-order Møller-Plesset perturbation theory applied to extended systems. I. Within the projector-augmented-wave formalism using a plane wave basis set.

    PubMed

    Marsman, M; Grüneis, A; Paier, J; Kresse, G

    2009-05-14

    We present an implementation of the canonical formulation of second-order Møller-Plesset (MP2) perturbation theory within the projector-augmented-wave method under periodic boundary conditions using a plane wave basis set. To demonstrate the accuracy of our approach we show that our result for the atomization energy of a LiH molecule at the Hartree-Fock+MP2 level is in excellent agreement with well converged Gaussian-type-orbital calculations. To establish the feasibility of employing MP2 perturbation theory in its canonical form to systems that are periodic in three dimensions we calculated the cohesive energy of bulk LiH.

  1. A wavelet-based Projector Augmented-Wave (PAW) method: Reaching frozen-core all-electron precision with a systematic, adaptive and localized wavelet basis set

    NASA Astrophysics Data System (ADS)

    Rangel, T.; Caliste, D.; Genovese, L.; Torrent, M.

    2016-11-01

    We present a Projector Augmented-Wave (PAW) method based on a wavelet basis set. We implemented our wavelet-PAW method as a PAW library in the ABINIT package [http://www.abinit.org] and into BigDFT [http://www.bigdft.org]. We test our implementation in prototypical systems to illustrate the potential usage of our code. By using the wavelet-PAW method, we can simulate charged and special boundary condition systems with frozen-core all-electron precision. Furthermore, our work paves the way to large-scale and potentially order- N simulations within a PAW method.

  2. Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review.

    PubMed

    Wu, Xing-Gang; Ma, Yang; Wang, Sheng-Quan; Fu, Hai-Bing; Ma, Hong-Hao; Brodsky, Stanley J; Mojaza, Matin

    2015-12-01

    A valid prediction for a physical observable from quantum field theory should be independent of the choice of renormalization scheme--this is the primary requirement of renormalization group invariance (RGI). Satisfying scheme invariance is a challenging problem for perturbative QCD (pQCD), since a truncated perturbation series does not automatically satisfy the requirements of the renormalization group. In a previous review, we provided a general introduction to the various scale setting approaches suggested in the literature. As a step forward, in the present review, we present a discussion in depth of two well-established scale-setting methods based on RGI. One is the 'principle of maximum conformality' (PMC) in which the terms associated with the β-function are absorbed into the scale of the running coupling at each perturbative order; its predictions are scheme and scale independent at every finite order. The other approach is the 'principle of minimum sensitivity' (PMS), which is based on local RGI; the PMS approach determines the optimal renormalization scale by requiring the slope of the approximant of an observable to vanish. In this paper, we present a detailed comparison of the PMC and PMS procedures by analyzing two physical observables R(e+e-) and [Formula: see text] up to four-loop order in pQCD. At the four-loop level, the PMC and PMS predictions for both observables agree within small errors with those of conventional scale setting assuming a physically-motivated scale, and each prediction shows small scale dependences. However, the convergence of the pQCD series at high orders, behaves quite differently: the PMC displays the best pQCD convergence since it eliminates divergent renormalon terms; in contrast, the convergence of the PMS prediction is questionable, often even worse than the conventional prediction based on an arbitrary guess for the renormalization scale. PMC predictions also have the property that any residual dependence on the choice

  3. On a distinctive feature of problems of calculating time-average characteristics of nuclear reactor optimal control sets

    NASA Astrophysics Data System (ADS)

    Trifonenkov, A. V.; Trifonenkov, V. P.

    2017-01-01

    This article deals with a feature of problems of calculating time-average characteristics of nuclear reactor optimal control sets. The operation of a nuclear reactor during threatened period is considered. The optimal control search problem is analysed. The xenon poisoning causes limitations on the variety of statements of the problem of calculating time-average characteristics of a set of optimal reactor power off controls. The level of xenon poisoning is limited. There is a problem of choosing an appropriate segment of the time axis to ensure that optimal control problem is consistent. Two procedures of estimation of the duration of this segment are considered. Two estimations as functions of the xenon limitation were plot. Boundaries of the interval of averaging are defined more precisely.

  4. A generalized gradient projection method based on a new working set for minimax optimization problems with inequality constraints.

    PubMed

    Ma, Guodong; Zhang, Yufeng; Liu, Meixing

    2017-01-01

    Combining the techniques of the working set identification and generalized gradient projection, we present a new generalized gradient projection algorithm for minimax optimization problems with inequality constraints. In this paper, we propose a new optimal identification function, from which we provide a new working set. At each iteration, the improved search direction is generated by only one generalized gradient projection explicit formula, which is simple and could reduce the computational cost. Under some mild assumptions, the algorithm possesses the global and strong convergence. Finally, the numerical results show that the proposed algorithm is promising.

  5. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule

    PubMed Central

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2014-01-01

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets. PMID:24526929

  6. Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

    PubMed

    Li, Y Q; Varandas, A J C

    2010-09-16

    An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

  7. Improving the accuracy of ground-state correlation energies within a plane-wave basis set: The electron-hole exchange kernel

    NASA Astrophysics Data System (ADS)

    Dixit, Anant; Ángyán, János G.; Rocca, Dario

    2016-09-01

    A new formalism was recently proposed to improve random phase approximation (RPA) correlation energies by including approximate exchange effects [B. Mussard et al., J. Chem. Theory Comput. 12, 2191 (2016)]. Within this framework, by keeping only the electron-hole contributions to the exchange kernel, two approximations can be obtained: An adiabatic connection analog of the second order screened exchange (AC-SOSEX) and an approximate electron-hole time-dependent Hartree-Fock (eh-TDHF). Here we show how this formalism is suitable for an efficient implementation within the plane-wave basis set. The response functions involved in the AC-SOSEX and eh-TDHF equations can indeed be compactly represented by an auxiliary basis set obtained from the diagonalization of an approximate dielectric matrix. Additionally, the explicit calculation of unoccupied states can be avoided by using density functional perturbation theory techniques and the matrix elements of dynamical response functions can be efficiently computed by applying the Lanczos algorithm. As shown by several applications to reaction energies and weakly bound dimers, the inclusion of the electron-hole kernel significantly improves the accuracy of ground-state correlation energies with respect to RPA and semi-local functionals.

  8. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule.

    PubMed

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2013-10-08

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets.

  9. Searching for optimal setting conditions in technological processes using parametric estimation models and neural network mapping approach: a tutorial.

    PubMed

    Fjodorova, Natalja; Novič, Marjana

    2015-09-03

    Engineering optimization is an actual goal in manufacturing and service industries. In the tutorial we represented the concept of traditional parametric estimation models (Factorial Design (FD) and Central Composite Design (CCD)) for searching optimal setting parameters of technological processes. Then the 2D mapping method based on Auto Associative Neural Networks (ANN) (particularly, the Feed Forward Bottle Neck Neural Network (FFBN NN)) was described in comparison with traditional methods. The FFBN NN mapping technique enables visualization of all optimal solutions in considered processes due to the projection of input as well as output parameters in the same coordinates of 2D map. This phenomenon supports the more efficient way of improving the performance of existing systems. Comparison of two methods was performed on the bases of optimization of solder paste printing processes as well as optimization of properties of cheese. Application of both methods enables the double check. This increases the reliability of selected optima or specification limits.

  10. Optimization of super-resolution processing using incomplete image sets in PET imaging.

    PubMed

    Chang, Guoping; Pan, Tinsu; Clark, John W; Mawlawi, Osama R

    2008-12-01

    Super-resolution (SR) techniques are used in PET imaging to generate a high-resolution image by combining multiple low-resolution images that have been acquired from different points of view (POVs). The number of low-resolution images used defines the processing time and memory storage necessary to generate the SR image. In this paper, the authors propose two optimized SR implementations (ISR-1 and ISR-2) that require only a subset of the low-resolution images (two sides and diagonal of the image matrix, respectively), thereby reducing the overall processing time and memory storage. In an N x N matrix of low-resolution images, ISR-1 would be generated using images from the two sides of the N x N matrix, while ISR-2 would be generated from images across the diagonal of the image matrix. The objective of this paper is to investigate whether the two proposed SR methods can achieve similar performance in contrast and signal-to-noise ratio (SNR) as the SR image generated from a complete set of low-resolution images (CSR) using simulation and experimental studies. A simulation, a point source, and a NEMA/IEC phantom study were conducted for this investigation. In each study, 4 (2 x 2) or 16 (4 x 4) low-resolution images were reconstructed from the same acquired data set while shifting the reconstruction grid to generate images from different POVs. SR processing was then applied in each study to combine all as well as two different subsets of the low-resolution images to generate the CSR, ISR-1, and ISR-2 images, respectively. For reference purpose, a native reconstruction (NR) image using the same matrix size as the three SR images was also generated. The resultant images (CSR, ISR-1, ISR-2, and NR) were then analyzed using visual inspection, line profiles, SNR plots, and background noise spectra. The simulation study showed that the contrast and the SNR difference between the two ISR images and the CSR image were on average 0.4% and 0.3%, respectively. Line profiles of

  11. Sea ice in the Baltic Sea - revisiting BASIS ice, a~historical data set covering the period 1960/1961-1978/1979

    NASA Astrophysics Data System (ADS)

    Löptien, U.; Dietze, H.

    2014-06-01

    The Baltic Sea is a seasonally ice-covered, marginal sea, situated in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised 1981 in a joint project of the Finnish Institute of Marine Research (today Finish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website www.baltic-ocean.org hosts the post-prossed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science PANGEA (doi:10.1594/PANGEA.832353).

  12. Sea ice in the Baltic Sea - revisiting BASIS ice, a historical data set covering the period 1960/1961-1978/1979

    NASA Astrophysics Data System (ADS)

    Löptien, U.; Dietze, H.

    2014-12-01

    The Baltic Sea is a seasonally ice-covered, marginal sea in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961 to 1978/1979. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised in 1981 in a joint project of the Finnish Institute of Marine Research (today the Finnish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website http://www.baltic-ocean.org hosts the post-processed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science, PANGAEA (doi:10.1594/PANGAEA.832353).

  13. Photoionization cross sections of H2(+) and H2 with complex Gaussian-type basis functions optimized for the frequency-dependent polarizabilities.

    PubMed

    Morita, Masato; Yabushita, Satoshi

    2008-11-15

    Within the framework of the complex basis function method, the photoionization cross sections of H(2)(+) and H(2) were calculated based on the variational principle for the frequency-dependent polarizabilities. In these calculations, complex orbital exponents of Gaussian-type basis functions for the final state continuum wavefunctions were fully optimized for each photon energy with the numerical Newton-Raphson method. In most cases, the use of only one or two complex Gaussian-type basis functions was enough to obtain excellent agreement with previous high precision calculations and available experimental results. However, there were a few cases, in which the use of complex basis functions having various angular momentum quantum numbers was crucial to obtain the accurate results. The behavior of the complex orbital exponents as a function of photon energy was discussed in relation to the scaling relation and the effective charge for photoelectron. The success of this method implies the effectiveness of the optimization of orbital exponents to reduce the number of basis functions and shows the possibility to calculate photoionization cross sections of general molecules using only Gaussian-type basis functions.

  14. Level Set Methods for Optimization Problems Involving Geometry and Constraints. I. Frequencies of a Two-Density Inhomogeneous Drum

    NASA Astrophysics Data System (ADS)

    Osher, Stanley J.; Santosa, Fadil

    2001-07-01

    Many problems in engineering design involve optimizing the geometry to maximize a certain design objective. Geometrical constraints are often imposed. In this paper, we use the level set method devised in (Osher and Sethian, J. Comput. Phys.79, 12 (1988)), the variational level set calculus presented in (Zhao et al., J. Comput. Phys.127, 179 (1996)), and the projected gradient method, as in (Rudin et al., Physica D.60, 259 (1992)), to construct a simple numerical approach for problems of this type. We apply this technique to a model problem involving a vibrating system whose resonant frequency or whose spectral gap is to be optimized subject to constraints on geometry. Our numerical results are quite promising. We expect to use this approach to deal with a wide class of optimal design problems in the future.

  15. Selection of appropriate training and validation set chemicals for modelling dermal permeability by U-optimal design.

    PubMed

    Xu, G; Hughes-Oliver, J M; Brooks, J D; Yeatts, J L; Baynes, R E

    2013-01-01

    Quantitative structure-activity relationship (QSAR) models are being used increasingly in skin permeation studies. The main idea of QSAR modelling is to quantify the relationship between biological activities and chemical properties, and thus to predict the activity of chemical solutes. As a key step, the selection of a representative and structurally diverse training set is critical to the prediction power of a QSAR model. Early QSAR models selected training sets in a subjective way and solutes in the training set were relatively homogenous. More recently, statistical methods such as D-optimal design or space-filling design have been applied but such methods are not always ideal. This paper describes a comprehensive procedure to select training sets from a large candidate set of 4534 solutes. A newly proposed 'Baynes' rule', which is a modification of Lipinski's 'rule of five', was used to screen out solutes that were not qualified for the study. U-optimality was used as the selection criterion. A principal component analysis showed that the selected training set was representative of the chemical space. Gas chromatograph amenability was verified. A model built using the training set was shown to have greater predictive power than a model built using a previous dataset [1].

  16. Optimization to the Culture Conditions for Phellinus Production with Regression Analysis and Gene-Set Based Genetic Algorithm

    PubMed Central

    Li, Zhongwei; Xin, Yuezhen; Wang, Xun; Sun, Beibei; Xia, Shengyu; Li, Hui

    2016-01-01

    Phellinus is a kind of fungus and is known as one of the elemental components in drugs to avoid cancers. With the purpose of finding optimized culture conditions for Phellinus production in the laboratory, plenty of experiments focusing on single factor were operated and large scale of experimental data were generated. In this work, we use the data collected from experiments for regression analysis, and then a mathematical model of predicting Phellinus production is achieved. Subsequently, a gene-set based genetic algorithm is developed to optimize the values of parameters involved in culture conditions, including inoculum size, PH value, initial liquid volume, temperature, seed age, fermentation time, and rotation speed. These optimized values of the parameters have accordance with biological experimental results, which indicate that our method has a good predictability for culture conditions optimization. PMID:27610365

  17. Efficiency of the MO method using a Slater-type basis set and non-local density functional formalism for describing DNA base stacking energy

    NASA Astrophysics Data System (ADS)

    Kurita, Noriyuki; Araki, Masahiro; Nakao, Kenji; Kobayashi, Kinya

    1999-11-01

    We have developed a molecular-orbital (MO) method based on a Slater-type basis set and non-local density functional theory (DFT) for describing the DNA base stacking properties, and its efficiency has been confirmed by investigating the stacking energy of cytosine dimer. Our DFT method can reproduce the dependence of stacking energy on the stacking conformation obtained by the ab initio second-order Møller-Plesset (MP2) calculation. The stable structures of hydrogen-bonded Watson-Crick base pairs and (PO 4H 2) -1 ion have been investigated and the structures obtained by our DFT method are comparable with those from the MP2 and DFT methods in Gaussian94. Therefore, our DFT method may be applicable for investigating the stable structures of more realistic models for stacked DNA base pairs including backbones.

  18. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets.

    PubMed

    Thorvaldsen, Andreas J; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-07

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  19. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets

    NASA Astrophysics Data System (ADS)

    Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-01

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  20. Minimum Total-Squared-Correlation Quaternary Signature Sets: New Bounds and Optimal Designs

    DTIC Science & Technology

    2009-12-01

    multiple ac- cess communications, statistical signal processing, steganography and steganalysis. Mr. Li is a student member of the IEEE Communications...spectrum com- munications, supervised and unsupervised optimization, distributed detection, sensor networks, covert communications and steganography . Dr

  1. Enumerating a Diverse Set of Building Designs Using Discrete Optimization: Preprint

    SciTech Connect

    Hale, E.; Long, N.

    2010-08-01

    Numerical optimization is a powerful method for identifying energy-efficient building designs. Automating the search process facilitates the evaluation of many more options than is possible with one-off parametric simulation runs. However, input data uncertainties and qualitative aspects of building design work against standard optimization formulations that return a single, so-called optimal design. This paper presents a method for harnessing a discrete optimization algorithm to obtain significantly different, economically viable building designs that satisfy an energy efficiency goal. The method is demonstrated using NREL's first-generation building analysis platform, Opt- E-Plus, and two example problems. We discuss the information content of the results, and the computational effort required by the algorithm.

  2. The optimization of single mode basis functions for polyatomic vibrational problems with application to the water molecule

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.

    1992-01-01

    The optimization of the wave functions is considered for coupled vibrations represented by linear combinations of products of functions depending only on a single vibrational coordinate. The functions themselves are optimized as well as configuration list. For the H2O molecule highly accurate results are obtained for the lowest 15 levels using significantly shorter expansions than would otherwise be possible.

  3. Experimental evaluation and basis function optimization of the spatially variant image-space PSF on the Ingenuity PET/MR scanner

    SciTech Connect

    Kotasidis, Fotis A.; Zaidi, Habib

    2014-06-15

    Purpose: The Ingenuity time-of-flight (TF) PET/MR is a recently developed hybrid scanner combining the molecular imaging capabilities of PET with the excellent soft tissue contrast of MRI. It is becoming common practice to characterize the system's point spread function (PSF) and understand its variation under spatial transformations to guide clinical studies and potentially use it within resolution recovery image reconstruction algorithms. Furthermore, due to the system's utilization of overlapping and spherical symmetric Kaiser-Bessel basis functions during image reconstruction, its image space PSF and reconstructed spatial resolution could be affected by the selection of the basis function parameters. Hence, a detailed investigation into the multidimensional basis function parameter space is needed to evaluate the impact of these parameters on spatial resolution. Methods: Using an array of 12 × 7 printed point sources, along with a custom made phantom, and with the MR magnet on, the system's spatially variant image-based PSF was characterized in detail. Moreover, basis function parameters were systematically varied during reconstruction (list-mode TF OSEM) to evaluate their impact on the reconstructed resolution and the image space PSF. Following the spatial resolution optimization, phantom, and clinical studies were subsequently reconstructed using representative basis function parameters. Results: Based on the analysis and under standard basis function parameters, the axial and tangential components of the PSF were found to be almost invariant under spatial transformations (∼4 mm) while the radial component varied modestly from 4 to 6.7 mm. Using a systematic investigation into the basis function parameter space, the spatial resolution was found to degrade for basis functions with a large radius and small shape parameter. However, it was found that optimizing the spatial resolution in the reconstructed PET images, while having a good basis function

  4. MAXBAND Version 3.1: Heuristic and optimal approach for setting the left turn phase sequences in signalized networks

    SciTech Connect

    Pillai, R.S.; Rathi, A.K.

    1995-02-01

    The main objective of synchronized signal timing is to keep traffic moving along arterials in platoons throughout the signal system by proper setting of left turn phase sequence at signals along the arterials/networks. The synchronization of traffic signals located along the urban/suburban arterials in metropolitan areas is perhaps one of the most cost-effective methods for improving traffic flow along these streets. MAXBAND Version 2.1 (formerly known as MAXBAND-86), a progression-based optimization model, is used for generating signal timing plan for urban networks. This model formulates the problem as a mixed integer linear program and uses Land and Powell branch and bound search to arrive at the optimal solution. The computation time of MAXBAND Version 2.1 tends to be excessive for realistic multiarterial network problems due to the exhaustive nature of the branch and bound search technique. Furthermore, the Land and Powell branch and bound code is known to be numerically unstable, which results in suboptimal solutions for network problems with a range on the cycle time variable. This report presents the development of a new version of MAXBAND called MAXBAND Version 3.1. This new version has a fast heuristic algorithm and a fast optimal algorithm for generating signal timing plan for arterials and networks. MAXBAND 3.1 can generate optimal/near-optimal solutions in fraction of the time needed to compute the optimal solution by Version 2.1. The heuristic algorithm in the new model is based on restricted search using branch and bound technique. The algorithm for generating the optimal solution is faster and more efficient than version 2.1 algorithm. Furthermore, the new version is numerically stable. The efficiency of the new model is demonstrated by numerical results for a set of test problems.

  5. 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).

  6. Benchmark Structures and Harmonic Vibrational Frequencies Near the CCSD(T) Complete Basis Set Limit for Small Water Clusters: (H2O)n = 2, 3, 4, 5, 6.

    PubMed

    Howard, J Coleman; Tschumper, Gregory S

    2015-05-12

    A series of (H2O)n clusters ranging from the dimer to the hexamer have been characterized with the CCSD(T) and the 2-body:Many-body CCSD(T):MP2 methods near the complete basis set (CBS) limit to generate benchmark-quality optimized structures and harmonic vibrational frequencies for these important systems. Quadruple-ζ correlation-consistent basis sets that augment the O atoms with diffuse functions have been employed in the analytic computation of harmonic vibrational frequencies for the global minima of the dimer, trimer, tetramer, and pentamer as well as the ring, book, cage, and prism isomers of the hexamer. Prior calibration [J. Chem. Phys. 2013, 139, 184113 and J. Chem. Theory Comput. 2014, 10, 5426] suggests that harmonic frequencies computed with this approach will lie within a few cm(-1) of the canonical CCSD(T) CBS limit. These data are used as reference values to gauge the performance of harmonic frequencies obtained with other ab initio methods (e.g., LCCSD(T) and MP2) and water potentials (e.g., TTM3-F and WHBB). This comparison reveals that it is far more challenging to converge harmonic vibrational frequencies for the bound OH stretching modes in these (H2O)n clusters to the CCSD(T) CBS limit than the free OH stretches, the n intramonomer HOH bending modes and even the 6n - 6 intermonomer modes. Deviations associated with the bound OH stretching harmonic frequencies increase rapidly with the size of the cluster for all methods and potentials examined, as do the corresponding frequency shifts relative to the monomer OH stretches.

  7. Partial spectral projected gradient method with active-set strategy for linearly constrained optimization

    NASA Astrophysics Data System (ADS)

    Andretta, Marina; Birgin, Ernesto; Martínez, J.

    2010-01-01

    A method for linearly constrained optimization which modifies and generalizes recent box-constraint optimization algorithms is introduced. The new algorithm is based on a relaxed form of Spectral Projected Gradient iterations. Intercalated with these projected steps, internal iterations restricted to faces of the polytope are performed, which enhance the efficiency of the algorithm. Convergence proofs are given and numerical experiments are included and commented. Software supporting this paper is available through the Tango Project web page: http://www.ime.usp.br/˜egbirgin/tango/.

  8. Bayesian Models of Cognition Revisited: Setting Optimality Aside and Letting Data Drive Psychological Theory.

    PubMed

    Tauber, Sean; Navarro, Daniel J; Perfors, Amy; Steyvers, Mark

    2017-03-30

    Recent debates in the psychological literature have raised questions about the assumptions that underpin Bayesian models of cognition and what inferences they license about human cognition. In this paper we revisit this topic, arguing that there are 2 qualitatively different ways in which a Bayesian model could be constructed. The most common approach uses a Bayesian model as a normative standard upon which to license a claim about optimality. In the alternative approach, a descriptive Bayesian model need not correspond to any claim that the underlying cognition is optimal or rational, and is used solely as a tool for instantiating a substantive psychological theory. We present 3 case studies in which these 2 perspectives lead to different computational models and license different conclusions about human cognition. We demonstrate how the descriptive Bayesian approach can be used to answer different sorts of questions than the optimal approach, especially when combined with principled tools for model evaluation and model selection. More generally we argue for the importance of making a clear distinction between the 2 perspectives. Considerable confusion results when descriptive models and optimal models are conflated, and if Bayesians are to avoid contributing to this confusion it is important to avoid making normative claims when none are intended. (PsycINFO Database Record

  9. Fast-Solving Quasi-Optimal LS-S$³$VM Based on an Extended Candidate Set.

    PubMed

    Ma, Yuefeng; Liang, Xun; Kwok, James T; Li, Jianping; Zhou, Xiaoping; Zhang, Haiyan

    2017-02-14

    The semisupervised least squares support vector machine (LS-S³VM) is an important enhancement of least squares support vector machines in semisupervised learning. Given that most data collected from the real world are without labels, semisupervised approaches are more applicable than standard supervised approaches. Although a few training methods for LS-S³VM exist, the problem of deriving the optimal decision hyperplane efficiently and effectually has not been solved. In this paper, a fully weighted model of LS-S³VM is proposed, and a simple integer programming (IP) model is introduced through an equivalent transformation to solve the model. Based on the distances between the unlabeled data and the decision hyperplane, a new indicator is designed to represent the possibility that the label of an unlabeled datum should be reversed in each iteration during training. Using the indicator, we construct an extended candidate set consisting of the indices of unlabeled data with high possibilities, which integrates more information from unlabeled data. Our algorithm is degenerated into a special scenario of the previous algorithm when the extended candidate set is reduced into a set with only one element. Two strategies are utilized to determine the descent directions based on the extended candidate set. Furthermore, we developed a novel method for locating a good starting point based on the properties of the equivalent IP model. Combined with the extended candidate set and the carefully computed starting point, a fast algorithm to solve LS-S³VM quasi-optimally is proposed. The choice of quasi-optimal solutions results in low computational cost and avoidance of overfitting. Experiments show that our algorithm equipped with the two designed strategies is more effective than other algorithms in at least one of the following three aspects: 1) computational complexity; 2) generalization ability; and 3) flexibility. However, our algorithm and other algorithms have similar

  10. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    PubMed

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-07

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  11. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

    PubMed Central

    Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

    2008-01-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner , J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT’s inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G*, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal∕mol [obtained with B3LYP∕6-311++G(3df,3pd)] to 0.8 kcal∕mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies. PMID:19063542

  12. Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior.

    PubMed

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

  13. New basis set superposition error free ab initio MO-VB interaction potential: Molecular-dynamics simulation of water at critical and supercritical conditions

    NASA Astrophysics Data System (ADS)

    Famulari, Antonino; Specchio, Roberto; Sironi, Maurizio; Raimondi, Mario

    1998-02-01

    Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site-site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed by nonorthogonal CI (configuration interaction) calculations was used to determine a new water-water interaction potential, which is BSSE (basis set superposition error) free in an a priori fashion. Extensive calculations were performed on water dimer and trimer and a new parametrization of a NCC-like (Niesar-Corongiu-Clementi) potential was accomplished. This was employed in the molecular-dynamics simulation of water. The effect of temperature and density variations was examined. Acceptable agreement between site-site correlation functions derived from neutron diffraction data and from computer simulation was reached. In particular, a weakening of the hydrogen bonded structure was observed on approaching the critical point, which reproduces the experimental behavior. The simulations were performed using the MOTECC (modern techniques in computational chemistry) suite of programs. The present results show the importance of BSSE-free nonorthogonal orbitals in an accurate description of the intermolecular potential of water.

  14. Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions

    NASA Astrophysics Data System (ADS)

    Lee, Hee-Seung; Tuckerman, Mark E.

    2008-12-01

    An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N4/3)] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N2 and a water dimer.

  15. Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions.

    PubMed

    Lee, Hee-Seung; Tuckerman, Mark E

    2008-12-14

    An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer.

  16. Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

    SciTech Connect

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.; Vargas, Rubicelia; Garza, Jorge

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

  17. The evaluation of bond dissociation energies for NO2 scission in nitro compounds using density functional and complete basis set methods

    NASA Astrophysics Data System (ADS)

    Shao, Ju-Xiang; Cheng, Xin-Lu; Yang, Xiang-Dong; He, Bi

    2006-02-01

    By using the density functional theory (B3LYP) and four highly accurate complete basis set (CBS-Q, CBS-QB3, CBS-Lq and CBS-4M) ab initio methods, the X(C, N, O)-NO2 bond dissociation energies (BDEs) for CH3NO2, C2H3NO2, C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 (CH3)2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy (BDE); however, all four CBS models are generally able to give reliable predication of the X(C, N, O)-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered. Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.

  18. Optimal Assembly of Tests with Item Sets. Research Report 98-12.

    ERIC Educational Resources Information Center

    van der Linden, Wim J.

    Six methods for assembling tests from a pool with an item-set structure are presented. All methods are computational and based on the technique of mixed integer programming. The methods are evaluated using such criteria as the feasibility of their linear programming problems and their expected solution times. The methods are illustrated for two…

  19. Creative Self-Efficacy and Innovative Behavior in a Service Setting: Optimism as a Moderator

    ERIC Educational Resources Information Center

    Hsu, Michael L. A.; Hou, Sheng-Tsung; Fan, Hsueh-Liang

    2011-01-01

    Creativity research on the personality approach has focused on the relationship between individual attributes and innovative behavior. However, few studies have empirically examined the effects of positive psychological traits on innovative behavior in an organizational setting. This study examines the relationships among creative self-efficacy,…

  20. REGRESSION APPROXIMATIONS FOR TRANSPORT MODEL CONSTRAINT SETS IN COMBINED AQUIFER SIMULATION-OPTIMIZATION STUDIES.

    USGS Publications Warehouse

    Alley, William M.

    1986-01-01

    Problems involving the combined use of contaminant transport models and nonlinear optimization schemes can be very expensive to solve. This paper explores the use of transport models with ordinary regression and regression on ranks to develop approximate response functions of concentrations at critical locations as a function of pumping and recharge at decision wells. These response functions combined with other constraints can often be solved very easily and may suggest reasonable starting points for combined simulation-management modeling or even relatively efficient operating schemes in themselves.

  1. Data set of optimal parameters for colorimetric red assay of epoxide hydrolase activity.

    PubMed

    de Oliveira, Gabriel Stephani; Adriani, Patricia Pereira; Borges, Flavia Garcia; Lopes, Adriana Rios; Campana, Patricia T; Chambergo, Felipe S

    2016-09-01

    The data presented in this article are related to the research article entitled "Epoxide hydrolase of Trichoderma reesei: Biochemical properties and conformational characterization" [1]. Epoxide hydrolases (EHs) are enzymes that catalyze the hydrolysis of epoxides to the corresponding vicinal diols. This article describes the optimal parameters for the colorimetric red assay to determine the enzymatic activity, with an emphasis on the characterization of the kinetic parameters, pH optimum and thermal stability of this enzyme. The effects of reagents that are not resistant to oxidation by sodium periodate on the reactions can generate false positives and interfere with the final results of the red assay.

  2. Integrated platform for optimized solar PV system design and engineering plan set generation

    SciTech Connect

    Adeyemo, Samuel

    2015-12-30

    The Aurora team has developed software that allows users to quickly generate a three-dimensional model for a building, with a corresponding irradiance map, from any two-dimensional image with associated geo-coordinates. The purpose of this project is to build upon that technology by developing and distributing to solar installers a software platform that automatically retrieves engineering, financial and geographic data for a specific site, and quickly generates an optimal customer proposal and corresponding engineering plans for that site. At the end of the project, Aurora’s optimization platform would have been used to make at least one thousand proposals from at least ten unique solar installation companies, two of whom would sign economically viable contracts to use the software. Furthermore, Aurora’s algorithms would be tested to show that in at least seventy percent of cases, Aurora automatically generated a design equivalent to or better than what a human could have done manually. A ‘better’ design is one that generates more energy for the same cost, or that generates a higher return on investment, while complying with all site-specific aesthetic, electrical and spatial requirements.

  3. Optimizing undergraduate nursing education: demystifying care of older adults in the home setting.

    PubMed

    Neal-Boylan, Leslie

    2006-01-01

    It is a challenge to provide experiences for nursing students that allow them to experience a professional relationship with older adults in the home setting. Home health agencies are under pressure related to productivity demands and may not provide preceptored experiences for students. Nursing students may not know any older adults outside of the institutional setting and consequently may have many misconceptions about what is and is not normal aging. This article describes an undergraduate nursing class and the out-of-classroom assignments that increased student understanding of nursing practice in the home, the effects of the home environment on the care of older adults, and the experiences of older adults living in the community. This article has relevance to nurses because it is important that we participate in creative methods of teaching students to value older adults and how to care for them in the community.

  4. Stochastic Set-Based Particle Swarm Optimization Based on Local Exploration for Solving the Carpool Service Problem.

    PubMed

    Chou, Sheng-Kai; Jiau, Ming-Kai; Huang, Shih-Chia

    2016-08-01

    The growing ubiquity of vehicles has led to increased concerns about environmental issues. These concerns can be mitigated by implementing an effective carpool service. In an intelligent carpool system, an automated service process assists carpool participants in determining routes and matches. It is a discrete optimization problem that involves a system-wide condition as well as participants' expectations. In this paper, we solve the carpool service problem (CSP) to provide satisfactory ride matches. To this end, we developed a particle swarm carpool algorithm based on stochastic set-based particle swarm optimization (PSO). Our method introduces stochastic coding to augment traditional particles, and uses three terminologies to represent a particle: 1) particle position; 2) particle view; and 3) particle velocity. In this way, the set-based PSO (S-PSO) can be realized by local exploration. In the simulation and experiments, two kind of discrete PSOs-S-PSO and binary PSO (BPSO)-and a genetic algorithm (GA) are compared and examined using tested benchmarks that simulate a real-world metropolis. We observed that the S-PSO outperformed the BPSO and the GA thoroughly. Moreover, our method yielded the best result in a statistical test and successfully obtained numerical results for meeting the optimization objectives of the CSP.

  5. Optimal design for sustainable development of a material recovery facility in a fast-growing urban setting.

    PubMed

    Chang, Ni-Bin; Davila, Eric; Dyson, Brian; Brown, Ron

    2005-01-01

    Installing material recovery facilities (MRFs) in a solid waste management system could be a feasible alternative to achieve sustainable development goals in urban areas if current household and curbside recycling cannot prove successful in the long run. This paper addresses the optimal site selection and capacity planning for a MRF in conjunction with an optimal shipping strategy of solid waste streams in a multi-district urban region. Screening of material recovery and disposal capacity alternatives can be achieved in terms of economic feasibility, technology limitation, recycling potential, and site availability. The optimization objectives include economic impacts characterized by recycling income and cost components for waste management, while the constraint set consists of mass balance, capacity limitation, recycling limitation, scale economy, conditionality, and relevant screening constraints. A case study for the City of San Antonio, Texas (USA) presents a vivid example where scenario planning demonstrates the robustness and flexibility of this modeling analysis. It proves especially useful when determining MRF ownership structure. Each scenario experiences two case settings: (1) two MRF sites are proposed for selection and (2) a single MRF site is sought. Cost analysis confirms processing fees are not the driving force in the City's operation, but rather shipping cost. Sensitivity analysis solidifies the notion that significant public participation plays the most important role in minimizing solid waste management expenses.

  6. Optimal mix of renewable power generation in the MENA region as a basis for an efficient electricity supply to europe

    NASA Astrophysics Data System (ADS)

    Alhamwi, Alaa; Kleinhans, David; Weitemeyer, Stefan; Vogt, Thomas

    2014-12-01

    Renewable Energy sources are gaining importance in the Middle East and North Africa (MENA) region. The purpose of this study is to quantify the optimal mix of renewable power generation in the MENA region, taking Morocco as a case study. Based on hourly meteorological data and load data, a 100% solar-plus-wind only scenario for Morocco is investigated. For the optimal mix analyses, a mismatch energy modelling approach is adopted with the objective to minimise the required storage capacities. For a hypothetical Moroccan energy supply system which is entirely based on renewable energy sources, our results show that the minimum storage capacity is achieved at a share of 63% solar and 37% wind power generations.

  7. Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: a path for the optimization of low-energy many-body basis expansions

    SciTech Connect

    Kim, Jeongnim; Reboredo, Fernando A

    2014-01-01

    The self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo J. Chem. Phys. {\\bf 136}, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys. {\\bf 89}, 6316 (1988)] are blended to obtain a method for the calculation of thermodynamic properties of many-body systems at low temperatures. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric trial wave functions. A statistical method is derived for the calculation of finite temperature properties of many-body systems near the ground state. In the process we also obtain a parallel algorithm that optimizes the many-body basis of a small subspace of the many-body Hilbert space. This small subspace is optimized to have maximum overlap with the one expanded by the lower energy eigenstates of a many-body Hamiltonian. We show in a model system that the Helmholtz free energy is minimized within this subspace as the iteration number increases. We show that the subspace expanded by the small basis systematically converges towards the subspace expanded by the lowest energy eigenstates. Possible applications of this method to calculate the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can be also used to accelerate the calculation of the ground or excited states with Quantum Monte Carlo.

  8. Recommendations for optimal distraction protocols for various animal models on the basis of a systematic review of the literature.

    PubMed

    Djasim, U M; Wolvius, E B; van Neck, J W; Weinans, H; van der Wal, K G H

    2007-10-01

    The principles of orthopaedic distraction osteogenesis (DO) have been successfully applied to the craniofacial skeleton, but the latency time, rate and rhythm of distraction, and length of the consolidation period that are optimal for long-bone distraction may be suboptimal for craniofacial DO. The aim of this study was to provide recommendations for optimal distraction parameters in animal experimental research on craniofacial DO. The data used were from studies, added to the PubMed database between 1 January 1973 and 1 January 2007, on the outcome of DO resulting from variations in a single distraction parameter while standardizing the other distraction parameters. Although experimental animal group sizes were rather small, especially in those studies that used large animals, and both skeletally mature and immature animals were used, the (in most cases quantitative) data provided useful information on the optimal parameters in craniofacial DO. A latency period may not be necessary at all. Distraction should be performed at a rate of 1mm/day (this may be halved when small animals such as rats are used) preferably with a continuous rhythm, followed by a consolidation period of 6-8 weeks. These recommendations can be used as basic guidelines for further animal experimental studies on craniofacial DO.

  9. Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets

    PubMed Central

    Xiao, Xun; Geyer, Veikko F.; Bowne-Anderson, Hugo; Howard, Jonathon; Sbalzarini, Ivo F.

    2016-01-01

    Biological filaments, such as actin filaments, microtubules, and cilia, are often imaged using different light-microscopy techniques. Reconstructing the filament curve from the acquired images constitutes the filament segmentation problem. Since filaments have lower dimensionality than the image itself, there is an inherent trade-off between tracing the filament with sub-pixel accuracy and avoiding noise artifacts. Here, we present a globally optimal filament segmentation method based on B-spline vector level-sets and a generalized linear model for the pixel intensity statistics. We show that the resulting optimization problem is convex and can hence be solved with global optimality. We introduce a simple and efficient algorithm to compute such optimal filament segmentations, and provide an open-source implementation as an ImageJ/Fiji plugin. We further derive an information-theoretic lower bound on the filament segmentation error, quantifying how well an algorithm could possibly do given the information in the image. We show that our algorithm asymptotically reaches this bound in the spline coefficients. We validate our method in comprehensive benchmarks, compare with other methods, and show applications from fluorescence, phase-contrast, and dark-field microscopy. PMID:27104582

  10. Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets.

    PubMed

    Xiao, Xun; Geyer, Veikko F; Bowne-Anderson, Hugo; Howard, Jonathon; Sbalzarini, Ivo F

    2016-08-01

    Biological filaments, such as actin filaments, microtubules, and cilia, are often imaged using different light-microscopy techniques. Reconstructing the filament curve from the acquired images constitutes the filament segmentation problem. Since filaments have lower dimensionality than the image itself, there is an inherent trade-off between tracing the filament with sub-pixel accuracy and avoiding noise artifacts. Here, we present a globally optimal filament segmentation method based on B-spline vector level-sets and a generalized linear model for the pixel intensity statistics. We show that the resulting optimization problem is convex and can hence be solved with global optimality. We introduce a simple and efficient algorithm to compute such optimal filament segmentations, and provide an open-source implementation as an ImageJ/Fiji plugin. We further derive an information-theoretic lower bound on the filament segmentation error, quantifying how well an algorithm could possibly do given the information in the image. We show that our algorithm asymptotically reaches this bound in the spline coefficients. We validate our method in comprehensive benchmarks, compare with other methods, and show applications from fluorescence, phase-contrast, and dark-field microscopy.

  11. Evaluation of the Volatility Basis-Set Approach for Modeling Primary and Secondary Organic Aerosol in the Mexico City Metropolitan Area

    NASA Astrophysics Data System (ADS)

    Tsimpidi, A. P.; Karydis, V. A.; Pandis, S. N.; Zavala, M.; Lei, W.; Molina, L. T.

    2007-12-01

    Anthropogenic air pollution is an increasingly serious problem for public health, agriculture, and global climate. Organic material (OM) contributes ~ 20-50% to the total fine aerosol mass at continental mid-latitudes. Although OM accounts for a large fraction of PM2.5 concentration worldwide, the contributions of primary and secondary organic aerosol have been difficult to quantify. In this study, new primary and secondary organic aerosol modules were added to PMCAMx, a three dimensional chemical transport model (Gaydos et al., 2007), for use with the SAPRC99 chemistry mechanism (Carter, 2000; ENVIRON, 2006) based on recent smog chamber studies (Robinson et al., 2007). The new modeling framework is based on the volatility basis-set approach (Lane et al., 2007): both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The emission inventory, which uses as starting point the MCMA 2004 official inventory (CAM, 2006), is modified and the primary organic aerosol (POA) emissions are distributed by volatility based on dilution experiments (Robinson et al., 2007). Sensitivity tests where POA is considered as nonvolatile and POA and SOA as chemically reactive are also described. In all cases PMCAMx is applied in the Mexico City Metropolitan Area during March 2006. The modeling domain covers a 180x180x6 km region in the MCMA with 3x3 km grid resolution. The model predictions are compared with Aerodyne's Aerosol Mass Spectrometry (AMS) observations from the MILAGRO Campaign. References Robinson, A. L.; Donahue, N. M.; Shrivastava, M. K.; Weitkamp, E. A.; Sage, A. M.; Grieshop, A. P.; Lane, T. E.; Pandis, S. N.; Pierce, J. R., 2007. Rethinking organic aerosols: semivolatile emissions and photochemical aging. Science 315, 1259-1262. Gaydos, T. M.; Pinder, R. W.; Koo, B.; Fahey, K. M.; Pandis, S. N., 2007. Development and application of a three- dimensional aerosol

  12. Setting the optimal erythrocyte protoporphyrin screening decision threshold for lead poisoning: a decision analytic approach

    SciTech Connect

    DeBaun, M.R.; Sox, H.C. Jr. )

    1991-07-01

    Erythrocyte protoporphyrin (EP) was introduced in the 1970s as an inexpensive screening test for lead poisoning. As greater knowledge of lead poisoning has accumulated, the recommended EP level at which further evaluation for lead poisoning should be initiated has been lowered from greater than or equal to 50 micrograms/dL to greater than or equal to 35 micrograms/dL. The purpose of this study was to evaluate the utility of this EP threshold. A receiver operator characteristic curve was constructed to assess the relationship between the true-positive rate and false-positive rate of EP at various decision thresholds. The receiver operator characteristic curve was constructed with data from the second National Health and Nutrition Examination Survey from 1976 to 1980, which included 2673 children 6 years of age or younger who had both blood lead and EP level determinations. Decision analysis was then used to determine the optimal EP decision threshold for detecting a blood lead level greater than or equal to 25 micrograms/dL. The receiver operator characteristic curve demonstrated that EP is a poor predictor of a blood lead level greater than or equal to 25 micrograms/dL. At the currently recommended EP decision threshold of 35 micrograms/dL, the true-positive rates and false-positive rates of EP are 0.23 and 0.04, respectively. As a result of the inadequate performance of EP screening for lead poisoning, when the prevalence of lead poisoning is greater than 8%, there is no EP decision threshold that optimizes the relationship between the cost of screening normal children and the benefit of detecting lead-poisoned children. Erythrocyte protoporphyrin measurement is not sufficiently sensitive to be recommended uniformly as a screening test for lead poisoning.

  13. Estimating the importance of multi-phase processing on secondary organic aerosol based on a functional-group resolving volatility basis set approach

    NASA Astrophysics Data System (ADS)

    Knote, C. J.; Hodzic, A.; Aumont, B.; Madronich, S.

    2014-12-01

    Traditional understanding views secondary organic aerosol (SOA) formation in the atmosphere as continuous gas-phase oxidation of precursors such as isoprene, aromatics or alkanes. Recent research found that these oxidation products are also highly water soluble. It is further understood that the liquid-phase of cloud droplets as well as deliquesced particles could mediate SOA formation through chemistry in the aqueous-phase. While the effect of multi-phase processing has been studied in detailed for specific compounds like glyoxal or methylglyoxal, an integrated approach that considers the large number of individual compounds has been missing due to the complexity involved. In our work we explore the effects of multi-phase processing on secondary organic aerosol from an explicit modeling perspective.Volatility and solubility determine in which phase a given molecule will be found under given atmospheric conditions. Volatility has already been used to simplify the description of SOA formation in the gas-phase in what became known as the Volatility Basis Set approach (VBS). Compounds contributing to SOA formation are grouped by volatility and then treated as a whole. A number of studies extended the VBS by adding a second dimension like oxygen to carbon ratio or the mean oxidation state. In our work we use functional groups as second dimension.Using explicit oxidation chemistry modeling (GECKO-A) we derive SOA yields as well as their composition in terms of functional groups for commonly used precursors. We then investigate the effect of simply partitioning functional-group specific organic mass into cloud droplets and deliquesced aerosol based on their estimated solubility. Finally we apply simple chemistry in the aqueous-phase and relate changes in functional groups to changes in volatility and subsequent changes in partitioning between gas- and aerosol-phase.In our presentation we will explore the sensitivites of the multi-phase system in a box model setting with

  14. Optimization of Compressor Vane and Bleed Settings. User’s Manual - Customer Computer Deck 1182-0.0.

    DTIC Science & Technology

    1981-06-01

    TO 14.00 DZC-?EES _________ SET VtNE 3 TO 11.00 OEC’IEES __SET VNlE 4 TO _7.00 0EC-EES_ HOLD PFiC CONSTANT AT A VALUE OF 5567.500 HS!t9 CL CZ’,:STAJT...U) JUN G1 J E GARBEROGLIO, J 0 SONG F33615 79-C 2013 UNCLASSIFIED PWA-FR 3 96 AFWAL-TR-82-207 NL hhhEhEhE moEmoEohhohhEI ArgM-a227 NOTICE When...Deck CCD 1182). The programn includles the capacity of handling four variable vanes and 3 one blssd The basi goal-sekitg algorithm a the COPH8IVONWIN

  15. A Combined Kinetic and Volatility Basis Set Approach to Model Secondary Organic Aerosol from Toluene and Diesel Exhaust/Meat Cooking Mixtures

    NASA Astrophysics Data System (ADS)

    Parikh, H. M.; Carlton, A. G.; Zhang, H.; Kamens, R.; Vizuete, W.

    2011-12-01

    Secondary organic aerosol (SOA) is simulated for 6 outdoor smog chamber experiments using a SOA model based on a kinetic chemical mechanism in conjunction with a volatility basis set (VBS) approach. The experiments include toluene, a non-SOA-forming hydrocarbon mixture, diesel exhaust or meat cooking emissions and NOx, and are performed under varying conditions of relative humidity. SOA formation from toluene is modeled using a condensed kinetic aromatic mechanism that includes partitioning of lumped semi-volatile products in particle organic-phase and incorporates particle aqueous-phase chemistry to describe uptake of glyoxal and methylglyoxal. Modeling using the kinetic mechanism alone, along with primary organic aerosol (POA) from diesel exhaust (DE) /meat cooking (MC) fails to simulate the rapid SOA formation at the beginning hours of the experiments. Inclusion of a VBS approach with the kinetic mechanism to characterize the emissions and chemistry of complex mixture of intermediate volatility organic compounds (IVOCs) from DE/MC, substantially improves SOA predictions when compared with observed data. The VBS model includes photochemical aging of IVOCs and evaporation of POA after dilution. The relative contribution of SOA mass from DE/MC is as high as 95% in the morning, but substantially decreases after mid-afternoon. For high humidity experiments, aqueous-phase SOA fraction dominates the total SOA mass at the end of the day (approximately 50%). In summary, the combined kinetic and VBS approach provides a new and improved framework to semi-explicitly model SOA from VOC precursors in conjunction with a VBS approach that can be used on complex emission mixtures comprised with hundreds of individual chemical species.

  16. Volatility basis-set approach simulation of organic aerosol formation in East Asia: implications for anthropogenic-biogenic interaction and controllable amounts

    SciTech Connect

    Matsui, H.; Koike, Makoto; Kondo, Yutaka; Takami, A.; Fast, Jerome D.; Kanaya, Y.; Takigawa, M.

    2014-09-16

    Organic aerosol (OA) simulations using the volatility basis-set approach were made for East Asia and its outflow region. Model simulations were evaluated through comparisons with OA measured by aerosol mass spectrometers in and around Tokyo (at Komaba and Kisai in summer 2003 and 2004) and over the outflow region in East Asia (at Fukue and Hedo in spring 2009). The simulations with aging processes of organic vapors reasonably well reproduced mass concentrations, temporal variations, and formation efficiency of observed OA at all sites. As OA mass was severely underestimated in the simulations without the aging processes, the oxidations of organic vapors are essential for reasonable OA simulations over East Asia. By considering the aging processes, simulated OA concentrations considerably increased from 0.24 to 1.28 µg m-3 in the boundary layer over the whole of East Asia. OA formed from the interaction of anthropogenic and biogenic sources was also enhanced by the aging processes. The fraction of controllable OA was estimated to be 87 % of total OA over the whole of East Asia, showing that most of the OA in our simulations formed anthropogenically (controllable). A large portion of biogenic secondary OA (78 % of biogenic secondary OA) formed through the influence of anthropogenic sources. The high fraction of controllable OA in our simulations is likely because anthropogenic emissions are dominant over East Asia and OA formation is enhanced by anthropogenic sources and their aging processes. Both the amounts (from 0.18 to 1.12 µg m-3) and the fraction (from 75 % to 87 %) of controllable OA were increased by aging processes of organic vapors over East Asia.

  17. A simple and efficient dispersion correction to the Hartree-Fock theory (2): Incorporation of a geometrical correction for the basis set superposition error.

    PubMed

    Yoshida, Tatsusada; Hayashi, Takahisa; Mashima, Akira; Chuman, Hiroshi

    2015-10-01

    One of the most challenging problems in computer-aided drug discovery is the accurate prediction of the binding energy between a ligand and a protein. For accurate estimation of net binding energy ΔEbind in the framework of the Hartree-Fock (HF) theory, it is necessary to estimate two additional energy terms; the dispersion interaction energy (Edisp) and the basis set superposition error (BSSE). We previously reported a simple and efficient dispersion correction, Edisp, to the Hartree-Fock theory (HF-Dtq). In the present study, an approximation procedure for estimating BSSE proposed by Kruse and Grimme, a geometrical counterpoise correction (gCP), was incorporated into HF-Dtq (HF-Dtq-gCP). The relative weights of the Edisp (Dtq) and BSSE (gCP) terms were determined to reproduce ΔEbind calculated with CCSD(T)/CBS or /aug-cc-pVTZ (HF-Dtq-gCP (scaled)). The performance of HF-Dtq-gCP (scaled) was compared with that of B3LYP-D3(BJ)-bCP (dispersion corrected B3LYP with the Boys and Bernadi counterpoise correction (bCP)), by taking ΔEbind (CCSD(T)-bCP) of small non-covalent complexes as 'a golden standard'. As a critical test, HF-Dtq-gCP (scaled)/6-31G(d) and B3LYP-D3(BJ)-bCP/6-31G(d) were applied to the complex model for HIV-1 protease and its potent inhibitor, KNI-10033. The present results demonstrate that HF-Dtq-gCP (scaled) is a useful and powerful remedy for accurately and promptly predicting ΔEbind between a ligand and a protein, albeit it is a simple correction procedure.

  18. An optimized gene set for transcriptomics based neurodevelopmental toxicity prediction in the neural embryonic stem cell test.

    PubMed

    Pennings, Jeroen L A; Theunissen, Peter T; Piersma, Aldert H

    2012-10-28

    The murine neural embryonic stem cell test (ESTn) is an in vitro model for neurodevelopmental toxicity testing. Recent studies have shown that application of transcriptomics analyses in the ESTn is useful for obtaining more accurate predictions as well as mechanistic insights. Gene expression responses due to stem cell neural differentiation versus toxicant exposure could be distinguished using the Principal Component Analysis based differentiation track algorithm. In this study, we performed a de novo analysis on combined raw data (10 compounds, 19 exposures) from three previous transcriptomics studies to identify an optimized gene set for neurodevelopmental toxicity prediction in the ESTn. By evaluating predictions of 200,000 randomly selected gene sets, we identified genes which significantly contributed to the prediction reliability. A set of 100 genes was obtained, predominantly involved in (neural) development. Further stringency restrictions resulted in a set of 29 genes that allowed for 84% prediction accuracy (area under the curve 94%). We anticipate these gene sets will contribute to further improve ESTn transcriptomics studies aimed at compound risk assessment.

  19. Side scan sonar image segmentation based on neutrosophic set and quantum-behaved particle swarm optimization algorithm

    NASA Astrophysics Data System (ADS)

    Zhao, Jianhu; Wang, Xiao; Zhang, Hongmei; Hu, Jun; Jian, Xiaomin

    2016-09-01

    To fulfill side scan sonar (SSS) image segmentation accurately and efficiently, a novel segmentation algorithm based on neutrosophic set (NS) and quantum-behaved particle swarm optimization (QPSO) is proposed in this paper. Firstly, the neutrosophic subset images are obtained by transforming the input image into the NS domain. Then, a co-occurrence matrix is accurately constructed based on these subset images, and the entropy of the gray level image is described to serve as the fitness function of the QPSO algorithm. Moreover, the optimal two-dimensional segmentation threshold vector is quickly obtained by QPSO. Finally, the contours of the interested target are segmented with the threshold vector and extracted by the mathematic morphology operation. To further improve the segmentation efficiency, the single threshold segmentation, an alternative algorithm, is recommended for the shadow segmentation by considering the gray level characteristics of the shadow. The accuracy and efficiency of the proposed algorithm are assessed with experiments of SSS image segmentation.

  20. Decision Optimization of Machine Sets Taking Into Consideration Logical Tree Minimization of Design Guidelines

    NASA Astrophysics Data System (ADS)

    Deptuła, A.; Partyka, M. A.

    2014-08-01

    The method of minimization of complex partial multi-valued logical functions determines the degree of importance of construction and exploitation parameters playing the role of logical decision variables. Logical functions are taken into consideration in the issues of modelling machine sets. In multi-valued logical functions with weighting products, it is possible to use a modified Quine - McCluskey algorithm of multi-valued functions minimization. Taking into account weighting coefficients in the logical tree minimization reflects a physical model of the object being analysed much better

  1. Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography.

    PubMed

    Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L; Armour, Wes; Waterman, David G; Iwata, So; Evans, Gwyndaf

    2013-08-01

    The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

  2. Architecture-Driven Level Set Optimization: From Clustering to Subpixel Image Segmentation.

    PubMed

    Balla-Arabe, Souleymane; Gao, Xinbo; Ginhac, Dominique; Brost, Vincent; Yang, Fan

    2016-12-01

    Thanks to their effectiveness, active contour models (ACMs) are of great interest for computer vision scientists. The level set methods (LSMs) refer to the class of geometric active contours. Comparing with the other ACMs, in addition to subpixel accuracy, it has the intrinsic ability to automatically handle topological changes. Nevertheless, the LSMs are computationally expensive. A solution for their time consumption problem can be hardware acceleration using some massively parallel devices such as graphics processing units (GPUs). But the question is: which accuracy can we reach while still maintaining an adequate algorithm to massively parallel architecture? In this paper, we attempt to push back the compromise between, speed and accuracy, efficiency and effectiveness, to a higher level, comparing with state-of-the-art methods. To this end, we designed a novel architecture-aware hybrid central processing unit (CPU)-GPU LSM for image segmentation. The initialization step, using the well-known k -means algorithm, is fast although executed on a CPU, while the evolution equation of the active contour is inherently local and therefore suitable for GPU-based acceleration. The incorporation of local statistics in the level set evolution allowed our model to detect new boundaries which are not extracted by the used clustering algorithm. Comparing with some cutting-edge LSMs, the introduced model is faster, more accurate, less subject to giving local minima, and therefore suitable for automatic systems. Furthermore, it allows two-phase clustering algorithms to benefit from the numerous LSM advantages such as the ability to achieve robust and subpixel accurate segmentation results with smooth and closed contours. Intensive experiments demonstrate, objectively and subjectively, the good performance of the introduced framework both in terms of speed and accuracy.

  3. Making use of optimization, nondeterministic analysis, and numerical simulation to assess firing set robustness in a fire

    SciTech Connect

    Romero, V.J.

    1996-08-01

    One emphasis of weapon surety (safety and security) at Sandia National Laboratories is the assessment of fire-related risk to weapon systems. New developments in computing hardware and software make possible the application of a new generation of very powerful analysis tools for surety assessment. This paper illustrates the application of some of these computational tools to assess the robustness of a conceptual firing set design in severe thermal environments. With these assessment tools, systematic interrogation of the parameter space governing the thermal robustness of the firing set has revealed much greater vulnerability than traditional ad hoc techniques had indicated. These newer techniques should be routinely applied in weapon design and assessment to produce more fully characterized and robust systems where weapon surety is paramount. As well as helping expose and quantify vulnerabilities in systems, these tools can be used in design and resource allocation processes to build safer, more reliable, more optimal systems.

  4. Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

    PubMed

    May, Damon H; Tamura, Kaipo; Noble, William S

    2017-03-13

    In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidates considered for each spectrum. Fragment mass tolerance or bin size determines how close observed and theoretical fragments must be to be considered a match. For either of these two parameters, too wide a setting yields randomly high-scoring false PSMs, whereas too narrow a setting erroneously excludes true PSMs, in both cases, lowering the yield of peptides detected at a given false discovery rate. We describe a strategy for inferring optimal search parameters by assembling and analyzing pairs of spectra that are likely to have been generated by the same peptide ion to infer precursor and fragment mass error. This strategy does not rely on a database search, making it usable in a wide variety of settings. In our experiments on data from a variety of instruments including Orbitrap and Q-TOF acquisitions, this strategy yields more high-confidence PSMs than using settings based on instrument defaults or determined by experts. Param-Medic is open-source and cross-platform. It is available as a standalone tool ( http://noble.gs.washington.edu/proj/param-medic/ ) and has been integrated into the Crux proteomics toolkit ( http://crux.ms ), providing automatic parameter selection for the Comet and Tide search engines.

  5. Myosin-II sets the optimal response time scale of chemotactic amoeba

    NASA Astrophysics Data System (ADS)

    Hsu, Hsin-Fang; Westendorf, Christian; Tarantola, Marco; Bodenschatz, Eberhard; Beta, Carsten

    2014-03-01

    The response dynamics of the actin cytoskeleton to external chemical stimuli plays a fundamental role in numerous cellular functions. One of the key players that governs the dynamics of the actin network is the motor protein myosin-II. Here we investigate the role of myosin-II in the response of the actin system to external stimuli. We used a microfluidic device in combination with a photoactivatable chemoattractant to apply stimuli to individual cells with high temporal resolution. We directly compare the actin dynamics in Dictyostelium discodelium wild type (WT) cells to a knockout mutant that is deficient in myosin-II (MNL). Similar to the WT a small population of MNL cells showed self-sustained oscillations even in absence of external stimuli. The actin response of MNL cells to a short pulse of chemoattractant resembles WT during the first 15 sec but is significantly delayed afterward. The amplitude of the dominant peak in the power spectrum from the response time series of MNL cells to periodic stimuli with varying period showed a clear resonance peak at a forcing period of 36 sec, which is significantly delayed as compared to the resonance at 20 sec found for the WT. This shift indicates an important role of myosin-II in setting the response time scale of motile amoeba. Institute of Physics und Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.

  6. Optimization of a solid-state electron spin qubit using gate set tomography

    NASA Astrophysics Data System (ADS)

    Dehollain, Juan P.; Muhonen, Juha T.; Blume-Kohout, Robin; Rudinger, Kenneth M.; King Gamble, John; Nielsen, Erik; Laucht, Arne; Simmons, Stephanie; Kalra, Rachpon; Dzurak, Andrew S.; Morello, Andrea

    2016-10-01

    State of the art qubit systems are reaching the gate fidelities required for scalable quantum computation architectures. Further improvements in the fidelity of quantum gates demands characterization and benchmarking protocols that are efficient, reliable and extremely accurate. Ideally, a benchmarking protocol should also provide information on how to rectify residual errors. Gate set tomography (GST) is one such protocol designed to give detailed characterization of as-built qubits. We implemented GST on a high-fidelity electron-spin qubit confined by a single 31P atom in 28Si. The results reveal systematic errors that a randomized benchmarking analysis could measure but not identify, whereas GST indicated the need for improved calibration of the length of the control pulses. After introducing this modification, we measured a new benchmark average gate fidelity of 99.942(8) % , an improvement on the previous value of 99.90(2) % . Furthermore, GST revealed high levels of non-Markovian noise in the system, which will need to be understood and addressed when the qubit is used within a fault-tolerant quantum computation scheme.

  7. Optimal Geometrical Set for Automated Marker Placement to Virtualized Real-Time Facial Emotions.

    PubMed

    Maruthapillai, Vasanthan; Murugappan, Murugappan

    2016-01-01

    In recent years, real-time face recognition has been a major topic of interest in developing intelligent human-machine interaction systems. Over the past several decades, researchers have proposed different algorithms for facial expression recognition, but there has been little focus on detection in real-time scenarios. The present work proposes a new algorithmic method of automated marker placement used to classify six facial expressions: happiness, sadness, anger, fear, disgust, and surprise. Emotional facial expressions were captured using a webcam, while the proposed algorithm placed a set of eight virtual markers on each subject's face. Facial feature extraction methods, including marker distance (distance between each marker to the center of the face) and change in marker distance (change in distance between the original and new marker positions), were used to extract three statistical features (mean, variance, and root mean square) from the real-time video sequence. The initial position of each marker was subjected to the optical flow algorithm for marker tracking with each emotional facial expression. Finally, the extracted statistical features were mapped into corresponding emotional facial expressions using two simple non-linear classifiers, K-nearest neighbor and probabilistic neural network. The results indicate that the proposed automated marker placement algorithm effectively placed eight virtual markers on each subject's face and gave a maximum mean emotion classification rate of 96.94% using the probabilistic neural network.

  8. Optimization of multiplanar reformations from isotropic data sets acquired with 16-detector row helical CT scanner.

    PubMed

    Jaffe, Tracy A; Nelson, Rendon C; Johnson, G Allan; Lee, Ellie R; Yoshizumi, Terry T; Lowry, Carolyn R; Bullard, Anthony B; DeLong, David M; Paulson, Erik K

    2006-01-01

    Institutional review board approval and waiver of consent were obtained for the patient component of this retrospective HIPAA-compliant study. By using an anthropomorphic phantom and metal oxide semiconductor field effect transistor detectors, radiation dose was determined for one eight-detector row and two 16-detector row computed tomographic (CT) protocols. A custom phantom was scanned by using the three protocols to identify isotropy. Contrast-to-noise ratios (CNRs) were determined for the same protocols by using a third phantom. Seven patients had undergone isotropic 16-detector row CT of the abdomen and pelvis. Anonymized coronal reformations at various thicknesses were ranked qualitatively by three radiologists. Effective dose equivalents were similar for the eight- and 16-detector row protocols. When transverse and coronal reformations of data acquired in the custom phantom were compared, coronal reformations obtained with the 16-detector row and 0.625-mm section thickness protocol were found to be nearly identical to the transverse image for all sets of line pairs. CNRs were consistently highest on 5-mm-thick coronal reformations (CNR range, 1.2-3.3). For qualitative assessment, 2- and 3-mm-thick coronal reformations were consistently preferred.

  9. [Optimal rehabilitation of patients with coronary heart disease in outpatient setting].

    PubMed

    Korzhenkov, N P; Kuzichkina, S F; Shcherbakova, N A; Kukhaleishvili, N R; Iarlykov, I I

    2012-01-01

    The problem of invalid rehabilitation in Russia is an important state task and dictates necessity of design of an effective state program of primary prevention of cardiovascular diseases. Common global practice of medico-social model is based on complex detailed medico-social aid. Rehabilitation of postmyocardial infarction patients consists of three phases (stages): hospital posthospital (readaptation) and postreconvalescent (supportive). The program includes physical, psychological and pharmacological rehabilitation. Departments of readaptation and medico-social rehabilitation provide effective conduction of all kinds of rehabilitation. The Moscow North-East Regional Administration has a rich experience in organization of departments of readaptation and medico-social rehabilitation. The departments practice an individual approach to the patients and work in a close contact with bureaus of medico-social commission of experts. Management of patients by cardiologist, rehabilitation specialist and outpatient clinic's physicians provides uninterrupted staged rehabilitation, timely correction of pharmacotherapy, early patient referral to invasive investigations and treatment of coronary heart disease. A course of rehabilitative measures lasts 2 months. Setting up departments of medico-social rehabilitation in outpatient clinics provides more effective use of money assigned by the state for social support of invalids.

  10. Optimal Geometrical Set for Automated Marker Placement to Virtualized Real-Time Facial Emotions

    PubMed Central

    Maruthapillai, Vasanthan; Murugappan, Murugappan

    2016-01-01

    In recent years, real-time face recognition has been a major topic of interest in developing intelligent human-machine interaction systems. Over the past several decades, researchers have proposed different algorithms for facial expression recognition, but there has been little focus on detection in real-time scenarios. The present work proposes a new algorithmic method of automated marker placement used to classify six facial expressions: happiness, sadness, anger, fear, disgust, and surprise. Emotional facial expressions were captured using a webcam, while the proposed algorithm placed a set of eight virtual markers on each subject’s face. Facial feature extraction methods, including marker distance (distance between each marker to the center of the face) and change in marker distance (change in distance between the original and new marker positions), were used to extract three statistical features (mean, variance, and root mean square) from the real-time video sequence. The initial position of each marker was subjected to the optical flow algorithm for marker tracking with each emotional facial expression. Finally, the extracted statistical features were mapped into corresponding emotional facial expressions using two simple non-linear classifiers, K-nearest neighbor and probabilistic neural network. The results indicate that the proposed automated marker placement algorithm effectively placed eight virtual markers on each subject’s face and gave a maximum mean emotion classification rate of 96.94% using the probabilistic neural network. PMID:26859884

  11. Optimization of Physical Working Environment Setting to Improve Productivity and Minimize Error by Taguchi and VIKOR Methods

    NASA Astrophysics Data System (ADS)

    Ilma Rahmillah, Fety

    2016-01-01

    The working environment is one factor that has contribution to the worker's performance, especially for continuous and monotonous works. L9 Taguchi design experiment for inner array is used to design the experiment which was carried out in laboratory whereas L4 is for outer array. Four control variables with three levels of each are used to get the optimal combination of working environment setting. Four responses are also measured to know the effect of four control factors. Results shown that by using ANOVA, the effect of illumination, temperature, and instrumental music to the number of ouput, number of error, and rating perceived discomfort is significant with the total variance explained of 54,67%, 60,67%, and 75,22% respectively. By using VIKOR method, it yields the optimal combination of experiment 66 with the setting condition of A3-B2-C1-D3. The illumination is 325-350 lux, temperature is 240-260C, fast category of instrumental music, and 70-80 dB for intensity of the music being played.

  12. Optimal set of EEG features for emotional state classification and trajectory visualization in Parkinson's disease.

    PubMed

    Yuvaraj, R; Murugappan, M; Ibrahim, Norlinah Mohamed; Sundaraj, Kenneth; Omar, Mohd Iqbal; Mohamad, Khairiyah; Palaniappan, R

    2014-12-01

    In addition to classic motor signs and symptoms, individuals with Parkinson's disease (PD) are characterized by emotional deficits. Ongoing brain activity can be recorded by electroencephalograph (EEG) to discover the links between emotional states and brain activity. This study utilized machine-learning algorithms to categorize emotional states in PD patients compared with healthy controls (HC) using EEG. Twenty non-demented PD patients and 20 healthy age-, gender-, and education level-matched controls viewed happiness, sadness, fear, anger, surprise, and disgust emotional stimuli while fourteen-channel EEG was being recorded. Multimodal stimulus (combination of audio and visual) was used to evoke the emotions. To classify the EEG-based emotional states and visualize the changes of emotional states over time, this paper compares four kinds of EEG features for emotional state classification and proposes an approach to track the trajectory of emotion changes with manifold learning. From the experimental results using our EEG data set, we found that (a) bispectrum feature is superior to other three kinds of features, namely power spectrum, wavelet packet and nonlinear dynamical analysis; (b) higher frequency bands (alpha, beta and gamma) play a more important role in emotion activities than lower frequency bands (delta and theta) in both groups and; (c) the trajectory of emotion changes can be visualized by reducing subject-independent features with manifold learning. This provides a promising way of implementing visualization of patient's emotional state in real time and leads to a practical system for noninvasive assessment of the emotional impairments associated with neurological disorders.

  13. Basis-set limit of the aurophilic attraction using the MP2 method: The examples of [ClAuPH3]2 dimer and [P(AuPH3)4]+ ion

    NASA Astrophysics Data System (ADS)

    Pyykkö, Pekka; Zaleski-Ejgierd, Patryk

    2008-03-01

    The basis-set limit of the aurophilic attraction is studied at the MP2 level for the free model dimer [ClAuPH3]2 and for a [P(AuPH3)4]+ ion. The latter system is found to prefer a C4v symmetry, instead of Td, in agreement with Li and Pyykkö [Inorg. Chem. 32, 2630 (1993)] but in contradiction to recent results of Fang and Wang [J. Phys. Chem. A. 111, 1562 (2006)]. The Karlsruhe split valence and the Dunning correlation-consistent basis sets converge to the same limit.

  14. On the performance of long-range-corrected density functional theory and reduced-size polarized LPol-n basis sets in computations of electric dipole (hyper)polarizabilities of π-conjugated molecules.

    PubMed

    Baranowska-Łączkowska, Angelika; Bartkowiak, Wojciech; Góra, Robert W; Pawłowski, Filip; Zaleśny, Robert

    2013-04-05

    Static longitudinal electric dipole (hyper)polarizabilities are calculated for six medium-sized π-conjugated organic molecules using recently developed LPol-n basis set family to assess their performance. Dunning's correlation-consistent basis sets of triple-ζ quality combined with MP2 method and supported by CCSD(T)/aug-cc-pVDZ results are used to obtain the reference values of analyzed properties. The same reference is used to analyze (hyper)polarizabilities predicted by selected exchange-correlation functionals, particularly those asymptotically corrected.

  15. Efficient Implementation of an Optimal Interpolator for Large Spatial Data Sets

    NASA Technical Reports Server (NTRS)

    Memarsadeghi, Nargess; Mount, David M.

    2007-01-01

    Scattered data interpolation is a problem of interest in numerous areas such as electronic imaging, smooth surface modeling, and computational geometry. Our motivation arises from applications in geology and mining, which often involve large scattered data sets and a demand for high accuracy. The method of choice is ordinary kriging. This is because it is a best unbiased estimator. Unfortunately, this interpolant is computationally very expensive to compute exactly. For n scattered data points, computing the value of a single interpolant involves solving a dense linear system of size roughly n x n. This is infeasible for large n. In practice, kriging is solved approximately by local approaches that are based on considering only a relatively small'number of points that lie close to the query point. There are many problems with this local approach, however. The first is that determining the proper neighborhood size is tricky, and is usually solved by ad hoc methods such as selecting a fixed number of nearest neighbors or all the points lying within a fixed radius. Such fixed neighborhood sizes may not work well for all query points, depending on local density of the point distribution. Local methods also suffer from the problem that the resulting interpolant is not continuous. Meyer showed that while kriging produces smooth continues surfaces, it has zero order continuity along its borders. Thus, at interface boundaries where the neighborhood changes, the interpolant behaves discontinuously. Therefore, it is important to consider and solve the global system for each interpolant. However, solving such large dense systems for each query point is impractical. Recently a more principled approach to approximating kriging has been proposed based on a technique called covariance tapering. The problems arise from the fact that the covariance functions that are used in kriging have global support. Our implementations combine, utilize, and enhance a number of different

  16. The maximum overlap method: A general and efficient scheme for reducing basis sets. Application to the generation of approximate AO's for the 3 d transition metal atoms and ions

    NASA Astrophysics Data System (ADS)

    Francisco, E.; Seijo, L.; Pueyo, L.

    1986-07-01

    The method of maximum overlap, often applied to the problem of basis set reduction, is formulated in terms of weighted least squares with orthogonality restrictions. An analytical solution for the linear parameters of the reduced set is given. In this form, the method is a general and efficient scheme for reducing basis sets. As an application, orthogonal radial wavefunctions of the STO type have been obtained for the 3 d transition metal atoms and ions by simulation of the high-quality sets of Clementi and Roetti. The performance of the reduction has been evaluated by examining several one- and two-electron interactions. Results of these tests reveal that the new functions are highly accurate simulations of the reference AO's. They appear to be appropriate for molecular and solid state calculations.

  17. Implementing a Volatility Basis Set Approach for Simulation of Secondary Organic Aerosol and its Climatic Impacts in CESM-CAM5

    NASA Astrophysics Data System (ADS)

    Glotfelty, T.; He, J.; Gantt, B.; Zhang, Y.

    2013-12-01

    Organic aerosols (OA) affect climate by serving as cloud condensation nuclei, which impact the cloud droplet number concentration (CDNC) and ultimately the radiation budget of the planet through aerosol direct and indirect effects. Accurately quantifying OA in climate models is important as they account for 20-90% of submicron aerosols. In order to better represent the formation of OA and their impact on climate, a volatility basis set (VBS) approach for the formation of secondary organic aerosols (SOA) has been implemented into the NCSU version of the Community Atmosphere Model version 5.1 (CAM5) in the Community Earth System Model (CESM). Compared to the officially released version of CESM/CAM5, the NCSU version used in this study features advanced inorganic aerosol treatments and aerosol activation parameterizations. In addition to the typical SOA precursors, SOA formation from semi-volatile primary organic aerosol (POA), polycyclic aromatic hydrocarbons, and glyoxal are being treated. To assess the performance of the improved model, two full year simulations of 2001 and 2010 will be conducted and evaluated against available observations including the total organic carbon (TOC) measurements from the Interagency Monitoring of Protected Visual Environments (IMPROVE), total carbon (TC) measurements from Speciation Trends Network (STN), and global aerosol mass spectrometer measurements of hydrocarbon-like aerosol (HOA) and oxygenated organic aerosol (OOA). Preliminary simulations for summer 2001 show that the VBS treatment increases the SOA concentration by 0.2 μg m-3 on global average but by 0.6-9.7 μg m-3 over Europe, East Asia, and North America. There is, however, a slight decrease in the SOA formed over rainforest areas; resulting from differences in SOA production from a single lumped precursor in the default treatment verses the species-dependent treatment in the VBS treatment. Compared to the baseline simulation, the simulation with the VBS treatment tends

  18. An evaluation of correlation-consistent basis sets in calculating the structure and energetics of (H{sub 3}Si){sub 2}O, H{sub 3}SiOH, and H{sub 3}SiO{sup {minus}}

    SciTech Connect

    Nicholas, J.B.; Feyereisen, M.

    1995-11-08

    We studied the structure of disiloxane (H{sub 3}Si--O--SiH{sub 3}), silanol (H{sub 3}Si--OH), and the silanol anion (H{sub 3}Si--O{sup {minus}}) with {ital ab} {ital initio} molecular orbital theory and the correlation consistent polarized basis sets of Dunning and co-workers. We present results for the correlation consistent polarized valence double zeta (cc-pVDZ), triple zeta (cc-pVTZ), and quadruple zeta [cc-pVQZ(-{ital g})] basis sets. Optimized geometries and energies are given at both the restricted Hartree--Fock (RHF) level and with the inclusion of electron correlation by second order Moller--Plesset perturbation theory (MP2). The correlation consistent basis sets provide a systematic expansion of the orbital basis set, with each set of additional functions adding a similar contribution to the correlation energy. We find that the calculated molecular properties show exponential convergence with increasing basis set size. These calculations answer long-standing questions regarding the structure and barrier to linearization of disiloxane. Results at the highest level of theory [MP2/cc-pVQZ(-{ital g})] for disiloxane gave a Si--O--Si bond angle of 147.0{degree}, a Si--O bond length of 1.641 A, and a barrier to linearization of 0.4 kcal/mol. All of these values are in excellent agreement with experimental results. Similar calculations for silanol gave a Si--O bond length of 1.655 A, an O--H bond of 0.955 A, and a Si--O--H angle of 117.9{degree}. The MP2/cc-pVQZ(-{ital g}) deprotonation energy ({Delta}{ital E}{sup 0}) for silanol, calculated as the energy difference between silanol and its anion, is {minus}366.6 kcal/mol. The effects of electron correlation at the MP4 level are studied in all three molecules using the cc-pVDZ and cc-pVTZ basis sets. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  19. Multi-criteria decision-making methods with optimism and pessimism based on Atanassov's intuitionistic fuzzy sets

    NASA Astrophysics Data System (ADS)

    Chen, Ting-Yu

    2012-05-01

    The theory of Atanassov's intuitionistic fuzzy sets (A-IFSs) developed over the last several decades has found useful application in fields requiring multiple-criteria decision analysis. Since the membership-nonmembership pair in A-IFSs belongs to the bivariate unipolarity type, this article describes an approach that relates optimism and pessimism to multi-criteria decision analysis in an intuitionistic fuzzy-decision environment. First, several optimistic and pessimistic point operators were defined to alter the estimation of decision outcomes. Next, based on the core of the estimations, optimistic and pessimistic score functions were developed to evaluate each alternative with respect to each criterion. The suitability function was then established to determine the degree to which each an alternative satisfies the decision maker's requirement. Because the information on multiple criteria corresponding to decision importance is often incomplete, this study included suitability functions in the optimisation models to account for poorly known membership grades. Using a linear equal-weighted summation method, these models were transformed into a single objective optimisation model to generate the optimal weights for criteria. The feasibility and effectiveness of the proposed methods were illustrated through a practical example. Finally, computational experiments with enormous amounts of simulation data were designed to conduct a comparative analysis on the ranking orders yielded by different optimistic/pessimistic point operators.

  20. All-electron all-virtual spinor space relativistic coupled-cluster calculations for molecules of heavy elements using contracted basis set: Prediction of atomization energy of PbH4*

    NASA Astrophysics Data System (ADS)

    Malli, Gulzari L.; Siegert, Martin; Turner, David P.

    All-electron all-virtual spinor space (AVSS) relativistic second order Møller-Plesset (RMP2), coupled-cluster singles doubles (RCCSD), RCCSD(T) (RCCSD plus the triple excitation correction included perturbationally) calculations are reported for tetrahedral (Td) PbH4 at various bond lengths using our finite contracted universal Gaussian basis set. Our relativistic calculations predict the RMP2, RCCSD, and RCCD(T) molecular correlation energy for PbH4 as -2.2563, -2.1917, and -2.2311 au, respectively. Ours are the first AVSS RMP2, RCCSD, and RCCSD(T) molecular calculations for electron correlation energy of the heavy element molecule PbH4. All-electron AVSS coupled-cluster calculations for the Pb atom are also reported and these were used (in conjunction with the corresponding molecular electron correlation energy calculations for PbH4) to predict atomization energy (Ae) of PbH4 at various levels of coupled-cluster electron correlation. Our predicted atomization energy for PbH4 (at the optimized bond length of 1.749 Å) with our Dirac-Fock, RMP2, RCCSD, and RCCSD(T) calculations is 5.73, 7.27, 11.24, and 11.62 eV, respectively. Neither such relativistic molecular correlation energy nor atomization energy has been reported so far for heavy polyatomic with 86 electrons. Calculation of relativistic molecular correlation energy is no more a nightmare, and bottlenecks are broken for the calculation of relativistic correlation as well as atomization energy for molecules of heavy elements.

  1. Accurate ab initio potential energy curves for the classic Li-F ionic-covalent interaction by extrapolation to the complete basis set limit and modeling of the radial nonadiabatic coupling.

    PubMed

    Varandas, A J C

    2009-09-28

    Multireference configuration interaction calculations using large correlation consistent basis sets and full configuration interaction calculations with the smallest of such basis are utilized to describe the ionic-neutral curve crossing for the title system. The results of the former calculations have then been extrapolated to the complete basis set limit using the uniform singlet- and triplet-pair extrapolation scheme. A recent suggestion for locating the nonadiabatic matrix terms at the point where the dynamical correlation split vanishes has also been tested. Additionally, a consistent formalism is suggested to model the radial dependence of the nonadiabatic matrix terms that warrants an overlap dependence away from the crossing. When applied to LiF, the overall approach yields results in excellent agreement with the commonly accepted values for the geometric and energetic attributes at both the equilibrium and diabatic crossing regions.

  2. Design of Multi-Parameter Steerable Functions Using Cascade Basis Reduction

    NASA Technical Reports Server (NTRS)

    Teo, P.; Hel-Or, Y.; Null, Cynthia H. (Technical Monitor)

    1996-01-01

    A new cascade basis reduction method of computing the optimal least-squares set of basis functions steering a given function is presented. The method combines the Lie group-theoretic and the singular value decomposition approaches in such a way that their respective strengths complement each other. Since the Lie group-theoretic approach is used, the set of basis and steering functions computed can be expressed analytically. Because the singular value decomposition method is used, this set of basis and steering functions is optimal in the least-squares sense. Furthermore, the computational complexity in designing basis functions for transformation groups with large numbers of parameters is significantly reduced. The efficiency of the cascade basis reduction method is demonstrated by designing a set of basis functions that steers a Gabor function under the four-parameter linear transformation group.

  3. Thermodynamic limits set relevant constraints to the soil-plant-atmosphere system and to optimality in terrestrial vegetation

    NASA Astrophysics Data System (ADS)

    Kleidon, Axel; Renner, Maik

    2016-04-01

    , which then links this thermodynamic approach to optimality in vegetation. We also contrast this approach to common, semi-empirical approaches of surface-atmosphere exchange and discuss how thermodynamics may set a broader range of transport limitations and optimality in the soil-plant-atmosphere system.

  4. Validation of an optimized SPM procedure for FDG-PET in dementia diagnosis in a clinical setting

    PubMed Central

    Perani, Daniela; Della Rosa, Pasquale Anthony; Cerami, Chiara; Gallivanone, Francesca; Fallanca, Federico; Vanoli, Emilia Giovanna; Panzacchi, Andrea; Nobili, Flavio; Pappatà, Sabina; Marcone, Alessandra; Garibotto, Valentina; Castiglioni, Isabella; Magnani, Giuseppe; Cappa, Stefano F.; Gianolli, Luigi

    2014-01-01

    Diagnostic accuracy in FDG-PET imaging highly depends on the operating procedures. In this clinical study on dementia, we compared the diagnostic accuracy at a single-subject level of a) Clinical Scenarios, b) Standard FDG Images and c) Statistical Parametrical (SPM) Maps generated via a new optimized SPM procedure. We evaluated the added value of FDG-PET, either Standard FDG Images or SPM Maps, to Clinical Scenarios. In 88 patients with neurodegenerative diseases (Alzheimer's Disease—AD, Frontotemporal Lobar Degeneration—FTLD, Dementia with Lewy bodies—DLB and Mild Cognitive Impairment—MCI), 9 neuroimaging experts made a forced diagnostic decision on the basis of the evaluation of the three types of information. There was also the possibility of a decision of normality on the FDG-PET images. The clinical diagnosis confirmed at a long-term follow-up was used as the gold standard. SPM Maps showed higher sensitivity and specificity (96% and 84%), and better diagnostic positive (6.8) and negative (0.05) likelihood ratios compared to Clinical Scenarios and Standard FDG Images. SPM Maps increased diagnostic accuracy for differential diagnosis (AD vs. FTD; beta 1.414, p = 0.019). The AUC of the ROC curve was 0.67 for SPM Maps, 0.57 for Clinical Scenarios and 0.50 for Standard FDG Images. In the MCI group, SPM Maps showed the highest predictive prognostic value (mean LOC = 2.46), by identifying either normal brain metabolism (exclusionary role) or hypometabolic patterns typical of different neurodegenerative conditions. PMID:25389519

  5. Comparison of different theory models and basis sets in the calculations of structures and 13C NMR spectra of [Pt(en)(CBDCA-O, O')], an analogue of the antitumor drug carboplatin.

    PubMed

    Gao, Hongwei; Wei, Xiujuan; Liu, Xuting; Yan, Tingxia

    2010-03-25

    Comparisons of various density functional theory (DFT) methods at different basis sets in predicting the molecular structures and (13)C NMR spectra for [Pt(en)(CBDCA-O, O')], an analogue of the antitumor drug carboplatin, are reported. DFT methods including B3LYP, B3PW91, mPW1PW91, PBE1PBE, BPV86, PBEPBE, and LSDA are examined. Different basis sets including LANL2DZ, SDD, LANL2MB, CEP-4G, CEP-31G, and CEP-121G are also considered. It is remarkable that the LSDA/SDD level is clearly superior to all of the remaining density functional methods in predicting the structure of [Pt(en)(CBDCA-O, O')]. The results also indicate that the B3LYP/SDD level is the best to predict (13)C NMR spectra for [Pt(en)(CBDCA-O, O')] among all DFT methods.

  6. Computational analysis of the potential energy surfaces of glycerol in the gas and aqueous phases: effects of level of theory, basis set, and solvation on strongly intramolecularly hydrogen-bonded systems.

    PubMed

    Callam, C S; Singer, S J; Lowary, T L; Hadad, C M

    2001-11-28

    The 126 possible conformations of 1,2,3-propanetriol (glycerol) have been studied by ab initio molecular orbital and density functional theory calculations in the gas and aqueous phases at multiple levels of theory and basis sets. The partial potential energy surface for glycerol as well as an analysis of the conformational properties and hydrogen-bonding trends in both phases have been obtained. In the gas phase at the G2(MP2) and CBS-QB3 levels of theory, the important, low-energy conformers are structures 100 and 95. In the aqueous phase at the SM5.42/HF/6-31G* level of theory, the lowest energy conformers are structures 95 and 46. Boltzmann distributions have been determined from these high-level calculations, and good agreement is observed when these distributions are compared to the available experimental data. These calculations indicate that the enthalpic and entropic contributions to the Gibbs free energy are important for an accurate determination of the conformational and energetic preferences of glycerol. Different levels of theory and basis sets were used in order to understand the effects of nonbonded interactions (i.e., intramolecular hydrogen bonding). The efficiency of basis set and level of theory in dealing with the issue of intramolecular hydrogen bonding and reproducing the correct energetic and geometrical trends is discussed, especially with relevance to practical computational methods for larger polyhydroxylated compounds, such as oligosaccharides.

  7. Exploring the Neural Basis of Real-Life Joint Action: Measuring Brain Activation during Joint Table Setting with Functional Near-Infrared Spectroscopy

    PubMed Central

    Egetemeir, Johanna; Stenneken, Prisca; Koehler, Saskia; Fallgatter, Andreas J.; Herrmann, Martin J.

    2011-01-01

    Many every-day life situations require two or more individuals to execute actions together. Assessing brain activation during naturalistic tasks to uncover relevant processes underlying such real-life joint action situations has remained a methodological challenge. In the present study, we introduce a novel joint action paradigm that enables the assessment of brain activation during real-life joint action tasks using functional near-infrared spectroscopy (fNIRS). We monitored brain activation of participants who coordinated complex actions with a partner sitting opposite them. Participants performed table setting tasks, either alone (solo action) or in cooperation with a partner (joint action), or they observed the partner performing the task (action observation). Comparing joint action and solo action revealed stronger activation (higher [oxy-Hb]-concentration) during joint action in a number of areas. Among these were areas in the inferior parietal lobule (IPL) that additionally showed an overlap of activation during action observation and solo action. Areas with such a close link between action observation and action execution have been associated with action simulation processes. The magnitude of activation in these IPL areas also varied according to joint action type and its respective demand on action simulation. The results validate fNIRS as an imaging technique for exploring the functional correlates of interindividual action coordination in real-life settings and suggest that coordinating actions in real-life situations requires simulating the actions of the partner. PMID:21927603

  8. Estimated MP2 and CCSD(T) interaction energies of n-alkane dimers at the basis set limit: Comparison of the methods of Helgaker et al. and Feller

    NASA Astrophysics Data System (ADS)

    Tsuzuki, Seiji; Honda, Kazumasa; Uchimaru, Tadafumi; Mikami, Masuhiro

    2006-03-01

    The MP2 (the second-order Møller-Plesset calculation) and CCSD(T) (coupled cluster calculation with single and double substitutions with noniterative triple excitations) interaction energies of all-trans n-alkane dimers were calculated using Dunning's [J. Chem. Phys. 90, 1007 (1989)] correlation consistent basis sets. The estimated MP2 interaction energies of methane, ethane, and propane dimers at the basis set limit [EMP2(limit)] by the method of Helgaker et al. [J. Chem. Phys. 106, 9639 (1997)] from the MP2/aug-cc-pVXZ (X =D and T) level interaction energies are very close to those estimated from the MP2/aug-cc-pVXZ (X =T and Q) level interaction energies. The estimated EMP2(limit) values of n-butane to n-heptane dimers from the MP2/cc-pVXZ (X =D and T) level interaction energies are very close to those from the MP2/aug-cc-pVXZ (X =D and T) ones. The EMP2(limit) values estimated by Feller's [J. Chem. Phys. 96, 6104 (1992)] method from the MP2/cc-pVXZ (X =D, T, and Q) level interaction energies are close to those estimated by the method of Helgaker et al. from the MP2/cc-pVXZ (X =T and Q) ones. The estimated EMP2(limit) values by the method of Helgaker et al. using the aug-cc-pVXZ (X =D and T) are close to these values. The estimated EMP2(limit) of the methane, ethane, propane, n-butane, n-pentane, n-hexane, n-heptane, n-octane, n-nonane, and n-decane dimers by the method of Helgaker et al. are -0.48, -1.35, -2.08, -2.97, -3.92, -4.91, -5.96, -6.68, -7.75, and -8.75kcal /mol, respectively. Effects of electron correlation beyond MP2 are not large. The estimated CCSD(T) interaction energies of the methane, ethane, propane, and n-butane dimers at the basis set limit by the method of Helgaker et al. (-0.41, -1.22, -1.87, and -2.74kcal/mol, respectively) from the CCSD(T )/cc-pVXZ (X =D and T) level interaction energies are close to the EMP2(limit) obtained using the same basis sets. The estimated EMP2(limit) values of the ten dimers were fitted to the form m0+m1X (X

  9. Sporogonic Cycles Calculated Using Degree-Days, as a Basis for Comparison of Malaria Parasite Development in Different Eco-Epidemiological Settings in India.

    PubMed

    Singh, Poonam; Dhiman, Ramesh C

    2016-01-01

    In India, malaria transmission is prevalent across diverse geologies and ecologies. Temperature is one of the key determinants of malarial transmission, causing low endemicity in some areas than in others. Using a degree-day model, we estimated the maximum and minimum possible number of days needed to complete a malarial sporogonic cycle (SC), in addition to the possible number of SCs for Plasmodium vivax and Plasmodium falciparum under two different ecological settings with either low or high endemicity for malaria at different elevations. In Raikhalkhatta (in the Himalayan foothills) SCs were modeled as not occurring from November to February, whereas in Gandhonia village (forested hills), all but only one month were suitable for malarial SCs. A minimum of 6 days and maximum of 46 days were required for completion of one SC. Forested hilly areas were more suitable for malaria parasite development in terms of SCs (25 versus 21 for P. falciparum and 32 versus 27 for P. vivax). Degree-days also provided a climatic explanation for the current transmission of malaria at different elevations. The calculation of degree-days and possible SC has applications in the regional analysis of transmission dynamics and management of malaria in view of climate change.

  10. Accurate density-functional calculation of core-electron binding energies with a scaled polarized triple-zeta basis set. Twelve test cases and application to three C 2H 4O 2 isomers

    NASA Astrophysics Data System (ADS)

    Chong, Delano P.; Hu, Ching-Han; Duffy, Patrick

    1996-02-01

    A scaling procedure based on Clementi and Raimondi's rules for atomic screening was proposed for atomic orbital basis sets in the unrestricted generalized transition state (uGTS) model of density functional calculation of core-electron binding energies (CEBEs). The exchange-correlation potential is based on a combined functional of Becke's exchange (B88) and Perdew's correlation (P86). This proposal was tested on CEBEs of twelve small molecules, including F 2, N 2 and H 2O, and applied to the computation of CEBEs of three isomers of C 2H 4O 2: acetic acid (CH 3COOH), methyl formate (HCOOCH 3), and glycolic aldehyde (CH 2OHCHO). In all cases, the new scaled pVTZ basis performs almost as well as the much larger cc-pV5Z and the average absolute difference between the results from the scaled pVTZ and estimated complete basis set limits is 0.04 eV.

  11. Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies.

    PubMed

    Schneebeli, Severin T; Bochevarov, Arteum D; Friesner, Richard A

    2011-03-08

    A vast number of non-covalent interaction energies at the counterpoise corrected CCSD(T) level have been collected from the literature to build a diverse new dataset. The whole dataset, which consists of 2027 CCSD(T) energies, includes most of the published data at this level. A large subset of the data was then used to train a novel, B3LYP specific, empirical correction scheme for non-covalent interactions and basis set superposition error (abbreviated as B3LYP-MM). Results obtained with our new correction scheme were directly compared to benchmark results obtained with B3LYP-D3(1) and M06-2X(2) (two popular density functions designed specifically to accurately model non-covalent interactions). For non-covalent complexes dominated by dispersion or dipole-dipole interactions all three tested methods give accurate results with the medium size aug-cc-pVDZ(3-6) basis set with MUE's of 0.27 (B3LYP-MM), 0.32 (B3LYP-D3) and 0.47 kcal/mol (M06-2X) (with explicit counterpoise corrections). These results validate both B3LYP-D3 and M06-2X for interactions of this type using a much larger data set than was presented in prior work. However, our new dispersion correction scheme shows some clear advantages for dispersion and dipole-dipole dominated complexes with the small LACVP* basis set, which is very popular in use due to its low associated computational cost: The MUE for B3LYP-MM with the LACVP* basis set for this subset of complexes (without explicit counterpoise corrections) is only 0.28 kcal/mol, compared to 0.65 kcal/mol for M06-2X or 1.16 kcal/mol for B3LYP-D3. Additionally, our new correction scheme also shows major improvements in accuracy for hydrogen-bonded systems and for systems involving ionic interactions, for example cation-π interactions. Compared to B3LYP-D3 and M06-2X, we also find that our new B3LYP-MM correction scheme gives results of higher or equal accuracy for a large dataset of conformer energies of di- and tripeptides, sugars, and cysteine.

  12. Optimism

    PubMed Central

    Carver, Charles S.; Scheier, Michael F.; Segerstrom, Suzanne C.

    2010-01-01

    Optimism is an individual difference variable that reflects the extent to which people hold generalized favorable expectancies for their future. Higher levels of optimism have been related prospectively to better subjective well-being in times of adversity or difficulty (i.e., controlling for previous well-being). Consistent with such findings, optimism has been linked to higher levels of engagement coping and lower levels of avoidance, or disengagement, coping. There is evidence that optimism is associated with taking proactive steps to protect one's health, whereas pessimism is associated with health-damaging behaviors. Consistent with such findings, optimism is also related to indicators of better physical health. The energetic, task-focused approach that optimists take to goals also relates to benefits in the socioeconomic world. Some evidence suggests that optimism relates to more persistence in educational efforts and to higher later income. Optimists also appear to fare better than pessimists in relationships. Although there are instances in which optimism fails to convey an advantage, and instances in which it may convey a disadvantage, those instances are relatively rare. In sum, the behavioral patterns of optimists appear to provide models of living for others to learn from. PMID:20170998

  13. Simulation of fruit-set and trophic competition and optimization of yield advantages in six Capsicum cultivars using functional–structural plant modelling

    PubMed Central

    Ma, Y. T.; Wubs, A. M.; Mathieu, A.; Heuvelink, E.; Zhu, J. Y.; Hu, B. G.; Cournède, P. H.; de Reffye, P.

    2011-01-01

    Background and aims Many indeterminate plants can have wide fluctuations in the pattern of fruit-set and harvest. Fruit-set in these types of plants depends largely on the balance between source (assimilate supply) and sink strength (assimilate demand) within the plant. This study aims to evaluate the ability of functional–structural plant models to simulate different fruit-set patterns among Capsicum cultivars through source–sink relationships. Methods A greenhouse experiment of six Capsicum cultivars characterized with different fruit weight and fruit-set was conducted. Fruit-set patterns and potential fruit sink strength were determined through measurement. Source and sink strength of other organs were determined via the GREENLAB model, with a description of plant organ weight and dimensions according to plant topological structure established from the measured data as inputs. Parameter optimization was determined using a generalized least squares method for the entire growth cycle. Key Results and Conclusions Fruit sink strength differed among cultivars. Vegetative sink strength was generally lower for large-fruited cultivars than for small-fruited ones. The larger the size of the fruit, the larger variation there was in fruit-set and fruit yield. Large-fruited cultivars need a higher source–sink ratio for fruit-set, which means higher demand for assimilates. Temporal heterogeneity of fruit-set affected both number and yield of fruit. The simulation study showed that reducing heterogeneity of fruit-set was obtained by different approaches: for example, increasing source strength; decreasing vegetative sink strength, source–sink ratio for fruit-set and flower appearance rate; and harvesting individual fruits earlier before full ripeness. Simulation results showed that, when we increased source strength or decreased vegetative sink strength, fruit-set and fruit weight increased. However, no significant differences were found between large-fruited and

  14. Calculation of the first static hyperpolarizability tensor of three-dimensional periodic compounds with a local basis set: A comparison of LDA, PBE, PBE0, B3LYP, and HF results

    NASA Astrophysics Data System (ADS)

    Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth

    2010-06-01

    The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (ɛ∞) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of ɛ∞ and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.

  15. Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

    PubMed Central

    Rincent, R.; Laloë, D.; Nicolas, S.; Altmann, T.; Brunel, D.; Revilla, P.; Rodríguez, V.M.; Moreno-Gonzalez, J.; Melchinger, A.; Bauer, E.; Schoen, C-C.; Meyer, N.; Giauffret, C.; Bauland, C.; Jamin, P.; Laborde, J.; Monod, H.; Flament, P.; Charcosset, A.; Moreau, L.

    2012-01-01

    Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix–best linear unbiased predictions model (RA–BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request. PMID:22865733

  16. Optimal encryption of quantum bits

    SciTech Connect

    Boykin, P. Oscar; Roychowdhury, Vwani

    2003-04-01

    We show that 2n random classical bits are both necessary and sufficient for encrypting any unknown state of n quantum bits in an informationally secure manner. We also characterize the complete set of optimal protocols in terms of a set of unitary operations that comprise an orthonormal basis in a canonical inner product space. Moreover, a connection is made between quantum encryption and quantum teleportation that allows for a different proof of optimality of teleportation.

  17. Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets.

    PubMed

    Khajehzadeh, Mostafa; Moghadam, Majid

    2017-02-24

    Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ→σ∗ and π→π∗ and LP(1)→σ∗ and LP(2)→σ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H2O, CH3CN and C6H12. UV

  18. Improved Fuzzy C-Means based Particle Swarm Optimization (PSO) initialization and outlier rejection with level set methods for MR brain image segmentation.

    PubMed

    Mekhmoukh, Abdenour; Mokrani, Karim

    2015-11-01

    In this paper, a new image segmentation method based on Particle Swarm Optimization (PSO) and outlier rejection combined with level set is proposed. A traditional approach to the segmentation of Magnetic Resonance (MR) images is the Fuzzy C-Means (FCM) clustering algorithm. The membership function of this conventional algorithm is sensitive to the outlier and does not integrate the spatial information in the image. The algorithm is very sensitive to noise and in-homogeneities in the image, moreover, it depends on cluster centers initialization. To improve the outlier rejection and to reduce the noise sensitivity of conventional FCM clustering algorithm, a novel extended FCM algorithm for image segmentation is presented. In general, in the FCM algorithm the initial cluster centers are chosen randomly, with the help of PSO algorithm the clusters centers are chosen optimally. Our algorithm takes also into consideration the spatial neighborhood information. These a priori are used in the cost function to be optimized. For MR images, the resulting fuzzy clustering is used to set the initial level set contour. The results confirm the effectiveness of the proposed algorithm.

  19. A generating set direct search augmented Lagrangian algorithm for optimization with a combination of general and linear constraints.

    SciTech Connect

    Lewis, Robert Michael (College of William and Mary, Williamsburg, VA); Torczon, Virginia Joanne (College of William and Mary, Williamsburg, VA); Kolda, Tamara Gibson

    2006-08-01

    We consider the solution of nonlinear programs in the case where derivatives of the objective function and nonlinear constraints are unavailable. To solve such problems, we propose an adaptation of a method due to Conn, Gould, Sartenaer, and Toint that proceeds by approximately minimizing a succession of linearly constrained augmented Lagrangians. Our modification is to use a derivative-free generating set direct search algorithm to solve the linearly constrained subproblems. The stopping criterion proposed by Conn, Gould, Sartenaer and Toint for the approximate solution of the subproblems requires explicit knowledge of derivatives. Such information is presumed absent in the generating set search method we employ. Instead, we show that stationarity results for linearly constrained generating set search methods provide a derivative-free stopping criterion, based on a step-length control parameter, that is sufficient to preserve the convergence properties of the original augmented Lagrangian algorithm.

  20. Full CI Benchmark Potentials for the 6e^- System Li_2 with a CBS Extrapolation from aug-cc-pCV5Z and aug-cc-pCV6Z Basis Sets Using Fciqmc and Dmrg

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.; Sharma, Sandeep; Alavi, Ali

    2016-06-01

    Being the simplest uncharged homonuclear dimer after H_2 that has a stable ground state, Li_2 is one of the most important benchmark systems for theory and experiment. In 1930, Delbruck used Li_2 to test his theory of homopolar binding, and it was used again and again as a prototype to test what have now become some of the most ubiquitous concepts in molecular physics (LCAO, SCF, MO, just to name a few). Experimentally, Roscoe and Schuster studied alkali dimers back in 1874. At the dawn of quantum mechanics, the emerging types of spectroscopic analyses we now use today, were tested on Li_2 in the labs of Wurm (1928), Harvey (1929), Lewis (1931), and many others, independently. Li_2 was at the centre of the development of PFOODR in the 80s, and PAS in the 90s; and Lithium Bose-Einstein condensates were announced only 1 month after the Nobel Prize winning BEC announcement in 1995. Even now in the 2010s, numerous experimental and theoretical studies on Li have tested QED up to the 7th power of the fine structure constant. Li_2 has also been of interest to sub-atomic physicists, as it was spectroscopic measurements on ^7Li_2 that determined the spin of ^7Li to be 3/2 in 1931; and Li_2 has been proposed in 2014 as a candidate for the first ``halo nucleonic molecule". The lowest triplet state a(1^3Σ_u^+) is an excellent benchmark system for all newly emerging ab initio techniques because it has only 6e^-, its potential is only 334 cm-1 deep, it avoids harsh complications from spin-orbit coupling, and it is the deepest potential for which all predicted vibrational energy levels have been observed with 0.0001 cm-1 precision. However the current best ab initio potentials do not even yield all vibrational energy spacings correct to within 1 cm-1. This could be because the calculation was only done on a cc-pV5Z basis set, or because the QCISD(T,full) method that the authors used, only considered triple excitations while a full CI calculation should include up to hexuple

  1. An optimized solution of multi-criteria evaluation analysis of landslide susceptibility using fuzzy sets and Kalman filter

    NASA Astrophysics Data System (ADS)

    Gorsevski, Pece V.; Jankowski, Piotr

    2010-08-01

    The Kalman recursive algorithm has been very widely used for integrating navigation sensor data to achieve optimal system performances. This paper explores the use of the Kalman filter to extend the aggregation of spatial multi-criteria evaluation (MCE) and to find optimal solutions with respect to a decision strategy space where a possible decision rule falls. The approach was tested in a case study in the Clearwater National Forest in central Idaho, using existing landslide datasets from roaded and roadless areas and terrain attributes. In this approach, fuzzy membership functions were used to standardize terrain attributes and develop criteria, while the aggregation of the criteria was achieved by the use of a Kalman filter. The approach presented here offers advantages over the classical MCE theory because the final solution includes both the aggregated solution and the areas of uncertainty expressed in terms of standard deviation. A comparison of this methodology with similar approaches suggested that this approach is promising for predicting landslide susceptibility and further application as a spatial decision support system.

  2. An Optimized Spline-Based Registration of a 3D CT to a Set of C-Arm Images.

    PubMed

    Jonić, S; Thévenaz, P; Zheng, G; Nolte, L-P; Unser, M

    2006-01-01

    We have developed an algorithm for the rigid-body registration of a CT volume to a set of C-arm images. The algorithm uses a gradient-based iterative minimization of a least-squares measure of dissimilarity between the C-arm images and projections of the CT volume. To compute projections, we use a novel method for fast integration of the volume along rays. To improve robustness and speed, we take advantage of a coarse-to-fine processing of the volume/image pyramids. To compute the projections of the volume, the gradient of the dissimilarity measure, and the multiresolution data pyramids, we use a continuous image/volume model based on cubic B-splines, which ensures a high interpolation accuracy and a gradient of the dissimilarity measure that is well defined everywhere. We show the performance of our algorithm on a human spine phantom, where the true alignment is determined using a set of fiducial markers.

  3. Accurate double many-body expansion potential energy surface for N3((4)A'') from correlation scaled ab initio energies with extrapolation to the complete basis set limit.

    PubMed

    Galvão, B R L; Varandas, A J C

    2009-12-31

    A new global potential energy surface is reported for the (4)A'' ground electronic state of the N(3) system from double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. It shows three equivalent metastable potential wells for C(2v) geometries that are separated from the three N((4)S) + N(2) asymptotes by energy barriers as predicted from previous ab initio work. The potential well and barrier height now predicted lie 42.9 and 45.9 kcal mol(-1) above the atom-diatom dissociation limit, respectively, being about 1 kcal mol(-1) lower than previous theoretical estimates. The ab initio calculations here reported predict also a (4)B(1)/(4)A(2) conical intersection and reveal a new minimum with D(3h) symmetry that lies 147 kcal mol(-1) above the atom-diatom asymptote. All major topographical features of the potential energy surface are accurately described by the DMBE function, including the weakly bound van der Waals minima at large atom-diatom separations.

  4. Accurate ab initio-based adiabatic global potential energy surface for the 2{sup 2}A″ state of NH{sub 2} by extrapolation to the complete basis set limit

    SciTech Connect

    Li, Y. Q.; Ma, F. C.; Sun, M. T.

    2013-10-21

    A full three-dimensional global potential energy surface is reported first time for the title system, which is important for the photodissociation processes. It is obtained using double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. Such a work can be recommended for dynamics studies of the N({sup 2}D) + H{sub 2} reaction, a reliable theoretical treatment of the photodissociation dynamics and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen containing systems. In turn, a preliminary theoretical study of the reaction N({sup 2}D)+H{sub 2}(X{sup 1}Σ{sub g}{sup +})(ν=0,j=0)→NH(a{sup 1}Δ)+H({sup 2}S) has been carried out with the method of quasi-classical trajectory on the new potential energy surface. Integral cross sections and thermal rate constants have been calculated, providing perhaps the most reliable estimate of the integral cross sections and the rate constants known thus far for such a reaction.

  5. Methodology for optimal in situ alignment and setting of bendable optics for nearly diffraction-limited focusing of soft x-rays

    NASA Astrophysics Data System (ADS)

    Merthe, Daniel J.; Yashchuk, Valeriy V.; Goldberg, Kenneth A.; Kunz, Martin; Tamura, Nobumichi; McKinney, Wayne R.; Artemiev, Nikolay A.; Celestre, Richard S.; Morrison, Gregory Y.; Anderson, Erik H.; Smith, Brian V.; Domning, Edward E.; Rekawa, Senajith B.; Padmore, Howard A.

    2013-03-01

    We demonstrate a comprehensive and broadly applicable methodology for the optimal in situ configuration of bendable soft x-ray Kirkpatrick-Baez mirrors. The mirrors used for this application are preset at the Advanced Light Source Optical Metrology Laboratory prior to beamline installation. The in situ methodology consists of a new technique for simultaneously setting the height and pitch angle of each mirror. The benders of both mirrors were then optimally tuned in order to minimize ray aberrations to a level below the diffraction-limited beam waist size of 200 nm (horizontal)×100 nm (vertical). After applying this methodology, we measured a beam waist size of 290 nm (horizontal)×130 nm (vertical) with 1 nm light using the Foucault knife-edge test. We also discuss the utility of using a grating-based lateral shearing interferometer with quantitative wavefront feedback for further improvement of bendable optics.

  6. Methodology for optimal in situ alignment and setting of bendable optics for diffraction-limited focusing of soft x-rays

    NASA Astrophysics Data System (ADS)

    Merthe, Daniel J.; Yashchuk, Valeriy V.; Goldberg, Kenneth A.; Kunz, Martin; Tamura, Nobumichi; McKinney, Wayne R.; Artemiev, Nikolay A.; Celestre, Richard S.; Morrison, Gregory Y.; Anderson, Erik; Smith, Brian V.; Domning, Edward E.; Rekawa, Senajith B.; Padmore, Howard A.

    2012-09-01

    We demonstrate a comprehensive and broadly applicable methodology for the optimal in situ configuration of bendable soft x-ray Kirkpatrick-Baez mirrors. The mirrors used for this application are preset at the ALS Optical Metrology Laboratory prior to beamline installation. The in situ methodology consists of a new technique for simultaneously setting the height and pitch angle of each mirror. The benders of both mirrors were then optimally tuned in order to minimize ray aberrations to a level below the diffraction-limited beam waist size of 200 nm (horizontal) × 100 nm (vertical). After applying this methodology, we measured a beam waist size of 290 nm (horizontal) × 130 nm (vertical) with 1 nm light using the Foucault knife-edge test. We also discuss the utility of using a grating-based lateral shearing interferometer with quantitative wavefront feedback for further improvement of bendable optics.

  7. A machine learning framework for auto classification of imaging system exams in hospital setting for utilization optimization.

    PubMed

    Patil, Meru A; Patil, Ravindra B; Krishnamoorthy, P; John, Jacob

    2016-08-01

    In clinical environment, Interventional X-Ray (IXR) system is used on various anatomies and for various types of the procedures. It is important to classify correctly each exam of IXR system into respective procedures and/or assign to correct anatomy. This classification enhances productivity of the system in terms of better scheduling of the Cath lab, also provides means to perform device usage/revenue forecast of the system by hospital management and focus on targeted treatment planning for a disease/anatomy. Although it may appear classification of each exam into respective procedure/anatomy a simple task. However, in real-life hospital settings, it is well-known that same system settings are used to perform different types of procedures. Though, such usage leads to under-utilization of the system. In this work, a method is developed to classify exams into respective anatomical type by applying machine-learning techniques (SVM, KNN and decision trees) on log information of the systems. The classification result is promising with accuracy of greater than 90%.

  8. An Optimized Spline-Based Registration of a 3D CT to a Set of C-Arm Images

    PubMed Central

    Thévenaz, P.; Zheng, G.; Nolte, L. -P.; Unser, M.

    2006-01-01

    We have developed an algorithm for the rigid-body registration of a CT volume to a set of C-arm images. The algorithm uses a gradient-based iterative minimization of a least-squares measure of dissimilarity between the C-arm images and projections of the CT volume. To compute projections, we use a novel method for fast integration of the volume along rays. To improve robustness and speed, we take advantage of a coarse-to-fine processing of the volume/image pyramids. To compute the projections of the volume, the gradient of the dissimilarity measure, and the multiresolution data pyramids, we use a continuous image/volume model based on cubic B-splines, which ensures a high interpolation accuracy and a gradient of the dissimilarity measure that is well defined everywhere. We show the performance of our algorithm on a human spine phantom, where the true alignment is determined using a set of fiducial markers. PMID:23165033

  9. [Optimization of devices for antibiotic phoretic physiotherapy on the basis of a two-barrier model of diffusion and diffusion-osmotic migration of antibiotic anions].

    PubMed

    Mazur, V V; Varakin, A I; Serianov, Iu V

    2006-01-01

    One-, two-, three-, and four-component low-amplitude field phoretic effects on permeability of placental and muscular biological barriers to levomycetin, benzylpenicillin, and oxacillin anions were studied. Experimental data on exposure to constant electric fields, sinusoidal alternating magnetic field, thermal heating, and vibroacoustic and UHF effects were used to determine the mean coefficients of acceleration of antibiotic anion migration through placental and muscular barriers. The effect of physical fields was interpreted in terms of the sensitivity coefficient, total factor of systemic response of human body, and trade-off optimization index. The results of calculation of trade-off optimization index showed that the maximal relative therapeutic efficiency was observed for optimal numbers of combined fields (2-3) both for placental and muscular barriers. The obtained results showed that optimal stimulated migration of antibiotic anions in placental or muscular barrier was already observed in two-component physical fields, such as magnetoelectric, UHF-magnetic, UHF-electric, UHF-vibroacoustic, magnetovibroacoustic, electrovibroacoustic, etc. Clinical use of stimulated anion migration is illustrated by the example of its physiotherapeutic effect in male urology, ophthalmology, dentistry, and dental implantation.

  10. Systematic description of direct push sensor systems: A conceptual framework for system decomposition as a basis for the optimal sensor system design

    NASA Astrophysics Data System (ADS)

    Bumberger, Jan; Paasche, Hendrik; Dietrich, Peter

    2015-11-01

    Systematic decomposition and evaluation of existing sensor systems as well as the optimal design of future generations of direct push probes are of high importance for optimized geophysical experiments since the employed equipment is a constrain on the data space. Direct push technologies became established methods in the field of geophysical, geotechnical, hydrogeological, and environmental sciences for the investigation of the near subsurface. By using direct push sensor systems it is possible to measure in-situ parameters with high vertical resolution. Such information is frequently used for quantitative geophysical model calibration of interpretation of geotechnical and hydrological subsurface conditions. Most of the available direct push sensor systems are largely based on empirical testing and consecutively evaluated under field conditions. Approaches suitable to identify specific characteristics and problems of direct push sensor systems have not been established, yet. We develop a general systematic approach for the classification, analysis, and optimization of direct push sensor systems. First, a classification is presented for different existing sensor systems. The following systematic description, which is based on the conceptual decomposition of an existing sensor system into subsystems, is a suitable way to analyze and explore the transfer behavior of the system components and therefore of the complete system. Also, this approach may serve as guideline for the synthesis and the design of new and optimized direct push sensor systems.

  11. An optimal set of landmarks for metopic craniosynostosis diagnosis from shape analysis of pediatric CT scans of the head

    NASA Astrophysics Data System (ADS)

    Mendoza, Carlos S.; Safdar, Nabile; Myers, Emmarie; Kittisarapong, Tanakorn; Rogers, Gary F.; Linguraru, Marius George

    2013-02-01

    Craniosynostosis (premature fusion of skull sutures) is a severe condition present in one of every 2000 newborns. Metopic craniosynostosis, accounting for 20-27% of cases, is diagnosed qualitatively in terms of skull shape abnormality, a subjective call of the surgeon. In this paper we introduce a new quantitative diagnostic feature for metopic craniosynostosis derived optimally from shape analysis of CT scans of the skull. We built a robust shape analysis pipeline that is capable of obtaining local shape differences in comparison to normal anatomy. Spatial normalization using 7-degree-of-freedom registration of the base of the skull is followed by a novel bone labeling strategy based on graph-cuts according to labeling priors. The statistical shape model built from 94 normal subjects allows matching a patient's anatomy to its most similar normal subject. Subsequently, the computation of local malformations from a normal subject allows characterization of the points of maximum malformation on each of the frontal bones adjacent to the metopic suture, and on the suture itself. Our results show that the malformations at these locations vary significantly (p<0.001) between abnormal/normal subjects and that an accurate diagnosis can be achieved using linear regression from these automatic measurements with an area under the curve for the receiver operating characteristic of 0.97.

  12. Joint optimization of segmentation and shape prior from level-set-based statistical shape model, and its application to the automated segmentation of abdominal organs.

    PubMed

    Saito, Atsushi; Nawano, Shigeru; Shimizu, Akinobu

    2016-02-01

    The goal of this study is to provide a theoretical framework for accurately optimizing the segmentation energy considering all of the possible shapes generated from the level-set-based statistical shape model (SSM). The proposed algorithm solves the well-known open problem, in which a shape prior may not be optimal in terms of an objective functional that needs to be minimized during segmentation. The algorithm allows the selection of an optimal shape prior from among all possible shapes generated from an SSM by conducting a branch-and-bound search over an eigenshape space. The proposed algorithm does not require predefined shape templates or the construction of a hierarchical clustering tree before graph-cut segmentation. It jointly optimizes an objective functional in terms of both the shape prior and segmentation labeling, and finds an optimal solution by considering all possible shapes generated from an SSM. We apply the proposed algorithm to both pancreas and spleen segmentation using multiphase computed tomography volumes, and we compare the results obtained with those produced by a conventional algorithm employing a branch-and-bound search over a search tree of predefined shapes, which were sampled discretely from an SSM. The proposed algorithm significantly improves the segmentation performance in terms of the Jaccard index and Dice similarity index. In addition, we compare the results with the state-of-the-art multiple abdominal organs segmentation algorithm, and confirmed that the performances of both algorithms are comparable to each other. We discuss the high computational efficiency of the proposed algorithm, which was determined experimentally using a normalized number of traversed nodes in a search tree, and the extensibility of the proposed algorithm to other SSMs or energy functionals.

  13. Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

    SciTech Connect

    Morgado, Claudio A.; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jiri

    2009-06-09

    We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFTSAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geome