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Sample records for optimal basis set

  1. 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.

  2. 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

    2015-03-01

    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. PMID:25747068

  3. Property-optimized Gaussian basis sets for molecular response calculations

    NASA Astrophysics Data System (ADS)

    Rappoport, Dmitrij; Furche, Filipp

    2010-10-01

    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 C720 using hybrid density functional theory.

  4. Optimization of selected molecular orbitals in group basis sets.

    PubMed

    Ferenczy, György G; Adams, William H

    2009-04-01

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

  5. Molecule-optimized basis sets and Hamiltonians for accelerated electronic structure calculations of atoms and molecules.

    PubMed

    Gidofalvi, Gergely; Mazziotti, David A

    2014-01-16

    Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multireferenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schrödinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACSE improves the accuracy of the equivalent standard atom-optimized basis set at little additional computational cost. We illustrate the method with the potential energy curves of hydrogen fluoride and diatomic nitrogen. Relative to the hydrogen fluoride potential energy curve from the ACSE in a polarized triple-ζ basis set, the ACSE curve in a molecule-optimized basis set, equivalent in size to a polarized double-ζ basis, has a nonparallelity error of 0.0154 au, which is significantly better than the nonparallelity error of 0.0252 au from the polarized double-ζ basis set. PMID:24387056

  6. Pulay forces from localized orbitals optimized in situ using a psinc basis set.

    PubMed

    Ruiz-Serrano, Álvaro; Hine, Nicholas D M; Skylaris, Chris-Kriton

    2012-06-21

    In situ optimization of a set of localized orbitals with respect to a systematically improvable basis set independent of the position of the atoms, such as psinc functions, would theoretically eliminate the correction due to Pulay forces from the total ionic forces. We demonstrate that for strict localization constraints, especially with small localization regions, there can be non-negligible Pulay forces that must be calculated as a correction to the Hellmann-Feynman forces in the ground state. Geometry optimization calculations, which rely heavily upon accurate evaluation of the total ionic forces, show much better convergence when Pulay forces are included. The more conventional case, where the local orbitals remain fixed to pseudo-atomic orbital multiple-ζ basis sets, also benefits from this implementation. We have validated the method on several test cases, including a DNA fragment with 1045 atoms. PMID:22779575

  7. 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.

  8. 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.

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

    PubMed

    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. PMID:26723656

  10. Reply to ``Comment on `Nonanalyticity of the optimized effective potential with finite basis sets' ''

    NASA Astrophysics Data System (ADS)

    Gidopoulos, Nikitas I.; Lathiotakis, Nektarios N.

    2013-10-01

    The Comment by Friedrich does not dispute the central result of our paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052508 85, 052508 (2012)] that nonanalytic behavior is present in long-established mathematical pathologies arising in the solution of finite basis optimized effective potential (OEP) equations. In the Comment, the terms “balancing of basis sets” and “basis-set convergence” imply a particular order towards the limit of a large orbital basis sets where the large-orbital-base limit is always taken first, before the large-auxiliary-base limit, until overall convergence is achieved, at a high computational cost. The authors claim that, on physical grounds, this order of limits is not only sufficient, but also necessary in order to avoid the mathematical pathologies. In response to the Comment, we remark that it is already written in our paper that the nonanalyticity trivially disappears with large orbital basis sets. We point out that the authors of the Comment give an incorrect proof of this statement. We also show that the order of limits towards convergence of the potential is immaterial. A recent paper by the authors of the Comment proposes a partial correction for the incomplete orbital basis error in the full-potential linearized augmented-plane-wave method. Similar to the correction developed in our paper, this correction also benefits from an effectively complete orbital basis, even though only a finite orbital basis is employed in the calculation. This shows that it is unnecessary to take, in practice, the limit of an infinite orbital basis in order to avoid mathematical pathologies in the OEP. Our paper is a significant contribution in that direction with general applicability to any choice of basis sets. Finally, contrary to an allusion in the abstract and assertions in the main text of the Comment that unphysical oscillations of the OEP are supposedly attributed to the common energy denominator approximation, in fact, such

  11. An 'optimal' spawning algorithm for adaptive basis set expansion in nonadiabatic dynamics

    SciTech Connect

    Yang, Sandy; Coe, Joshua D.; Kaduk, Benjamin; Martinez, Todd J.

    2009-04-07

    The full multiple spawning (FMS) method has been developed to simulate quantum dynamics in the multistate electronic problem. In FMS, the nuclear wave function is represented in a basis of coupled, frozen Gaussians, and a 'spawning' procedure prescribes a means of adaptively increasing the size of this basis in order to capture population transfer between electronic states. Herein we detail a new algorithm for specifying the initial conditions of newly spawned basis functions that minimizes the number of spawned basis functions needed for convergence. 'Optimally' spawned basis functions are placed to maximize the coupling between parent and child trajectories at the point of spawning. The method is tested with a two-state, one-mode avoided crossing model and a two-state, two-mode conical intersection model.

  12. 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)

  13. 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}.

  14. Optimal site-centered electronic structure basis set from a displaced-center expansion: Improved results via a priori estimates of saddle points in the density

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Johnson, D. D.

    2009-09-01

    Site-centered, electronic-structure methods use an expansion inside nonoverlapping “muffin-tin” (MT) spheres plus an interstitial basis set. As the boundary separating the more spherical from nonspherical density between atoms, the “saddle-point” radii (SPR) in the density provide an optimal spherical region for expanding in spherical harmonics, as used in augmented plane wave, muffin-tin orbital, and multiple-scattering [Korringa, Kohn, and Rostoker (KKR)] methods. These MT-SPR guarantee unique, convex Voronoi polyhedra at each site, in distinction to Bader topological cells. We present a numerically fast, two-center expansion to find SPR a priori from overlapping atomic charge densities, valid also for disordered alloys. We adopt this MT-SPR basis for KKR in the atomic sphere approximation and study (dis)ordered alloys with large differences in atomic size (fcc CoPt and bcc CrW). For this simple and unique improvement, we find formation energies and structural parameters in strikingly better agreement with more exact methods or experiment, and resolve issues with former results.

  15. Atomic orbital basis sets for use with effective core potentials

    SciTech Connect

    Blaudeau, J.P.; Brozell, S.R.; Matsika, S.; Zhang, Z.; Pitzer, R.M.

    2000-03-15

    Basis sets developed for use with effective core potentials describe pseudo-orbitals rather than orbitals. The primitive Gaussian functions and the contraction coefficients in the basis set must therefore both describe the valence region effectively and allow the pseudo-orbital to be small in the core region. The latter is particularly difficult using 1s primitive functions, which have their maxima at the nucleus. Several methods of choosing contraction coefficients are tried, and it is found that natural orbitals give the best results. The number and optimization of primitive functions are done following Dunning's correlation-consistent procedure. Optimization of orbital exponents for larger atoms frequently results in coalescence of adjacent exponents; use of orbitals with higher principal quantum number is one alternative. Actinide atoms or ions provide the most difficult cases in that basis sets must be optimized for valence shells of different radial size simultaneously considering correlation energy and spin-orbit energy.

  16. 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.

  17. 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.

  18. Many-Body Basis Set Superposition Effect.

    PubMed

    Ouyang, John F; Bettens, Ryan P A

    2015-11-10

    The basis set superposition effect (BSSE) arises in electronic structure calculations of molecular clusters when questions relating to interactions between monomers within the larger cluster are asked. The binding energy, or total energy, of the cluster may be broken down into many smaller subcluster calculations and the energies of these subsystems linearly combined to, hopefully, produce the desired quantity of interest. Unfortunately, BSSE can plague these smaller fragment calculations. In this work, we carefully examine the major sources of error associated with reproducing the binding energy and total energy of a molecular cluster. In order to do so, we decompose these energies in terms of a many-body expansion (MBE), where a "body" here refers to the monomers that make up the cluster. In our analysis, we found it necessary to introduce something we designate here as a many-ghost many-body expansion (MGMBE). The work presented here produces some surprising results, but perhaps the most significant of all is that BSSE effects up to the order of truncation in a MBE of the total energy cancel exactly. In the case of the binding energy, the only BSSE correction terms remaining arise from the removal of the one-body monomer total energies. Nevertheless, our earlier work indicated that BSSE effects continued to remain in the total energy of the cluster up to very high truncation order in the MBE. We show in this work that the vast majority of these high-order many-body effects arise from BSSE associated with the one-body monomer total energies. Also, we found that, remarkably, the complete basis set limit values for the three-body and four-body interactions differed very little from that at the MP2/aug-cc-pVDZ level for the respective subclusters embedded within a larger cluster. PMID:26574311

  19. 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.

  20. Gravitational Lens Modeling with Basis Sets

    NASA Astrophysics Data System (ADS)

    Birrer, Simon; Amara, Adam; Refregier, Alexandre

    2015-11-01

    We present a strong lensing modeling technique based on versatile basis sets for the lens and source planes. Our method uses high performance Monte Carlo algorithms, allows for an adaptive build up of complexity, and bridges the gap between parametric and pixel based reconstruction methods. We apply our method to a Hubble Space Telescope image of the strong lens system RX J1131-1231 and show that our method finds a reliable solution and is able to detect substructure in the lens and source planes simultaneously. Using mock data, we show that our method is sensitive to sub-clumps with masses four orders of magnitude smaller than the main lens, which corresponds to about {10}8{M}⊙ , without prior knowledge of the position and mass of the sub-clump. The modeling approach is flexible and maximizes automation to facilitate the analysis of the large number of strong lensing systems expected in upcoming wide field surveys. The resulting search for dark sub-clumps in these systems, without mass-to-light priors, offers promise for probing physics beyond the standard model in the dark matter sector.

  1. 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.

  2. Correlation consistent basis sets for the atoms In–Xe

    SciTech Connect

    Mahler, Andrew; Wilson, Angela K.

    2015-02-28

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

  3. QUALITY: A program to assess basis set quality

    NASA Astrophysics Data System (ADS)

    Sordo, J. A.

    1998-09-01

    A program to analyze in detail the quality of basis sets is presented. The information provided by the application of a wide variety of (atomic and/or molecular) quality criteria is processed by using a methodology that allows one to determine the most appropriate quality test to select a basis set to compute a given (atomic or molecular) property. Fuzzy set theory is used to choose the most adequate basis set to compute simultaneously a set of properties.

  4. Tests for Wavelets as a Basis Set

    NASA Astrophysics Data System (ADS)

    Baker, Thomas; Evenbly, Glen; White, Steven

    A wavelet transformation is a special type of filter usually reserved for image processing and other applications. We develop metrics to evaluate wavelets for general problems on test one-dimensional systems. The goal is to eventually use a wavelet basis in electronic structure calculations. We compare a variety of orthogonal wavelets such as coiflets, symlets, and daubechies wavelets. We also evaluate a new type of orthogonal wavelet with dilation factor three which is both symmetric and compact in real space. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award #DE-SC008696.

  5. 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.

  6. 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.

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

    SciTech Connect

    Hill, J. Grant E-mail: kipeters@wsu.edu; Peterson, Kirk A. E-mail: kipeters@wsu.edu

    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.

  8. Segmented contracted basis sets for one- and two-component Dirac-Fock effective core potentials.

    PubMed

    Weigend, Florian; Baldes, Alexander

    2010-11-01

    Segmented contracted basis sets for 4d, 5d, 5s, and 6s elements of split (double zeta) valence to quadruple zeta valence quality optimized for Dirac-Fock effective core potentials (ECPs) are presented. They were obtained from previous bases optimized for Wood-Boring ECPs by comparably small modifications and reoptimizations. Additionally extensions for two-component self-consistent-field treatments accounting for spin-orbit (SO) coupling were designed and optimized. Reliability for chemical applications was assessed by comparing results to those obtained with a very large (19s16p17d7f6g) reference basis for a set of more than 80 representatively chosen 5s-5d compounds. Moreover, the effect of different types of ECPs and that of the SO-coupling at the basis set limit of density functional theory is documented for the above set of molecules extended by 40 5p-6p compounds. PMID:21054001

  9. Point Set Denoising Using Bootstrap-Based Radial Basis Function

    PubMed Central

    Ramli, Ahmad; Abd. Majid, Ahmad

    2016-01-01

    This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study. PMID:27315105

  10. Basis Set Dependence of Vibrational Raman and Raman Optical Activity Intensities.

    PubMed

    Cheeseman, James R; Frisch, Michael J

    2011-10-11

    We present a systematic study of the basis set dependence of the backscattering vibrational Raman intensities and Raman Optical Activity (ROA) intensity differences. The accuracies of computed Raman intensities and ROA intensity differences for a series of commonly used basis sets are reported, relative to large reference basis sets, using the B3LYP density functional. This study attempts to separately quantify the relative accuracies obtained from particular basis set combinations: one for the geometry optimization and force field computation and the other for the computation of Raman and ROA tensors. We demonstrate here that the basis set requirements for the geometry and force fields are not similar to those of the Raman and ROA tensors. The Raman and ROA tensors require basis sets with diffuse functions, while geometry optimizations and force field computations typically do not. Eleven molecules were examined: (S)-methyloxirane, (S)-methylthirane, (R)-epichlorhydrin, (S)-CHFClBr, (1S,5S)-α-pinene, (1S,5S)-β-pinene, (1S,4S)-norborneneone, (M)-σ-[4]-helicene, an enone precursor to a cytotoxic sesquiterpene, the gauche-gauche conformer of the monosaccharide methyl-β-d-glucopyranose, and the dipeptide Ac-(alanine)2-NH2. For the molecules examined here, intensities and intensity differences obtained from Raman and ROA tensors computed using the aug-cc-pVDZ basis set are nearly equivalent to those computed with the larger aug-cc-pVTZ basis set. We find that modifying the aug-cc-pVDZ basis set by removing the set of diffuse d functions on all atoms (while keeping the diffuse s and p sets), denoted as aug(sp)-cc-pVDZ, results in a basis set which is significantly faster without much reduction in the overall accuracy. In addition, the popular rDPS basis set introduced by Zuber and Hug offers a good compromise between accuracy and efficiency. The combination of either the aug(sp)-pVDZ or rDPS basis for the computation of the Raman and ROA tensors with the 6-31G

  11. Localized orbitals from basis sets augmented with diffuse functions

    NASA Astrophysics Data System (ADS)

    Høyvik, Ida-Marie; Jørgensen, Poul

    2013-05-01

    Orbital localization of occupied and virtual Hartree-Fock orbitals generated from basis sets augmented with diffuse functions is performed using the Pipek-Mezey, Boys, powers of the second central moment, and powers of the fourth central moment localizations. The locality of the obtained orbital sets are presented in terms of second and fourth moment orbital spreads. The results show that both local occupied and virtual orbitals may be obtained when using powers of the second central moment and powers of the fourth central moment localizations, while the Pipek-Mezey and Boys localizations fail to produce sets of local virtual orbitals. The locality of the fourth central moment virtual orbitals exhibits a locality similar to the locality of a Boys localization for non-augmented basis sets.

  12. 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.

  13. Basis-set extensions for two-component spin-orbit treatments of heavy elements.

    PubMed

    Armbruster, Markus K; Klopper, Wim; Weigend, Florian

    2006-11-14

    The accuracy of standard basis sets of quadruple-zeta and lower quality for the use in two-component self-consistent field procedures including spin-orbit coupling is investigated for the elements In-I and Au-At. Spin-orbit coupling leads to energetic and spatial splittings of inner shells, which are not described accurately with standard basis sets optimized for scalar relativistic calculations. This results in large errors in total atomic energies and significant errors in atomization energies of compounds containing these atoms. We show how these errors can be corrected by adding just a few steep sets of basis functions and demonstrate the quality of the resulting extended basis sets. PMID:17066175

  14. Accurate Complete Basis Set Extrapolation of Direct Random Phase Correlation Energies.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn

    2015-08-11

    The direct random phase approximation (dRPA) is a promising way to obtain improvements upon the standard semilocal density functional results in many aspects of computational chemistry. In this paper, we address the slow convergence of the calculated dRPA correlation energy with the increase of the quality and size of the popular Gaussian-type Dunning's correlation consistent aug-cc-pVXZ split valence atomic basis set family. The cardinal number X controls the size of the basis set, and we use X = 3-6 in this study. It is known that even the very expensive X = 6 basis sets lead to large errors for the dRPA correlation energy, and thus complete basis set extrapolation is necessary. We study the basis set convergence of the dRPA correlation energies on a set of 65 hydrocarbon isomers from CH4 to C6H6. We calculate the iterative density fitted dRPA correlation energies using an efficient algorithm based on the CC-like form of the equations using the self-consistent HF orbitals. We test the popular inverse cubic, the optimized exponential, and inverse power formulas for complete basis set extrapolation. We have found that the optimized inverse power based extrapolation delivers the best energies. Further analysis showed that the optimal exponent depends on the molecular structure, and the most efficient two-point energy extrapolations that use X = 3 and 4 can be improved considerably by considering the atomic composition and hybridization states of the atoms in the molecules. Our results also show that the optimized exponents that yield accurate X = 3 and 4 extrapolated dRPA energies for atoms or small molecules might be inaccurate for larger molecules. PMID:26574475

  15. 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.

  16. Full Waveform Inversion with Optimal Basis Functions

    NASA Astrophysics Data System (ADS)

    Sun, Gang; Chang, Qianshun; Sheng, Ping

    2003-03-01

    Based on the approach suggested by Tarantola, and Gauthier etal., we show that the alternate use of the step (linear) function basis and the block function (quasi-δ function) basis can give accurate full waveform inversion results for the layered acoustic systems, starting from a uniform background. Our method is robust against additive white noise (up to 20% of the signal) and can resolve layers that are comparable to or smaller than a wavelength in thickness. The physical reason for the success of our approach is illustrated through a simple example.

  17. Universal perturbative explicitly correlated basis set incompleteness correction

    NASA Astrophysics Data System (ADS)

    Torheyden, Martin; Valeev, Edward F.

    2009-11-01

    Basis set incompleteness error for an arbitrary approximate electronic wave function is robustly reduced using a second-order perturbative correction into a basis of explicitly correlated, internally contracted geminal functions. The Hylleraas functional for the second-order energy correction is evaluated algebraically involving at most a four-electron reduced density matrix and four-electron integrals. By using the R12 technology in combination with screening approximations such a correction only requires a two-electron reduced density matrix and two-electron integrals. Preliminary investigations of potential energy surfaces of hydrogen fluoride and nitrogen molecules at the multireference configuration interaction singles and doubles indicate that with the perturbative correction only an aug-cc-pVDZ basis is necessary to compute correlation energies of an aug-cc-pVQZ quality, or better. The proposed correction, dubbed [2]R12, can in principle be combined with any single reference and multireference method in use today.

  18. Informatics-Based Energy Fitting Scheme for Correlation Energy at Complete Basis Set Limit.

    PubMed

    Seino, Junji; Nakai, Hiromi

    2016-09-30

    Energy fitting schemes based on informatics techniques using hierarchical basis sets with small cardinal numbers were numerically investigated to estimate correlation energies at the complete basis set limits. Numerical validations confirmed that the conventional two-point extrapolation models can be unified into a simple formula with optimal parameters obtained by the same test sets. The extrapolation model was extended to two-point fitting models by a relaxation of the relationship between the extrapolation coefficients or a change of the fitting formula. Furthermore, n-scheme fitting models were developed by the combinations of results calculated at several theory levels and basis sets to compensate for the deficiencies in the fitting model at one level of theory. Systematic assessments on the Gaussian-3X and Gaussian-2 sets revealed that the fitting models drastically reduced errors with equal or smaller computational effort. © 2016 Wiley Periodicals, Inc. PMID:27454327

  19. 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

  20. 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.

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

    PubMed

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

    2016-03-14

    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 ⟨r(n)⟩ (-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. PMID:26979680

  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. PMID:26905100

  3. Global and Local Optimization Algorithms for Optimal Signal Set Design

    PubMed Central

    Kearsley, Anthony J.

    2001-01-01

    The problem of choosing an optimal signal set for non-Gaussian detection was reduced to a smooth inequality constrained mini-max nonlinear programming problem by Gockenbach and Kearsley. Here we consider the application of several optimization algorithms, both global and local, to this problem. The most promising results are obtained when special-purpose sequential quadratic programming (SQP) algorithms are embedded into stochastic global algorithms.

  4. Fuzzy set applications in engineering optimization: Multilevel fuzzy optimization

    NASA Technical Reports Server (NTRS)

    Diaz, Alejandro R.

    1989-01-01

    A formulation for multilevel optimization with fuzzy objective functions is presented. With few exceptions, formulations for fuzzy optimization have dealt with a one-level problem in which the objective is the membership function of a fuzzy set formed by the fuzzy intersection of other sets. In the problem examined here, the goal set G is defined in a more general way, using an aggregation operator H that allows arbitrary combinations of set operations (union, intersection, addition) on the individual sets Gi. This is a straightforward extension of the standard form, but one that makes possible the modeling of interesting evaluation strategies. A second, more important departure from the standard form will be the construction of a multilevel problem analogous to the design decomposition problem in optimization. This arrangement facilitates the simulation of a system design process in which different components of the system are designed by different teams, and different levels of design detail become relevant at different time stages in the process: global design features early, local features later in the process.

  5. 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).

  6. 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.

  7. 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.

  8. 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. PMID:27475350

  9. 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.

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

    PubMed

    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)] 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. PMID:23902066

  11. 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.

  12. 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.

  13. 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 ...

  14. Extension of the basis set of linearized augmented plane wave (LAPW) method by using supplemented tight binding basis functions

    NASA Astrophysics Data System (ADS)

    Nikolaev, A. V.; Lamoen, D.; Partoens, B.

    2016-07-01

    In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the u ˙ l -component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.

  15. Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: a basis set and correlation study.

    PubMed

    Kjaer, Hanna; Nielsen, Monia R; Pagola, Gabriel I; Ferraro, Marta B; Lazzeretti, Paolo; Sauer, Stephan P A

    2012-09-01

    In this article, we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the nuclear magnetic resonance (NMR) indirect nuclear spin-spin coupling constant with respect to an external electric field and play an important role for both chiral discrimination and solvation effects on NMR coupling constants. In this study, we illustrate the effects of one-electron basis sets and electron correlation both at the level of density functional theory as well as second-order polarization propagator approximation for the small molecule hydrogen peroxide, which allowed us to perform calculations with the largest available basis sets optimized for the calculation of NMR coupling constants. We find a systematic but rather slow convergence with the one-electron basis set and that augmentation functions are required. We observe also large and nonsystematic correlation effects with significant differences between the density functional and wave function theory methods. PMID:22618604

  16. On the performance of atomic natural orbital basis sets: A full configuration interaction study

    SciTech Connect

    Illas, F. Departament de Quimica Fisica, Grup de Quimica Quantica, Facultat de Quimica, Universitat de Barcelona, C Ricart, J.M. ); Rubio, J. ); Bagus, P.S. )

    1990-10-01

    The performance of atomic natural orbital (ANO) basis sets has been studied by comparing self-consistant field (SCF) and full configuration interaction (CI) results obtained for the first row atoms and hydrides. The ANO results have been compared with those obtained using a segmented basis set containing the same number of contracted basis functions. The total energies obtained with the ANO basis sets are always lower than the one obtained by using the segmented one. However, for the hydrides, differential electronic correlation energy obtained with the ANO basis set may be smaller than the one recovered with the segmented set. We relate this poorer differential correlation energy for the ANO basis set to the fact that only one contracted {ital d} function is used for the ANO and segmented basis sets.

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

    NASA Astrophysics Data System (ADS)

    Chen, Mingzhou; Dholakia, Kishan; Mazilu, Michael

    2016-03-01

    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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Lombardini, Richard; Nowara, Ewa; Johnson, Bruce

    2015-03-01

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

  20. Extension of the basis set of linearized augmented plane wave (LAPW) method by using supplemented tight binding basis functions.

    PubMed

    Nikolaev, A V; Lamoen, D; Partoens, B

    2016-07-01

    In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the u̇l-component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets. PMID:27394093

  1. Optimal Assembly of Tests with Item Sets.

    ERIC Educational Resources Information Center

    van der Linden, Wim J.

    2000-01-01

    Presents six computational methods based on mixed-integer programming for assembling tests from a bank with an item-set structure and evaluated these methods using mathematical programming feasibiity and expected solution times. Illustrates these methods with two data sets from the Law School Admission Test. Discusses the best approximations to…

  2. General approach for representing and propagating partially coherent terahertz fields with application to Gabor basis sets.

    PubMed

    Berry, Rachel H; Hobson, Michael P; Withington, Stafford

    2004-05-01

    We discuss a general theoretical framework for representing and propagating fully coherent, fully incoherent, and the intermediate regime of partially coherent submillimeter-wave fields by means of general sampled basis functions, which may have any degree of completeness. Partially coherent fields arise when finite-throughput systems induce coherence on incoherent fields. This powerful extension to traditional modal analysis methods by using undercomplete Gaussian-Hermite modes can be employed to analyze and optimize such Gaussian quasi-optical techniques. We focus on one particular basis set, the Gabor basis, which consists of overlapping translated and modulated Gaussian beams. We present high-accuracy numerical results from field reconstructions and propagations. In particular, we perform one-dimensional analyses illustrating the Van Cittert-Zernike theorem and then extend our simulations to two dimensions, including simple models of horn and bolometer arrays. Our methods and results are of practical importance as a method for analyzing terahertz fields, which are often partially coherent and diffraction limited so that ray tracing is inaccurate and physical optics computationally prohibitive. PMID:15139431

  3. Atomic self-consistent-field program by the basis set expansion method: Columbus version

    NASA Astrophysics Data System (ADS)

    Pitzer, Russell M.

    2005-08-01

    A revised and extended (Columbus) version of the Chicago atomic self-consistent-field (Hartree-Fock) program of 1963 is described. Its principal present use is in developing Gaussian basis sets for molecular calculations. Complete memory allocation (using Fortran 90) has been added as well as improved integral formulas and efficient and simple programming features. Energy-expression coefficients have been added sufficient to treat the ground states of all atoms to the extent that Russell-Saunders (LS) coupling applies. Excited states with large angular-momentum orbitals can be treated. Relativistic effects can be included to the extent possible with relativistic effective core potentials. A review of earlier work is included. Program summaryProgram title: atmscf Catalogue identifier: ADVR Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVR Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Programming language: Fortran 90 Computer: Sun, SGI, PC Operating system: Solaris, Irix, Linux RAM: 10 Mbytes No. of lines in distributed program, including test data, etc.: 2113 No. of bytes in distributed program, including test data, etc.: 15 379 Distribution format: tar.gz Nature of problem: Energies and wave functions, at the Hartree-Fock level Solution method: Expansions in Gaussian or Slater functions. Iterative minimization of the total energy. Optimization of exponential parameters. Used frequently for developing Gaussian basis sets for molecular use Running time: Typical 30 s per calculation

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

    PubMed

    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. PMID:26026434

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Shirkov, Leonid; Makarewicz, Jan

    2015-05-01

    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.

  7. 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.

  8. 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.

  9. 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

  10. A Hartree-Fock study of the confined helium atom: Local and global basis set approaches

    NASA Astrophysics Data System (ADS)

    Young, Toby D.; Vargas, Rubicelia; Garza, Jorge

    2016-02-01

    Two different basis set methods are used to calculate atomic energy within Hartree-Fock theory. The first is a local basis set approach using high-order real-space finite elements and the second is a global basis set approach using modified Slater-type orbitals. These two approaches are applied to the confined helium atom and are compared by calculating one- and two-electron contributions to the total energy. As a measure of the quality of the electron density, the cusp condition is analyzed.

  11. 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.

  12. 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

  13. Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness.

    PubMed

    Kulik, Heather J; Seelam, Natasha; Mar, Brendan D; Martínez, Todd J

    2016-07-28

    Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors. PMID:27383567

  14. What is the most efficient way to reach the canonical MP2 basis set limit?

    NASA Astrophysics Data System (ADS)

    Liakos, Dimitrios G.; Izsák, Róbert; Valeev, Edward F.; Neese, Frank

    2013-09-01

    Various ways of reaching the complete basis set limit at the second-order Møller-Plesset perturbation theory (MP2) level are compared with respect to their cost-to-accuracy ratio. These include: (1) traditional MP2 calculations with correlation consistent basis sets of increasing size, with and without the resolution of identity for Coulomb and exchange (RIJK) or the combined RIJ and 'chain of spheres' (RIJCOSX) approximations; (2) basis set extrapolation obtained with the same MP2 variants; and (3) explicitly correlated F12-MP2 methods. The time required to solve the Hartree-Fock equations is part of the evaluation because the overall efficiency is of central interest in this work. Results were obtained for the ISO34, DC9 and S66 test sets and were analysed in terms of efficiency and accuracy for total energies, reaction energies and their effect on the basis set superposition error. Among the methods studied, the RIJK-MP2-F12 and RIJK-MP2-EP1 (where EP1 stands for 'Extrapolation Protocol 1' as explained in the text) methods perform outstandingly well. Although extrapolation is, in general, slightly faster than explicit correlation, it is found that for reaction energies, RIJK-MP2-F12 performs systematically better. This holds especially in combination with a triple zeta basis set, in which case it even outperforms the much more costly extrapolation involving quadruple- and quintuple-zeta correlation consistent basis sets.

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

    PubMed

    Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

    2011-10-01

    In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections. PMID:21992293

  16. From correlation-consistent to polarization-consistent basis sets estimation of NMR spin spin coupling constant in the B3LYP Kohn Sham basis set limit

    NASA Astrophysics Data System (ADS)

    Kupka, Teobald

    2008-08-01

    Based on B3LYP spin-spin coupling constants (SSCC) of several molecules calculated with cc-pV xZ, cc-pCV xZ, cc-pCV xZ-sd and cc-pCV xZ-sd+ t basis sets, a reasonably fit, using the two-parameter formula, to the Kohn-Sham complete basis set limit (CBS) is shown. Improvement in the CBS values going from cc-pV xZ to the most elaborated cc-pCV xZ-sd+ t basis set family is observed: standard deviation for all data drops from 33.7 to 23.1, and from 6.0 to 4.8 Hz after excluding problematic 1J(F,H) and 1J(F,C). Calculation of water's 1J(OH) using B3LYP/cc-pCV xZ and B3LYP/pcJ- n significantly improved the FC term convergence.

  17. 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.

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

    SciTech Connect

    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.

  19. An active set algorithm for nonlinear optimization with polyhedral constraints

    NASA Astrophysics Data System (ADS)

    Hager, William W.; Zhang, Hongchao

    2016-08-01

    A polyhedral active set algorithm PASA is developed for solving a nonlinear optimization problem whose feasible set is a polyhedron. Phase one of the algorithm is the gradient projection method, while phase two is any algorithm for solving a linearly constrained optimization problem. Rules are provided for branching between the two phases. Global convergence to a stationary point is established, while asymptotically PASA performs only phase two when either a nondegeneracy assumption holds, or the active constraints are linearly independent and a strong second-order sufficient optimality condition holds.

  20. An explicitly correlated approach to basis set incompleteness in full configuration interaction quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Booth, George H.; Cleland, Deidre; Alavi, Ali; Tew, David P.

    2012-10-01

    By performing a stochastic dynamic in a space of Slater determinants, the full configuration interaction quantum Monte Carlo (FCIQMC) method has been able to obtain energies which are essentially free from systematic error to the basis set correlation energy, within small and systematically improvable error bars. However, the weakly exponential scaling with basis size makes converging the energy with respect to basis set costly and in larger systems, impossible. To ameliorate these basis set issues, here we use perturbation theory to couple the FCIQMC wavefunction to an explicitly correlated strongly orthogonal basis of geminals, following the { [2]_{{R12}} } approach of Valeev et al. The required one- and two-particle density matrices are computed on-the-fly during the FCIQMC dynamic, using a sampling procedure which incurs relatively little additional computation expense. The F12 energy corrections are shown to converge rapidly as a function of sampling, both in imaginary time and number of walkers. Our pilot calculations on the binding curve for the carbon dimer, which exhibits strong correlation effects as well as substantial basis set dependence, demonstrate that the accuracy of the FCIQMC-F12 method surpasses that of all previous FCIQMC calculations, and that the F12 correction improves results equivalent to increasing the quality of the one-electron basis by two cardinal numbers.

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

    PubMed

    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 H2, O2, and N2, 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. PMID:26277128

  2. 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.

  3. 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

    2016-08-01

    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. PMID:27087397

  4. 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. PMID:26579898

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.

    1992-01-01

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

  12. 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.

  13. 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.

  14. 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

  15. 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.

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

    PubMed

    Hofer, Thomas S

    2013-01-01

    A systematic investigation of three different electron-electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li(+) and Be(2+) using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one-electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li(+) and Be(2+). In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used. PMID:24790952

  17. 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

  18. Discrete Optimization with Polynomially Detectable Boundaries and Restricted Level Sets

    NASA Astrophysics Data System (ADS)

    Zinder, Yakov; Memar, Julia; Singh, Gaurav

    The paper describes an optimization procedure for a class of discrete optimization problems which is defined by certain properties of the boundary of the feasible region and level sets of the objective function. It is shown that these properties are possessed, for example, by various scheduling problems, including a number of well-known NP-hard problems which play an important role in scheduling theory. For an important particular case the presented optimization procedure is compared with a version of the branch-and-bound algorithm by means of computational experiments.

  19. Intermolecular transfer integrals for organic molecular materials: can basis set convergence be achieved?

    NASA Astrophysics Data System (ADS)

    Huang, Jingsong; Kertesz, Miklos

    2004-05-01

    Intermolecular transfer integrals, and associated band-structures of organic molecular materials can be calculated through a dimer approach. Extensive numerical studies are performed on an ethylene π-dimer to investigate the basis sets dependence of transfer integrals. Convergence of calculated transfer integrals is achieved with respect to both Gaussian and plane-wave basis sets, provided the same level of theory is used. Effects of diffuse and polarization Gaussian functions on transfer integrals are identified. Comparison of experimental and theoretical values of transfer integrals of the TTF-TCNQ charge transfer salt is also presented.

  20. Strategies for reducing basis set superposition error (BSSE) in O/AU and O/Ni

    NASA Astrophysics Data System (ADS)

    Shuttleworth, I. G.

    2015-11-01

    The effect of basis set superposition error (BSSE) and effective strategies for the minimisation have been investigated using the SIESTA-LCAO DFT package. Variation of the energy shift parameter ΔEPAO has been shown to reduce BSSE for bulk Au and Ni and across their oxygenated surfaces. Alternative strategies based on either the expansion or contraction of the basis set have been shown to be ineffective in reducing BSSE. Comparison of the binding energies for the surface systems obtained using LCAO were compared with BSSE-free plane wave energies.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  2. 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

    2016-10-01

    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. PMID:27510431

  3. 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 at the CCSD(T)/ Complete Basis Set limit and examine the validity of the BSSE-correction, previously challenged by Kalescky, Kraka and Cremer [J. Chem. Phys. 140 (2014) 084315]. Our best estimate of D0=14.3±0.1 kcal/mol is in excellent agreement with the experimental value of 14.22±0.12 kcal/mol. The BSSE correction is indeed valid for this system since it exhibits the expected behavior of decreasing with increasing basis set size and its inclusion produces the same limit (within 0.1 kcal/mol) as the one obtained from extrapolation of the uncorrected binding energy. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. A portion of this research was performed using the Molecular Science Computing Facility (MSCF) in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at PNNL.

  4. Molecular Dipole Moments within the Incremental Scheme Using the Domain-Specific Basis-Set Approach.

    PubMed

    Fiedler, Benjamin; Coriani, Sonia; Friedrich, Joachim

    2016-07-12

    We present the first implementation of the fully automated incremental scheme for CCSD unrelaxed dipole moments using the domain-specific basis-set approach. Truncation parameters are varied, and the accuracy of the method is statistically analyzed for a test set of 20 molecules. The local approximations introduce small errors at second order and negligible ones at third order. For a third-order incremental CCSD expansion with a CC2 error correction, a cc-pVDZ/SV domain-specific basis set (tmain = 3.5 Bohr), and the truncation parameter f = 30 Bohr, we obtain a mean error of 0.00 mau (-0.20 mau) and a standard deviation of 1.95 mau (2.17 mau) for the total dipole moments (Cartesian components of the dipole vectors). By analyzing incremental CCSD energies, we demonstrate that the MP2 and CC2 error correction schemes are an exclusive correction for the domain-specific basis-set error. Our implementation of the incremental scheme provides fully automated computations of highly accurate dipole moments at reduced computational cost and is fully parallelized in terms of the calculation of the increments. Therefore, one can utilize the incremental scheme, on the same hardware, to extend the basis set in comparison to standard CCSD and thus obtain a better total accuracy. PMID:27300371

  5. 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}.

  6. Orthonormal curvature polynomials over a unit circle: basis set derived from curvatures of Zernike polynomials.

    PubMed

    Zhao, Chunyu; Burge, James H

    2013-12-16

    Zernike polynomials are an orthonormal set of scalar functions over a circular domain, and are commonly used to represent wavefront phase or surface irregularity. In optical testing, slope or curvature of a surface or wavefront is sometimes measured instead, from which the surface or wavefront map is obtained. Previously we derived an orthonormal set of vector polynomials that fit to slope measurement data and yield the surface or wavefront map represented by Zernike polynomials. Here we define a 3-element curvature vector used to represent the second derivatives of a continuous surface, and derive a set of orthonormal curvature basis functions that are written in terms of Zernike polynomials. We call the new curvature functions the C polynomials. Closed form relations for the complete basis set are provided, and we show how to determine Zernike surface coefficients from the curvature data as represented by the C polynomials. PMID:24514717

  7. 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.

  8. A Novel Gaussian-Sinc mixed Basis Set for Electronic Structure calculations

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    A Gaussian-Sinc mixed basis set for the computation of the electronic structure of atoms and molecules is presented. Excellent bases functions are known for ``core'' and ``valence'' separately, such as Gaussians for the ``core'' wave functions and Plane-waves for ``valance'' wave functions, but as yet no method is known that can accurately deal with both regimes in a single basis. A Gaussian-Sinc mixed basis can do both. This method resolves several issues such as: i) the Sincs basis spans the same space as the plane-waves basis, yet are semi-local enough to define all interaction elements including Exchange; ii) the Gaussians span the spherically symmetric core states and can be mixed with the Sinc functions in a computationally efficient methodology; iii) together, this mixed basis set is a flexible, computationally efficient and a highly accurate method for solving atomic and molecular problems. This methodology has been implemented within the Hartree-Fock level of theory within ultra-strong magnetic fields. To demonstrate the utility of this new method, we calculated the ground state Hartree-Fock energies to five digits accuracy in ultra strong magnetic fields for Helium to Neon, Molecular Hydrogen, Water, Carbon dioxide and Benzene. Welch Foundation (Grant J-1675), the ARO (Grant W911Nf-13-1-0162), the Texas Southern University High Performance Computing Center (http:/hpcc.tsu.edu/; Grant PHY-1126251) and NSF-CREST CRCN project (Grant HRD-1137732).

  9. 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...

  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 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 determ...

  11. 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

  12. 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. PMID:25702000

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

    NASA Astrophysics Data System (ADS)

    Peterson, Kirk A.

    2015-02-01

    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.

  14. Level set based structural topology optimization for minimizing frequency response

    NASA Astrophysics Data System (ADS)

    Shu, Lei; Wang, Michael Yu; Fang, Zongde; Ma, Zhengdong; Wei, Peng

    2011-11-01

    For the purpose of structure vibration reduction, a structural topology optimization for minimizing frequency response is proposed based on the level set method. The objective of the present study is to minimize the frequency response at the specified points or surfaces on the structure with an excitation frequency or a frequency range, subject to the given amount of the material over the admissible design domain. The sensitivity analysis with respect to the structural boundaries is carried out, while the Extended finite element method (X-FEM) is employed for solving the state equation and the adjoint equation. The optimal structure with smooth boundaries is obtained by the level set evolution with advection velocity, derived from the sensitivity analysis and the optimization algorithm. A number of numerical examples, in the frameworks of two-dimension (2D) and three-dimension (3D), are presented to demonstrate the feasibility and effectiveness of the proposed approach.

  15. 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.

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

    PubMed

    Borges, A; Solomon, G C

    2016-05-21

    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. PMID:27208940

  17. Sensitivity of the properties of ruthenium ``blue dimer'' to method, basis set, and continuum model

    NASA Astrophysics Data System (ADS)

    Ozkanlar, Abdullah; Clark, Aurora E.

    2012-05-01

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

  18. 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.

  19. Relativistic Prolapse-Free Gaussian Basis Set of Quadruple-ζ Quality: (aug-)RPF-4Z. I. The s- and p-Block Elements.

    PubMed

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

    2014-09-01

    This study reports a new relativistic prolapse-free Gaussian basis set series of quadruple-ζ quality, RPF-4Z, and an augmented version that includes extra diffuse functions, aug-RPF-4Z, for all the s- and p-block elements. The relativistic adapted Gaussian basis sets (RAGBSs), which are free of variational prolapse, were used as the starting primitive sets. Exponents of correlating/polarization functions were taken from a polynomial version of the generator coordinate Dirac-Fock (p-GCDF) method, in which the previously optimized RAGBS parameters are applied. By using such procedure we aimed to reduce the computational demand of these sets in comparison with fully optimized ones. The effect of these basis set increments on the correlation energy was evaluated by atomic multireference configuration interaction calculations with single and double excitations out of the valence shell. Finally, atomic and molecular calculations of fundamental properties (bond lengths, vibrational frequencies, dipole moments and electron affinities) corroborate the quadruple-ζ quality of these new sets that are also about half-time-consuming than the correspondent Dyall's v4z sets. The read-to use format of these (aug-)RPF-4Fz sets are available as Supporting Information files and can also be found at http://basis-sets.iqsc.usp.br/ . PMID:26588525

  20. 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.

  1. 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.

  2. Truncated spherical-wave basis set for first-principles pseudopotential calculations

    NASA Astrophysics Data System (ADS)

    Monserrat, B.; Haynes, P. D.

    2010-11-01

    Analytic results for two- and three-centre integrals are derived for the truncated spherical-wave basis set designed for first-principles pseudopotential calculations within density-functional theory. These allow the overlap, kinetic energy and non-local pseudopotential matrix elements to be calculated efficiently and accurately. In particular, the scaling of the computational effort with maximum angular momentum component is dramatically improved and the projection method takes full account of the discontinuities in the basis functions arising from their localization within spherical regions.

  3. Benchmarks of electronically excited states: Basis set effects on CASPT2 results

    NASA Astrophysics Data System (ADS)

    Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.; Thiel, Walter

    2010-11-01

    Vertical excitation energies and one-electron properties are computed for the valence excited states of 28 medium-sized organic benchmark molecules using multistate multiconfigurational second-order perturbation theory (MS-CASPT2) and the augmented correlation-consistent aug-cc-pVTZ basis set. They are compared with previously reported MS-CASPT2 results obtained with the smaller TZVP basis. The basis set extension from TZVP to aug-cc-pVTZ causes rather minor and systematic shifts in the vertical excitation energies that are normally slightly reduced (on average by 0.11 eV for the singlets and by 0.09 eV for the triplets), whereas the changes in the calculated oscillator strengths and dipole moments are somewhat more pronounced on a relative scale. These basis set effects at the MS-CASPT2 level are qualitatively and quantitatively similar to those found at the coupled cluster level for the same set of benchmark molecules. The previously proposed theoretical best estimates (TBE-1) for the vertical excitation energies for 104 singlet and 63 triplet excited states of the benchmark molecules are upgraded by replacing TZVP with aug-cc-pVTZ data that yields a new reference set (TBE-2). Statistical evaluations of the performance of density functional theory (DFT) and semiempirical methods lead to the same ranking and very similar quantitative results for TBE-1 and TBE-2, with slightly better performance measures with respect to TBE-2. DFT/MRCI is most accurate among the investigated DFT-based approaches, while the OMx methods with orthogonalization corrections perform best at the semiempirical level.

  4. Method and Basis Set Analysis of Oxorhenium(V) Complexes for Theoretical Calculations

    PubMed Central

    Demoin, Dustin Wayne; Li, Yawen; Jurisson, Silvia S.; Deakyne, Carol A.

    2012-01-01

    A variety of method and basis set combinations has been evaluated for monooxorhenium(V) complexes with N, O, P, S, Cl, and Se donor atoms. The geometries and energies obtained are compared to both high-level computations and literature structures. These calculations show that the PBE0 method outperforms the B3LYP method with respect to both structure and energetics. The combination of 6-31G** basis set on the nonmetal atoms and LANL2TZ effective core potential on the rhenium center gives reliable equilibrium structures with minimal computational resources for both model and literature compounds. Single-point energy calculations at the PBE0/LANL2TZ,6-311+G* level of theory are recommended for energetics. PMID:23087847

  5. 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.

  6. Elimination of the linearization error and improved basis-set convergence within the FLAPW method

    NASA Astrophysics Data System (ADS)

    Michalicek, Gregor; Betzinger, Markus; Friedrich, Christoph; Blügel, Stefan

    2013-12-01

    We analyze in detail the error that arises from the linearization in linearized augmented-plane-wave (LAPW) basis functions around predetermined energies El and show that it can lead to undesirable dependences of the calculated results on method-inherent parameters such as energy parameters El and muffin-tin sphere radii. To overcome these dependences, we evaluate approaches that eliminate the linearization error systematically by adding local orbitals (LOs) to the basis set. We consider two kinds of LOs: (i) constructed from solutions ul(r,E) to the scalar-relativistic approximation of the radial Dirac equation with E>El and (ii) constructed from second energy derivatives ∂2ul(r,E)/∂E2 at E=El. We find that the latter eliminates the error most efficiently and yields the density functional answer to many electronic and materials properties with very high precision. Finally, we demonstrate that the so constructed LAPW +LO basis shows a more favorable convergence behavior than the conventional LAPW basis due to a better decoupling of muffin-tin and interstitial regions, similarly to the related APW +lo approach, which, however, requires an extra set of LOs to reach the same total energy.

  7. Representing the behavior of partially coherent optical systems by using overcomplete basis sets

    NASA Astrophysics Data System (ADS)

    Withington, Stafford; Hobson, Michael P.; Berry, Rachel H.

    2004-02-01

    A technique is described for representing the behavior of partially coherent optical systems by using overcomplete basis sets. The scheme is closely related to Gabor function theory. Through singular-value decomposition it is shown that if E is a matrix containing the sampled basis functions, then all of the information needed for optical calculations is contained in S=EE† and R=E†E. For overcomplete sets, S can be inverted to give a dual basis set, E~=S-1E, which can be used to find the correlation matrix elements A of a sampled bimodal expansion of the spatial coherence function. Overcomplete correlation matrices can be scattered easily at optical components. They can be used to determine (i) the natural modes of a field; (ii) the total power in a field, Pt=Tr[RA] (iii) the power coupled between two fields, A and B, that are in different states of coherence, Pc=Tr[RARB] and (iv) the entropy of a field, Q=Tr[ZΣr(I-Z)r/r], where Z=RA/Tr[RA].

  8. Representing the behavior of partially coherent optical systems by using overcomplete basis sets.

    PubMed

    Withington, Stafford; Hobson, Michael P; Berry, Rachel H

    2004-02-01

    A technique is described for representing the behavior of partially coherent optical systems by using overcomplete basis sets. The scheme is closely related to Gabor function theory. Through singular-value decomposition it is shown that if E is a matrix containing the sampled basis functions, then all of the information needed for optical calculations is contained in S = EE(dagger) and R = E(dagger)E. For overcomplete sets, S can be inverted to give a dual basis set, E = S(-1)E, which can be used to find the correlation matrix elements A of a sampled bimodal expansion of the spatial coherence function. Overcomplete correlation matrices can be scattered easily at optical components. They can be used to determine (i) the natural modes of a field; (ii) the total power in a field, Pt = Tr[RA]; (iii) the power coupled between two fields, A and B, that are in different states of coherence, Pc = Tr[RARB]; and (iv) the entropy of a field, Q = Tr[Zsigmar(I-Z)r/r], where Z = RA/Tr[RA]. PMID:14763763

  9. 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.

  10. On fast computation of finite-time coherent sets using radial basis functions

    NASA Astrophysics Data System (ADS)

    Froyland, Gary; Junge, Oliver

    2015-08-01

    Finite-time coherent sets inhibit mixing over finite times. The most expensive part of the transfer operator approach to detecting coherent sets is the construction of the operator itself. We present a numerical method based on radial basis function collocation and apply it to a recent transfer operator construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] that has been designed specifically for purely advective dynamics. The construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] is based on a "dynamic" Laplace operator and minimises the boundary size of the coherent sets relative to their volume. The main advantage of our new approach is a substantial reduction in the number of Lagrangian trajectories that need to be computed, leading to large speedups in the transfer operator analysis when this computation is costly.

  11. On fast computation of finite-time coherent sets using radial basis functions.

    PubMed

    Froyland, Gary; Junge, Oliver

    2015-08-01

    Finite-time coherent sets inhibit mixing over finite times. The most expensive part of the transfer operator approach to detecting coherent sets is the construction of the operator itself. We present a numerical method based on radial basis function collocation and apply it to a recent transfer operator construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] that has been designed specifically for purely advective dynamics. The construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] is based on a "dynamic" Laplace operator and minimises the boundary size of the coherent sets relative to their volume. The main advantage of our new approach is a substantial reduction in the number of Lagrangian trajectories that need to be computed, leading to large speedups in the transfer operator analysis when this computation is costly. PMID:26328580

  12. 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. PMID:17508413

  13. XFEM schemes for level set based structural optimization

    NASA Astrophysics Data System (ADS)

    Li, Li; Wang, Michael Yu; Wei, Peng

    2012-12-01

    In this paper, some elegant extended finite element method (XFEM) schemes for level set method structural optimization are proposed. Firstly, two-dimension (2D) and three-dimension (3D) XFEM schemes with partition integral method are developed and numerical examples are employed to evaluate their accuracy, which indicate that an accurate analysis result can be obtained on the structural boundary. Furthermore, the methods for improving the computational accuracy and efficiency of XFEM are studied, which include the XFEM integral scheme without quadrature sub-cells and higher order element XFEM scheme. Numerical examples show that the XFEM scheme without quadrature sub-cells can yield similar accuracy of structural analysis while prominently reducing the time cost and that higher order XFEM elements can improve the computational accuracy of structural analysis in the boundary elements, but the time cost is increasing. Therefore, the balance of time cost between FE system scale and the order of element needs to be discussed. Finally, the reliability and advantages of the proposed XFEM schemes are illustrated with several 2D and 3D mean compliance minimization examples that are widely used in the recent literature of structural topology optimization. All numerical results demonstrate that the proposed XFEM is a promising structural analysis approach for structural optimization with the level set method.

  14. 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.

  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. 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

  17. 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

  18. Optimization of the generator settings for endobiliary radiofrequency ablation

    PubMed Central

    Barret, Maximilien; Leblanc, Sarah; Vienne, Ariane; Rouquette, Alexandre; Beuvon, Frederic; Chaussade, Stanislas; Prat, Frederic

    2015-01-01

    AIM: To determine the optimal generator settings for endobiliary radiofrequency ablation. METHODS: Endobiliary radiofrequency ablation was performed in live swine on the ampulla of Vater, the common bile duct and in the hepatic parenchyma. Radiofrequency ablation time, “effect”, and power were allowed to vary. The animals were sacrificed two hours after the procedure. Histopathological assessment of the depth of the thermal lesions was performed. RESULTS: Twenty-five radiofrequency bursts were applied in three swine. In the ampulla of Vater (n = 3), necrosis of the duodenal wall was observed starting with an effect set at 8, power output set at 10 W, and a 30 s shot duration, whereas superficial mucosal damage of up to 350 μm in depth was recorded for an effect set at 8, power output set at 6 W and a 30 s shot duration. In the common bile duct (n = 4), a 1070 μm, safe and efficient ablation was obtained for an effect set at 8, a power output of 8 W, and an ablation time of 30 s. Within the hepatic parenchyma (n = 18), the depth of tissue damage varied from 1620 μm (effect = 8, power = 10 W, ablation time = 15 s) to 4480 μm (effect = 8, power = 8 W, ablation time = 90 s). CONCLUSION: The duration of the catheter application appeared to be the most important parameter influencing the depth of the thermal injury during endobiliary radiofrequency ablation. In healthy swine, the currently recommended settings of the generator may induce severe, supratherapeutic tissue damage in the biliary tree, especially in the high-risk area of the ampulla of Vater. PMID:26566429

  19. Optimal exposure sets for high dynamic range scenes

    NASA Astrophysics Data System (ADS)

    Valli Kumari, V.; RaviKiran, B.; Raju, K. V. S. V. N.; Shajahan Basha, S. A.

    2011-10-01

    The dynamic range of many natural scenes is far greater than the dynamic range of the imaging devices. These scenes present a challenge to the consumer digital cameras. The well-known technique to capture the full dynamic range of the scene is by fusing multiple images of the same scene. Usually people combine three or five different exposures to get the full dynamic range of the scene. Some cameras like Pentax K-7, always combines fixed exposures together to produce the output result. However, this should be adaptive to the scene characteristics. We propose an optimal solution for dynamically selecting the exposure sets.

  20. 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.

  1. 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

  2. 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

  3. Imputing gene expression from optimally reduced probe sets

    PubMed Central

    Donner, Yoni; Feng, Ting; Benoist, Christophe; Koller, Daphne

    2012-01-01

    Measuring complete gene expression profiles for a large number of experiments is costly. We propose an approach in which a small subset of probes is selected based on a preliminary set of full expression profiles. In subsequent experiments, only the subset is measured, and the missing values are imputed. We develop several algorithms to simultaneously select probes and impute missing values, and demonstrate that these probe selection for imputation (PSI) algorithms can successfully reconstruct missing gene expression values in a wide variety of applications, as evaluated using multiple metrics of biological importance. We analyze the performance of PSI methods under varying conditions, provide guidelines for choosing the optimal method based on the experimental setting, and indicate how to estimate imputation accuracy. Finally, we apply our approach to a large-scale study of immune system variation. PMID:23064520

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

    PubMed

    Lu, Qing; Peterson, Kirk A

    2016-08-01

    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. PMID:27497543

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

    NASA Astrophysics Data System (ADS)

    Lu, Qing; Peterson, Kirk A.

    2016-08-01

    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.

  6. 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.

  7. 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.

  8. Many-body calculations of molecular electric polarizabilities in asymptotically complete basis sets

    NASA Astrophysics Data System (ADS)

    Monten, Ruben; Hajgató, Balázs; Deleuze, Michael S.

    2011-10-01

    The static dipole polarizabilities of Ne, CO, N2, F2, HF, H2O, HCN, and C2H2 (acetylene) have been determined close to the Full-CI limit along with an asymptotically complete basis set (CBS), according to the principles of a Focal Point Analysis. For this purpose the results of Finite Field calculations up to the level of Coupled Cluster theory including Single, Double, Triple, Quadruple and perturbative Pentuple excitations [CCSDTQ(P)] were used, in conjunction with suited extrapolations of energies obtained using augmented and doubly-augmented Dunning's correlation consistent polarized valence basis sets of improving quality. The polarizability characteristics of C2H4 (ethylene) and C2H6 (ethane) have been determined on the same grounds at the CCSDTQ level in the CBS limit. Comparison is made with results obtained using lower levels in electronic correlation, or taking into account the relaxation of the molecular structure due to an adiabatic polarization process. Vibrational corrections to electronic polarizabilities have been empirically estimated according to Born-Oppenheimer Molecular Dynamical simulations employing Density Functional Theory. Confrontation with experiment ultimately indicates relative accuracies of the order of 1 to 2%.

  9. Spectral fitting using basis set modified by measured B0 field distribution.

    PubMed

    Li, Ningzhi; An, Li; Shen, Jun

    2015-12-01

    This study sought to demonstrate and evaluate a novel spectral fitting method to improve quantification accuracy in the presence of large magnetic field distortion, especially with high fields. MRS experiments were performed using a point-resolved spectroscopy (PRESS)-type sequence at 7 T. A double-echo gradient echo (GRE) sequence was used to acquire B0 maps following MRS experiments. The basis set was modified based on the measured B0 distribution within the MRS voxel. Quantification results were obtained after fitting the measured MRS data using the modified basis set. The proposed method was validated using numerical Monte Carlo simulations, phantom measurements, and comparison of occipital lobe MRS measurements under homogeneous and inhomogeneous magnetic field conditions. In vivo results acquired from voxels placed in thalamus and prefrontal cortex regions close to the frontal sinus agreed well with published values. Instead of noise-amplifying complex division, the proposed method treats field variations as part of the signal model, thereby avoiding inherent statistical bias associated with regularization. Simulations and experiments showed that the proposed approach reliably quantified results in the presence of relatively large magnetic field distortion. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. PMID:26503305

  10. 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}

  11. Nonlinearly-constrained optimization using asynchronous parallel generating set search.

    SciTech Connect

    Griffin, Joshua D.; Kolda, Tamara Gibson

    2007-05-01

    Many optimization problems in computational science and engineering (CS&E) are characterized by expensive objective and/or constraint function evaluations paired with a lack of derivative information. Direct search methods such as generating set search (GSS) are well understood and efficient for derivative-free optimization of unconstrained and linearly-constrained problems. This paper addresses the more difficult problem of general nonlinear programming where derivatives for objective or constraint functions are unavailable, which is the case for many CS&E applications. We focus on penalty methods that use GSS to solve the linearly-constrained problems, comparing different penalty functions. A classical choice for penalizing constraint violations is {ell}{sub 2}{sup 2}, the squared {ell}{sub 2} norm, which has advantages for derivative-based optimization methods. In our numerical tests, however, we show that exact penalty functions based on the {ell}{sub 1}, {ell}{sub 2}, and {ell}{sub {infinity}} norms converge to good approximate solutions more quickly and thus are attractive alternatives. Unfortunately, exact penalty functions are discontinuous and consequently introduce theoretical problems that degrade the final solution accuracy, so we also consider smoothed variants. Smoothed-exact penalty functions are theoretically attractive because they retain the differentiability of the original problem. Numerically, they are a compromise between exact and {ell}{sub 2}{sup 2}, i.e., they converge to a good solution somewhat quickly without sacrificing much solution accuracy. Moreover, the smoothing is parameterized and can potentially be adjusted to balance the two considerations. Since many CS&E optimization problems are characterized by expensive function evaluations, reducing the number of function evaluations is paramount, and the results of this paper show that exact and smoothed-exact penalty functions are well-suited to this task.

  12. On Optimizing Joint Inversion of Constrained Geophysical Data Sets

    NASA Astrophysics Data System (ADS)

    Sosa Aguirre, U. A.; Velazquez, L.; Argaez, M.; Velasco, A. A.; Romero, R.

    2010-12-01

    We implemented a joint inversion least-squares (LSQ) algorithm to characterize 1-D crustal velocity Earth structure using geophysical data sets with two different optimization methods: truncated singular value decomposition (TSVD), and primal-dual interior-point (PDIP). We used receiver function and surface wave dispersion velocity observations, and created a framework to incorporate other data sets. An improvement in the final outcome (model) is expected by providing better physical constraints than using just one single data set. The TSVD and PDIP methods solve a regularized unconstrained and an inherent regularized constrained minimization problems, respectively. Both techniques implement the inclusion of bounds into the layered shear velocities in a different fashion. We conduct a numerical experimentation with synthetic data, and find that the PDID method’s solution was more robust in terms of satisfying geophysical constraints, accuracy, and efficiency than the TSVD approach. Finally, we apply the PDIP method for characterizing material properties of the Rio Grande Rift region using real recorded seismic data with promising numerical results.

  13. 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.

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

    DOE PAGESBeta

    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 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

  15. 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.

  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. Crystal orbital Hamilton population (COHP) analysis as projected from plane-wave basis sets.

    PubMed

    Deringer, Volker L; Tchougréeff, Andrei L; Dronskowski, Richard

    2011-06-01

    Simple, yet predictive bonding models are essential achievements of chemistry. In the solid state, in particular, they often appear in the form of visual bonding indicators. Because the latter require the crystal orbitals to be constructed from local basis sets, the application of the most popular density-functional theory codes (namely, those based on plane waves and pseudopotentials) appears as being ill-fitted to retrieve the chemical bonding information. In this paper, we describe a way to re-extract Hamilton-weighted populations from plane-wave electronic-structure calculations to develop a tool analogous to the familiar crystal orbital Hamilton population (COHP) method. We derive the new technique, dubbed "projected COHP" (pCOHP), and demonstrate its viability using examples of covalent, ionic, and metallic crystals (diamond, GaAs, CsCl, and Na). For the first time, this chemical bonding information is directly extracted from the results of plane-wave calculations. PMID:21548594

  18. 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.

  19. 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.

  20. A two-dimensional volatility basis set - Part 3: Prognostic modeling and NOx dependence

    NASA Astrophysics Data System (ADS)

    Chuang, W. K.; Donahue, N. M.

    2015-06-01

    When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2-D-VBS) to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in AMS measurements. We also discuss the mathematical methods underlying the implementation of the 2-D-VBS and provide the complete code in the Supplemental material. A developer version is available on Bitbucket, an online community repository.

  1. A two-dimensional volatility basis set - Part 3: Prognostic modeling and NOx dependence

    NASA Astrophysics Data System (ADS)

    Chuang, W. K.; Donahue, N. M.

    2016-01-01

    When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2D-VBS) to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in Aerosol Mass Spectrometer (AMS) measurements. We also discuss the mathematical methods underlying the implementation of the 2D-VBS and provide the complete code in the Supplement. A developer version is available on Bitbucket, an online community repository.

  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. 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.

  4. 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

  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. 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

  7. Model for the fast estimation of basis set superposition error in biomolecular systems

    PubMed Central

    Faver, John C.; Zheng, Zheng; Merz, Kenneth M.

    2011-01-01

    Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds. PMID:22010701

  8. Excitation of helium Rydberg states and doubly excited resonances in strong extreme ultraviolet fields: Full-dimensional quantum dynamics using exponentially tempered Gaussian basis sets

    SciTech Connect

    Kaprálová-Žďánská, Petra Ruth; Šmydke, Jan; Department of Radiation and Chemical Physics, Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague 8 ; Civiš, Svatopluk

    2013-09-14

    Recently optimized exponentially tempered Gaussian basis sets [P. R. Kapralova-Zdanska and J. Smydke, J. Chem. Phys. 138, 024105 (2013)] are employed in quantitative simulations of helium absorption cross-sections and two-photon excitation yields of doubly excited resonances. Linearly polarized half-infinite and Gaussian laser pulses at wavelengths 38–58 nm and large intensities up to 100 TW/cm{sup 2} are considered. The emphasis is laid on convergence of the results with respect to the quality of the Gaussian basis sets (typically limited by a number of partial waves, density, and spatial extent of the basis functions) as well as to the quality of the basis set of field-free states (typically limited by the maximum rotational quantum number and maximum excitation of the lower electron). Particular attention is paid to stability of the results with respect to varying complex scaling parameter. Moreover, the study of the dynamics is preceded by a thorough check of helium energies and oscillator strengths as they are obtained with the exponentially tempered Gaussian basis sets, being also compared with yet unpublished emission wavelengths measured in electric discharge experiments.

  9. A mathematical basis for the design and 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

    A mathematical basis for the optimal design of adaptive trusses to be used in supporting precision equipment is provided. The general theory of adaptive structures is introduced, and the global optimization problem of placing a limited number, q, of actuators, so as to maximally achieve precision control and provide prestress, is stated. Two serialized optimization problems, namely, optimal actuator placement for prestress and optimal actuator placement for precision control, are addressed. In the case of prestressing, the computation of a 'desired' prestress is discussed, the interaction between actuators and redundants in conveying the prestress is shown in its mathematical form, and a methodology for arriving at the optimal placement of actuators and additional redundants is discussed. With regard to precision control, an optimal placement scheme (for q actuators) for maximum 'authority' over the precision points is suggested. The results of the two serialized optimization problems are combined to give a suboptimal solution to the global optimization problem. A method for improving this suboptimal actuator placement scheme by iteration is presented.

  10. 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.

  11. 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

  12. Toward accurate thermochemical models for transition metals : G3large basis sets for atoms Sc-Zn.

    SciTech Connect

    Mayhall, N. J.; Raghavachari, K.; Redfern, P. C.; Curtiss, L. A.; Rassolov, V.; Indiana Univ.; Univ. of South Carolina

    2008-04-01

    An augmented valence triple-zeta basis set, referred to as G3Large, is reported for the first-row transition metal elements Sc through Zn. The basis set is constructed in a manner similar to the G3Large basis set developed previously for other elements (H-Ar, K, Ca, Ga-Kr) and used as a key component in Gaussian-3 theory. It is based on a contraction of a set of 15s13p5d Gaussian primitives to 8s7p3d, and also includes sets of f and g polarization functions, diffuse spd functions, and core df polarization functions. The basis set is evaluated with triples-augmented coupled cluster [CCSD(T)] and Brueckner orbital [BD(T)] methods for a small test set involving energies of atoms, atomic ions, and diatomic hydrides. It performs well for the low-lying s{yields}d excitation energies of atoms, atomic ionization energies, and the dissociation energies of the diatomic hydrides. The Brueckner orbital-based BD(T) method performs substantially better than Hartree-Fock-based CCSD(T) for molecules such as NiH, where the starting unrestricted Hartree-Fock wavefunction suffers from a high degree of spin contamination. Comparison with available data for geometries of transition metal hydrides also shows good agreement. A smaller basis set without core polarization functions, G3MP2Large, is also defined.

  13. Structural Basis for WDR5 Interaction (Win) Motif Recognition in Human SET1 Family Histone Methyltransferases*

    PubMed Central

    Dharmarajan, Venkatasubramanian; Lee, Jeong-Heon; Patel, Anamika; Skalnik, David G.; Cosgrove, Michael S.

    2012-01-01

    Translocations and amplifications of the mixed lineage leukemia-1 (MLL1) gene are associated with aggressive myeloid and lymphocytic leukemias in humans. MLL1 is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, which are required for transcription of genes involved in hematopoiesis and development. MLL1 associates with a subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD), which together form the MLL1 core complex that is required for sequential mono- and dimethylation of H3K4. We previously demonstrated that WDR5 binds the conserved WDR5 interaction (Win) motif of MLL1 in vitro, an interaction that is required for the H3K4 dimethylation activity of the MLL1 core complex. In this investigation, we demonstrate that arginine 3765 of the MLL1 Win motif is required to co-immunoprecipitate WRAD from mammalian cells, suggesting that the WDR5-Win motif interaction is important for the assembly of the MLL1 core complex in vivo. We also demonstrate that peptides that mimic SET1 family Win motif sequences inhibit H3K4 dimethylation by the MLL1 core complex with varying degrees of efficiency. To understand the structural basis for these differences, we determined structures of WDR5 bound to six different naturally occurring Win motif sequences at resolutions ranging from 1.9 to 1.2 Å. Our results reveal that binding energy differences result from interactions between non-conserved residues C-terminal to the Win motif and to a lesser extent from subtle variation of residues within the Win motif. These results highlight a new class of methylation inhibitors that may be useful for the treatment of MLL1-related malignancies. PMID:22665483

  14. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions

    SciTech Connect

    Kendall, R.A.; Dunning, T.H. Jr. ); Harrison, R.J. )

    1992-05-01

    The calculation of accurate electron affinities (EAs) of atomic or molecular species is one of the most challenging tasks in quantum chemistry. We describe a reliable procedure for calculating the electron affinity of an atom and present results for hydrogen, boron, carbon, oxygen, and fluorine (hydrogen is included for completeness). This procedure involves the use of the recently proposed correlation-consistent basis sets augmented with functions to describe the more diffuse character of the atomic anion coupled with a straightforward, uniform expansion of the reference space for multireference singles and doubles configuration-interaction (MRSD-CI) calculations. Comparison with previous results and with corresponding full CI calculations are given. The most accurate EAs obtained from the MRSD-CI calculations are (with experimental values in parentheses) hydrogen 0.740 eV (0.754), boron 0.258 (0.277), carbon 1.245 (1.263), oxygen 1.384 (1.461), and fluorine 3.337 (3.401). The EAs obtained from the MR-SDCI calculations differ by less than 0.03 eV from those predicted by the full CI calculations.

  15. 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

  16. Analytical GIAO and hybrid-basis integral derivatives: application to geometry optimization of molecules in strong magnetic fields.

    PubMed

    Tellgren, Erik I; Reine, Simen S; Helgaker, Trygve

    2012-07-14

    Analytical integral evaluation is a central task of modern quantum chemistry. Here we present a general method for evaluating differentiated integrals over standard Gaussian and mixed Gaussian/plane-wave hybrid orbitals. The main idea is to have a representation of basis sets that is flexible enough to enable differentiated integrals to be reinterpreted as standard integrals over modified basis functions. As an illustration of the method, we report a very simple implementation of Hartree-Fock level geometrical derivatives in finite magnetic fields for gauge-origin independent atomic orbitals, within the London program. As a quantum-chemical application, we optimize the structure of helium clusters and some well-known covalently bound molecules (water, ammonia and benzene) subject to strong magnetic fields. PMID:22653039

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Temperature dependence of source specific volatility basis sets for motor vehicle exhaust

    NASA Astrophysics Data System (ADS)

    Roy, Anirban; Choi, Yunsoo

    2015-10-01

    Recent work on emissions testing has focused on developing source specific volatility distributions which could be used to improve emissions inventories. One problem about these volatility profiles is that they are evaluated only at one temperature which is usually 298 K. This study uses a simple statistical model to evaluate the temperature dependence of the source-resolved volatility basis set, considering gasoline and diesel vehicle exhaust. The steps involved (a) fitting a distribution to the emissions data (b) evaluating the goodness of fit using a statistical test (c) updating the volatility bins using the Clausius-Clayperon equation; calculating the heats of vaporization of each volatility class using a regression model (d) assessing how the volatility of different VOC classes-Extremely Low Volatile, Low Volatile, Semi-Volatile, Intermediate Volatile and Volatile Organic Compounds - are affected by temperature. The results indicated that there could be significant changes in gas-particle partitioning of these emissions. For diesel exhaust at 298 K, the fractions are 5.4 × 10-4 (ELVOC), 0.074 (LVOC), 0.76 (SVOC), 0.17 (IVOC) and 10-5 (VOC) respectively. Looking at a window of ∓20 K, the partitioning for 278 K is 3 × 10-3 (ELVOC), 0.26 (LVOC), 0.67 (SVOC), 0.07 (IVOC) with no VOC fraction; while at 318 K it is 1.5 × 10-7 (ELVOC), 9 × 10-3 (LVOC), 0.64 (SVOC), 0.35 (IVOC) and 2 × 10-5 (VOC); demonstrating a significant change with temperature. The parameterizations developed in this work could be used to improve motor vehicle emissions inventory models such as MOVES.

  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. PMID:26508426

  3. Comparison of the polarizabilities and hyperpolarizabilities obtained from finite basis set and finite difference Hartree Fock calculations for diatomic molecules: II. Refinement of basis sets and grids for hyperpolarizability calculations

    NASA Astrophysics Data System (ADS)

    Kobus, J.; Moncrieff, D.; Wilson, S.

    2004-02-01

    In a previous paper, we have made a comparison of the accuracy with which the electric dipole polarizability agrzz and hyperpolarizability bgrzzz can be calculated by using either the finite basis set approach (the algebraic approximation) or the finite difference method in calculations for the ground states of the H2, LiH, BH and FH molecules, at their respective experimental equilibrium geometries, within the Hartree-Fock model. A re-examination of the hyperpolarizability of the BH molecule shows it to be very sensitive both to the choice of grid employed in the finite difference Hartree-Fock calculation and the construction of the basis set used in the matrix Hartree-Fock study. A new comparison of finite difference and finite basis set hyperpolarizabilities for the BH molecule is made, together with new calculations for the LiH and FH ground states.

  4. Simulating the oxygen content of ambient organic aerosol with the 2D volatility basis set

    NASA Astrophysics Data System (ADS)

    Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Pandis, S. N.

    2011-08-01

    A module predicting the oxidation state of organic aerosol (OA) has been developed using the two-dimensional volatility basis set (2D-VBS) framework. This model is an extension of the 1D-VBS framework and tracks saturation concentration and oxygen content of organic species during their atmospheric lifetime. The host model, a one-dimensional Lagrangian transport model, is used to simulate air parcels arriving at Finokalia, Greece during the Finokalia Aerosol Measurement Experiment in May 2008 (FAME-08). Extensive observations were collected during this campaign using an aerosol mass spectrometer (AMS) and a thermodenuder to determine the chemical composition and volatility, respectively, of the ambient OA. Although there are several uncertain model parameters, the consistently high oxygen content of OA measured during FAME-08 (O:C = 0.8) can help constrain these parameters and elucidate OA formation and aging processes that are necessary for achieving the high degree of oxygenation observed. The base-case model reproduces observed OA mass concentrations (measured mean = 3.1 μg m-3, predicted mean = 3.3 μg m-3) and O:C (predicted O:C = 0.78) accurately. A suite of sensitivity studies explore uncertainties due to (1) the anthropogenic secondary OA (SOA) aging rate constant, (2) assumed enthalpies of vaporization, (3) the volatility change and number of oxygen atoms added for each generation of aging, (4) heterogeneous chemistry, (5) the oxidation state of the first generation of compounds formed from SOA precursor oxidation, and (6) biogenic SOA aging. Perturbations in most of these parameters do impact the ability of the model to predict O:C well throughout the simulation period. By comparing measurements of the O:C from FAME-08, several sensitivity cases including a high oxygenation case, a low oxygenation case, and biogenic SOA aging case are found to unreasonably depict OA aging, keeping in mind that this study does not consider possibly important processes

  5. Simulating the oxygen content of ambient organic aerosol with the 2D volatility basis set

    NASA Astrophysics Data System (ADS)

    Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Pandis, S. N.

    2011-03-01

    A module predicting the oxidation state of organic aerosol (OA) has been developed using the two-dimensional volatility basis set (2D-VBS) framework. This model is an extension of the 1D-VBS framework and tracks saturation concentration and oxygen content of organic species during their atmospheric lifetime. The host model, a one-dimensional Lagrangian transport model, is used to simulate air parcels arriving at Finokalia, Greece during the Finokalia Aerosol Measurement Experiment in May 2008 (FAME-08). Extensive observations were collected during this campaign using an aerosol mass spectrometer (AMS) and a thermodenuder to determine the chemical composition and volatility, respectively, of the ambient OA. Although there are several uncertain model parameters, the consistently high oxygen content of OA measured during FAME-08 (O:C = 0.8) can help constrain these parameters and elucidate OA formation and aging processes that are necessary for achieving the high degree of oxygenation observed. The base-case model reproduces observed OA mass concentrations (measured mean = 3.1 μg m-3, predicted mean = 3.3 μg m-3) and O:C ratio (predicted O:C = 0.78) accurately. A suite of sensitivity studies explore uncertainties due to (1) the anthropogenic secondary OA (SOA) aging rate constant, (2) assumed enthalpies of vaporization, (3) the volatility change and number of oxygen atoms added for each generation of aging, (4) heterogeneous chemistry, (5) the oxidation state of the first generation of compounds formed from SOA precursor oxidation, and (6) biogenic SOA aging. Perturbations in most of these parameters do impact the ability of the model to predict O:C ratios well throughout the simulation period. By comparing measurements of the O:C ratio from FAME-08, several sensitivity cases including a high oxygenation case, low oxygenation case, and biogenic SOA aging case are found to unreasonably depict OA aging. However, many of the cases chosen for this study predict average

  6. Finite-basis correction applied to the optimized effective potential within the FLAPW method

    NASA Astrophysics Data System (ADS)

    Friedrich, Christoph; Betzinger, Markus; Blügel, Stefan

    2011-03-01

    The optimized-effective-potential (OEP) method is a special technique to construct local exchange-correlation (xc) potentials from general orbital-dependent xc energy functionals for density-functional theory. Recently, we showed that particular care must be taken to construct local potentials within the all-electron full-potential augmented-plane-wave (FLAPW) approach. In fact, we found that the LAPW basis had to be converged to an accuracy that was far beyond that in calculations using conventional functionals, leading to a very high computational cost. This could be traced back to the convergence behavior of the density response function: only a highly converged basis lends the density enough flexibility to react adequately to changes of the potential. In this work we derive a numerical correction for the response function, which vanishes in the limit of an infinite, complete basis. It is constructed in the atomic spheres from the response of the basis functions themselves to changes of the potential. We show that such a finite-basis correction reduces the computational demand of OEP calculations considerably. We also discuss a similar correction scheme for GW calculations.

  7. A Complete Basis Set Estimate of Cation-p Bond Strengths: Na+(ethylene) and Na+(benzene)

    SciTech Connect

    Feller, David F.

    2000-06-02

    Large scale second order perturbation theory and couple cluster theory calculations were performed on the Na+(ethylene) and Na+(benzene) complexes in an effort to estimate binding enthalpies in the complete basis set limit. The resulting best estimates are DH0[Na+(ethylene)] = -13.7 ? 0.2 kcal/mol and DH0[Na+(benzene)] = -23.9 ? 0.3 kcal/mol, which include small corrections for core/valence correlation effects. The former value can be compared to a measurement of -10.3 ? 1.0 kcal/mol obtained from collision induced dissociation, while the latter value is approximately midway between the two existing experimental values which differed by 6.5 kcal/mol. For the basis sets considered in this study, the counterpoise-corrected binding energies were found to be in much worse agreement with the complete basis set limit than the raw values.

  8. Potential and matrix elements of the hamiltonian of internal rotation in molecules in the basis set of Mathieu functions

    NASA Astrophysics Data System (ADS)

    Turovtsev, V. V.; Orlov, Yu. D.; Tsirulev, A. N.

    2015-08-01

    The advantages of the orthonormal basis set of 2π-periodic Mathieu functions compared to the trigonometric basis set in calculations of torsional states of molecules are substantiated. Explicit expressions are derived for calculating the Hamiltonian matrix elements of a one-dimensional torsional Schrödinger equation with a periodic potential of the general form in the basis set of Mathieu functions. It is shown that variation of a parameter of Mathieu functions allows the rotation potential and the structural function to be approximated with a good accuracy by a small number of series terms. The conditions for the best choice of this parameter are specified, and approximations are obtained for torsional potentials of n-butane upon rotation about the central C-C bond and of its univalent radical n-butyl C2H5C·H2 upon rotation of the C·H2 group. All algorithms are implemented in the Maple package.

  9. Parallel Douglas-Kroll energy and gradients in NWChem: Estimating scalar relativistic effects using Douglas-Kroll contracted basis sets

    NASA Astrophysics Data System (ADS)

    de Jong, W. A.; Harrison, R. J.; Dixon, D. A.

    2001-01-01

    A parallel implementation of the spin-free one-electron Douglas-Kroll-Hess (DKH) Hamiltonian in NWChem is discussed. An efficient and accurate method to calculate DKH gradients is introduced. It is shown that the use of a standard (nonrelativistic) contracted basis set can produce erroneous results for elements beyond the first row elements. The generation of DKH contracted cc-pVXZ(X=D,T,Q,5) basis sets for H, He, B-Ne, Al-Ar, and Ga-Br is discussed. The effect of DKH at the Hartree-Fock level on the bond distances, vibrational frequencies, and total dissociation energies for CF4, SiH4, SiF4, and Br2CO is discussed. It is suggested that the predominant effect of the scalar relativistic correction on the total dissociation energy can be calculated at the Hartree-Fock level if an adequate basis set is used.

  10. 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. PMID:26574270

  11. 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.

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

    SciTech Connect

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

    2001-01-01

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

  14. All-electron LCAO calculations of the LiF crystal phonon spectrum: Influence of the basis set, the exchange-correlation functional, and the supercell size.

    PubMed

    Evarestov, R A; Losev, M V

    2009-12-01

    For the first time the convergence of the phonon frequencies and dispersion curves in terms of the supercell size is studied in ab initio frozen phonon calculations on LiF crystal. Helmann-Feynman forces over atomic displacements are found in all-electron calculations with the localized atomic functions (LCAO) basis using CRYSTAL06 program. The Parlinski-Li-Kawazoe method and FROPHO program are used to calculate the dynamical matrix and phonon frequencies of the supercells. For fcc lattice, it is demonstrated that use of the full supercell space group (including the supercell inner translations) enables to reduce essentially the number of the displacements under consideration. For Hartree-Fock (HF), PBE and hybrid PBE0, B3LYP, and B3PW exchange-correlation functionals the atomic basis set optimization is performed. The supercells up to 216 atoms (3 x 3 x 3 conventional unit cells) are considered. The phonon frequencies using the supercells of different size and shape are compared. For the commensurate with supercell k-points the best agreement of the theoretical results with the experimental data is found for B3PW exchange-correlation functional calculations with the optimized basis set. The phonon frequencies at the most non-commensurate k-points converged for the supercell consisting of 4 x 4 x 4 primitive cells and ensures the accuracy 1-2% in the thermodynamic properties calculated (the Helmholtz free energy, entropy, and heat capacity at the room temperature). PMID:19382176

  15. Optimal Experience among Campers in a Resident Camp Setting.

    ERIC Educational Resources Information Center

    Bialeschki, M. Deborah; Henderson, Karla A.

    The purpose of this study was to assess optimal experience, also known as "flow" and "quality of experience" in a private, coeducational resident camp program for children. Flow refers to those times in work and leisure when people report feelings of enjoyment, concentration, and deep involvement. Flow theory predicts that an experience will be…

  16. 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.

  17. 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

    2015-06-01

    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.

  18. Optimal continuous variable quantum teleportation protocol for realistic settings

    NASA Astrophysics Data System (ADS)

    Luiz, F. S.; Rigolin, Gustavo

    2015-03-01

    We show the optimal setup that allows Alice to teleport coherent states | α > to Bob giving the greatest fidelity (efficiency) when one takes into account two realistic assumptions. The first one is the fact that in any actual implementation of the continuous variable teleportation protocol (CVTP) Alice and Bob necessarily share non-maximally entangled states (two-mode finitely squeezed states). The second one assumes that Alice's pool of possible coherent states to be teleported to Bob does not cover the whole complex plane (| α | < ∞). The optimal strategy is achieved by tuning three parameters in the original CVTP, namely, Alice's beam splitter transmittance and Bob's displacements in position and momentum implemented on the teleported state. These slight changes in the protocol are currently easy to be implemented and, as we show, give considerable gain in performance for a variety of possible pool of input states with Alice.

  19. MSE optimal bit-rate allocation in JPEG2000 Part 2 compression applied to a 3D data set

    NASA Astrophysics Data System (ADS)

    Kosheleva, Olga M.; Cabrera, Sergio D.; Usevitch, Bryan E.; Aguirre, Alberto; Vidal, Edward, Jr.

    2004-10-01

    A bit rate allocation (BRA) strategy is needed to optimally compress three-dimensional (3-D) data on a per-slice basis, treating it as a collection of two-dimensional (2-D) slices/components. This approach is compatible with the framework of JPEG2000 Part 2 which includes the option of pre-processing the slices with a decorrelation transform in the cross-component direction so that slices of transform coefficients are compressed. In this paper, we illustrate the impact of a recently developed inter-slice rate-distortion optimal bit-rate allocation approach that is applicable to this compression system. The approach exploits the MSE optimality of all JPEG2000 bit streams for all slices when each is produced in the quality progressive mode. Each bit stream can be used to produce a rate-distortion curve (RDC) for each slice that is MSE optimal at each bit rate of interest. The inter-slice allocation approach uses all RDCs for all slices to optimally select an overall optimal set of bit rates for all the slices using a constrained optimization procedure. The optimization is conceptually similar to Post-Compression Rate-Distortion optimization that is used within JPEG2000 to optimize bit rates allocated to codeblocks. Results are presented for two types of data sets: a 3-D computed tomography (CT) medical image, and a 3-D metereological data set derived from a particular modeling program. For comparison purposes, compression results are also illustrated for the traditional log-variance approach and for a uniform allocation strategy. The approach is illustrated using two decorrelation tranforms (the Karhunen Loeve transform, and the discrete wavelet transform) for which the inter-slice allocation scheme has the most impact.

  20. 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

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Conditions for payment on a fee schedule basis for physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICARE PROGRAM SERVICES FURNISHED BY PHYSICIANS IN PROVIDERS,...

  1. Desiccation tolerance of recalcitrant Theobroma cacao embryonic axes: the optimal drying rate and its physiological basis.

    PubMed

    Liang, Y; Sun, W Q

    2000-11-01

    Recalcitrant seed axes were reported to survive to lower water contents under fast-drying conditions. The present study was to examine the hypothesis that drying rate and dehydration duration could interact to determine desiccation tolerance through different physico-chemical mechanisms. The effect of drying rate on desiccation tolerance of Theobroma cacao seed axes at 16 degrees C was examined. Rapid-drying at low relative humidity (RH) and slow-drying at high RH were more harmful to cocoa axes, because electrolyte leakage began to increase and axis viability began to decrease at high water contents. Maximum desiccation tolerance was observed with intermediate drying rates at RH between 88% and 91%, indicating the existence of an optimal drying rate or optimal desiccation duration. This maximum level of desiccation tolerance for cocoa axes (corresponding to a critical water potential of -9 MPa) was also detected using the equilibration method, in which axes were dehydrated over a series of salt solutions or glycerol solutions until the equilibrium. These data confirmed that the physiological basis of the optimal drying rate is related to both mechanical stress during desiccation and the length of desiccation duration during which deleterious reactions may occur. The optimal drying rate represents a situation where combined damages from mechanical and metabolic stresses become minimal. PMID:11113169

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  4. 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.

  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. PMID:23947824

  6. 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.

  7. Optimal electrocardiographic limb lead set for rapid emphysema screening

    PubMed Central

    Bajaj, Rishi; Chhabra, Lovely; Basheer, Zainab; Spodick, David H

    2013-01-01

    Background Pulmonary emphysema of any etiology has been shown to be strongly and quasidiagnostically associated with a vertical frontal P wave axis. A vertical P wave axis (>60 degrees) during sinus rhythm can be easily determined by a P wave in lead III greater than the P wave in lead I (bipolar lead set) or a dominantly negative P wave in aVL (unipolar lead set). The purpose of this investigation was to determine which set of limb leads may be better for identifying the vertical P vector of emphysema in adults. Methods Unselected consecutive electrocardiograms from 100 patients with a diagnosis of emphysema were analyzed to determine the P wave axis. Patients aged younger than 45 years, those not in sinus rhythm, and those with poor quality tracings were excluded. The electrocardiographic data were divided into three categories depending on the frontal P wave axis, ie, >60 degrees, 60 degrees, or <60 degrees, by each criterion (P amplitude lead III > lead I and a negative P wave in aVL). Results Sixty-six percent of patients had a P wave axis > 60 degrees based on aVL, and 88% of patients had a P wave axis > 60 degrees based on the P wave in lead III being greater than in lead I. Conclusion A P wave in lead III greater than that in lead I is a more sensitive marker than a negative P wave in aVL for diagnosing emphysema and is recommended for rapid routine screening. PMID:23378754

  8. Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections

    NASA Astrophysics Data System (ADS)

    Ma, Zhonghua; Zhang, Yanli; Tuckerman, Mark E.

    2012-07-01

    It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)], 10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.

  9. 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.

  10. Solving the Dirac equation, using the large component only, in a Dirac-type Slater orbital basis set

    NASA Astrophysics Data System (ADS)

    van Lenthe, E.; Baerends, E. J.; Snijders, J. G.

    1995-04-01

    We solve the Dirac equation by solving the two-component energy-dependent equation for the large component that results from the elimination of the small component. This requires for every occupied orbital the diagonalization of a Hamiltonian. Advantages are, however, that these Hamiltonians are all bounded from below, unlike the Dirac Hamiltonian, and that only a basis set for the large component is needed. We use Dirac-type Slater orbitals, adapted from solutions to the hydrogen-like atom. This offers the perspective of performing relativistic calculations to the same accuracy as non-relativistic ones, with a comparable number of basis functions.

  11. Non-homogeneous solutions of a Coulomb Schrödinger equation as basis set for scattering problems

    SciTech Connect

    Del Punta, J. A.; Ambrosio, M. J.; Gasaneo, G.; Zaytsev, S. A.; Ancarani, L. U.

    2014-05-15

    We introduce and study two-body Quasi Sturmian functions which are proposed as basis functions for applications in three-body scattering problems. They are solutions of a two-body non-homogeneous Schrödinger equation. We present different analytic expressions, including asymptotic behaviors, for the pure Coulomb potential with a driven term involving either Slater-type or Laguerre-type orbitals. The efficiency of Quasi Sturmian functions as basis set is numerically illustrated through a two-body scattering problem.

  12. A decision support system to determine optimal ventilator settings

    PubMed Central

    2014-01-01

    Background Choosing the correct ventilator settings for the treatment of patients with respiratory tract disease is quite an important issue. Since the task of specifying the parameters of ventilation equipment is entirely carried out by a physician, physician’s knowledge and experience in the selection of these settings has a direct effect on the accuracy of his/her decisions. Nowadays, decision support systems have been used for these kinds of operations to eliminate errors. Our goal is to minimize errors in ventilation therapy and prevent deaths caused by incorrect configuration of ventilation devices. The proposed system is designed to assist less experienced physicians working in the facilities without having lung mechanics like cottage hospitals. Methods This article describes a decision support system proposing the ventilator settings required to be applied in the treatment according to the patients’ physiological information. The proposed model has been designed to minimize the possibility of making a mistake and to encourage more efficient use of time in support of the decision making process while the physicians make critical decisions about the patient. Artificial Neural Network (ANN) is implemented in order to calculate frequency, tidal volume, FiO2 outputs, and this classification model has been used for estimation of pressure support / volume support outputs. For the obtainment of the highest performance in both models, different configurations have been tried. Various tests have been realized for training methods, and a number of hidden layers mostly affect factors regarding the performance of ANNs. Results The physiological information of 158 respiratory patients over the age of 60 and were treated in three different hospitals between the years 2010 and 2012 has been used in the training and testing of the system. The diagnosed disease, core body temperature, pulse, arterial systolic pressure, diastolic blood pressure, PEEP, PSO2, pH, pCO2

  13. Accurate non-adiabatic quantum dynamics from pseudospectral sampling of time-dependent Gaussian basis sets

    NASA Astrophysics Data System (ADS)

    Heaps, Charles W.; Mazziotti, David A.

    2016-08-01

    Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schrödinger equation with N Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from O ( N 2 ) to O ( N ) . By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing the nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems: the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-dimensional model for collinear triatomic vibrational dynamics. In all cases, the pseudospectral Gaussian method is in quantitative agreement with numerically exact calculations. The results are promising for nonadiabatic molecular dynamics in molecular systems where strongly correlated ground or excited states require expensive electronic structure calculations.

  14. Approaching the complete basis set limit of CCSD(T) for large systems by the third-order incremental dual-basis set zero-buffer F12 method

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Dolg, Michael

    2014-01-01

    The third-order incremental dual-basis set zero-buffer approach was combined with CCSD(T)-F12x (x = a, b) theory to develop a new approach, i.e., the inc3-db-B0-CCSD(T)-F12 method, which can be applied as a black-box procedure to efficiently obtain the near complete basis set (CBS) limit of the CCSD(T) energies also for large systems. We tested this method for several cases of different chemical nature: four complexes taken from the standard benchmark sets S66 and X40, the energy difference between isomers of water hexamer and the rotation barrier of biphenyl. The results show that our method has an error relative to the best estimation of CBS energy of only 0.2 kcal/mol or less. By parallelization, our method can accomplish the CCSD(T)-F12 calculations of about 60 correlated electrons and 800 basis functions in only several days, which by standard implementation are impossible for ordinary hardware. We conclude that the inc3-db-B0-CCSD(T)-F12a/AVTZ method, which is of CCSD(T)/AV5Z quality, is close to the limit of accuracy that one can achieve for large systems currently.

  15. Approaching the complete basis set limit of CCSD(T) for large systems by the third-order incremental dual-basis set zero-buffer F12 method

    SciTech Connect

    Zhang, Jun Dolg, Michael

    2014-01-28

    The third-order incremental dual-basis set zero-buffer approach was combined with CCSD(T)-F12x (x = a, b) theory to develop a new approach, i.e., the inc3-db-B0-CCSD(T)-F12 method, which can be applied as a black-box procedure to efficiently obtain the near complete basis set (CBS) limit of the CCSD(T) energies also for large systems. We tested this method for several cases of different chemical nature: four complexes taken from the standard benchmark sets S66 and X40, the energy difference between isomers of water hexamer and the rotation barrier of biphenyl. The results show that our method has an error relative to the best estimation of CBS energy of only 0.2 kcal/mol or less. By parallelization, our method can accomplish the CCSD(T)-F12 calculations of about 60 correlated electrons and 800 basis functions in only several days, which by standard implementation are impossible for ordinary hardware. We conclude that the inc3-db-B0-CCSD(T)-F12a/AVTZ method, which is of CCSD(T)/AV5Z quality, is close to the limit of accuracy that one can achieve for large systems currently.

  16. Optimizing the application of entomopathogenic nematodes: experimental set-up.

    PubMed

    Brusselman, E; Steurbaut, W; Sonck, B

    2007-01-01

    The complex issue concerning the spray application of Entomopathogenic Nematodes (EPNs) with a hydraulic sprayer is still not solved. This research project focuses on the effect of spray application technique on the viability and deposition of EPNs. In this paper the experimental set-up used for this evaluation is described. A modular spray application system has been developed and is currently used to evaluate the effect of different parts of a sprayer on the viability of the EPNs. Based on the results of experiments using this modular spray application system, recommendations regarding pump type, mixing system, nozzle type and filter size will be formulated. Because of the large number of experiments in this research project, an image analysis system for the determination of the viability of the nematodes is developed. This paper describes two experiments comparing the new developed image processing technique with the standard microscopic counting technique. PMID:18399427

  17. 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.

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

    PubMed

    Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo

    2016-08-01

    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. PMID:27434607

  19. 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.

  20. 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.

  1. All-electron double zeta basis sets for the lanthanides: Application in atomic and molecular property calculations

    NASA Astrophysics Data System (ADS)

    Jorge, F. E.; Martins, L. S. C.; Franco, M. L.

    2016-01-01

    Segmented all-electron basis sets of valence double zeta quality plus polarization functions (DZP) for the elements from Ce to Lu are generated to be used with the non-relativistic and Douglas-Kroll-Hess (DKH) Hamiltonians. At the B3LYP level, the DZP-DKH atomic ionization energies and equilibrium bond lengths and atomization energies of the lanthanide trifluorides are evaluated and compared with benchmark theoretical and experimental data reported in the literature. In general, this compact size set shows to have a regular, efficient, and reliable performance. It can be particularly useful in molecular property calculations that require explicit treatment of the core electrons.

  2. Pure-state noninteracting v-representability of electron densities from Kohn-Sham calculations with finite basis sets

    NASA Astrophysics Data System (ADS)

    de Silva, Piotr; Wesolowski, Tomasz A.

    2012-03-01

    Within the linear combination of atomic orbitals (LCAO) approximation, one can distinguish two different Kohn-Sham potentials. One is the potential available numerically in calculations, and the other is the exact potential corresponding to the LCAO density. The latter is usually not available, but can be obtained from the total density by a numerical inversion procedure or, as is done here, analytically using only one LCAO Kohn-Sham orbital. In the complete basis-set limit, the lowest-lying Kohn-Sham orbital suffices to perform the analytical inversion, and the two potentials differ by no more than a constant. The relation between these two potentials is investigated here for diatomic molecules and several atomic basis sets of increasing size and quality. The differences between the two potentials are usually qualitative (wrong behavior at nuclear cusps and far from the molecule even if Slater-type orbitals are used) and δ-like features at nodal planes of the lowest-lying LCAO Kohn-Sham orbital. Such nodes occur frequently in LCAO calculations and are not physical. Whereas the behavior of the potential can be systematically improved locally by the increase of the basis sets, the occurrence of nodes is not correlated with the size of the basis set. The presence of nodes in the lowest-lying LCAO orbital can be used to monitor whether the effective potential in LCAO Kohn-Sham equations can be interpreted as the potential needed for pure-state noninteracting v-representability of the LCAO density. Squares of such node-containing lowest-lying LCAO Kohn-Sham orbitals are nontrivial examples of two-electron densities which are not pure-state noninteracting v-representable.

  3. Selection of optimal muscle set for 16-channel standing neuroprosthesis

    PubMed Central

    Gartman, Steven J.; Audu, Musa L.; Kirsch, Robert F.; Triolo, Ronald J.

    2009-01-01

    The Case Western Reserve University/Department of Veterans Affairs 8-channel lower-limb neuroprosthesis can restore standing to selected individuals with paraplegia by application of functional electrical stimulation. The second generation of this system will include 16 channels of stimulation and a closed-loop control scheme to provide automatic postural corrections. This study used a musculoskeletal model of the legs and trunk to determine which muscles to target with the new system in order to maximize the range of postures that can be statically maintained, which should increase the system’s ability to provide adequate support to maintain standing when the user’s posture moves away from a neutral stance, either by an external disturbance or a volitional change in posture by the user. The results show that the prime muscle targets should be the medial gastrocnemius, tibialis anterior, vastus lateralis, semimembranosus, gluteus maximus, gluteus medius, adductor magnus, and erector spinae. This set of 16 muscles supports 42 percent of the standing postures that are attainable by the nondisabled model. Coactivation of the lateral gastrocnemius and peroneus longus with the medial gastrocnemius and of the peroneus tertius with the tibialis anterior increased the percentage of feasible postures to 71 percent. PMID:16847793

  4. Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

    NASA Astrophysics Data System (ADS)

    Kolmann, Stephen J.; Jordan, Meredith J. T.

    2010-02-01

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

  5. 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

    2010-02-01

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented. PMID:20136303

  6. Robust, basis-set independent method for the evaluation of charge-transfer energy in noncovalent complexes.

    PubMed

    Řezáč, Jan; de la Lande, Aurélien

    2015-02-10

    Separation of the energetic contribution of charge transfer to interaction energy in noncovalent complexes would provide important insight into the mechanisms of the interaction. However, the calculation of charge-transfer energy is not an easy task. It is not a physically well-defined term, and the results might depend on how it is described in practice. Commonly, the charge transfer is defined in terms of molecular orbitals; in this framework, however, the charge transfer vanishes as the basis set size increases toward the complete basis set limit. This can be avoided by defining the charge transfer in terms of the spatial extent of the electron densities of the interacting molecules, but the schemes used so far do not reflect the actual electronic structure of each particular system and thus are not reliable. We propose a spatial partitioning of the system, which is based on a charge transfer-free reference state, namely superimposition of electron densities of the noninteracting fragments. We show that this method, employing constrained DFT for the calculation of the charge-transfer energy, yields reliable results and is robust with respect to the strength of the charge transfer, the basis set size, and the DFT functional used. Because it is based on DFT, the method is applicable to rather large systems. PMID:26580910

  7. Matrix-product-state method with local basis optimization for nonequilibrium electron-phonon systems

    NASA Astrophysics Data System (ADS)

    Heidrich-Meisner, Fabian; Brockt, Christoph; Dorfner, Florian; Vidmar, Lev; Jeckelmann, Eric

    We present a method for simulating the time evolution of quasi-one-dimensional correlated systems with strongly fluctuating bosonic degrees of freedom (e.g., phonons) using matrix product states. For this purpose we combine the time-evolving block decimation (TEBD) algorithm with a local basis optimization (LBO) approach. We discuss the performance of our approach in comparison to TEBD with a bare boson basis, exact diagonalization, and diagonalization in a limited functional space. TEBD with LBO can reduce the computational cost by orders of magnitude when boson fluctuations are large and thus it allows one to investigate problems that are out of reach of other approaches. First, we test our method on the non-equilibrium dynamics of a Holstein polaron and show that it allows us to study the regime of strong electron-phonon coupling. Second, the method is applied to the scattering of an electronic wave packet off a region with electron-phonon coupling. Our study reveals a rich physics including transient self-trapping and dissipation. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 1807.

  8. [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. PMID:22748725

  9. Generally Contracted Valence-Core/Valence Basis Sets for Use with Relativistic Effective Core Potentials and Spin-Orbit Coupling Operators

    SciTech Connect

    Ermler, Walter V.; Tilson, Jeffrey L.

    2012-12-15

    A procedure for structuring generally contracted valence-core/valence basis sets of Gaussian-type functions for use with relativistic effective core potentials (gcv-c/v-RECP basis sets) is presented. Large valence basis sets are enhanced using a compact basis set derived for outer core electrons in the presence of small-core RECPs. When core electrons are represented by relativistic effective core potentials (RECPs), and appropriate levels of theory, these basis sets are shown to provide accurate representations of atomic and molecular valence and outer-core electrons. Core/valence polarization and correlation effects can be calculated using these basis sets through standard methods for treating electron correlation. Calculations of energies and spectra for Ru, Os, Ir, In and Cs are reported. Spectroscopic constants for RuO2+, OsO2+, Cs2 and InH are calculated and compared with experiment.

  10. 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

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

    PubMed

    Kruse, Holger; Grimme, Stefan

    2012-04-21

    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. PMID:22519309

  12. Full Glowworm Swarm Optimization Algorithm for Whole-Set Orders Scheduling in Single Machine

    PubMed Central

    Yu, Zhang; Yang, Xiaomei

    2013-01-01

    By analyzing the characteristics of whole-set orders problem and combining the theory of glowworm swarm optimization, a new glowworm swarm optimization algorithm for scheduling is proposed. A new hybrid-encoding schema combining with two-dimensional encoding and random-key encoding is given. In order to enhance the capability of optimal searching and speed up the convergence rate, the dynamical changed step strategy is integrated into this algorithm. Furthermore, experimental results prove its feasibility and efficiency. PMID:24294135

  13. Analysis of the optimal laminated target made up of discrete set of materials

    NASA Technical Reports Server (NTRS)

    Aptukov, Valery N.; Belousov, Valentin L.

    1991-01-01

    A new class of problems was analyzed to estimate an optimal structure of laminated targets fabricated from the specified set of homogeneous materials. An approximate description of the perforation process is based on the model of radial hole extension. The problem is solved by using the needle-type variation technique. The desired optimization conditions and quantitative/qualitative estimations of optimal targets were obtained and are discussed using specific examples.

  14. 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. PMID:27208948

  15. 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

  16. 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. PMID:26216969

  17. Describing the Complexity of Systems: Multivariable “Set Complexity” and the Information Basis of Systems Biology

    PubMed Central

    Sakhanenko, Nikita A.; Skupin, Alexander; Ignac, Tomasz

    2014-01-01

    Abstract 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. PMID:24377753

  18. 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. PMID:25581402

  19. POSSIBILITIES FOR ASSESSMENT AND OPTIMIZATION OF NPP PHYSICAL PROTECTION SYSTEMS IN UKRAINE ON THE BASIS OF NUCLEAR SAFETY ANALYSIS

    SciTech Connect

    Shcherbinin, Konstantin

    2011-10-01

    The design requirements for physical protection systems currently adopted at Ukrainian NPPs were established in the middle of the nineties on the basis of deterministic analyses and expert evaluations of the vulnerabilities of reactor facilities. At the present time the in-depth assessment of the nuclear safety of Ukrainian NPPs with VVER-1000/B320 reactors has been completed using Probabilistic Safety Assessment (PSA). PSA has established and provided a qualitative assessment of the significance of the equipment for maintaining the integrity of a reactor core and preventing an abnormal radioactive release. The availability of qualitative assessments of the importance of equipment for nuclear safety allows one to assess the existing physical protection system using (1) comparative analysis: to determine whether all equipment and zones that may be affected, as established by the nuclear safety assessment, are actually included into the vital zones protected by the existing physical protection system; (2) specific analysis of dominant contributors: since nuclear safety analyses provide qualitative assessment of the equipment’s importance for safety, it is easy to select a limited group of essential equipment that makes the major contribution to safety, and (3) specific equipment analysis included in dominant emergency sets: part of the components might not be included in the essential equipment group, but it might be included in the dominant emergency sets. If some equipment is found not to be covered by the physical protection system, it is possible, using qualitative assessment of the importance of this equipment for safety, to assess the required degree of enhancement of physical protection. Such analysis will permit an assessment of the sufficiency of the existing physical protection system, to define the "tight" system areas and, therefore, to develop a justified optimization of a PPS with the objective of implementing priority upgrades to enhance safety, and

  20. 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…

  1. An expanded calibration study of the explicitly correlated CCSD(T)-F12b method using large basis set standard CCSD(T) atomization energies

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.

    2013-08-01

    The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 Eh) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.

  2. 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.

  3. Generation of pareto optimal ensembles of calibrated parameter sets for climate models.

    SciTech Connect

    Dalbey, Keith R.; Levy, Michael Nathan

    2010-12-01

    Climate models have a large number of inputs and outputs. In addition, diverse parameters sets can match observations similarly well. These factors make calibrating the models difficult. But as the Earth enters a new climate regime, parameters sets may cease to match observations. History matching is necessary but not sufficient for good predictions. We seek a 'Pareto optimal' ensemble of calibrated parameter sets for the CCSM climate model, in which no individual criteria can be improved without worsening another. One Multi Objective Genetic Algorithm (MOGA) optimization typically requires thousands of simulations but produces an ensemble of Pareto optimal solutions. Our simulation budget of 500-1000 runs allows us to perform the MOGA optimization once, but with far fewer evaluations than normal. We devised an analytic test problem to aid in the selection MOGA settings. The test problem's Pareto set is the surface of a 6 dimensional hypersphere with radius 1 centered at the origin, or rather the portion of it in the [0,1] octant. We also explore starting MOGA from a space-filling Latin Hypercube sample design, specifically Binning Optimal Symmetric Latin Hypercube Sampling (BOSLHS), instead of Monte Carlo (MC). We compare the Pareto sets based on: their number of points, N, larger is better; their RMS distance, d, to the ensemble's center, 0.5553 is optimal; their average radius, {mu}(r), 1 is optimal; their radius standard deviation, {sigma}(r), 0 is optimal. The estimated distributions for these metrics when starting from MC and BOSLHS are shown in Figs. 1 and 2.

  4. Chemical bonding analysis for solid-state systems using intrinsic oriented quasiatomic minimal-basis-set orbitals

    SciTech Connect

    Yao, Y. X.; Wang, C. Z.; Ho, K. M.

    2010-06-16

    A chemical bonding scheme is presented for the analysis of solid-state systems. The scheme is based on the intrinsic oriented quasiatomic minimal-basis-set orbitals (IO-QUAMBOs) previously developed by Ivanic and Ruedenberg for molecular systems. In the solid-state scheme, IO-QUAMBOs are generated by a unitary transformation of the quasiatomic orbitals located at each site of the system with the criteria of maximizing the sum of the fourth power of interatomic orbital bond order. Possible bonding and antibonding characters are indicated by the single particle matrix elements, and can be further examined by the projected density of states. We demonstrate the method by applications to graphene and (6,0) zigzag carbon nanotube. The oriented-orbital scheme automatically describes the system in terms of sp{sup 2} hybridization. The effect of curvature on the electronic structure of the zigzag carbon nanotube is also manifested in the deformation of the intrinsic oriented orbitals as well as a breaking of symmetry leading to nonzero single particle density matrix elements. In an additional study, the analysis is performed on the Al{sub 3}V compound. The main covalent bonding characters are identified in a straightforward way without resorting to the symmetry analysis. Our method provides a general way for chemical bonding analysis of ab initio electronic structure calculations with any type of basis sets.

  5. 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.

  6. Optimized face recognition algorithm using radial basis function neural networks and its practical applications.

    PubMed

    Yoo, Sung-Hoon; Oh, Sung-Kwun; Pedrycz, Witold

    2015-09-01

    In this study, we propose a hybrid method of face recognition by using face region information extracted from the detected face region. In the preprocessing part, we develop a hybrid approach based on the Active Shape Model (ASM) and the Principal Component Analysis (PCA) algorithm. At this step, we use a CCD (Charge Coupled Device) camera to acquire a facial image by using AdaBoost and then Histogram Equalization (HE) is employed to improve the quality of the image. ASM extracts the face contour and image shape to produce a personal profile. Then we use a PCA method to reduce dimensionality of face images. In the recognition part, we consider the improved Radial Basis Function Neural Networks (RBF NNs) to identify a unique pattern associated with each person. The proposed RBF NN architecture consists of three functional modules realizing the condition phase, the conclusion phase, and the inference phase completed with the help of fuzzy rules coming in the standard 'if-then' format. In the formation of the condition part of the fuzzy rules, the input space is partitioned with the use of Fuzzy C-Means (FCM) clustering. In the conclusion part of the fuzzy rules, the connections (weights) of the RBF NNs are represented by four kinds of polynomials such as constant, linear, quadratic, and reduced quadratic. The values of the coefficients are determined by running a gradient descent method. The output of the RBF NNs model is obtained by running a fuzzy inference method. The essential design parameters of the network (including learning rate, momentum coefficient and fuzzification coefficient used by the FCM) are optimized by means of Differential Evolution (DE). The proposed P-RBF NNs (Polynomial based RBF NNs) are applied to facial recognition and its performance is quantified from the viewpoint of the output performance and recognition rate. PMID:26163042

  7. 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.

  8. Parallel, linear-scaling building-block and embedding method based on localized orbitals and orbital-specific basis sets.

    PubMed

    Seijo, Luis; Barandiarán, Zoila

    2004-10-01

    We present a linear scaling method for the energy minimization step of semiempirical and first-principles Hartree-Fock and Kohn-Sham calculations. It is based on the self-consistent calculation of the optimum localized orbitals of any localization method of choice and on the use of orbital-specific basis sets. The full set of localized orbitals of a large molecule is seen as an orbital mosaic where each tessera is made of only a few of them. The orbital tesserae are computed out of a set of embedded cluster pseudoeigenvalue coupled equations which are solved in a building-block self-consistent fashion. In each iteration, the embedded cluster equations are solved independently of each other and, as a result, the method is parallel at a high level of the calculation. In addition to full system calculations, the method enables to perform simpler, much less demanding embedded cluster calculations, where only a fraction of the localized molecular orbitals are variational while the rest is frozen, taking advantage of the transferability of the localized orbitals of a given localization method between similar molecules. Monitoring single point energy calculations of large poly(ethylene oxide) molecules and three dimensional carbon monoxide clusters using an extended Huckel Hamiltonian are presented. PMID:15473725

  9. 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.

  10. Introduction of a fully relativistic capable basis set in the ab initio orthogonalized linear combination of atomic orbitals method

    NASA Astrophysics Data System (ADS)

    Thomas, Patrick Ryan

    Large simulation cell sizes, relativistic effects, and the need to correctly model excited state properties are major impediments to the accurate prediction of the optical properties of candidate materials for solid-state laser crystal and luminescent applications. To overcome these challenges, new methods must be created to improve the electron orbital wavefunction and interactions. In this work, a method has been developed to create new analytical four-component, fully-relativistic and single-component scalar relativistic descriptions of the atomic orbital wave functions from Grasp2K numerically represented atomic orbitals. In addition, adapted theory for the calculation of the relativistic kinetic energy contribution to Hamiltonian which bypasses directly solving the Dirac equation has been explicated. The orbital description improvements are tested against YAG, YBCO, SnO2 and BiF3. The improvements to the basis set reflect an improvement in both computational speed and accuracy.

  11. 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.

  12. Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods.

    PubMed

    Andrade, Xavier; Aspuru-Guzik, Alán

    2013-10-01

    We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs. PMID:26589153

  13. 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.

  14. Topology-optimized multiple-disk resonators obtained using level set expression incorporating surface effects.

    PubMed

    Fujii, Garuda; Ueta, Tsuyoshi; Mizuno, Mamoru; Nakamura, Masayuki

    2015-05-01

    Topology-optimized designs of multiple-disk resonators are presented using level-set expression that incorporates surface effects. Effects from total internal reflection at the surfaces of the dielectric disks are precisely simulated by modeling clearly defined dielectric boundaries during topology optimization. The electric field intensity in optimal resonators increases to more than four and a half times the initial intensity in a resonant state, whereas in some cases the Q factor increases by three and a half times that for the initial state. Wavelength-scale link structures between neighboring disks improve the performance of the multiple-disk resonators. PMID:25969226

  15. 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

  16. An adaptive multiquadric radial basis function method for expensive black-box mixed-integer nonlinear constrained optimization

    NASA Astrophysics Data System (ADS)

    Rashid, Kashif; Ambani, Saumil; Cetinkaya, Eren

    2013-02-01

    Many real-world optimization problems comprise objective functions that are based on the output of one or more simulation models. As these underlying processes can be time and computation intensive, the objective function is deemed expensive to evaluate. While methods to alleviate this cost in the optimization procedure have been explored previously, less attention has been given to the treatment of expensive constraints. This article presents a methodology for treating expensive simulation-based nonlinear constraints alongside an expensive simulation-based objective function using adaptive radial basis function techniques. Specifically, a multiquadric radial basis function approximation scheme is developed, together with a robust training method, to model not only the costly objective function, but also each expensive simulation-based constraint defined in the problem. The article presents the methodology developed for expensive nonlinear constrained optimization problems comprising both continuous and integer variables. Results from various test cases, both analytical and simulation-based, are presented.

  17. 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.

  18. Accurate Bond Energies of Hydrocarbons from Complete Basis Set Extrapolated Multi-Reference Singles and Doubles Configuration Interaction

    SciTech Connect

    Oyeyemi, Victor B.; Pavone, Michele; Carter, Emily A.

    2011-11-03

    Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: (1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; (2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and (3) DFT-B3LYP calculations of minimumenergy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of C*C and C*H bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules.

  19. A variational level set method for the topology optimization of steady-state Navier Stokes flow

    NASA Astrophysics Data System (ADS)

    Zhou, Shiwei; Li, Qing

    2008-12-01

    The smoothness of topological interfaces often largely affects the fluid optimization and sometimes makes the density-based approaches, though well established in structural designs, inadequate. This paper presents a level-set method for topology optimization of steady-state Navier-Stokes flow subject to a specific fluid volume constraint. The solid-fluid interface is implicitly characterized by a zero-level contour of a higher-order scalar level set function and can be naturally transformed to other configurations as its host moves. A variational form of the cost function is constructed based upon the adjoint variable and Lagrangian multiplier techniques. To satisfy the volume constraint effectively, the Lagrangian multiplier derived from the first-order approximation of the cost function is amended by the bisection algorithm. The procedure allows evolving initial design to an optimal shape and/or topology by solving the Hamilton-Jacobi equation. Two classes of benchmarking examples are presented in this paper: (1) periodic microstructural material design for the maximum permeability; and (2) topology optimization of flow channels for minimizing energy dissipation. A number of 2D and 3D examples well demonstrated the feasibility and advantage of the level-set method in solving fluid-solid shape and topology optimization problems.

  20. 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.

  1. 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

  2. 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. PMID:26367382

  3. 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.

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

    PubMed

    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

  5. 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

  6. Hyperpolarizability of H 2O revisited: accurate estimate of the basis set limit and the size of electron correlation effects

    NASA Astrophysics Data System (ADS)

    Maroulis, George

    1998-06-01

    A large (18s 13p 8d 5f / 12s 7p 3d 2f) basis set consisting of 256 uncontracted gaussian-type functions is expected to yield values near the Hartree-Fock limit for the static hyperpolarizability of H 2O: βzxx=-9.40, βzyy=-1.35, βzzz=-7.71 and β¯=-11.07 for βαβγ ( e3a03Eh-2) and γxxxx=569, γyyyy=1422, γzzzz=907, γxxyy=338, γyyzz=389, γzzxx=287 and γ¯=985 for γαβγδ ( e4a04Eh-3) at the experimental equilibrium geometry (with z as the C 2 axis, molecule on the xz plane). The respective electron correlation corrections obtained with the single, double and perturbatively linked triple excitations coupled-cluster method and a [9s 6p 6d 3f / 6s 4p 2d 1f] basis set are βzxx=-0.45, βzyy=-4.19, βzzz=-6.09, β¯=-6.44 and γxxxx=267, γyyyy=1228, γzzzz=574, γxxyy=295, γyyzz=322, γzzxx=152, γ¯=721 . For the static limit we propose β¯=-17.5±0.3 e3a03Eh-2 and γ¯=(171±6)×10 1e4a04Eh-3, in near agreement with the experimental findings of β¯=-19.2±0.9 e3a03Eh-2 and γ¯=1800±150 e4a04Eh-3 deduced from EFISH measurements at 1064 nm by Kaatz et al. [P. Kaatz, E.A. Donley, D.P. Shelton, J. Chem. Phys. 108 (1998) 849].

  7. 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

  8. 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)].

  9. 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.

  10. Implementation of a near-optimal global set point control method in a DDC controller

    SciTech Connect

    Cascia, M.A.

    2000-07-01

    A near-optimal global set point control method that can be implemented in an energy management system's (EMS) DDC controller is described in this paper. Mathematical models are presented for the power consumption of electric chillers, hot water boilers, chilled and hot water pumps, and air handler fans, which allow the calculation of near-optimal chilled water, hot water, and coil discharge air set points to minimize power consumption, based on data collected by the EMS. Also optimized are the differential and static pressure set points for the variable speed pumps and fans. A pilot test of this control methodology was implemented for a cooling plant at a pharmaceutical manufacturing facility near Dallas, Texas. Data collected at this site showed good agreement between the actual power consumed by the chillers, chilled water pumps, and air handlers and that predicted by the models. An approximate model was developed to calculate real-time power savings in the DDC controller. A third-party energy accounting program was used to track savings due to the near-optimal control, and results show a monthly KWH reduction ranging from 3% to 14%.

  11. Density and level set-XFEM schemes for topology optimization of 3-D structures

    NASA Astrophysics Data System (ADS)

    Villanueva, Carlos H.; Maute, Kurt

    2014-07-01

    As the capabilities of additive manufacturing techniques increase, topology optimization provides a promising approach to design geometrically sophisticated structures. Traditional topology optimization methods aim at finding conceptual designs, but they often do not resolve sufficiently the geometry and the structural response such that the optimized designs can be directly used for manufacturing. To overcome these limitations, this paper studies the viability of the extended finite element method (XFEM) in combination with the level-set method (LSM) for topology optimization of three dimensional structures. The LSM describes the geometry by defining the nodal level set values via explicit functions of the optimization variables. The structural response is predicted by a generalized version of the XFEM. The LSM-XFEM approach is compared against results from a traditional Solid Isotropic Material with Penalization method for two-phase "solid-void" and "solid-solid" problems. The numerical results demonstrate that the LSM-XFEM approach describes crisply the geometry and predicts the structural response with acceptable accuracy even on coarse meshes.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. A candidate-set-free algorithm for generating D-optimal split-plot designs

    PubMed Central

    Jones, Bradley; Goos, Peter

    2007-01-01

    We introduce a new method for generating optimal split-plot designs. These designs are optimal in the sense that they are efficient for estimating the fixed effects of the statistical model that is appropriate given the split-plot design structure. One advantage of the method is that it does not require the prior specification of a candidate set. This makes the production of split-plot designs computationally feasible in situations where the candidate set is too large to be tractable. The method allows for flexible choice of the sample size and supports inclusion of both continuous and categorical factors. The model can be any linear regression model and may include arbitrary polynomial terms in the continuous factors and interaction terms of any order. We demonstrate the usefulness of this flexibility with a 100-run polypropylene experiment involving 11 factors where we found a design that is substantially more efficient than designs that are produced by using other approaches. PMID:21197132

  17. Brodsky-Lepage-Mackenzie optimal renormalization scale setting for semihard processes

    NASA Astrophysics Data System (ADS)

    Caporale, F.; Ivanov, D. Yu.; Murdaca, B.; Papa, A.

    2015-06-01

    The Balitsky-Fadin-Kuraev-Lipatov (BFKL) approach for the investigation of semihard processes is plagued by large next-to-leading corrections, both in the kernel of the universal BFKL Green's function and in the process-dependent impact factors, as well as by large uncertainties in the renormalization scale setting. All that calls for an optimization procedure of the perturbative series. In this respect, one of the most common methods is the Brodsky-Lepage-Mackenzie (BLM) one, which eliminates the renormalization scale ambiguity by absorbing the nonconformal β0 terms into the running coupling. In this paper, we apply the BLM scale setting procedure directly to the amplitudes (cross sections) of several semihard processes. We show that, due to the presence of β0 terms in the next-to-leading expressions for the impact factors, the optimal renormalization scale is not universal but depends both on the energy and on the type of process in question.

  18. 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.

  19. 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.

  20. 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

  1. Architecture and settings optimization procedure of a TES frequency domain multiplexed readout firmware

    NASA Astrophysics Data System (ADS)

    Clenet, A.; Ravera, L.; Bertrand, B.; den Hartog, R.; Jackson, B.; van Leeuwen, B.-J.; van Loon, D.; Parot, Y.; Pointecouteau, E.; Sournac, A.

    2014-11-01

    IRAP is developing the readout electronics of the SPICA-SAFARI's TES bolometer arrays. Based on the frequency domain multiplexing technique the readout electronics provides the AC-signals to voltage-bias the detectors; it demodulates the data; and it computes a feedback to linearize the detection chain. The feedback is computed with a specific technique, so called baseband feedback (BBFB) which ensures that the loop is stable even with long propagation and processing delays (i.e. several μ s) and with fast signals (i.e. frequency carriers of the order of 5 MHz). To optimize the power consumption we took advantage of the reduced science signal bandwidth to decouple the signal sampling frequency and the data processing rate. This technique allowed a reduction of the power consumption of the circuit by a factor of 10. Beyond the firmware architecture the optimization of the instrument concerns the characterization routines and the definition of the optimal parameters. Indeed, to operate an array TES one has to properly define about 21000 parameters. We defined a set of procedures to automatically characterize these parameters and find out the optimal settings.

  2. Time-optimal path planning in dynamic flows using level set equations: realistic applications

    NASA Astrophysics Data System (ADS)

    Lolla, Tapovan; Haley, Patrick J.; Lermusiaux, Pierre F. J.

    2014-09-01

    The level set methodology for time-optimal path planning is employed to predict collision-free and fastest-time trajectories for swarms of underwater vehicles deployed in the Philippine Archipelago region. To simulate the multiscale ocean flows in this complex region, a data-assimilative primitive-equation ocean modeling system is employed with telescoping domains that are interconnected by implicit two-way nesting. These data-driven multiresolution simulations provide a realistic flow environment, including variable large-scale currents, strong jets, eddies, wind-driven currents, and tides. The properties and capabilities of the rigorous level set methodology are illustrated and assessed quantitatively for several vehicle types and mission scenarios. Feasibility studies of all-to-all broadcast missions, leading to minimal time transmission between source and receiver locations, are performed using a large number of vehicles. The results with gliders and faster propelled vehicles are compared. Reachability studies, i.e., determining the boundaries of regions that can be reached by vehicles for exploratory missions, are then exemplified and analyzed. Finally, the methodology is used to determine the optimal strategies for fastest-time pick up of deployed gliders by means of underway surface vessels or stationary platforms. The results highlight the complex effects of multiscale flows on the optimal paths, the need to utilize the ocean environment for more efficient autonomous missions, and the benefits of including ocean forecasts in the planning of time-optimal paths.

  3. Time-optimal path planning in dynamic flows using level set equations: realistic applications

    NASA Astrophysics Data System (ADS)

    Lolla, Tapovan; Haley, Patrick J.; Lermusiaux, Pierre F. J.

    2014-10-01

    The level set methodology for time-optimal path planning is employed to predict collision-free and fastest-time trajectories for swarms of underwater vehicles deployed in the Philippine Archipelago region. To simulate the multiscale ocean flows in this complex region, a data-assimilative primitive-equation ocean modeling system is employed with telescoping domains that are interconnected by implicit two-way nesting. These data-driven multiresolution simulations provide a realistic flow environment, including variable large-scale currents, strong jets, eddies, wind-driven currents, and tides. The properties and capabilities of the rigorous level set methodology are illustrated and assessed quantitatively for several vehicle types and mission scenarios. Feasibility studies of all-to-all broadcast missions, leading to minimal time transmission between source and receiver locations, are performed using a large number of vehicles. The results with gliders and faster propelled vehicles are compared. Reachability studies, i.e., determining the boundaries of regions that can be reached by vehicles for exploratory missions, are then exemplified and analyzed. Finally, the methodology is used to determine the optimal strategies for fastest-time pick up of deployed gliders by means of underway surface vessels or stationary platforms. The results highlight the complex effects of multiscale flows on the optimal paths, the need to utilize the ocean environment for more efficient autonomous missions, and the benefits of including ocean forecasts in the planning of time-optimal paths.

  4. 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.

  5. 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

  6. 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. PMID:25025089

  7. Temporal Data Set Reduction Based on D-Optimality for Quantitative FLIM-FRET Imaging

    PubMed Central

    Omer, Travis; Intes, Xavier; Hahn, Juergen

    2015-01-01

    Fluorescence lifetime imaging (FLIM) when paired with Förster resonance energy transfer (FLIM-FRET) enables the monitoring of nanoscale interactions in living biological samples. FLIM-FRET model-based estimation methods allow the quantitative retrieval of parameters such as the quenched (interacting) and unquenched (non-interacting) fractional populations of the donor fluorophore and/or the distance of the interactions. The quantitative accuracy of such model-based approaches is dependent on multiple factors such as signal-to-noise ratio and number of temporal points acquired when sampling the fluorescence decays. For high-throughput or in vivo applications of FLIM-FRET, it is desirable to acquire a limited number of temporal points for fast acquisition times. Yet, it is critical to acquire temporal data sets with sufficient information content to allow for accurate FLIM-FRET parameter estimation. Herein, an optimal experimental design approach based upon sensitivity analysis is presented in order to identify the time points that provide the best quantitative estimates of the parameters for a determined number of temporal sampling points. More specifically, the D-optimality criterion is employed to identify, within a sparse temporal data set, the set of time points leading to optimal estimations of the quenched fractional population of the donor fluorophore. Overall, a reduced set of 10 time points (compared to a typical complete set of 90 time points) was identified to have minimal impact on parameter estimation accuracy (≈5%), with in silico and in vivo experiment validations. This reduction of the number of needed time points by almost an order of magnitude allows the use of FLIM-FRET for certain high-throughput applications which would be infeasible if the entire number of time sampling points were used. PMID:26658308

  8. 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.

  9. 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. PMID:18270966

  10. Planting-Density Optimization Study Fortomato Fruit Set and Yield Based Onfunctional-Structural Model Greenlab

    NASA Astrophysics Data System (ADS)

    Yang, Lili; Wang, Yiming; Dong, Qiaoxue

    Quantification of tomato's fruit-sets depends on the level of competition for assimilate in different environment, and this paper presented some results of fruit yield and quality (fruit size) in response to environment (mainly respect to and planting-density and light). Some experiments had been carried out to find the relationship between growth rules of tomato and plant densities A structural-functional model GREENLAB has been developed to simulate it. The results show that increasing plant density results in an increment of biomass production on a ground area but in a reduction of single plant fresh weight. To find rules between organ sink and source relationship, calibrations Environmental conditions were introduced into the model checking the influence on Q/D over plant growth period and fruit set ratio. It is found that changing the Q/D ratio in some critical periods can be used to optimize fruit set and yield of greenhouse tomato.

  11. A PERFECT MATCH CONDITION FOR POINT-SET MATCHING PROBLEMS USING THE OPTIMAL MASS TRANSPORT APPROACH

    PubMed Central

    CHEN, PENGWEN; LIN, CHING-LONG; CHERN, I-LIANG

    2013-01-01

    We study the performance of optimal mass transport-based methods applied to point-set matching problems. The present study, which is based on the L2 mass transport cost, states that perfect matches always occur when the product of the point-set cardinality and the norm of the curl of the non-rigid deformation field does not exceed some constant. This analytic result is justified by a numerical study of matching two sets of pulmonary vascular tree branch points whose displacement is caused by the lung volume changes in the same human subject. The nearly perfect match performance verifies the effectiveness of this mass transport-based approach. PMID:23687536

  12. 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. PMID:24375320

  13. Modeling Organic Aerosols in a Megacity: Comparison of Simple and Complex Representations of the Volatility Basis Set Approach

    SciTech Connect

    Shrivastava, ManishKumar B.; Fast, Jerome D.; Easter, Richard C.; Gustafson, William I.; Zaveri, Rahul A.; Jimenez, Jose L.; Saide, Pablo; Hodzic, Alma

    2011-07-13

    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

  14. 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

  15. IIA: a novel method to optimize media instruction set of embedded processor

    NASA Astrophysics Data System (ADS)

    Chen, Keming; Yu, Guojun; Liu, Peng; Yao, Qingdong

    2006-02-01

    To accelerate media processing, many media enhancement instructions have been adopted into the instruction set of embedded processors. In this paper, a novel method, called interaction between instructions and algorithms (IIA), is proposed to optimize these media enhancement instructions. Based on the analysis for inherent characteristics of video processing algorithms and processor's architecture, three measures are proposed: three single-cycle instructions for manipulation on bit level are implemented to speed up variable-length decoding; a data path is designed to solve data misalignment in SIMD processing instead of software programs; a memory architecture is proposed to support 128-bit word parallel processing. All these suggestions are used in the optimization of an embedded processor, MediaDSP3200 which fuses RISC architecture and DSP computation capability thoroughly and achieves reduced instruction and 64-bit SIMD instruction set with various addressing mode in a unified RISC pipeline stage architecture. Simulation results show that this optimization method can reduce more than 26.4% of clock cycles for VLD, 47.8% for IDCT and 66.8% for MC in real-time processing.

  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.

    2014-09-01

    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. 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.

  18. 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

  19. 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.

  20. Matrix-product-state method with a dynamical local basis optimization for bosonic systems out of equilibrium

    NASA Astrophysics Data System (ADS)

    Brockt, C.; Dorfner, F.; Vidmar, L.; Heidrich-Meisner, F.; Jeckelmann, E.

    2015-12-01

    We present a method for simulating the time evolution of one-dimensional correlated electron-phonon systems which combines the time-evolving block decimation algorithm with a dynamical optimization of the local basis. This approach can reduce the computational cost by orders of magnitude when boson fluctuations are large. The method is demonstrated on the nonequilibrium Holstein polaron by comparison with exact simulations in a limited functional space and on the scattering of an electronic wave packet by local phonon modes. Our study of the scattering problem reveals a rich physics including transient self-trapping and dissipation.

  1. Approximating the optimal groundwater pumping policy in a multiaquifer stochastic conjunctive use setting

    NASA Astrophysics Data System (ADS)

    Provencher, Bill; Burt, Oscar

    1994-03-01

    This paper presents two methods for approximating the optimal groundwater pumping policy for several interrelated aquifers in a stochastic setting that also involves conjunctive use of surface water. The first method employs a policy iteration dynamic programming (DP) algorithm where the value function is estimated by Monte Carlo simulation combined with curve-fitting techniques. The second method uses a Taylor series approximation to the functional equation of DP which reduces the problem, for a given observed state, to solving a system of equations equal in number to the aquifers. The methods are compared using a four-state variable, stochastic dynamic programming model of Madera County, California. The two methods yield nearly identical estimates of the optimal pumping policy, as well as the steady state pumping depth, suggesting that either method can be used in similar applications.

  2. 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. PMID:25204003

  3. 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

  4. Process modeling and parameter optimization using radial basis function neural network and genetic algorithm for laser welding of dissimilar materials

    NASA Astrophysics Data System (ADS)

    Ai, Yuewei; Shao, Xinyu; Jiang, Ping; Li, Peigen; Liu, Yang; Yue, Chen

    2015-11-01

    The welded joints of dissimilar materials have been widely used in automotive, ship and space industries. The joint quality is often evaluated by weld seam geometry, microstructures and mechanical properties. To obtain the desired weld seam geometry and improve the quality of welded joints, this paper proposes a process modeling and parameter optimization method to obtain the weld seam with minimum width and desired depth of penetration for laser butt welding of dissimilar materials. During the process, Taguchi experiments are conducted on the laser welding of the low carbon steel (Q235) and stainless steel (SUS301L-HT). The experimental results are used to develop the radial basis function neural network model, and the process parameters are optimized by genetic algorithm. The proposed method is validated by a confirmation experiment. Simultaneously, the microstructures and mechanical properties of the weld seam generated from optimal process parameters are further studied by optical microscopy and tensile strength test. Compared with the unoptimized weld seam, the welding defects are eliminated in the optimized weld seam and the mechanical properties are improved. The results show that the proposed method is effective and reliable for improving the quality of welded joints in practical production.

  5. 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. PMID:23913741

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

    PubMed

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

    2016-07-01

    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

  7. 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

  8. 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.

  9. Automatic classification of Polish fricatives on the basis of optimization of the parameter space

    NASA Astrophysics Data System (ADS)

    Domagala, Piotr; Richter, Lutoslawa

    1994-08-01

    The subject of this article is a study of the possibility of automatic classification and recognition of fricatives on the basis of a certain linear combination of values of an autocorrelation function. Automatic classification of fricative consonants constituted one phase of a study which involves the classification of all Polish phones for the purpose of enabling automatic speech recognition regardless of the phonetic context or the speaker. The study was conducted using phonetic material consisting of 166 nonsense syllables which included fricatives and had CVCV and VCCV structures. There were a total of about 20 contexts for each consonant. Separate classifications were performed for 5 female voices and 5 male voices and then both groups of voices were classified together. The three series of classifications had success rates of 60%, 69%, and 60% respectively. These results were about 10% better than the results obtained using classical discrimination analysis (CSS:Statistica 3.1 software). The use of cluster analysis and multidimensional scaling yielded information on the relative probabilities of the acoustic patterns of these phones in reference to perception tests.

  10. Training set optimization and classifier performance in a top-down diabetic retinopathy screening system

    NASA Astrophysics Data System (ADS)

    Wigdahl, J.; Agurto, C.; Murray, V.; Barriga, S.; Soliz, P.

    2013-03-01

    Diabetic retinopathy (DR) affects more than 4.4 million Americans age 40 and over. Automatic screening for DR has shown to be an efficient and cost-effective way to lower the burden on the healthcare system, by triaging diabetic patients and ensuring timely care for those presenting with DR. Several supervised algorithms have been developed to detect pathologies related to DR, but little work has been done in determining the size of the training set that optimizes an algorithm's performance. In this paper we analyze the effect of the training sample size on the performance of a top-down DR screening algorithm for different types of statistical classifiers. Results are based on partial least squares (PLS), support vector machines (SVM), k-nearest neighbor (kNN), and Naïve Bayes classifiers. Our dataset consisted of digital retinal images collected from a total of 745 cases (595 controls, 150 with DR). We varied the number of normal controls in the training set, while keeping the number of DR samples constant, and repeated the procedure 10 times using randomized training sets to avoid bias. Results show increasing performance in terms of area under the ROC curve (AUC) when the number of DR subjects in the training set increased, with similar trends for each of the classifiers. Of these, PLS and k-NN had the highest average AUC. Lower standard deviation and a flattening of the AUC curve gives evidence that there is a limit to the learning ability of the classifiers and an optimal number of cases to train on.

  11. Optimal power settings of aluminum gallium arsenide lasers in caries inhibition — An in vitro study

    PubMed Central

    Sharma, Sonali; Hegde, Mithra N; Sadananda, Vandana; Mathews, Blessen

    2016-01-01

    Context: Incipient carious lesions are characterized by subsurface dissolution due to more fluoride ions in the 50-100 microns of the tooth's outer surface. Aims: To determine an optimal power setting for 810 nm aluminum gallium arsenide laser for caries inhibition. Materials and Methods: Fifty-four caries-free extracted teeth were sectioned mesiodistally. The samples were divided into 18 groups for each power setting being evaluated. Each group had six samples. The laser used is 810 nm aluminum gallium arsenide laser with power setting from 0.1 watts to 5 watts. Laser fluorescence based device was used to evaluate the effect of irradiation. Statistical Analysis Used: Paired “t” test, one-way analysis of variance (ANOVA), Tukey's post hoc test, and the Pearson's correlation test. Results: The paired t-test showed that there is minimum divergence from the control for 3.5 watts. Tukey's post hoc test also showed statistically significantly results for 3.5 watts. The Pearson's correlation test showed that there was negative correlation between the watts and irradiation. Conclusions: The power setting that gave statistically significant results was 3.5 watts. PMID:27099427

  12. 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. PMID:17523796

  13. A new theoretical basis for the bandwidth method and optimal power ratios for the damping estimation

    NASA Astrophysics Data System (ADS)

    Yin, H. P.

    2008-11-01

    Using the well-known bandwidth formula and the half power bandwidth formula [R.E.D. Bishop, G.M.L. Gladwell, An investigation into the theory of resonance testing, Philosophical Transactions of the Royal Society of London A 255 (1963) 241-280], in particular, is the simplest way to estimate modal damping for engineers. By using the half power bandwidth formula, the damping factor is estimated to be approximately the half bandwidth at the half power points. One of the major limitations that restrict the use of this method is the coupling effect between closely spaced modes. In this paper, the dependence of the damping estimation accuracy on the selected power ratios is studied with both analytical and experimental data of frequency response functions. The results show that by selecting adequate power ratio values, the coupling effect can be minimized and the estimation accuracy can be significantly improved for closely spaced modes. A further improvement of accuracy can be obtained by applying the algorithm of mode isolation [H.P. Yin, D. Duhamel, Substraction technique and finite difference formulas for modal parameter estimation, Mechanical Systems and Signal Processing 18 (2004) 1497-1503; M.S. Allen, J.H. Ginsberg, A global, single-input-multi-output (SIMO) implementation of the algorithm of mode isolation and application to analytical and experimental data, Mechanical Systems and Signal Processing 20 (2006) 1090-1111]. Also an exact bandwidth formula in case of a single degree of freedom system is presented and the link between the exact formula and the classical approximated formula is indicated. The exact bandwidth formula provides a new theoretical basis of the bandwidth method for the damping estimation from frequency response functions.

  14. 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

  15. Optimization of parameter settings in cine-MR imaging for diagnosis of swallowing.

    PubMed

    Ohkubo, Mai; Higaki, Takuo; Nishikawa, Keiichi; Otonari-Yamamoto, Mika; Sugiyama, Tetsuya; Ishida, Ryo; Wako, Mamoru; Sano, Tsukasa

    2014-01-01

    Videofluorography is frequently used to evaluate swallowing and is considered the "gold standard" among imaging modalities. This modality, however, has several disadvantages, including radiation exposure and limitations in the detection of soft tissues. Conversely, magnetic resonance imaging (MRI) offers excellent contrast resolution in soft tissue without radiation exposure. A major drawback of MRI in evaluating swallowing, however, is that temporal resolution is poor. The aim of this study was to investigate a new cine-MRI modality. Imaging parameters were optimized and the efficacy of this new technique is discussed. Three techniques for speeding up MRI were combined: true fast imaging with steady state precession, generalized auto-calibrating partially parallel acquisition, and key-hole imaging. The effects of the receiver coils used, receiving bandwidth, slice thickness, and flip angle on each image were determined. The optimal imaging parameters obtained comprised a reduction factor of 2, receiving bandwidth of 1,000 Hz/pixel (repetition time of 151.7 milliseconds and echo time of 1.4 milliseconds), flip angle of 50°, and slice thickness of 6 mm. Neck and spine coils were used. Under these conditions, the new cine-MR imaging technique investigated showed a temporal resolution of 0.1 sec/slice (10 frames/sec). Even with optimized parameter settings, this technique did not allow a true temporal resolution of 30 frames/sec by a large margin. Motion artifacts persisted. Further study is needed on how to speed up this technique. PMID:25212558

  16. 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.

  17. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    SciTech Connect

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  18. 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.

  19. Optimizing baryon acoustic oscillation surveys - II. Curvature, redshifts and external data sets

    NASA Astrophysics Data System (ADS)

    Parkinson, David; Kunz, Martin; Liddle, Andrew R.; Bassett, Bruce A.; Nichol, Robert C.; Vardanyan, Mihran

    2010-02-01

    We extend our study of the optimization of large baryon acoustic oscillation (BAO) surveys to return the best constraints on the dark energy, building on Paper I of this series by Parkinson et al. The survey galaxies are assumed to be pre-selected active, star-forming galaxies observed by their line emission with a constant number density across the redshift bin. Star-forming galaxies have a redshift desert in the region 1.6 < z < 2, and so this redshift range was excluded from the analysis. We use the Seo & Eisenstein fitting formula for the accuracies of the BAO measurements, using only the information for the oscillatory part of the power spectrum as distance and expansion rate rulers. We go beyond our earlier analysis by examining the effect of including curvature on the optimal survey configuration and updating the expected `prior' constraints from Planck and the Sloan Digital Sky Survey. We once again find that the optimal survey strategy involves minimizing the exposure time and maximizing the survey area (within the instrumental constraints), and that all time should be spent observing in the low-redshift range (z < 1.6) rather than beyond the redshift desert, z > 2. We find that, when assuming a flat universe, the optimal survey makes measurements in the redshift range 0.1 < z < 0.7, but that including curvature as a nuisance parameter requires us to push the maximum redshift to 1.35, to remove the degeneracy between curvature and evolving dark energy. The inclusion of expected other data sets (such as WiggleZ, the Baryon Oscillation Spectroscopic Survey and a stage III Type Ia supernova survey) removes the necessity of measurements below redshift 0.9, and pushes the maximum redshift up to 1.5. We discuss considerations in determining the best survey strategy in light of uncertainty in the true underlying cosmological model.

  20. 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.

  1. 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. PMID:26239947

  2. 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

  3. Quantifying and visualizing variations in sets of images using continuous linear optimal transport

    NASA Astrophysics Data System (ADS)

    Kolouri, Soheil; Rohde, Gustavo K.

    2014-03-01

    Modern advancements in imaging devices have enabled us to explore the subcellular structure of living organisms and extract vast amounts of information. However, interpreting the biological information mined in the captured images is not a trivial task. Utilizing predetermined numerical features is usually the only hope for quantifying this information. Nonetheless, direct visual or biological interpretation of results obtained from these selected features is non-intuitive and difficult. In this paper, we describe an automatic method for modeling visual variations in a set of images, which allows for direct visual interpretation of the most significant differences, without the need for predefined features. The method is based on a linearized version of the continuous optimal transport (OT) metric, which provides a natural linear embedding for the image data set, in which linear combination of images leads to a visually meaningful image. This enables us to apply linear geometric data analysis techniques such as principal component analysis and linear discriminant analysis in the linearly embedded space and visualize the most prominent modes, as well as the most discriminant modes of variations, in the dataset. Using the continuous OT framework, we are able to analyze variations in shape and texture in a set of images utilizing each image at full resolution, that otherwise cannot be done by existing methods. The proposed method is applied to a set of nuclei images segmented from Feulgen stained liver tissues in order to investigate the major visual differences in chromatin distribution of Fetal-Type Hepatoblastoma (FHB) cells compared to the normal cells.

  4. 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

  5. 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.

  6. Optimization of the information content of multitemporal Landsat TM data sets for monitoring forest cover disturbance

    NASA Technical Reports Server (NTRS)

    Coppin, Pol R.; Bauer, Marvin E.

    1992-01-01

    Procedures that were developed to optimize the information content of multitemporal thematic mapper (TM) data sets for forest cover disturbance monitoring in Minnesota are described. TM imagery from three different years was calibrated to exoatmospheric reflectance. An atmospheric correction routine was applied combining two major components, atmospheric normalization over time and transformation to ground reflectance. Atmospheric conditions were modeled over time using regression functions derived from five ground features known to be unchanged over the time interval of interest and spanning the entire image reflectance range. The correlation between digital data and the forest cover was subsequently maximized and irrelevant information content was reduced by converting the band-specific reflectances into seven vegetation indices that were assumed to carry unique information. The application of two change detection algorithms to these seven indices ultimately resulted in 14 change features for each time interval of interest. Results show that the preprocessing sequence is vital to forest cover monitoring methodology.

  7. The possibility of evaluating turbo-set bearing misalignment defects on the basis of bearing trajectory features

    NASA Astrophysics Data System (ADS)

    Rybczyński, Józef

    2011-02-01

    This paper presents the results of computer simulation of bearing misalignment defects in a power turbogenerator. This malfunction is typical for great multi-rotor and multi-bearing rotating machines and very common in power turbo-sets. Necessary calculations were carried out by the computer code system MESWIR, developed and used at the IFFM in Gdansk for calculating dynamics of rotors supported on oil bearings. The results are presented in the form of a set of journal and bush trajectories of all turbo-set bearings. Our analysis focuses on the vibrational effects of displacing the two most vulnerable machine bearings in horizontal and vertical directions by the maximum acceptable range calculated with regard to bearing vibration criterion. This assumption required preliminary assessment of the maximum values for the permissible bearing dislocations. We show the relations between the attributes of the particular bearing trajectories and the bearing displacements in relation to their base design position. The shape and dimensions of bearing trajectories are interpreted based on the theory of hydrodynamic lubrication of oil bearings. It was shown that the relative journal trajectories and absolute bush trajectories carry much important information about the dynamic state of the machine, indicating also the way in which bearings are loaded. Therefore, trajectories can be a source of information about the position and direction of bearing misalignments. This article indicates the potential of using trajectory patterns for diagnosing misalignment defects in rotating machines and suggests including sets of trajectory patterns to the knowledge base of a machine diagnostic system.

  8. Increasing the Pedagogical Sophistication of Parents: The Basis for Improving the Education of School Pupils in the Family Setting

    ERIC Educational Resources Information Center

    Grebennikov, I. V.

    1978-01-01

    Maintains that lack of pedagogical training of parents in the Soviet Union leads to errors in the education of children in the family setting. Methods to increase parents' pedagogical sophistication include media presentations about social education, community education clubs for young families, parent teacher conferences, and training sessions…

  9. Optimize flue gas settings to promote microalgae growth in photobioreactors via computer simulations.

    PubMed

    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 emissions(1). Microalgae not only capture solar energy more efficiently than plants(3), but also synthesize advanced biofuels(2-4). Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth(5). 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 configurations(4,6) and cultivation strategies(7,8) 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. 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

  11. A New Methodology to Select the Preferred Solutions from the Pareto-optimal Set: Application to Polymer Extrusion

    SciTech Connect

    Ferreira, Jose C.; Gaspar-Cunha, Antonio; Fonseca, Carlos M.

    2007-04-07

    Most of the real world optimization problems involve multiple, usually conflicting, optimization criteria. Generating Pareto optimal solutions plays an important role in multi-objective optimization, and the problem is considered to be solved when the Pareto optimal set is found, i.e., the set of non-dominated solutions. Multi-Objective Evolutionary Algorithms based on the principle of Pareto optimality are designed to produce the complete set of non-dominated solutions. However, this is not allays enough since the aim is not only to know the Pareto set but, also, to obtain one solution from this Pareto set. Thus, the definition of a methodology able to select a single solution from the set of non-dominated solutions (or a region of the Pareto frontier), and taking into account the preferences of a Decision Maker (DM), is necessary. A different method, based on a weighted stress function, is proposed. It is able to integrate the user's preferences in order to find the best region of the Pareto frontier accordingly with these preferences. This method was tested on some benchmark test problems, with two and three criteria, and on a polymer extrusion problem. This methodology is able to select efficiently the best Pareto-frontier region for the specified relative importance of the criteria.

  12. 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.

  13. Global optimization on set of mixed variables: continuous and discrete with unordered possible values

    NASA Astrophysics Data System (ADS)

    Mikhalev, A. S.; Rouban, A. I.

    2016-04-01

    The algorithms of global non-differentiable minimization of functions on set of the mixed variables: continuous and discrete with unordered specific possible values are constructed. The method of optimization is based on selective averaging of required variables, on adaptive reorganization of the sizes of admissible domain of trial movements and on use of relative values for minimised functions. Existence of discrete variables leads to solution of a sequence of global minimization problems of the functions in space of only continuous variables at the presence: 1) of their inequality restrictions for each problem; 2) of the general inequality restrictions for all problems (i.e. at the absence of dependence of functions fore inequality restrictions from discrete variables). In the first case, presence of discrete variables with unordered non-numeric possible values leads to solution of sequence of problems of global minimization of multiextreme functions on set only of continuous variables at the presence of their inequality restrictions. As a result, among the received optimum solutions the best is selected. In the second variant all minimized functions is convoluted in each sampling point in one multiextreme function and this function is minimised on continuous variables.

  14. 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

  15. The Fantastic Four: A plug `n' play set of optimal control pulses for enhancing NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Nimbalkar, Manoj; Luy, Burkhard; Skinner, Thomas E.; Neves, Jorge L.; Gershenzon, Naum I.; Kobzar, Kyryl; Bermel, Wolfgang; Glaser, Steffen J.

    2013-03-01

    We present highly robust, optimal control-based shaped pulses designed to replace all 90° and 180° hard pulses in a given pulse sequence for improved performance. Special attention was devoted to ensuring that the pulses can be simply substituted in a one-to-one fashion for the original hard pulses without any additional modification of the existing sequence. The set of four pulses for each nucleus therefore consists of 90° and 180° point-to-point (PP) and universal rotation (UR) pulses of identical duration. These 1 ms pulses provide uniform performance over resonance offsets of 20 kHz (1H) and 35 kHz (13C) and tolerate reasonably large radio frequency (RF) inhomogeneity/miscalibration of ±15% (1H) and ±10% (13C), making them especially suitable for NMR of small-to-medium-sized molecules (for which relaxation effects during the pulse are negligible) at an accessible and widely utilized spectrometer field strength of 600 MHz. The experimental performance of conventional hard-pulse sequences is shown to be greatly improved by incorporating the new pulses, each set referred to as the Fantastic Four (Fanta4).

  16. 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. PMID:27308221

  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. Accurate ab initio double many-body expansion potential energy surface for ground-state H2S by extrapolation to the complete basis set limit.

    PubMed

    Song, Y Z; Varandas, A J C

    2009-04-01

    A single-sheeted potential energy surface is reported for the electronic ground-state of H(2)S by fitting accurate multireference configuration interaction energies calculated using aug-cc-pVTZ and aug-cc-pVQZ basis sets with extrapolation of the electron correlation energy to the complete basis set limit, plus extrapolation to the complete basis set limit of the complete-active-space self-consistent field energy. A switching function formalism has been used to warrant the correct behavior at the H(2)(X (1)Sigma(g) (+))+S((1)D) and SH(X (2)Pi)+H((2)S) dissociation limits. The topographical features of the novel global potential energy surface are examined in detail, with the former being used for exploratory quasiclassical trajectory calculations of the thermal rate constant for the S((1)D)+H(2), S((1)D)+D(2), and S((1)D)+HD reactions at room temperature. A comparison with other available potential energy surfaces as well as kinetics data is also provided. PMID:19355742

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

    PubMed

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

    2006-07-28

    Examination of the convergence of full valence complete active space self-consistent-field configuration interaction including all single and double excitation (CASSCF-CISD) energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant energies. Calculations on the lowest four singlet states and the lowest four triplet states of N(2) with the sequence of n-tuple-zeta augmented polarized (nZaP) basis sets (n=2, 3, 4, 5, and 6) are used to establish the complete basis set limits. Full configuration-interaction (CI) and core electron contributions must be included for very accurate potential energy surfaces. However, a simple extrapolation scheme that has no adjustable parameters and requires nothing more demanding than CAS(10e(-),8orb)-CISD/3ZaP calculations gives the R(e), omega(e), omega(e)X(e), T(e), and D(e) for these eight states with rms errors of 0.0006 Angstrom, 4.43 cm(-1), 0.35 cm(-1), 0.063 eV, and 0.018 eV, respectively. PMID:16942134

  20. Comparison of the polarizabilities and hyperpolarizabilities obtained from finite basis set and finite difference Hartree-Fock calculations for diatomic molecules

    NASA Astrophysics Data System (ADS)

    Kobus, J.; Moncrieff, D.; Wilson, S.

    2001-12-01

    A comparison is made of the accuracy by which the electric dipole polarizability αzz and hyperpolarizability βzzz can be calculated by using the finite basis set approach (the algebraic approximation) and finite difference method in calculations employing the Hartree-Fock model. The numerical and algebraic methods were tested on the ground states of H2, LiH, BH and FH molecules at their respective experimental equilibrium geometries. For the FH molecule at its experimental equilibrium geometry, a sequence of distributed universal even-tempered basis sets have been used to explore the convergence pattern of the total energy, dipole moment and polarizabilities. The comparison of finite difference and finite basis set methods is extended to geometries for which the nuclear separation, RFH, lies in the range 1.5-2.2 b. The methods give consistent results to within 1% or better. In the case of the FH molecule the dependence of truncation errors of the total energy, dipole moment and polarizabilities on the geometry have been studied and are shown to be negligible.

  1. 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.

  2. 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.

  3. 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

  4. Investigation of optimal feature value set in false positive reduction process for automated abdominal lymph node detection method

    NASA Astrophysics Data System (ADS)

    Nakamura, Yoshihiko; Nimura, Yukitaka; Kitasaka, Takayuki; Mizuno, Shinji; Furukawa, Kazuhiro; Goto, Hidemi; Fujiwara, Michitaka; Misawa, Kazunari; Ito, Masaaki; Nawano, Shigeru; Mori, Kensaku

    2015-03-01

    This paper presents an investigation of optimal feature value set in false positive reduction process for the automated method of enlarged abdominal lymph node detection. We have developed the automated abdominal lymph node detection method to aid for surgical planning. Because it is important to understand the location and the structure of an enlarged lymph node in order to make a suitable surgical plan. However, our previous method was not able to obtain the suitable feature value set. This method was able to detect 71.6% of the lymph nodes with 12.5 FPs per case. In this paper, we investigate the optimal feature value set in the false positive reduction process to improve the method for automated abdominal lymph node detection. By applying our improved method by using the optimal feature value set to 28 cases of abdominal 3D CT images, we detected about 74.7% of the abdominal lymph nodes with 11.8 FPs/case.

  5. Influence of a strong magnetic field on the hydrogen molecular ion using B-spline-type basis-sets

    NASA Astrophysics Data System (ADS)

    Zhang, Yue-Xia; Xiao-Long, Zhang

    2015-12-01

    As an improvement on our previous work [J. Phys. B: At. Mol. Opt. Phys. 45 085101 (2012)], an accurate method combining the spheroidal coordinates and B-spline basis is applied to study the ground state 1σg and low excited states 1σu, 1πg,u,1δg,u,2σg of the in magnetic fields ranging from 109 Gs (1 Gs = 10-4 T) to 4.414 × 1013 Gs. Comparing the one-center method used in our previous work, the present method has a higher precision with a shorter computing time. Equilibrium distances of the states of the in strong magnetic fields were found to be accurate to 3˜5 significant digits (s.d.) and the total energies 6˜11 s.d., even for some antibonding state, such as 1πg, which is difficult for the one-center method to give reliable results while the field strength is B ≥ 1013 Gs. For the large disagreement in previous works, such as the equilibrium distances of the 1πg state at B = 109 Gs, the present data may be used as a reference. Further, the potential energy curves (PECs) and the electronic probability density distributions (EPDDs) of the bound states 1σg, 1πu, 1δg and antibonding states 1σu, 1πg, 1δu for B = 1, 10, 100, 1000 a.u. (atomic unit) are compared, so that the different influences of the magnetic fields on the chemical bonds of the bound states and antibonding states are discussed in detail. Project supported by the National Natural Science Foundation of China (Grant No. 11204389) and the Natural Science Foundation Project of Chongqing (Grant Nos. CSTC2012jjA50015 and CSTC2012jjA00012).

  6. Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

    NASA Astrophysics Data System (ADS)

    Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

    2015-06-01

    The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

  7. Visualization of large medical data sets using memory-optimized CPU and GPU algorithms

    NASA Astrophysics Data System (ADS)

    Kiefer, Gundolf; Lehmann, Helko; Weese, Juergen

    2005-04-01

    With the evolution of medical scanners towards higher spatial resolutions, the sizes of image data sets are increasing rapidly. To profit from the higher resolution in medical applications such as 3D-angiography for a more efficient and precise diagnosis, high-performance visualization is essential. However, to make sure that the performance of a volume rendering algorithm scales with the performance of future computer architectures, technology trends need to be considered. The design of such scalable volume rendering algorithms remains challenging. One of the major trends in the development of computer architectures is the wider use of cache memory hierarchies to bridge the growing gap between the faster evolving processing power and the slower evolving memory access speed. In this paper we propose ways to exploit the standard PC"s cache memories supporting the main processors (CPU"s) and the graphics hardware (graphics processing unit, GPU), respectively, for computing Maximum Intensity Projections (MIPs). To this end, we describe a generic and flexible way to improve the cache efficiency of software ray casting algorithms and show by means of cache simulations, that it enables cache miss rates close to the theoretical optimum. For GPU-based rendering we propose a similar, brick-based technique to optimize the utilization of onboard caches and the transfer of data to the GPU on-board memory. All algorithms produce images of identical quality, which enables us to compare the performance of their implementations in a fair way without eventually trading quality for speed. Our comparison indicates that the proposed methods perform superior, in particular for large data sets.

  8. A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp.

    PubMed

    Eaton, Carla J; Dupont, Pierre-Yves; Solomon, Peter; Clayton, William; Scott, Barry; Cox, Murray P

    2015-03-01

    Beneficial plant-fungal interactions play an important role in the ability of plants to survive changing environmental conditions. In contrast, phytopathogenic fungi fall at the opposite end of the symbiotic spectrum, causing reduced host growth or even death. In order to exploit beneficial interactions and prevent pathogenic ones, it is essential to understand the molecular differences underlying these alternative states. The association between the endophyte Epichloë festucae and Lolium perenne (perennial ryegrass) is an excellent system for studying these molecular patterns due to the existence of several fungal mutants that have an antagonistic rather than a mutualistic interaction with the host plant. By comparing gene expression in a wild-type beneficial association with three mutant antagonistic associations disrupted in key signaling genes, we identified a core set of 182 genes that show common differential expression patterns between these two states. These gene expression changes are indicative of a nutrient-starvation response, as supported by the upregulation of genes encoding degradative enzymes, transporters, and primary metabolism, and downregulation of genes encoding putative small-secreted proteins and secondary metabolism. These results suggest that disruption of a mutualistic symbiotic interaction may lead to an elevated uptake and degradation of host-derived nutrients and cell-wall components, reminiscent of phytopathogenic interactions. PMID:25496592

  9. Collaborative effects-based planning using adversary models and target set optimization

    NASA Astrophysics Data System (ADS)

    Pioch, Nicholas J.; Daniels, Troy; Pielech, Bradford

    2004-08-01

    The Strategy Development Tool (SDT), sponsored by AFRL-IFS, supports effects-based planning at multiple levels of war through three core capabilities: plan authoring, center of gravity (COG) modeling and analysis, and target system analysis. This paper describes recent extensions to all three of these capabilities. The extended plan authoring subsystem supports collaborative planning in which a user delegates elaboration of objectives to other registered users. A suite of collaboration tools allows planners to assign planning tasks, submit plan fragments, and review submitted plans, while a collaboration server transparently handles message routing and persistence. The COG modeling subsystem now includes an enhanced adversary modeling tool that provides a lightweight ontology for building temporal causal models relating enemy goals, beliefs, actions, and resources across multiple types of COGs. Users may overlay friendly interventions, analyze their impact on enemy COGs, and automatically incorporate the causal chains stemming from the best interventions into the current plan. Finally, the target system analysis subsystem has been extended with option generation tools that use network-based optimization algorithms to select candidate target set options to achieve specified effects.

  10. Defining the optimal animal model for translational research using gene set enrichment analysis.

    PubMed

    Weidner, Christopher; Steinfath, Matthias; Opitz, Elisa; Oelgeschläger, Michael; Schönfelder, Gilbert

    2016-01-01

    The mouse is the main model organism used to study the functions of human genes because most biological processes in the mouse are highly conserved in humans. Recent reports that compared identical transcriptomic datasets of human inflammatory diseases with datasets from mouse models using traditional gene-to-gene comparison techniques resulted in contradictory conclusions regarding the relevance of animal models for translational research. To reduce susceptibility to biased interpretation, all genes of interest for the biological question under investigation should be considered. Thus, standardized approaches for systematic data analysis are needed. We analyzed the same datasets using gene set enrichment analysis focusing on pathways assigned to inflammatory processes in either humans or mice. The analyses revealed a moderate overlap between all human and mouse datasets, with average positive and negative predictive values of 48 and 57% significant correlations. Subgroups of the septic mouse models (i.e., Staphylococcus aureus injection) correlated very well with most human studies. These findings support the applicability of targeted strategies to identify the optimal animal model and protocol to improve the success of translational research. PMID:27311961

  11. 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.

  12. Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review

    NASA Astrophysics Data System (ADS)

    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 Γ(H\\to b\\bar{b}) 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

  13. Distributed Gaussian basis sets: a comparison with finite difference Hartree Fock calculations for potential energy curves of H2, LiH and BH

    NASA Astrophysics Data System (ADS)

    Glushkov, V. N.; Kobus, J.; Wilson, S.

    2008-10-01

    Within the Hartree-Fock approximation, distributed basis sets of s-type Gaussian functions are used to compute those portions of the ground-state potential energy curves of the H2, LiH and BH molecules for which the model is appropriate. The exponents are generated using the even-tempered prescription and an anharmonic model is employed to distribute the basis functions. For few-electron diatomic systems, this approach is known to support sub-μHartree accuracy for electronic energies. For the molecules studied in the present work, matrix Hartree-Fock energy expectation values are compared with finite difference Hartree-Fock calculations carried out at the same geometries and using grids designed to support an accuracy of at least 1 nanoHartree. The distributed basis sets developed in this work support matrix Hartree-Fock energies which differ from the corresponding finite difference energies by 0.41, 0.58 and 0.68 μHartree, respectively, for the ground states of the H2, LiH and BH molecules at their equilibrium geometries. For each of these systems, a sub-μHartree level of accuracy is supported for a range of geometries.

  14. Constrained optimization by radial basis function interpolation for high-dimensional expensive black-box problems with infeasible initial points

    NASA Astrophysics Data System (ADS)

    Regis, Rommel G.

    2014-02-01

    This article develops two new algorithms for constrained expensive black-box optimization that use radial basis function surrogates for the objective and constraint functions. These algorithms are called COBRA and Extended ConstrLMSRBF and, unlike previous surrogate-based approaches, they can be used for high-dimensional problems where all initial points are infeasible. They both follow a two-phase approach where the first phase finds a feasible point while the second phase improves this feasible point. COBRA and Extended ConstrLMSRBF are compared with alternative methods on 20 test problems and on the MOPTA08 benchmark automotive problem (D.R. Jones, Presented at MOPTA 2008), which has 124 decision variables and 68 black-box inequality constraints. The alternatives include a sequential penalty derivative-free algorithm, a direct search method with kriging surrogates, and two multistart methods. Numerical results show that COBRA algorithms are competitive with Extended ConstrLMSRBF and they generally outperform the alternatives on the MOPTA08 problem and most of the test problems.

  15. A comparative assessment of the perturbative and renormalized coupled cluster theories with a noniterative treatment of triple excitations for thermochemical kinetics, including a study of basis set and core correlation effects

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Gour, Jeffrey R.; Lutz, Jesse J.; Włoch, Marta; Piecuch, Piotr; Truhlar, Donald G.

    2008-01-01

    The CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T +d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T +d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlation most reliably, a basis set including functions that correlate the core and that can treat core-valence correlation is required. On the other hand, the frozen-core approximation using valence-optimized basis sets that lead to relatively small computational costs of CCSD(T) and CR-CC(2,3) calculations can achieve almost as high accuracy as the analogous fully correlated calculations.

  16. Searching for optimal setting conditions in technological processes using parametric estimation models and neural network mapping approach: a tutorial.

    PubMed

    Fjodorova, Natalja; Novič, Marjana

    2015-09-01

    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. PMID:26388367

  17. Accurate adiabatic potential energy surface for 12A' state of FH2 based on ab initio data extrapolated to the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Li, Yong-Qing; Song, Yu-Zhi; Joaquim de Campos Varandas, António

    2015-01-01

    An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system. It is obtained by using the aug-cc-pVTZ and aug-cc-pVQZ basis sets with extrapolation of the electron correlation energy to the complete basis set limit, plus extrapolation to the complete basis set limit of the complete-active-space self-consistent field energy. The collinear and bending barrier heights of the new global potential energy surface is 2.301 and 1.768 kcal mol-1, in very good agreement with the values of 2.222 and 1.770 kcal mol-1 from the current best potential energy surface. In particular, the new potential energy surface describes well the important van der Waals interactions which is very useful for investigating the dynamics of the title system. Thus, the new potential energy surface can both be recommended for dynamics studies of the F + H2 reaction and as building block for constructing the potential energy surfaces of larger fluorine/hydrogen containing systems. Based on the new potential energy surface, a preliminary theoretical study of the reaction F(2P) + H2 (X1 Σg+) → FH(X1Σ+) + H(2S) has been carried out with the methods of quasi-classical trajectory and quantum mechanical. The results have shown that the new PES is suitable for any kind of dynamics studies. Supplementary material in the form of one pdf file available from the Journal web page at http://dx.doi.org/10.1140/epjd/e2014-50445-3

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

    NASA Astrophysics Data System (ADS)

    Varandas, A. J. C.; Pansini, F. N. N.

    2014-12-01

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

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

    SciTech Connect

    Varandas, A. J. C.; Pansini, F. N. N.

    2014-12-14

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

  20. 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.

  1. Optimal body balance disturbance tolerance skills as a methodological basis for selection of firefighters to solve difficult rescue tasks.

    PubMed

    Jagiełło, Władysław; Wójcicki, Zbigniew; Barczyński, Bartłomiej J; Litwiniuk, Artur; Kalina, Roman Maciej

    2014-01-01

    The aim of this study is the methodology of optimal choice of firefighters to solve difficult rescue tasks. 27 firefighters were analyzed: aged from 22-50 years of age, and with 2-27 years of work experience. Body balance disturbance tolerance skills (BBDTS) measured by the 'Rotational Test' (RT) and time of transition (back and forth) on a 4 meter beam located 3 meters above the ground, was the criterion for simulation of a rescue task (SRT). RT and SRT were carried out first in a sports tracksuit and then in protective clothing. A total of 4 results of the RT and SRT is the substantive base of the 4 rankings. The correlation of the RT and SRT results with 3 criteria for estimating BBDTS and 2 categories ranged from 0.478 (p<0.01) - 0.884 (p<0.01) and the results of SRT 0.911 (p<0.01). The basic ranking very highly correlated indicators of SRT (0.860 and 0.844), while the 6 indicators of RT only 2 (0.396 and 0.381; p<0.05). There was no correlation between the results of the RT and SRT, but there was an important partial correlation of these variables, but only then was the effect stabilized. The Rotational Test is a simple and easy to use tool for measuring body balance disturbance tolerance skills. However, the BBDTS typology is an accurate criteria for forecasting on this basis, including the results of accurate motor simulations, and the periodic ability of firefighters to solve the most difficult rescue tasks. PMID:24738515

  2. 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

  3. Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

    NASA Astrophysics Data System (ADS)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

    Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.

  4. Optimized Fluoroscopy Setting and Appropriate Project Position Can Reduce X-ray Radiation Doses Rates during Electrophysiology Procedures

    PubMed Central

    Hou, Bing-Bo; Yao, Yan; Wu, Ling-Min; Qiao, Yu; Zheng, Li-Hui; Ding, Li-Gang; Chen, Gang; Zhang, Shu

    2015-01-01

    Background: Nonfluoroscopic three-dimensional electroanatomical system is widely used nowadays, but X-ray remains indispensable for complex electrophysiology procedures. This study aimed to evaluate the value of optimized parameter setting and different projection position to reduce X-ray radiation dose rates. Methods: From June 2013 to October 2013, 105 consecutive patients who underwent complex ablation were enrolled in the study. After the ablation, the radiation dose rates were measured by two different settings (default setting and optimized setting) with three projection positions (posteroanterior [PA] projection; left anterior oblique [LAO] 30° projection; and LAO 45° projection). The parameter of preset voltage, pulse width, critical voltage, peak voltage, noise reduction, edge enhancement, pulse rate, and dose per frame was modified in the optimized setting. Results: The optimized setting reduced radiation dose rates by 87.5% (1.7 Gy/min vs. 13.6 Gy/min, P < 0.001) in PA, 87.3% (2.5 Gy/min vs. 19.7 Gy/min, P < 0.001) in LAO 30°, 85.9% (3.1 Gy/min vs. 22.1 Gy/min, P < 0.001) in LAO 45°. Increase the angle of projection position will increase the radiation dose rate. Conclusions: We can reduce X-ray radiation dose rates by adjusting the parameter setting of X-ray system. Avoiding oblique projection of large angle is another way to reduce X-ray radiation dose rates. PMID:25947395

  5. 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

  6. Optimization to the Culture Conditions for Phellinus Production with Regression Analysis and Gene-Set Based Genetic Algorithm.

    PubMed

    Li, Zhongwei; Xin, Yuezhen; Wang, Xun; Sun, Beibei; Xia, Shengyu; Li, Hui; Zhu, Hu

    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

  7. 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).

  8. 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).

  9. 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.

  10. Optimized Dual Threshold Entity Resolution For Electronic Health Record Databases – Training Set Size And Active Learning

    PubMed Central

    Joffe, Erel; Byrne, Michael J.; Reeder, Phillip; Herskovic, Jorge R.; Johnson, Craig W.; McCoy, Allison B.; Bernstam, Elmer V.

    2013-01-01

    Clinical databases may contain several records for a single patient. Multiple general entity-resolution algorithms have been developed to identify such duplicate records. To achieve optimal accuracy, algorithm parameters must be tuned to a particular dataset. The purpose of this study was to determine the required training set size for probabilistic, deterministic and Fuzzy Inference Engine (FIE) algorithms with parameters optimized using the particle swarm approach. Each algorithm classified potential duplicates into: definite match, non-match and indeterminate (i.e., requires manual review). Training sets size ranged from 2,000–10,000 randomly selected record-pairs. We also evaluated marginal uncertainty sampling for active learning. Optimization reduced manual review size (Deterministic 11.6% vs. 2.5%; FIE 49.6% vs. 1.9%; and Probabilistic 10.5% vs. 3.5%). FIE classified 98.1% of the records correctly (precision=1.0). Best performance required training on all 10,000 randomly-selected record-pairs. Active learning achieved comparable results with 3,000 records. Automated optimization is effective and targeted sampling can reduce the required training set size. PMID:24551372

  11. Evaluation of the vibration-rotation-tunneling dynamics at the basis set superposition error corrected global minimum geometry of the ammonia dimer

    NASA Astrophysics Data System (ADS)

    Muguet, Francis F.; Robinson, G. Wilse; Bassez-Muguet, M. Palmyre

    1995-03-01

    With the help of a new scheme to correct for the basis set superposition error (BSSE), we find that an eclipsed nonlinear geometry becomes energetically favored over the eclipsed linear hydrogen-bonded geometry. From a normal mode analysis of the potential energy surface (PES) in the vicinity of the nonlinear geometry, we suggest that several dynamical interchange pathways must be taken into account. The minimal molecular symmetry group to be considered should be the double group of G36, but still larger multiple groups may be required. An interpretation of experimental vibration-rotation-tunneling (VRT) data in terms of the G144 group, which implies monomer inversions, may not be the only alternative. It appears that group theoretical considerations alone are insufficient for understanding the complex VRT dynamics of the ammonia dimer.

  12. Variational (time-independent) calculations of reactive S matrix elements: application of negative imaginary absorbing potentials and contracted L 2 basis sets

    NASA Astrophysics Data System (ADS)

    Last, Isidore; Baer, Michael

    1992-01-01

    Recently we introduced a time-independent approach to treat reactive collisions employing the negative imaginary absorbing potentials and L 2 basis sets. The application of these potentials led to the formulation of a method whereby only one arrangement channel has to be considered in a given calculation. In the present work we further extend this approach. (a) We show how this method is capable of yielding reactive state-to-state S-matrix elements. (In the previous versions of this method, these could not be obtained.) (b) We show that by employing contracted vibrational adiabatic and translational Gaussian functions the number of algebraic equations to be solved within this approach is significantly reduced (by a factor of four).

  13. Microstructure Modeling in Integrated Computational Materials Engineering (ICME) Settings: Can HDF5 Provide the Basis for an Emerging Standard for Describing Microstructures?

    NASA Astrophysics Data System (ADS)

    Schmitz, G. J.

    2016-01-01

    The importance of microstructure simulation in integrated computational materials engineering settings in relation to the added value provided for macroscopic process simulation, as well as the contribution this kind of simulation can make in predicting material properties, are discussed. The roles of microstructure simulation in integrating scales ranging from component/process scales down to atomistic scales, and also in integrating experimental and virtual worlds, are highlighted. The hierarchical data format (HDF5) as a basis for enhancing the interoperability of the heterogeneous range of simulation tools and experimental datasets in the area of computational materials engineering is discussed. Several ongoing developments indicate that HDF5 might evolve into a de facto standard for digital microstructure representation of all length scales.

  14. Choice of atomic basis set for the study of two electrons in a harmonic anisotropic quantum dot using a configuration interaction approach

    NASA Astrophysics Data System (ADS)

    Olavo, L. S. F.; Maniero, A. M.; de Carvalho, C. R.; Prudente, F. V.; Jalbert, Ginette

    2016-07-01

    We have developed a computational code based on the Hartree–Fock and full interaction configuration approaches which allows the study of N-electron confined quantum systems with different confining potentials and external conditions. The code employs Cartesian anisotropic Gaussian-type orbitals as the atomic basis set, which enables the use of different exponents for each direction space in order to better exploit the characteristics of the confining potential. As an illustration, we have employed it to study a system consisting of two electrons confined by a three-dimensional harmonic potential for different values of confinement strength, leading to different confinement conditions: an isotropic three-dimensional and an anisotropic oblate (or quasi-two dimensional) quantum dot. A central aspect of this study is to propose efficient procedures for choosing the exponents of the atomic basis functions. In particular, we note that the use of more than one function for each atomic orbital can improve the convergence of the electronic energy levels. The present results are compared with other theoretical values published previously.

  15. Assessing optimal set of implemented physical parameterization schemes in a multi-physics land surface model using genetic algorithm

    NASA Astrophysics Data System (ADS)

    Hong, S.; Yu, X.; Park, S. K.; Choi, Y.-S.; Myoung, B.

    2014-10-01

    Optimization of land surface models has been challenging due to the model complexity and uncertainty. In this study, we performed scheme-based model optimizations by designing a framework for coupling "the micro-genetic algorithm" (micro-GA) and "the Noah land surface model with multiple physics options" (Noah-MP). Micro-GA controls the scheme selections among eight different land surface parameterization categories, each containing 2-4 schemes, in Noah-MP in order to extract the optimal scheme combination that achieves the best skill score. This coupling framework was successfully applied to the optimizations of evapotranspiration and runoff simulations in terms of surface water balance over the Han River basin in Korea, showing outstanding speeds in searching for the optimal scheme combination. Taking advantage of the natural selection mechanism in micro-GA, we explored the model sensitivity to scheme selections and the scheme interrelationship during the micro-GA evolution process. This information is helpful for better understanding physical parameterizations and hence it is expected to be effectively used for further optimizations with uncertain parameters in a specific set of schemes.

  16. 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

  17. Accurate ab initio-based adiabatic global potential energy surface for the 2(2)A" state of NH2 by extrapolation to the complete basis set limit.

    PubMed

    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((2)D) + H2 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((2)D)+H2(X(1)Σg (+))(ν=0,j=0)→NH(a(1)Δ)+H((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. PMID:24160511

  18. Accurate ab initio-based adiabatic global potential energy surface for the 22A″ state of NH2 by extrapolation to the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Li, Y. Q.; Ma, F. C.; Sun, M. T.

    2013-10-01

    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(2D) + H2 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(^2D)+H_2(X^1Σ _g^+)(ν =0,j=0)rArr NH(a^1Δ )+H(^2S) 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.

  19. Estimation of an optimal chemotherapy utilisation rate for cancer: setting an evidence-based benchmark for quality cancer care.

    PubMed

    Jacob, S A; Ng, W L; Do, V

    2015-02-01

    There is wide variation in the proportion of newly diagnosed cancer patients who receive chemotherapy, indicating the need for a benchmark rate of chemotherapy utilisation. This study describes an evidence-based model that estimates the proportion of new cancer patients in whom chemotherapy is indicated at least once (defined as the optimal chemotherapy utilisation rate). The optimal chemotherapy utilisation rate can act as a benchmark for measuring and improving the quality of care. Models of optimal chemotherapy utilisation were constructed for each cancer site based on indications for chemotherapy identified from evidence-based treatment guidelines. Data on the proportion of patient- and tumour-related attributes for which chemotherapy was indicated were obtained, using population-based data where possible. Treatment indications and epidemiological data were merged to calculate the optimal chemotherapy utilisation rate. Monte Carlo simulations and sensitivity analyses were used to assess the effect of controversial chemotherapy indications and variations in epidemiological data on our model. Chemotherapy is indicated at least once in 49.1% (95% confidence interval 48.8-49.6%) of all new cancer patients in Australia. The optimal chemotherapy utilisation rates for individual tumour sites ranged from a low of 13% in thyroid cancers to a high of 94% in myeloma. The optimal chemotherapy utilisation rate can serve as a benchmark for planning chemotherapy services on a population basis. The model can be used to evaluate service delivery by comparing the benchmark rate with patterns of care data. The overall estimate for other countries can be obtained by substituting the relevant distribution of cancer types. It can also be used to predict future chemotherapy workload and can be easily modified to take into account future changes in cancer incidence, presentation stage or chemotherapy indications. PMID:25455844

  20. 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. PMID:26574415

  1. 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,…

  2. 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…

  3. Maximizing device-independent randomness from a Bell experiment by optimizing the measurement settings

    NASA Astrophysics Data System (ADS)

    Assad, S. M.; Thearle, O.; Lam, P. K.

    2016-07-01

    The rates at which a user can generate device-independent quantum random numbers from a Bell-type experiment depend on the measurements that the user performs. By numerically optimizing over these measurements, we present lower bounds on the randomness generation rates for a family of two-qubit states composed from a mixture of partially entangled states and the completely mixed state. We also report on the randomness generation rates from a tomographic measurement. Interestingly in this case, the randomness generation rates are not monotonic functions of entanglement.

  4. 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. PMID:27366781

  5. 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.

  6. Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets.

    PubMed

    Bauer, Matthias R; Ibrahim, Tamer M; Vogel, Simon M; Boeckler, Frank M

    2013-06-24

    The application of molecular benchmarking sets helps to assess the actual performance of virtual screening (VS) workflows. To improve the efficiency of structure-based VS approaches, the selection and optimization of various parameters can be guided by benchmarking. With the DEKOIS 2.0 library, we aim to further extend and complement the collection of publicly available decoy sets. Based on BindingDB bioactivity data, we provide 81 new and structurally diverse benchmark sets for a wide variety of different target classes. To ensure a meaningful selection of ligands, we address several issues that can be found in bioactivity data. We have improved our previously introduced DEKOIS methodology with enhanced physicochemical matching, now including the consideration of molecular charges, as well as a more sophisticated elimination of latent actives in the decoy set (LADS). We evaluate the docking performance of Glide, GOLD, and AutoDock Vina with our data sets and highlight existing challenges for VS tools. All DEKOIS 2.0 benchmark sets will be made accessible at http://www.dekois.com. PMID:23705874

  7. A method of hidden Markov model optimization for use with geophysical data sets

    NASA Technical Reports Server (NTRS)

    Granat, R. A.

    2003-01-01

    Geophysics research has been faced with a growing need for automated techniques with which to process large quantities of data. A successful tool must meet a number of requirements: it should be consistent, require minimal parameter tuning, and produce scientifically meaningful results in reasonable time. We introduce a hidden Markov model (HMM)-based method for analysis of geophysical data sets that attempts to address these issues.

  8. The Role of eHealth in Optimizing Preventive Care in the Primary Care Setting.

    PubMed

    Carey, Mariko; Noble, Natasha; Mansfield, Elise; Waller, Amy; Henskens, Frans; Sanson-Fisher, Rob

    2015-01-01

    Modifiable health risk behaviors such as smoking, overweight and obesity, risky alcohol consumption, physical inactivity, and poor nutrition contribute to a substantial proportion of the world's morbidity and mortality burden. General practitioners (GPs) play a key role in identifying and managing modifiable health risk behaviors. However, these are often underdetected and undermanaged in the primary care setting. We describe the potential of eHealth to help patients and GPs to overcome some of the barriers to managing health risk behaviors. In particular, we discuss (1) the role of eHealth in facilitating routine collection of patient-reported data on lifestyle risk factors, and (2) the role of eHealth in improving clinical management of identified risk factors through provision of tailored feedback, point-of-care reminders, tailored educational materials, and referral to online self-management programs. Strategies to harness the capacity of the eHealth medium, including the use of dynamic features and tailoring to help end users engage with, understand, and apply information need to be considered and maximized. Finally, the potential challenges in implementing eHealth solutions in the primary care setting are discussed. In conclusion, there is significant potential for innovative eHealth solutions to make a contribution to improving preventive care in the primary care setting. However, attention to issues such as data security and designing eHealth interfaces that maximize engagement from end users will be important to moving this field forward. PMID:26001983

  9. Optimal design for sustainable development of a material recovery facility in a fast-growing urban setting

    SciTech Connect

    Chang, Ni-Bin . E-mail: nchang@even.tamuk.edu; Davila, Eric; Dyson, Brian; Brown, Ron

    2005-10-15

    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.

  10. 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. PMID:26890944

  11. Optimization of gas condensate Field A development on the basis of "reservoir - gathering facilities system" integrated model

    NASA Astrophysics Data System (ADS)

    Demidova, E. A.; Maksyutina, O. V.

    2015-02-01

    It is known that many gas condensate fields are challenged with liquid loading and condensate banking problems. Therefore, gas production is declining with time. In this paper hydraulic fracturing treatment was considered as a method to improve the productivity of wells and consequently to exclude the factors that lead to production decline. This paper presents the analysis of gas condensate Field A development optimization with the purpose of maintaining constant gas production at the 2013 level for 8 years taking into account mentioned factors . To optimize the development of the filed, an integrated model was created. The integrated model of the field implies constructing the uniform model of the field consisting of the coupling models of the reservoir, wells and surface facilities. This model allowed optimizing each of the elements of the model separately and also taking into account the mutual influence of these elements. Using the integrated model, five development scenarios were analyzed and an optimal scenario was chosen. The NPV of this scenario equals 7,277 mln RUR, cumulative gas production - 12,160.6 mln m3, cumulative condensate production - 1.8 mln tons.

  12. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules I. Reference Data at the CCSD(T) Complete Basis Set Limit.

    PubMed

    Richard, Ryan M; Marshall, Michael S; Dolgounitcheva, O; Ortiz, J V; Brédas, Jean-Luc; Marom, Noa; Sherrill, C David

    2016-02-01

    In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates. PMID:26731487

  13. 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. PMID:19071908

  14. Effect of noncovalent interactions on conformers of the n-butylbenzene monomer studied by mass analyzed threshold ionization spectroscopy and basis-set convergent ab initio computations.

    PubMed

    Tong, Xin; Cerný, Jirí; Müller-Dethlefs, Klaus; Dessent, Caroline E H

    2008-07-01

    Two conformational isomers of the aromatic hydrocarbon n-butylbenzene have been studied using two-color MATI (mass analyzed threshold ionization) spectroscopy to explore the effect of conformation on ionization dynamics. Cationic states of g auche-conformer III and anti- conformers IV were selectively produced by two-color excitation via the respective S 1 origins. Adiabatic ionization potentials of the gauche- and anti-conformations were determined to be 70146 and 69872 +/- 5 cm (-1) respectively. Spectral features and vibrational modes are interpreted with the aid of MP2/cc-pVDZ ab initio calculations, and ionization-induced changes in the molecular conformations are discussed. Complete basis set (CBS) ab initio studies at MP2 level reveal reliable energetics for all four n-butylbenzene conformers observed in earlier two-color REMPI (resonance enhanced multiphoton ionization) spectra. For the S 0 state, the energies of conformer III, IV and V are above conformer I by 130, 289, 73 cm (-1), respectively. Furthermore, the combination of the CBS calculations with the measured REMPI, MATI spectra allowed the determination of the energetics of all four conformers in the S 1 and D 0 states. PMID:18533642

  15. Complete basis set limit second-order Møller-Plesset calculations for the fcc lattices of neon, argon, krypton, and xenon.

    PubMed

    Hermann, Andreas; Schwerdtfeger, Peter

    2009-12-28

    Complete basis set (CBS) limit calculations using second-order Møller-Plesset (MP2) theory for electron correlation within a many-body expansion of the interaction potential up to third order are carried out for the fcc lattices of Ne, Ar, Kr, and Xe. Lattice constants and cohesive energies from recent localized MP2 solid-state calculations by Halo et al. [Chem. Phys. Lett. 467, 294 (2009)] are in reasonable agreement with our CBS limit results. A detailed analysis reveals that MP2 severely underestimates long-range three-body effects, thus the Axilrod-Teller term is incorrectly described causing bond contractions for all rare gas solids considered. Further, any deviations in the MP2 lattice constant, cohesive energy, and bulk modulus can be traced back to inaccuracies in the binding energy and equilibrium distance of the rare gas dimer. Without inclusion of phonon dispersion, MP2 prefers the hcp over the fcc crystal structure for all rare gas solids considered. PMID:20059080

  16. Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

    NASA Astrophysics Data System (ADS)

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.; Vargas, Rubicelia; Garza, Jorge

    2015-07-01

    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. 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.

  18. H/D isotope effect on structures, binding energies, and basis set superposition errors in F-(H2O)n (n = 1-3) clusters

    NASA Astrophysics Data System (ADS)

    Udagawa, Taro; Ishimoto, Takayoshi; Tachikawa, Masanori

    2014-09-01

    The H/D isotope effects on structures, binding energies, and basis set superposition errors (BSSEs) of hydrated fluoride anion clusters, F-(H2O)n (n = 1-3), are theoretically analyzed by using the MP2 level of multi-component molecular orbital (MC_MO-MP2) method, in which quantum nature of proton/deuteron and electron-electron correlation are directly taken account. Our results clearly show that the additional water molecule to F-(H2O)n-1 cluster forms stronger water-water hydrogen bond than that in simple water cluster, whereas the additional F--water hydrogen bond formation in F-(H2O)n cluster weakens the original F--water hydrogen bonds in F-(H2O)n-1 cluster. The BSSEs estimated in the MC_MO-MP2 calculations are slightly larger than those in the conventional MP2 calculations, due to the H/D geometrical isotope effect on the intermolecular distances. Consequently, the order of stability in several F-(H2O)3 cluster isomers cannot be adequately evaluated without BSSE corrections in our MC_MO-MP2 calculations, rather than the conventional MP2 ones.

  19. 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. PMID:26203010

  20. Quantum dot nanoparticle for optimization of breast cancer diagnostics and therapy in a clinical setting.

    PubMed

    Radenkovic, Dina; Kobayashi, Hisataka; Remsey-Semmelweis, Ernö; Seifalian, Alexander M

    2016-08-01

    Breast cancer is the most common cancer in the world. Sentinel lymph node (SLN) biopsy is used for staging of axillary lymph nodes. Organic dyes and radiocolloid are currently used for SLN mapping, but expose patients to ionizing radiation, are unstable during surgery and cause local tissue damage. Quantum dots (QD) could be used for SLN mapping without the need for biopsy. Surgical resection of the primary tumor is the optimal treatment for early-diagnosed breast cancer, but due to difficulties in defining tumor margins, cancer cells often remain leading to reoccurrences. Functionalized QD could be used for image-guided tumor resection to allow visualization of cancer cells. Near Infrared QD are photostable and have improved deep tissue penetration. Slow elimination of QD raises concerns of potential accumulation. Nevertheless, promising findings with cadmium-free QD in recent in vivo studies and first in-human trial suggest huge potential for cancer diagnostic and therapy. PMID:27013132

  1. 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.

  2. Global nonlinear kernel prediction for large data set with a particle swarm-optimized interval support vector regression.

    PubMed

    Ding, Yongsheng; Cheng, Lijun; Pedrycz, Witold; Hao, Kuangrong

    2015-10-01

    A new global nonlinear predictor with a particle swarm-optimized interval support vector regression (PSO-ISVR) is proposed to address three issues (viz., kernel selection, model optimization, kernel method speed) encountered when applying SVR in the presence of large data sets. The novel prediction model can reduce the SVR computing overhead by dividing input space and adaptively selecting the optimized kernel functions to obtain optimal SVR parameter by PSO. To quantify the quality of the predictor, its generalization performance and execution speed are investigated based on statistical learning theory. In addition, experiments using synthetic data as well as the stock volume weighted average price are reported to demonstrate the effectiveness of the developed models. The experimental results show that the proposed PSO-ISVR predictor can improve the computational efficiency and the overall prediction accuracy compared with the results produced by the SVR and other regression methods. The proposed PSO-ISVR provides an important tool for nonlinear regression analysis of big data. PMID:25974954

  3. Optimal Location and Parameter Setting of TCSC for Loss Minimization Based on Differential Evolution and Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Rashed, Ghamgeen I.; Sun, Yuanzhang; Shaheen, H. I.

    Flexible Alternating Current Transmission Systems (FACTS) devices have been proposed as an effective solution for controlling power flow and regulating bus voltage in electrical power systems, resulting in an increased transfer capability, low system losses, and improve stability. However to what extent the performance of FACTS devices can be brought out highly depends upon the location and the parameters of these devices. In this paper, we propose two Evolutionary Optimization Techniques, namely Differential Evolution (DE) and Genetic Algorithm (GA) to select the optimal location and the optimal parameter setting of TCSC which minimize the active power losses in the power network, and compare their performances. To show the validity of the proposed techniques and for comparison purposes, simulations are carried out on several power systems, a three-bus power system, a five-bus power system, and an IEEE-14 bus power system. The results, we have obtained, indicate that DE is an easy to use, fast, robust and powerful optimization technique compared with genetic algorithm (GA). The results are presented in the paper together with appropriate discussion.

  4. 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. PMID:27104582

  5. Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting

    PubMed Central

    Temiz, N. A.; Trapp, A.; Prokopyev, O. A.; Camacho, C. J.

    2010-01-01

    Motivation: A major limitation in modeling protein interactions is the difficulty of assessing the over-fitting of the training set. Recently, an experimentally based approach that integrates crystallographic information of C2H2 zinc finger–DNA complexes with binding data from 11 mutants, 7 from EGR finger I, was used to define an improved interaction code (no optimization). Here, we present a novel mixed integer programming (MIP)-based method that transforms this type of data into an optimized code, demonstrating both the advantages of the mathematical formulation to minimize over- and under-fitting and the robustness of the underlying physical parameters mapped by the code. Results: Based on the structural models of feasible interaction networks for 35 mutants of EGR–DNA complexes, the MIP method minimizes the cumulative binding energy over all complexes for a general set of fundamental protein–DNA interactions. To guard against over-fitting, we use the scalability of the method to probe against the elimination of related interactions. From an initial set of 12 parameters (six hydrogen bonds, five desolvation penalties and a water factor), we proceed to eliminate five of them with only a marginal reduction of the correlation coefficient to 0.9983. Further reduction of parameters negatively impacts the performance of the code (under-fitting). Besides accurately predicting the change in binding affinity of validation sets, the code identifies possible context-dependent effects in the definition of the interaction networks. Yet, the approach of constraining predictions to within a pre-selected set of interactions limits the impact of these potential errors to related low-affinity complexes. Contact: ccamacho@pitt.edu; droleg@pitt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19965883

  6. Civilian field surgery in the rural trauma setting: a proposal for providing optimal care.

    PubMed Central

    Foil, M. B.; Cunningham, P. R.; Hale, J. C.; Benson, N. H.; Treurniet, S.

    1992-01-01

    Rural trauma presents unique problems for surgical care. While military surgeons are prepared to provide care at or near the scene of battle, civilian literature is devoid of reports for care provided by surgeons at sites of injury occurrences. Although these injuries are infrequent, they are more likely to occur in rural trauma settings. This article describes two cases of extremity injury that required amputation at the scene and presents a proposal for swift mobilization of appropriately trained surgeons to the scene with adequate instrumentation and lighting, which can significantly reduce the morbidity and mortality of these victims. PMID:1404476

  7. 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

    2016-06-01

    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.

  8. 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.

  9. Modeling and predicting optimal treatment scheduling between the antiangiogenic drug sunitinib and irinotecan in preclinical settings.

    PubMed

    Wilson, S; Tod, M; Ouerdani, A; Emde, A; Yarden, Y; Adda Berkane, A; Kassour, S; Wei, M X; Freyer, G; You, B; Grenier, E; Ribba, B

    2015-12-01

    We present a system of nonlinear ordinary differential equations used to quantify the complex dynamics of the interactions between tumor growth, vasculature generation, and antiangiogenic treatment. The primary dataset consists of longitudinal tumor size measurements (1,371 total observations) in 105 colorectal tumor-bearing mice. Mice received single or combination administration of sunitinib, an antiangiogenic agent, and/or irinotecan, a cytotoxic agent. Depending on the dataset, parameter estimation was performed either using a mixed-effect approach or by nonlinear least squares. Through a log-likelihood ratio test, we conclude that there is a potential synergistic interaction between sunitinib when administered in combination with irinotecan in preclinical settings. Model simulations were then compared to data from a follow-up preclinical experiment. We conclude that the model has predictive value in identifying the therapeutic window in which the timing between the administrations of these two drugs is most effective. PMID:26904386

  10. Optimization of legacy lidar data sets for measuring near-field earthquake displacements

    NASA Astrophysics Data System (ADS)

    Glennie, Craig L.; Hinojosa-Corona, Alejandro; Nissen, Edwin; Kusari, Arpan; Oskin, Michael E.; Arrowsmith, J. Ramon; Borsa, Adrian

    2014-05-01

    Airborne lidar (light detection and ranging) topography, acquired before and after an earthquake, can provide an estimate of the coseismic surface displacement field by differencing the preevent and postevent lidar point clouds. However, estimated displacements can be contaminated by the presence of large systematic errors in either of the point clouds. We present three-dimensional displacements obtained by differencing airborne lidar point clouds collected before and after the El Mayor-Cucapah earthquake, a Mw 7.2 earthquake that occurred in 2010. The original surface displacement estimates contained large, periodic artifacts caused by systematic errors in the preevent lidar data. Reprocessing the preevent data, detailed herein, removed a majority of these systematic errors that were largely due to misalignment between the scanning mirror and the outgoing laser beam. The methodology presented can be applied to other legacy airborne laser scanning data sets in order to improve change estimates from temporally spaced lidar acquisitions.

  11. NOTE: Optimization of megavoltage CT scan registration settings for thoracic cases on helical tomotherapy

    NASA Astrophysics Data System (ADS)

    Woodford, Curtis; Yartsev, Slav; Van Dyk, Jake

    2007-08-01

    This study aims to investigate the settings that provide optimum registration accuracy when registering megavoltage CT (MVCT) studies acquired on tomotherapy with planning kilovoltage CT (kVCT) studies of patients with lung cancer. For each experiment, the systematic difference between the actual and planned positions of the thorax phantom was determined by setting the phantom up at the planning isocenter, generating and registering an MVCT study. The phantom was translated by 5 or 10 mm, MVCT scanned, and registration was performed again. A root-mean-square equation that calculated the residual error of the registration based on the known shift and systematic difference was used to assess the accuracy of the registration process. The phantom study results for 18 combinations of different MVCT/kVCT registration options are presented and compared to clinical registration data from 17 lung cancer patients. MVCT studies acquired with coarse (6 mm), normal (4 mm) and fine (2 mm) slice spacings could all be registered with similar residual errors. No specific combination of resolution and fusion selection technique resulted in a lower residual error. A scan length of 6 cm with any slice spacing registered with the full image fusion selection technique and fine resolution will result in a low residual error most of the time. On average, large corrections made manually by clinicians to the automatic registration values are infrequent. Small manual corrections within the residual error averages of the registration process occur, but their impact on the average patient position is small. Registrations using the full image fusion selection technique and fine resolution of 6 cm MVCT scans with coarse slices have a low residual error, and this strategy can be clinically used for lung cancer patients treated on tomotherapy. Automatic registration values are accurate on average, and a quick verification on a sagittal MVCT slice should be enough to detect registration outliers.

  12. 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

  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. 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. PMID:26292629

  15. 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.

  16. Karhunen-Loève expansion revisited for vector-valued random fields: Scaling, errors and optimal basis.

    NASA Astrophysics Data System (ADS)

    Perrin, G.; Soize, C.; Duhamel, D.; Funfschilling, C.

    2013-06-01

    Due to scaling effects, when dealing with vector-valued random fields, the classical Karhunen-Loève expansion, which is optimal with respect to the total mean square error, tends to favorize the components of the random field that have the highest signal energy. When these random fields are to be used in mechanical systems, this phenomenon can introduce undesired biases for the results. This paper presents therefore an adaptation of the Karhunen-Loève expansion that allows us to control these biases and to minimize them. This original decomposition is first analyzed from a theoretical point of view, and is then illustrated on a numerical example.

  17. 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.

  18. 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

  19. Optimization of Geriatric Pharmacotherapy: Role of Multifaceted Cooperation in the Hospital Setting.

    PubMed

    Petrovic, Mirko; Somers, Annemie; Onder, Graziano

    2016-03-01

    Because older patients are more vulnerable to adverse drug-related events, there is a need to ensure appropriate pharmacotherapy in these patients. This narrative review describes approaches to improve pharmacotherapy in older people in the hospital setting. Screening to identify older patients at risk of drug-related problems and adverse drug reactions (ADRs) is the first critical step within a multistep approach to geriatric pharmacotherapy. Two methods that have been developed are the GerontoNet ADR risk score and the Brighton Adverse Drug Reactions Risk (BADRI) model, which take into account a number of factors, the most important of which is the number of medicines. In order to reduce potentially inappropriate prescribing in older patients, different types of interventions exist, such as pharmacist-led medication reviews, educational interventions, computerized decision support systems, and comprehensive geriatric assessment. The effects of these interventions have been studied, sometimes in a multifaceted approach, by combining different techniques. None of the existing interventions shows a clear beneficial effect on patients' health outcomes if applied in isolation; however, when these interventions are combined within the context of a multidisciplinary team, positive effects on patients' health outcomes can be expected. Appropriate geriatric pharmacotherapy, global assessment of patients' clinical and functional parameters, and integration of skills from different healthcare professionals are needed to address medical complexity of older adults. PMID:26884392

  20. 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. PMID:26859884

  1. A systematic study of basis set, electron correlation, and geometry effects on the electric multipole moments, polarizability, and hyperpolarizability of HCl

    NASA Astrophysics Data System (ADS)

    Maroulis, George

    1998-04-01

    The electric multipole moments, dipole and quadrupole polarizability and hyperpolarizability of hydrogen chloride have been determined from an extensive and systematic study based on finite-field fourth-order many-body perturbation theory and coupled-cluster calculations. Our best values for the dipole, quadrupole, octopole and hexadecapole moment at the experimental internuclear separation of Re=2.408645a0 are μ=0.4238ea0, Θ=2.67ea02, Ω=3.94ea03, and Φ=13.37ea04, respectively. For the mean and the anisotropy of the dipole polarizability ααβ we recommend ᾱ=17.41±0.02 and Δα=1.60±0.03e2a02Eh-1. For the mean value of the first dipole hyperpolarizability βαβγ we advance β¯=-6.8±0.3e3a03Eh-2. Extensive calculations with a [8s6p6d3f/5s4p2d1f] basis set at the CCSD(T) level of theory yield the R-dependence of the Cartesian components and the mean of the second dipole hyperpolarizability γαβγδ(R)/e4a04Eh-3 around Re as γzzzz(R)=1907+1326(R-Re)+570(R-Re)2+10(R-Re)3-40(R-Re)4, γxxxx(R)=3900+747(R-Re)-65(R-Re)2-38(R-Re)3-7(R-Re)4, γxxzz(R)=962+222(R-Re)+88(R-Re)2+49(R-Re)3+5(R-Re)4, γ¯(R)=3230+841(R-Re)+151(R-Re)2+21(R-Re)3-9(R-Re)4, with z as the molecular axis. The present investigation suggests an estimate of (26.7±0.3)×102e4a04Eh-3 for the Hartree-Fock limit of the mean value γ¯ at Re. CCSD(T) calculations with basis sets of [8s6p6d3f/5s4p2d1f] and [9s7p5d4f/6s5p4d1f] size and MP4 calculations with the even larger [15s12p7d3f/12s7p2d1f] give (7.0±0.3)×102e4a04Eh-3 for the electron correlation effects for this property, thus leading to a recommended value of γ¯=(33.7±0.6)×102e4a04Eh-3. For the quadrupole polarizability Cαβ,γδ/e2a04Eh-1 at Re our best values are Czz,zz=41.68, Cxz,xz=26.11, and Cxx,xx=35.38, calculated with the [9s7p5d4f/6s5p4d1f] basis set at the CCSD(T) level of theory. The following CCSD(T) values were obtained with [8s6p6d3f/5s4p2d1f] at Re: dipole-quadrupole polarizability Aα,βγ/e2a03Eh-1, Az,zz=14.0, and

  2. OptiTope—a web server for the selection of an optimal set of peptides for epitope-based vaccines

    PubMed Central

    Toussaint, Nora C.; Kohlbacher, Oliver

    2009-01-01

    Epitope-based vaccines (EVs) have recently been attracting significant interest. They trigger an immune response by confronting the immune system with immunogenic peptides derived from, e.g. viral- or cancer-related proteins. Binding of these peptides to proteins from the major histocompatibility complex (MHC) is crucial for immune system activation. However, since the MHC is highly polymorphic, different patients typically bind different repertoires of peptides. Furthermore, economical and regulatory issues impose strong limitations on the number of peptides that can be included in an EV. Hence, it is crucial to identify the optimal set of peptides for a vaccine, given constraints such as MHC allele probabilities in the target population, peptide mutation rates and maximum number of selected peptides. OptiTope aims at assisting immunologists in this critical task. With OptiTope, we provide an easy-to-use tool to determine a provably optimal set of epitopes with respect to overall immunogenicity in a specific individual (personalized medicine) or a target population (e.g. a certain ethnic group). OptiTope is available at http://www.epitoolkit.org/optitope. PMID:19420066

  3. 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.

  4. 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. PMID:25109433

  5. 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

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

    PubMed

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

    2010-12-28

    One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar

  7. 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.

  8. Roothaan--Hartree--Fock--Slater atomic wave functions. Single-zeta, double-zeta, and extended slater-type basis sets for /sub 87/Fr--/sub 103/Lr

    SciTech Connect

    Snijders, J.G.; Vernooijs, P.; Baerends, E.J.

    1981-11-01

    Basis-set expansions are presented for the Hartree--Fock--Slater (HFS) orbitals of the neutral elements Fr--Lr (Z = 87--103). The Slater-type functions used in these expansions are found by an efficient fitting procedure to the Herman--Skillman numerical HFS orbitals. The expansions are of single-zera, double-zeta, and triple-zeta-valence (extended) quality. Comparisons of orbital energies with the numerical values are given for all elements. similar basis sets for all the remaining elements are available on request.

  9. 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.

  10. Basis selection in LOBPCG

    NASA Astrophysics Data System (ADS)

    Hetmaniuk, U.; Lehoucq, R.

    2006-10-01

    The purpose of our paper is to discuss basis selection for Knyazev's locally optimal block preconditioned conjugate gradient (LOBPCG) method. An inappropriate choice of basis can lead to ill-conditioned Gram matrices in the Rayleigh-Ritz analysis that can delay convergence or produce inaccurate eigenpairs. We demonstrate that the choice of basis is not merely related to computing in finite precision arithmetic. We propose a representation that maintains orthogonality of the basis vectors and so has excellent numerical properties.

  11. Modeling organic aerosols over east China using a volatility basis-set approach with aging mechanism in a regional air quality model

    NASA Astrophysics Data System (ADS)

    Han, Zhiwei; Xie, Zuxin; Wang, Gehui; Zhang, Renjian; Tao, Jun

    2016-01-01

    A volatility basis set approach with chemical aging mechanism has been incorporated into a regional air quality model system (RAQMS) and used to investigate the distribution of organic aerosols (OA) over east China in April 2009, with focus on secondary organic aerosols (SOA) in fine particle and relative contributions from a series of anthropogenic and biogenic VOC precursors. The comparison between the VBS approach prediction and observation at four sites in east China demonstrates a significant improvement in SOA and OA concentrations compared with the traditional two-product model, which predicts very low SOA level. The average value of secondary organic carbon (SOC) for all sites predicted by the VBS approach with chemical aging is 2.8 μgC m-3, quite close to the estimated value of 3.3 μgC m-3. The SOC fraction of organic carbon (OC) also increases from just 5% predicted by the two-product model to 33% by the VBS approach with aging, close to the estimated fraction of 32%, suggesting a more realistic and precise representation of SOA formation by the VBS approach. The enhanced SOC prediction further improve OC prediction, reducing the normalized mean bias from -43% to -18%. The VBS approach with aging predicts SOA concentration in PM2.5 of 5-10 μg m-3 over most parts of east China. The predicted ASOA concentrations vary from 5.0 to 7.5 μg m-3 in the Pearl River Delta, the Yangtze River Delta and the wide areas north of the Yangtze River. BSOA is predicted to be 1.0-2.5 μg m-3 across the regions from southeast China to the middle reaches of the Yangtze River and the Yellow River. Prediction with the VBS approach exhibits that ASOA becomes dominant component of SOA, which is more realistic as compared to the BSOA dominance by the two-product model. The domain-average surface POA and SOA concentrations predicted by the VBS approach with aging over east China are 4.86 μg m-3 and 4.45 μg m-3, with the SOA fraction of total OA and the ASOA fraction of SOA

  12. A basis-set based Fortran program to solve the Gross Pitaevskii equation for dilute Bose gases in harmonic and anharmonic traps

    NASA Astrophysics Data System (ADS)

    Tiwari, Rakesh Prabhat; Shukla, Alok

    2006-06-01

    Inhomogeneous boson systems, such as the dilute gases of integral spin atoms in low-temperature magnetic traps, are believed to be well described by the Gross-Pitaevskii equation (GPE). GPE is a nonlinear Schrödinger equation which describes the order parameter of such systems at the mean field level. In the present work, we describe a Fortran 90 computer program developed by us, which solves the GPE using a basis set expansion technique. In this technique, the condensate wave function (order parameter) is expanded in terms of the solutions of the simple-harmonic oscillator (SHO) characterizing the atomic trap. Additionally, the same approach is also used to solve the problems in which the trap is weakly anharmonic, and the anharmonic potential can be expressed as a polynomial in the position operators x, y, and z. The resulting eigenvalue problem is solved iteratively using either the self-consistent-field (SCF) approach, or the imaginary time steepest-descent (SD) approach. Iterations can be initiated using either the simple-harmonic-oscillator ground state solution, or the Thomas-Fermi (TF) solution. It is found that for condensates containing up to a few hundred atoms, both approaches lead to rapid convergence. However, in the strong interaction limit of condensates containing thousands of atoms, it is the SD approach coupled with the TF starting orbitals, which leads to quick convergence. Our results for harmonic traps are also compared with those published by other authors using different numerical approaches, and excellent agreement is obtained. GPE is also solved for a few anharmonic potentials, and the influence of anharmonicity on the condensate is discussed. Additionally, the notion of Shannon entropy for the condensate wave function is defined and studied as a function of the number of particles in the trap. It is demonstrated numerically that the entropy increases with the particle number in a monotonic way. Program summaryTitle of program

  13. 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}.

  14. Trigonometric Basis Set Functions: Their Application to the C-H Stretching and Deformation Motions of Benzene and to Orbital Symmetry

    NASA Astrophysics Data System (ADS)

    Bor, G.; Kettle, Sidney F. A.

    1999-12-01

    The unifying power of the use of trigonometric basis functions in group character tables is demonstrated. Additionally, these functions provide a simple way of generating pictures of symmetry coordinates. This is illustrated for the in-plane stretch and out-of-plane deformation motions of the C-H bonds in benzene. Their application to orbital symmetry applications is also indicated.

  15. 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.

  16. 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

  17. Optimal settings and accuracy of indocyanine green fluorescence imaging for sentinel node biopsy in early gastric cancer

    PubMed Central

    KINAMI, SHINICHI; OONISHI, TOSHIO; FUJITA, JUN; TOMITA, YASUTO; FUNAKI, HIROSHI; FUJITA, HIDETO; NAKANO, YASUHARU; UEDA, NOBUHIKO; KOSAKA, TAKEO

    2016-01-01

    Indocyanine green (ICG) fluorescence imaging represents a promising method for sentinel node (SN) biopsy in laparoscopic gastric surgery due to its signal stability. In the present study, the suitability and optimal settings of ICG fluorescence imaging for SN biopsy in early gastric cancer were determined. Patients with single primary superficial-type adenocarcinoma of the stomach, lesions <5 cm in diameter, and no evident nodal metastasis and out of indication for endoscopic submucosal dissection were enrolled. The day prior to surgery, ICG solution was endoscopically injected into four quadrants of the submucosal layer of the tumor. The Photodynamic Eye was used to detect ICG fluorescence. Bright nodes were defined as clearly fluorescent nodes. A total of 72 patients were enrolled; 11 cases presented with metastasis, and of these, 10 could be diagnosed by bright node biopsy. The adequate concentration and injection volume of ICG was determined to be 50 µg/ml (×100) and 0.5 mlx4 points, respectively. There was 1 false-negative case, and this was attributed to the failure of the frozen section diagnosis. These results suggested that ICG fluorescence imaging for SN biopsy in laparoscopic surgery for early gastric cancer is feasible. However, a weakness of ICG fluorescence imaging is the subjectivity of bright node evaluation. PMID:27313740

  18. Intertwining Threshold Settings, Biological Data and Database Knowledge to Optimize the Selection of Differentially Expressed Genes from Microarray

    PubMed Central

    Chuchana, Paul; Holzmuller, Philippe; Vezilier, Frederic; Berthier, David; Chantal, Isabelle; Severac, Dany; Lemesre, Jean Loup; Cuny, Gerard; Nirdé, Philippe; Bucheton, Bruno

    2010-01-01

    Background Many tools used to analyze microarrays in different conditions have been described. However, the integration of deregulated genes within coherent metabolic pathways is lacking. Currently no objective selection criterion based on biological functions exists to determine a threshold demonstrating that a gene is indeed differentially expressed. Methodology/Principal Findings To improve transcriptomic analysis of microarrays, we propose a new statistical approach that takes into account biological parameters. We present an iterative method to optimise the selection of differentially expressed genes in two experimental conditions. The stringency level of gene selection was associated simultaneously with the p-value of expression variation and the occurrence rate parameter associated with the percentage of donors whose transcriptomic profile is similar. Our method intertwines stringency level settings, biological data and a knowledge database to highlight molecular interactions using networks and pathways. Analysis performed during iterations helped us to select the optimal threshold required for the most pertinent selection of differentially expressed genes. Conclusions/Significance We have applied this approach to the well documented mechanism of human macrophage response to lipopolysaccharide stimulation. We thus verified that our method was able to determine with the highest degree of accuracy the best threshold for selecting genes that are truly differentially expressed. PMID:20976008

  19. Advanced Procedure for the Monitoring of Settlement and Open Space Development on Basis of Topographical Geodata Sets in the Ioer-Monitor

    NASA Astrophysics Data System (ADS)

    Meinel, G.

    2011-08-01

    Concept, Procedures and Results of the Monitor of settlement and open space development are presented. The monitoring system will describe the state and the development of land use especially in regard to its sustainability for the entire Federal Republic of Germany. To this end, for the first time ever it makes use of topographical geobasis data (digital landscape model of the Authoritative Topographic-Cartographic Information System, short ATKIS). These data allow for a more precise spatial and contentwise description of land use than that of the land register data, which serve as the basis for the official land use statistics. On the basis of the geobasis data an automatic calculation of indicators from the fields of settlement, open space, nature reserves, population, traffic occurs and landscape fragmentation. The indicators are depicted in thematic maps, thus allowing for spatial and chronological comparisons. In addition to administrative spatial units (federal state, region, district, municipality), the indicator values are also presented in scales of various cell widths. For calculating building-based settlement indicators, the patented program SEMENTA® is used, which is based on an automated evaluation of analogue maps.

  20. Theory of nuclear magnetic resonance of higher spin nuclei. 3. A/sub 2/B/sub 2/ systems and many-spin basis sets

    SciTech Connect

    Siddall, T.H.

    1982-01-07

    A theory is developed for nuclear magnetic resonance spectra of A/sub 2/B/sub 2/ systems with nuclei of higher spin. It is assumed that all nuclei have the same spin value. Otherwise no arbitrary limit is set on the spin. Although the development is made for NMR it also has application to the magnetic properties of clusters of transition-metal ions.

  1. Comparison of the polarizabilities and hyperpolarizabilities obtained from finite basis set and finite difference Hartree Fock calculations for diatomic molecules: III. The ground states of N2, CO and BF

    NASA Astrophysics Data System (ADS)

    Kobus, J.; Moncrieff, D.; Wilson, S.

    2007-03-01

    We investigate the accuracy with which the electric dipole polarizability, αzz, and the hyperpolarizability, βzzz, can be calculated by using the algebraic approximation, i.e. finite basis set expansions, and by means of the finite difference method in calculations for the ground states of the 14 electron systems N2, CO and BF within the Hartree-Fock model at their respective experimental equilibrium geometries. For a well-chosen grid, the finite difference technique can provide Hartree-Fock energy and dipole moment expectation values approaching machine precision which can be used to assess the accuracy of corresponding calculations carried out within the algebraic approximation. The finite field approximation is used to determine polarizabilities and hyperpolarizabilities from finite difference Hartree-Fock dipole moment expectation values. The results are compared with finite basis set calculations of the corresponding quantities which are carried out analytically using coupled perturbed Hartree-Fock theory. For the N2 molecule, the Hartree-Fock polarizability is found to be 14.9512 au within the finite basis set approximation and 14.945 au within the finite difference approach. For the CO molecule, the corresponding results are 14.4668 au and 14.4668 au, whilst for the BF molecule the values are 16.6450 au and 16.6450 au, respectively. The Hartree-Fock hyperpolarizability of the CO molecule is found to be 31.4081 au and 31.411 au within the finite basis set and finite difference approximations, respectively. The corresponding hyperpolarizability values for the BF molecule are 63.9687 au and 63.969 au, respectively. This paper is dedicated to Victor R Saunders, on his official retirement from Daresbury Laboratory.

  2. Optimization of cancer chemotherapy on the basis of pharmacokinetics and pharmacodynamics: from patients enrolled in clinical trials to those in the 'real world'.

    PubMed

    Fujita, Ken-Ichi; Sasaki, Yasutsuna

    2014-01-01

      Cytotoxic anticancer drugs are the most challenging therapeutic agents among all medicines with relatively narrow efficacy profiles. Therefore, medical oncologists have to practically manage the risk of severe toxic effects to optimize treatment outcomes. Dose and treatment-schedule recommendations for cytotoxic anticancer agents are determined on the basis of clinical trials. Patients enrolled in clinical trials are those likely to receive the drug in clinical practice, excluding those with conditions such as organ dysfunction, obesity, advanced age, or comorbidity. On the other hand, the 'real world' includes large numbers of such patients who do not meet the eligibility criteria of clinical trials. However, there is a paucity of data from sufficiently powered pharmacokinetic and pharmacodynamic studies to support dosage recommendations in such patients. Consequently, dose levels and treatment schedules for chemotherapy in these subjects are somewhat arbitrary and not evidence-based. Pharmacokinetic and pharmacodynamic studies of patients in the 'real world' are needed to address this issue. In this review article, we describe general aspects of clinical pharmacology in cancer patients enrolled in clinical trials and those in the 'real world,' and introduce recent findings regarding the pharmacokinetic and pharmacodynamic properties of irinotecan and S-1 in 'real world' cancer patients. PMID:24256625

  3. 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

  4. Defining Falciparum-Malaria-Attributable Severe Febrile Illness in Moderate-to-High Transmission Settings on the Basis of Plasma PfHRP2 Concentration

    PubMed Central

    Hendriksen, Ilse C. E.; White, Lisa J.; Veenemans, Jacobien; Mtove, George; Woodrow, Charles; Amos, Ben; Saiwaew, Somporn; Gesase, Samwel; Nadjm, Behzad; Silamut, Kamolrat; Joseph, Sarah; Chotivanich, Kesinee; Day, Nicholas P. J.; von Seidlein, Lorenz; Verhoef, Hans; Reyburn, Hugh; White, Nicholas J.; Dondorp, Arjen M.

    2013-01-01

    Background. In malaria-endemic settings, asymptomatic parasitemia complicates the diagnosis of malaria. Histidine-rich protein 2 (HRP2) is produced by Plasmodium falciparum, and its plasma concentration reflects the total body parasite burden. We aimed to define the malaria-attributable fraction of severe febrile illness, using the distributions of plasma P. falciparum HRP2 (PfHRP2) concentrations from parasitemic children with different clinical presentations. Methods. Plasma samples were collected from and peripheral blood slides prepared for 1435 children aged 6−60 months in communities and a nearby hospital in northeastern Tanzania. The study population included children with severe or uncomplicated malaria, asymptomatic carriers, and healthy control subjects who had negative results of rapid diagnostic tests. The distributions of plasma PfHRP2 concentrations among the different groups were used to model severe malaria-attributable disease. Results. The plasma PfHRP2 concentration showed a close correlation with the severity of infection. PfHRP2 concentrations of >1000 ng/mL denoted a malaria-attributable fraction of severe disease of 99% (95% credible interval [CI], 96%–100%), with a sensitivity of 74% (95% CI, 72%–77%), whereas a concentration of <200 ng/mL denoted severe febrile illness of an alternative diagnosis in >10% (95% CI, 3%–27%) of patients. Bacteremia was more common among patients in the lowest and highest PfHRP2 concentration quintiles. Conclusions. The plasma PfHRP2 concentration defines malaria-attributable disease and distinguishes severe malaria from coincidental parasitemia in African children in a moderate-to-high transmission setting. PMID:23136222

  5. Determining the optimal dosimetric leaf gap setting for rounded leaf-end multileaf collimator systems by simple test fields.

    PubMed

    Yao, Weiguang; Farr, Jonathan B

    2015-01-01

    Individual QA for IMRT/VMAT plans is required by protocols. Sometimes plans cannot pass the institute's QA criteria. For the Eclipse treatment planning system (TPS) with rounded leaf-end multileaf collimator (MLC), one practical way to improve the agreement of planned and delivered doses is to tune the value of dosimetric leaf gap (DLG) in the TPS from the measured DLG. We propose that this step may be necessary due to the complexity of the MLC system, including dosimetry of small fields and the tongue-and-groove (T&G) effects, and report our use of test fields to obtain linac-specific optimal DLGs in TPSs. More than 20 original patient plans were reoptimized with the linac-specific optimal DLG value. We examined the distribution of gaps and T&G extensions in typical patient plans and the effect of using the optimal DLG on the distribution. The QA pass rate of patient plans using the optimal DLG was investigated. The dose-volume histograms (DVHs) of targets and organs at risk were checked. We tested three MLC systems (Varian millennium 120 MLC, high-definition 120 MLC, and Siemens 160 MLC) installed in four Varian linear accelerators (linacs) (TrueBEAM STx, Trilogy, Clinac 2300 iX, and Clinac 21 EX) and 1 Siemens linac (Artiste). With an optimal DLG, the individual QA for all those patient plans passed the institute's criteria (95% in DTA test or gamma test with 3%/3 mm/10%), even though most of these plans had failed to pass QA when using original DLGs optimized from typical patient plans or from the optimization process (automodeler) of Pinnacle TPS. Using either our optimal DLG or one optimized from typical patient plans or from the Pinnacle optimization process yielded similar DVHs. PMID:26218999

  6. Assessment of the "6-31+G** + LANL2DZ" Mixed Basis Set Coupled with Density Functional Theory Methods and the Effective Core Potential: Prediction of Heats of Formation and Ionization Potentials for First-Row-Transition-Metal Complexes

    NASA Astrophysics Data System (ADS)

    Yang, Yue; Weaver, Michael N.; Merz, Kenneth M.

    2009-08-01

    Computational chemists have long demonstrated great interest in finding ways to reliably and accurately predict the molecular properties for transition-metal-containing complexes. This study is a continuation of our validation efforts of density functional theory (DFT) methods when applied to transition-metal-containing systems (Riley, K.E.; Merz, K. M., Jr. J. Phys. Chem. 2007, 111, 6044-6053). In our previous work we examined DFT using all-electron basis sets, but approaches incorporating effective core potentials (ECPs) are effective in reducing computational expense. With this in mind, our efforts were expanded to include evaluation of the performance of the basis set derived to approximate such an approach as well on the same set of density functionals. Indeed, employing an ECP basis such as LANL2DZ (Los Alamos National Laboratory 2 double ζ) for transition metals, while using all-electron basis sets for all other non-transition-metal atoms, has become more and more popular in computations on transition-metal-containing systems. In this study, we assess the performance of 12 different DFT functionals, from the GGA (generalized gradient approximation), hybrid-GGA, meta-GGA, and hybrid-meta-GGA classes, respectively, along with the 6-31+G** + LANL2DZ (on the transition metal) mixed basis set in predicting two important molecular properties, heats of formation and ionization potentials, for 94 and 58 systems containing first-row transition metals from Ti to Zn, which are all in the third row of the periodic table. An interesting note is that the inclusion of the exact exchange term in density functional methods generally increases the accuracy of ionization potential prediction for the hybrid-GGA methods but decreases the reliability of determining the heats of formation for transition-metal-containing complexes for all hybrid density functional methods. The hybrid-GGA functional B3LYP gives the best performance in predicting the ionization potentials, while the

  7. 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. PMID:26073732

  8. Note on the choice of basis set in density functional theory calculations for electronic structures of molecules (test on the atoms from the first three rows of the periodic table (2 N Z 18), water, ammonia and pyrrole)

    NASA Astrophysics Data System (ADS)

    Kristyán, Sándor

    1995-12-01

    The effect of basis set in Kohn-Sham theory on estimating correlation energy was investigated using a density functional subroutine and a Hartree-Fock SCF one-electron density program (working with arbitrary basis set). Lee-Yang-Parr density functional estimation, MP2 perturbation calculation and Davidson's accurate configuration interactions calculations for correlation energies of atoms were used for this test. In the density functional estimation a simple 3-21G basis set has produced the same results as the huge triple-zeta basis set with polarization functions within the chemical accuracy (1 kcal/mol).

  9. 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

  10. The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set.

    PubMed

    Gao, Wei; Feng, Huajie; Xuan, Xiaopeng; Chen, Liuping

    2012-10-01

    An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA + DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA + BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA + BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics. PMID:22643965

  11. 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.

  12. Developing an optimally estimated earth gravity model to degree and order 360 from a global set of 30 deg x 30 deg mean surface gravity anomalies

    NASA Astrophysics Data System (ADS)

    Gleason, D. M.

    An optimally estimated earth gravity model (EGM), consisting of a set of geopotential coefficients through a maximum degree and order of 360, has been created from a global set of 259,200 30 deg by 30 deg surface mean gravity anomalies. The model is optimal in the sense that its derivation follows the principles of least-squares collocation which results in the coefficients' error variance/covariance matrix having a minimal trace value. This paper presents: (1) an overview of the mathematical and geodetic principles behind the construction of the model, (2) a discussion on the practical concerns and problems associated with the implementation of these principles on a present-day high speed computer, (3) a brief description of the global 30 deg input mean anomaly file used, (4) an analysis of the statistical properties of the coefficients and their accuracies, and (5) a prognosis for the future.

  13. Optimization from design rules, source and mask, to full chip with a single computational lithography framework: level-set-methods-based inverse lithography technology (ILT)

    NASA Astrophysics Data System (ADS)

    Pang, Linyong; Peng, Danping; Hu, Peter; Chen, Dongxue; Cecil, Tom; He, Lin; Xiao, Guangming; Tolani, Vikram; Dam, Thuc; Baik, Ki-Ho; Gleason, Bob

    2010-04-01

    For semiconductor manufacturers moving toward advanced technology nodes -32nm, 22nm and below - lithography presents a great challenge, because it is fundamentally constrained by basic principles of optical physics. Because no major lithography hardware improvements are expected over the next couple years, Computational Lithography has been recognized by the industry as the key technology needed to drive lithographic performance. This implies not only simultaneous co-optimization of all the lithographic enhancement tricks that have been learned over the years, but that they also be pushed to the limit by powerful computational techniques and systems. In this paper a single computational lithography framework for design, mask, and source co-optimization will be explained in non-mathematical language. A number of memory and logic device results at the 32nm node and below are presented to demonstrate the benefits of Level-Set-Method-based ILT in applications covering design rule optimization, SMO, and full-chip correction.

  14. 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. PMID:26299609

  15. 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.

  16. Analytic design method for optimal imaging: coupling three ray sets using two free-form lens profiles.

    PubMed

    Duerr, Fabian; Benítez, Pablo; Miñano, Juan C; Meuret, Youri; Thienpont, Hugo

    2012-02-27

    In this work, a new two-dimensional optics design method is proposed that enables the coupling of three ray sets with two lens surfaces. The method is especially important for optical systems designed for wide field of view and with clearly separated optical surfaces. Fermat's principle is used to deduce a set of functional differential equations fully describing the entire optical system. The presented general analytic solution makes it possible to calculate the lens profiles. Ray tracing results for calculated 15th order Taylor polynomials describing the lens profiles demonstrate excellent imaging performance and the versatility of this new analytic design method. PMID:22418364

  17. Setting a Census Date To Optimize Enrollment, Retention, and Tuition Revenue Projections. AIR 1995 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Borden, Victor M. H.; And Others

    The effect of alternative census dates on the determination of student enrollment and retention rates and the accuracy of tuition revenue projections was analyzed at Indiana University-Purdue University Indianapolis. A set of pseudo-extract files was created for the first 8 weeks of two consecutive fall semesters (1993 and 1994). The accuracy of…

  18. 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.

  19. 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.

  20. 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.

  1. 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. PMID:26716720

  2. 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.

  3. The use of nonpharmacological interventions to reduce anxiety in patients undergoing gastroscopy in a setting with an optimal soothing environment.

    PubMed

    Hoya, Yoshiyuki; Matsumura, Izumi; Fujita, Tetsuji; Yanaga, Katsuhiko

    2008-01-01

    Patients develop anxiety before undergoing gastroscopy. By removing such distressing feelings, patients are more likely to experience gastroscopy more smoothly. This study was designed to examine changes in anxiety levels in patients undergoing gastroscopy and the effect of an optimal soothing environment (OSE) as a new nonpharmacological intervention to reduce patient anxiety prior to gastroscopy. During a 6-month period, 50 outpatients referred for gastroscopy were randomly assigned to two groups (control group, n = 24 patients; OSE group, n = 26 patients). This study was performed at the digestive endoscopy service of a 150-bed acute care hospital in Japan. The patient anxiety was assessed using the Face Scale score. Pre- and postprocedural systolic blood pressures were measured and values were compared with blood pressure upon arrival at the hospital. The tools for an OSE, including a safe essential oil burner with lavender essential oil and a digital video disk program entitled "Flow" manufactured by NHK (Japan Broadcasting Corporation) software, were provided to patients in the waiting room before gastroscopy. The score for self-assessed anxiety level just before gastroscopy was significantly higher than that on arrival at the hospital but returned to baseline after gastroscopy in the control group, whereas the score did not increase before starting gastroscopy in the OSE group. Systolic blood pressure measurements just before and after gastroscopy were significantly higher than those on arrival at the hospital and the baseline values in the control group, whereas it was not increased before starting gastroscopy in the OSE group. Providing an OSE before and during gastroscopy is useful to minimize patient anxiety regarding experiencing a gastroscopy. This nonpharmacological method is a simple, inexpensive, and safe method of minimizing anxiety before and during gastroscopy. PMID:19077833

  4. Time-Dependent Selection of an Optimal Set of Sources to Define a Stable Celestial Reference Frame

    NASA Technical Reports Server (NTRS)

    Le Bail, Karine; Gordon, David

    2010-01-01

    Temporal statistical position stability is required for VLBI sources to define a stable Celestial Reference Frame (CRF) and has been studied in many recent papers. This study analyzes the sources from the latest realization of the International Celestial Reference Frame (ICRF2) with the Allan variance, in addition to taking into account the apparent linear motions of the sources. Focusing on the 295 defining sources shows how they are a good compromise of different criteria, such as statistical stability and sky distribution, as well as having a sufficient number of sources, despite the fact that the most stable sources of the entire ICRF2 are mostly in the Northern Hemisphere. Nevertheless, the selection of a stable set is not unique: studying different solutions (GSF005a and AUG24 from GSFC and OPA from the Paris Observatory) over different time periods (1989.5 to 2009.5 and 1999.5 to 2009.5) leads to selections that can differ in up to 20% of the sources. Observing, recording, and network improvement are some of the causes, showing better stability for the CRF over the last decade than the last twenty years. But this may also be explained by the assumption of stationarity that is not necessarily right for some sources.

  5. A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility.

    PubMed

    Perreault-Micale, Cynthia; Davie, Jocelyn; Breton, Benjamin; Hallam, Stephanie; Greger, Valerie

    2015-07-01

    Carrier screening for certain diseases is recommended by major medical and Ashkenazi Jewish (AJ) societies. Most carrier screening panels test only for common, ethnic-specific variants. However, with formerly isolated ethnic groups becoming increasingly intermixed, this approach is becoming inadequate. Our objective was to develop a rigorous process to curate all variants, for relevant genes, into a database and then apply stringent clinical validity classification criteria to each in order to retain only those with clear evidence for pathogenicity. The resulting variant set, in conjunction with next-generation DNA sequencing (NGS), then affords the capability for an ethnically diverse, comprehensive, highly specific carrier-screening assay. The clinical utility of our approach was demonstrated by screening a pan-ethnic population of 22,864 individuals for Bloom syndrome carrier status using a BLM variant panel comprised of 50 pathogenic variants. In addition to carriers of the common AJ founder variant, we identified 57 carriers of other pathogenic BLM variants. All variants reported had previously been curated and their clinical validity documented, or were of a type that met our stringent, preassigned validity criteria. Thus, it was possible to confidently report an increased number of Bloom's syndrome carriers compared to traditional, ethnicity-based screening, while not reducing the specificity of the screening due to reporting variants of unknown clinical significance. PMID:26247052

  6. A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility

    PubMed Central

    Perreault-Micale, Cynthia; Davie, Jocelyn; Breton, Benjamin; Hallam, Stephanie; Greger, Valerie

    2015-01-01

    Carrier screening for certain diseases is recommended by major medical and Ashkenazi Jewish (AJ) societies. Most carrier screening panels test only for common, ethnic-specific variants. However, with formerly isolated ethnic groups becoming increasingly intermixed, this approach is becoming inadequate. Our objective was to develop a rigorous process to curate all variants, for relevant genes, into a database and then apply stringent clinical validity classification criteria to each in order to retain only those with clear evidence for pathogenicity. The resulting variant set, in conjunction with next-generation DNA sequencing (NGS), then affords the capability for an ethnically diverse, comprehensive, highly specific carrier-screening assay. The clinical utility of our approach was demonstrated by screening a pan-ethnic population of 22,864 individuals for Bloom syndrome carrier status using a BLM variant panel comprised of 50 pathogenic variants. In addition to carriers of the common AJ founder variant, we identified 57 carriers of other pathogenic BLM variants. All variants reported had previously been curated and their clinical validity documented, or were of a type that met our stringent, preassigned validity criteria. Thus, it was possible to confidently report an increased number of Bloom’s syndrome carriers compared to traditional, ethnicity-based screening, while not reducing the specificity of the screening due to reporting variants of unknown clinical significance. PMID:26247052

  7. Optimally coherent sets in geophysical flows: a transfer-operator approach to delimiting the stratospheric polar vortex.

    PubMed

    Santitissadeekorn, Naratip; Froyland, Gary; Monahan, Adam

    2010-11-01

    The "edge" of the Antarctic polar vortex is known to behave as a barrier to the meridional (poleward) transport of ozone during the austral winter. This chemical isolation of the polar vortex from the middle and low latitudes produces an ozone minimum in the vortex region, intensifying the ozone hole relative to that which would be produced by photochemical processes alone. Observational determination of the vortex edge remains an active field of research. In this paper, we obtain objective estimates of the structure of the polar vortex by introducing a technique based on transfer operators that aims to find regions with minimal external transport. Applying this technique to European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-40 three-dimensional velocity data, we produce an improved three-dimensional estimate of the vortex location in the upper stratosphere where the vortex is most pronounced. This computational approach has wide potential application in detecting and analyzing mixing structures in a variety of atmospheric, oceanographic, and general fluid dynamical settings. PMID:21230580

  8. 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.

  9. Decentralization Does Not Assure Optimal Delivery of PMTCT and HIV-Exposed Infant Services in a Low Prevalence Setting

    PubMed Central

    Edmonds, Andrew; Feinstein, Lydia; Okitolonda, Vitus; Thompson, Deidre; Kawende, Bienvenu; Behets, Frieda

    2016-01-01

    Background The consequences of decentralizing prevention of mother-to-child HIV transmission and HIV-exposed infant services to antenatal care (ANC)/labor and delivery (L&D) sites from dedicated HIV care and treatment (C&T) centers remain unknown, particularly in low prevalence settings. Methods In a cohort of mother–infant pairs, we compared delivery of routine services at ANC/L&D and C&T facilities in Kinshasa, Democratic Republic of Congo from 2010–2013, using methods accounting for competing risks (eg, death). Women could opt to receive interventions at 90 decentralized ANC/L&D sites, or 2 affiliated C&T centers. Additionally, we assessed decentralization’s population-level impacts by comparing proportions of women and infants receiving interventions before (2009–2010) and after (2011–2013) decentralization. Results Among newly HIV-diagnosed women (N = 1482), the 14-week cumulative incidence of receiving the package of CD4 testing and zidovudine or antiretroviral therapy was less at ANC/L&D [66%; 95% confidence interval (CI): 63% to 69%] than at C&T (88%; 95% CI: 83% to 92%) sites (subdistribution hazard ratio, 0.62; 95% CI: 0.55 to 0.69). Delivery of cotrimoxazole and DNA polymerase chain reaction testing to HIV-exposed infants (N = 1182) was inferior at ANC/L&D sites (subdistribution hazard ratio, 0.84; 95% CI: 0.76 to 0.92); the 10-month cumulative incidence of the package at ANC/L&D sites was 89% (95% CI: 82% to 93%) versus 97% (95% CI: 93% to 99%) at C&T centers. Receipt of the pregnancy (20% of 1518, to 64% of 1405) and infant (16%–31%) packages improved post decentralization. Conclusions Services were delivered less efficiently at ANC/L&D sites than C&T centers. Although access improved with decentralization, its potential cannot be realized without sufficient and sustained support. PMID:26262776

  10. The through optimization of fail-safe branched injection trajectories of launch vehicles in view of aerodynamic load constraints on the basis of the maximum principle

    NASA Astrophysics Data System (ADS)

    Filatyev, A. S.; Yanova, O. V.

    2013-12-01

    A problem of through optimization of fail-safe branched trajectories of launchers in view of aerodynamic load constraints and restrictions on ground impact areas of separated parts (SP) is considered. The failsafety is regarded to the possibility of a recoverable vehicle (RV) to return from any point of the ascent trajectory to landing points without excess of allowable g-loads. So, the purpose is determination of the launcher optimal control in view of constraints on all trajectory branches: the main, corresponding to an active injection leg, and side branches, corresponding to SP fall trajectories and imaginary RV emergency trajectories, which form a continuum. The problem solution is based on the Pontryagin maximum principle (PMP).

  11. Optimization of ventilator setting by flow and pressure waveforms analysis during noninvasive ventilation for acute exacerbations of COPD: a multicentric randomized controlled trial

    PubMed Central

    2011-01-01

    Introduction The analysis of flow and pressure waveforms generated by ventilators can be useful in the optimization of patient-ventilator interactions, notably in chronic obstructive pulmonary disease (COPD) patients. To date, however, a real clinical benefit of this approach has not been proven. Methods The aim of the present randomized, multi-centric, controlled study was to compare optimized ventilation, driven by the analysis of flow and pressure waveforms, to standard ventilation (same physician, same initial ventilator setting, same time spent at the bedside while the ventilator screen was obscured with numerical data always available). The primary aim was the rate of pH normalization at two hours, while secondary aims were changes in PaCO2, respiratory rate and the patient's tolerance to ventilation (all parameters evaluated at baseline, 30, 120, 360 minutes and 24 hours after the beginning of ventilation). Seventy patients (35 for each group) with acute exacerbation of COPD were enrolled. Results Optimized ventilation led to a more rapid normalization of pH at two hours (51 vs. 26% of patients), to a significant improvement of the patient's tolerance to ventilation at two hours, and to a higher decrease of PaCO2 at two and six hours. Optimized ventilation induced physicians to use higher levels of external positive end-expiratory pressure, more sensitive inspiratory triggers and a faster speed of pressurization. Conclusions The analysis of the waveforms generated by ventilators has a significant positive effect on physiological and patient-centered outcomes during acute exacerbation of COPD. The acquisition of specific skills in this field should be encouraged. Trial registration ClinicalTrials.gov NCT01291303. PMID:22115190

  12. The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes.

    PubMed

    Roper, Ian P E; Besley, Nicholas A

    2016-03-21

    The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals. PMID:27004859

  13. Estimation of optimal b-value sets for obtaining apparent diffusion coefficient free from perfusion in non-small cell lung cancer

    NASA Astrophysics Data System (ADS)

    Karki, Kishor; Hugo, Geoffrey D.; Ford, John C.; Olsen, Kathryn M.; Saraiya, Siddharth; Groves, Robert; Weiss, Elisabeth

    2015-10-01

    The purpose of this study was to determine optimal sets of b-values in diffusion-weighted MRI (DW-MRI) for obtaining monoexponential apparent diffusion coefficient (ADC) close to perfusion-insensitive intravoxel incoherent motion (IVIM) model ADC (ADCIVIM) in non-small cell lung cancer. Ten subjects had 40 DW-MRI scans before and during radiotherapy in a 1.5 T MRI scanner. Respiratory triggering was applied to the echo-planar DW-MRI with \\text{TR}≈ 4500 ms, TE  =  74 ms, eight b-values of 0-1000 μs μm-2, pixel size  =  1.98× 1.98 mm2, slice thickness  =  6 mm, interslice gap  =  1.2 mm, 7 axial slices and total acquisition time ≈6 min. One or more DW-MRI scans together covered the whole tumour volume. Monoexponential model ADC values using various b-value sets were compared to reference-standard ADCIVIM values using all eight b-values. Intra-scan coefficient of variation (CV) of active tumour volumes was computed to compare the relative noise in ADC maps. ADC values for one pre-treatment DW-MRI scan of each of the 10 subjects were computed using b-value pairs from DW-MRI images synthesized for b-values of 0-2000 μs μm-2 from the estimated IVIM parametric maps and corrupted by various Rician noise levels. The square root of mean of squared error percentage (RMSE) of the ADC value relative to the corresponding ADCIVIM for the tumour volume of the scan was computed. Monoexponential ADC values for the b-value sets of 250 and 1000; 250, 500 and 1000; 250, 650 and 1000; 250, 800 and 1000; and 250-1000 μs μm-2 were not significantly different from ADCIVIM values (p>0.05 , paired t-test). Mean error in ADC values for these sets relative to ADCIVIM were within 3.5%. Intra-scan CVs for these sets were comparable to that for ADCIVIM. The monoexponential ADC values for other sets—0-1000 50-1000 100-1000 500-1000 and 250 and 800 μs μm-2 were significantly different from the ADCIVIM values. From Rician noise simulation

  14. The search for optimal cutoff points for apoptosis and proliferation rate in prognostification of early stage breast cancer patients treated with anthracyclines in adjuvant settings.

    PubMed

    Biesaga, Beata; Niemiec, Joanna; Wysocka, Joanna; Słonina, Dorota; Ziobro, Marek

    2016-06-01

    Cancer growth is determined by the proportion of proliferating to dying cells; thus, the aim of the study was to analyze how proliferation rate and apoptosis level affect disease-free survival (DFS) of breast cancer (BC) patients treated with anthracycline-based chemotherapy. For 172 BC, proliferation rate was investigated by Ki-67 labeling index (Ki-67 LI)-assessed immunohistochemically. Apoptosis level was analyzed by apoptotic index (AI) estimated by terminal deoxynucleotidyl transferase dUTP nick end labeling assay. To stratify patients into subgroups with higher and lower DFS and to achieve optimal categorization, optimal cutoff points were searching by minimal P value method. The best separation of DFS curves (P = 0.001) was observed for three categories of AI: (i) AI >1.8 % (DFS = 100 %), (ii) AI ≤0.3 % (DFS = 84.6 %), and (iii) 1.8 % <= AI >0.3 % (DFS = 64.0 %). The highest DFS (86.1 %) was shown for the subgroup with low-proliferating BC (Ki-67 LI ≤18.0 %), intermediate (73.9 %) for patients characterized by Ki-67 LI in the range 18.0-37.0 % and the lowest (60.0 %) for women with fast-proliferating tumors (Ki-67 LI >37.0 %) (P = 0.022). Summarized, minimal P value method allows for optimal separation of survival curves. Apoptosis level and proliferation rate have some prognostic potential for early stage breast cancer patients treated with anthracyclines in adjuvant setting, however, as suggested by multivariate analysis, not as independent prognostic factors. PMID:26687650

  15. Using a Pareto-optimal solution set to characterize trade-offs between a broad range of values and preferences in climate risk management

    NASA Astrophysics Data System (ADS)

    Garner, Gregory; Reed, Patrick; Keller, Klaus

    2015-04-01

    Integrated assessment models (IAMs) are often used to inform the design of climate risk management strategies. Previous IAM studies have broken important new ground on analyzing the effects of parametric uncertainties, but they are often silent on the implications of uncertainties regarding the problem formulation. Here we use the Dynamic Integrated model of Climate and the Economy (DICE) to analyze the effects of uncertainty surrounding the definition of the objective(s). The standard DICE model adopts a single objective to maximize a weighted sum of utilities of per-capita consumption. Decision makers, however, are often concerned with a broader range of values and preferences that may be poorly captured by this a priori definition of utility. We reformulate the problem by introducing three additional objectives that represent values such as (i) reliably limiting global average warming to two degrees Celsius and minimizing (ii) the costs of abatement and (iii) the climate change damages. We use advanced multi-objective optimization methods to derive a set of Pareto-optimal solutions over which decision makers can trade-off and assess performance criteria a posteriori. We illustrate the potential for myopia in the traditional problem formulation and discuss the capability of this multiobjective formulation to provide decision support.

  16. SETS. Set Equation Transformation System

    SciTech Connect

    Worrel, R.B.

    1992-01-13

    SETS is used for symbolic manipulation of Boolean equations, particularly the reduction of equations by the application of Boolean identities. It is a flexible and efficient tool for performing probabilistic risk analysis (PRA), vital area analysis, and common cause analysis. The equation manipulation capabilities of SETS can also be used to analyze noncoherent fault trees and determine prime implicants of Boolean functions, to verify circuit design implementation, to determine minimum cost fire protection requirements for nuclear reactor plants, to obtain solutions to combinatorial optimization problems with Boolean constraints, and to determine the susceptibility of a facility to unauthorized access through nullification of sensors in its protection system.

  17. Revising the retrieval technique of a long-term stratospheric HNO3 data set: from a constrained matrix inversion to the optimal estimation algorithm

    NASA Astrophysics Data System (ADS)

    Fiorucci, I.; Muscari, G.; de Zafra, R. L.

    2011-07-01

    The Ground-Based Millimeter-wave Spectrometer (GBMS) was designed and built at the State University of New York at Stony Brook in the early 1990s and since then has carried out many measurement campaigns of stratospheric O3, HNO3, CO and N2O at polar and mid-latitudes. Its HNO3 data set shed light on HNO3 annual cycles over the Antarctic continent and contributed to the validation of both generations of the satellite-based JPL Microwave Limb Sounder (MLS). Following the increasing need for long-term data sets of stratospheric constituents, we resolved to establish a long-term GMBS observation site at the Arctic station of Thule (76.5° N, 68.8° W), Greenland, beginning in January 2009, in order to track the long- and short-term interactions between the changing climate and the seasonal processes tied to the ozone depletion phenomenon. Furthermore, we updated the retrieval algorithm adapting the Optimal Estimation (OE) method to GBMS spectral data in order to conform to the standard of the Network for the Detection of Atmospheric Composition Change (NDACC) microwave group, and to provide our retrievals with a set of averaging kernels that allow more straightforward comparisons with other data sets. The new OE algorithm was applied to GBMS HNO3 data sets from 1993 South Pole observations to date, in order to produce HNO3 version 2 (v2) profiles. A sample of results obtained at Antarctic latitudes in fall and winter and at mid-latitudes is shown here. In most conditions, v2 inversions show a sensitivity (i.e., sum of column elements of the averaging kernel matrix) of 100 ± 20 % from 20 to 45 km altitude, with somewhat worse (better) sensitivity in the Antarctic winter lower (upper) stratosphere. The 1σ uncertainty on HNO3 v2 mixing ratio vertical profiles depends on altitude and is estimated at ~15 % or 0.3 ppbv, whichever is larger. Comparisons of v2 with former (v1) GBMS HNO3 vertical profiles, obtained employing the constrained matrix inversion method, show that

  18. Determining optimal clinical target volume margins on the basis of microscopic extracapsular extension of metastatic nodes in patients with non-small-cell lung cancer

    SciTech Connect

    Yuan Shuanghu; Meng Xue; Yu Jinming . E-mail: fishtigers@yahoo.com.cn; Mu Dianbin; Chao, K.S. Clifford; Zhang Jiandong; Zhong Weixia; Yu Yonghua; Wang Jialin; Sun Xindong; Yang Guoren; Wang Yongzheng

    2007-03-01

    Purpose: To determine the optimal clinical target volume (CTV) margins around the nodal gross tumor volume (GTV) in non-small-cell lung cancer (NSCLC) patients by assessing microscopic tumor extension beyond regional lymph node capsules. Methods and Materials: The incidence of nodal extracapsular extension (ECE) and relationship with nodal size were reviewed in 243 patients. Histologic sections of dissected regional lymph nodes up to 30 mm in size were examined to measure the extent of microscopic ECE. We determined the distribution of cases according to extent of ECE and the relationships between ECE extent and lymph node size, regional nodal disease extent, histologic type, and degree of differentiation. Results: The nodal ECE was seen in 41.6% of patients (101/243) and 33.4% of lymph nodes (214/640), and the incidence correlated to larger lymph node size positively. The extent of ECE was 0.7 mm in mean (range, 0-12.0 mm) and {<=}3 mm in 95% of the nodes. Positive correlations were found between extent of ECE and larger lymph node size ({>=}20 mm vs. 10-19 mm or <10 mm, p = 0.005), advanced nodal stage (N2 vs. N1, p = 0.046), and moderate or poor (vs. good or unknown) nodal differentiation (p = 0.002). ECE did not differ significantly by histologic type or nodal station. Conclusions: The incidence of ECE related to lymph node size, and ECE extent related to lymph node size, stage, and differentiation. It may be reasonable to recommend 3-mm CTV margins for pathologic lymph nodes <20 mm and more generous margins for lymph nodes {>=}20 mm.

  19. Analysis of Regional Timelines To Set Up a Global Phase III Clinical Trial in Breast Cancer: The Adjuvant Lapatinib and/or Trastuzumab Treatment Optimization Experience

    PubMed Central

    de Azambuja, Evandro; Bradbury, Ian; Saini, Kamal S.; Bines, José; Simon, Sergio D.; Dooren, Veerle Van; Aktan, Gursel; Pritchard, Kathleen I.; Wolff, Antonio C.; Smith, Ian; Jackisch, Christian; Lang, Istvan; Untch, Michael; Boyle, Frances; Xu, Binghe; Baselga, Jose; Perez, Edith A.; Piccart-Gebhart, Martine

    2013-01-01

    Purpose. This study measured the time taken for setting up the different facets of Adjuvant Lapatinib and/or Trastuzumab Treatment Optimization (ALTTO), an international phase III study being conducted in 44 participating countries. Methods. Time to regulatory authority (RA) approval, time to ethics committee/institutional review board (EC/IRB) approval, time from study approval by EC/IRB to first randomized patient, and time from first to last randomized patient were prospectively collected in the ALTTO study. Analyses were conducted by grouping countries into either geographic regions or economic classes as per the World Bank's criteria. Results. South America had a significantly longer time to RA approval (median: 236 days, range: 21–257 days) than Europe (median: 52 days, range: 0–151 days), North America (median: 26 days, range: 22–30 days), and Asia-Pacific (median: 62 days, range: 37–75 days). Upper-middle economies had longer times to RA approval (median: 123 days, range: 21–257 days) than high-income (median: 47 days, range: 0–112 days) and lower-middle income economies (median: 57 days, range: 37–62 days). No significant difference was observed for time to EC/IRB approval across the studied regions (median: 59 days, range 0–174 days). Overall, the median time from EC/IRB approval to first recruited patient was 169 days (range: 26–412 days). Conclusion. This study highlights the long time intervals required to activate a global phase III trial. Collaborative research groups, pharmaceutical industry sponsors, and regulatory authorities should analyze the current system and enter into dialogue for optimizing local policies. This would enable faster access of patients to innovative therapies and enhance the efficiency of clinical research. PMID:23359433

  20. WE-G-18C-02: Estimation of Optimal B-Value Set for Obtaining Apparent Diffusion Coefficient Free From Perfusion in Non-Small Cell Lung Cancer

    SciTech Connect

    Karki, K; Hugo, G; Ford, J; Saraiya, S; Weiss, E; Olsen, K; Groves, R

    2014-06-15

    Purpose: Diffusion-weighted MRI (DW-MRI) is increasingly being investigated for radiotherapy planning and response assessment. Selection of a limited number of b-values in DW-MRI is important to keep geometrical variations low and imaging time short. We investigated various b-value sets to determine an optimal set for obtaining monoexponential apparent diffusion coefficient (ADC) close to perfusion-insensitive intravoxel incoherent motion (IVIM) model ADC (ADCIVIM) in nonsmall cell lung cancer. Methods: Seven patients had 27 DW-MRI scans before and during radiotherapy in a 1.5T scanner. Respiratory triggering was applied to the echo-planar DW-MRI with TR=4500ms approximately, TE=74ms, pixel size=1.98X1.98mm{sub 2}, slice thickness=4–6mm and 7 axial slices. Diffusion gradients were applied to all three axes producing traceweighted images with eight b-values of 0–1000μs/μm{sup 2}. Monoexponential model ADC values using various b-value sets were compared to ADCIVIM using all b-values. To compare the relative noise in ADC maps, intra-scan coefficient of variation (CV) of active tumor volumes was computed. Results: ADCIVIM, perfusion coefficient and perfusion fraction for tumor volumes were in the range of 880-1622 μm{sup 2}/s, 8119-33834 μm{sup 2}/s and 0.104–0.349, respectively. ADC values using sets of 250, 800 and 1000; 250, 650 and 1000; and 250–1000μs/μm{sup 2} only were not significantly different from ADCIVIM(p>0.05, paired t-test). Error in ADC values for 0–1000, 50–1000, 100–1000, 250–1000, 500–1000, and three b-value sets- 250, 500 and 1000; 250, 650 and 1000; and 250, 800 and 1000μs/μm{sup 2} were 15.0, 9.4, 5.6, 1.4, 11.7, 3.7, 2.0 and 0.2% relative to the reference-standard ADCIVIM, respectively. Mean intrascan CV was 20.2, 20.9, 21.9, 24.9, 32.6, 25.8, 25.4 and 24.8%, respectively, whereas that for ADCIVIM was 23.3%. Conclusion: ADC values of two 3 b-value sets

  1. Fuzzy resource optimization for safeguards

    SciTech Connect

    Zardecki, A.; Markin, J.T.

    1991-01-01

    Authorization, enforcement, and verification -- three key functions of safeguards systems -- form the basis of a hierarchical description of the system risk. When formulated in terms of linguistic rather than numeric attributes, the risk can be computed through an algorithm based on the notion of fuzzy sets. Similarly, this formulation allows one to analyze the optimal resource allocation by maximizing the overall detection probability, regarded as a linguistic variable. After summarizing the necessary elements of the fuzzy sets theory, we outline the basic algorithm. This is followed by a sample computation of the fuzzy optimization. 10 refs., 1 tab.

  2. Establishing a Scientific Basis for Optimizing Compositions, Process Paths and Fabrication Methods for Nanostructured Ferritic Alloys for Use in Advanced Fission Energy Systems

    SciTech Connect

    Odette, G Robert; Cunningham, Nicholas J., Wu, Yuan; Etienne, Auriane; Stergar, Erich; Yamamoto, Takuya

    2012-02-21

    The broad objective of this NEUP was to further develop a class of 12-15Cr ferritic alloys that are dispersion strengthened and made radiation tolerant by an ultrahigh density of Y-Ti-O nanofeatures (NFs) in the size range of less than 5 nm. We call these potentially transformable materials nanostructured ferritic alloys (NFAs). NFAs are typically processed by ball milling pre-alloyed rapidly solidified powders and yttria (Y2O3) powders. Proper milling effectively dissolves the Ti, Y and O solutes that precipitate as NFs during hot consolidation. The tasks in the present study included examining alternative processing paths, characterizing and optimizing the NFs and investigating solid state joining. Alternative processing paths involved rapid solidification by gas atomization of Fe, 14% Cr, 3% W, and 0.4% Ti powders that are also pre-alloyed with 0.2% Y (14YWT), where the compositions are in wt.%. The focus is on exploring the possibility of minimizing, or even eliminating, the milling time, as well as producing alloys with more homogeneous distributions of NFs and a more uniform, fine grain size. Three atomization environments were explored: Ar, Ar plus O (Ar/O) and He. The characterization of powders and alloys occurred through each processing step: powder production by gas atomization; powder milling; and powder annealing or hot consolidation by hot isostatic pressing (HIPing) or hot extrusion. The characterization studies of the materials described here include various combinations of: a) bulk chemistry; b) electron probe microanalysis (EPMA); c) atom probe tomography (APT); d) small angle neutron scattering (SANS); e) various types of scanning and transmission electron microscopy (SEM and TEM); and f) microhardness testing. The bulk chemistry measurements show that preliminary batches of gas-atomized powders could be produced within specified composition ranges. However, EPMA and TEM showed that the Y is heterogeneously distributed and phase separated, but

  3. PS1-23: Capitalizing on the HMO Cancer Research Network (CRN): The Optimal Setting to Conduct Studies of Rare Complex Diseases

    PubMed Central

    Johnson, Christine Cole; Chao, Chun; Engel, Larry; Feigelson, Heather; Fortuny, Joan; Habel, Laurel; Koshiol, Jill; Roblin, Douglas; Spangler, Leslie; Wells, Karen; Yood, Marianne Ulcickas

    2013-01-01

    Background/Aims Rare cancers are challenging to study, both epidemiologically and clinically, as it is difficult to ascertain enough cases to achieve adequate statistical power or to be representative of a vast range of exposures. Further, as the complexity of unraveling the natural history of disease has increased, a large investigator team with diverse expertise is required to optimize the scientific contributions that can be mined from research projects. The HMOCRN provides a setting that can overcome these barriers. Although many studies evaluate all lymphomas combined, lymphoma consists of over 50 rare histological subtypes with varying incidence and survival rates and epidemiological features. Ideally, each histological subtype should be considered separately in etiological studies, but even the most common, diffuse large B cell lymphoma, has a SEER incidence of only 7.5 per 100,000 in men and 5.0 per 100,000 in women. Other lymphoma types range in incidence from <0.1 cases per 100,000 for NKT cell lymphoma to 2.8 per 100,000 for Hodgkin’s Disease in all race-sex groups combined, to the highest rate found for a population subgroup, only 8.8 per 100,000 for multiple myeloma in African American men. Methods We have assembled a multi-disciplinary team interested in lymphoma and pharmacoepidemiology that includes investigators with clinical, epidemiological and biostatistical expertise from six HMORN sites, two US universities, the NCI, and an international investigator who first initiated the project. Results Combining data from these HMOCRN sites from 1998–2008, we ascertained 1479 Hodgkin’s Disease cases, 3385 multiple myelomas, 771 T-cell lymphomas, (including 390 mycosis fungoides cases and 158 mature T-cell lymphomas), 3000 chronic lymphocytic leukemias, 1357 mature B cell lymphomas, 3883 diffuse large B cell lymphomas, 2188 follicular lymphomas, and 992 marginal zone B cell lymphomas. Conclusions These numbers provide a unique opportunity to analyze

  4. Optimal cost basis for seismic design

    SciTech Connect

    Hadjian, A.H.

    1993-09-01

    The paper summarizes a methodology for establishing seismic design levels based on a cost-benefit assessment. The methodology requires the development of costs and benefits for varying design levels of vibratory ground motion and surface fault displacements. The optimum design level for a given structure is that which gives the minimum total direct and earthquake consequence costs. The example used is the surface facilities of the proposed high-level waste repository at Yucca Mountain, Nevada.

  5. A Grobner Basis Solution for Lightning Ground Flash Fraction Retrieval

    NASA Technical Reports Server (NTRS)

    Solakiewicz, Richard; Attele, Rohan; Koshak, William

    2011-01-01

    A Bayesian inversion method was previously introduced for retrieving the fraction of ground flashes in a set of flashes observed from a (low earth orbiting or geostationary) satellite lightning imager. The method employed a constrained mixed exponential distribution model to describe the lightning optical measurements. To obtain the optimum model parameters, a scalar function was minimized by a numerical method. In order to improve this optimization, we introduce a Grobner basis solution to obtain analytic representations of the model parameters that serve as a refined initialization scheme to the numerical optimization. Using the Grobner basis, we show that there are exactly 2 solutions involving the first 3 moments of the (exponentially distributed) data. When the mean of the ground flash optical characteristic (e.g., such as the Maximum Group Area, MGA) is larger than that for cloud flashes, then a unique solution can be obtained.

  6. Hybridisations Of Simulated Annealing And Modified Simplex Algorithms On A Path Of Steepest Ascent With Multi-Response For Optimal Parameter Settings Of ACO

    NASA Astrophysics Data System (ADS)

    Luangpaiboon, P.

    2009-10-01

    Many entrepreneurs face to extreme conditions for instances; costs, quality, sales and services. Moreover, technology has always been intertwined with our demands. Then almost manufacturers or assembling lines adopt it and come out with more complicated process inevitably. At this stage, products and service improvement need to be shifted from competitors with sustainability. So, a simulated process optimisation is an alternative way for solving huge and complex problems. Metaheuristics are sequential processes that perform exploration and exploitation in the solution space aiming to efficiently find near optimal solutions with natural intelligence as a source of inspiration. One of the most well-known metaheuristics is called Ant Colony Optimisation, ACO. This paper is conducted to give an aid in complicatedness of using ACO in terms of its parameters: number of iterations, ants and moves. Proper levels of these parameters are analysed on eight noisy continuous non-linear continuous response surfaces. Considering the solution space in a specified region, some surfaces contain global optimum and multiple local optimums and some are with a curved ridge. ACO parameters are determined through hybridisations of Modified Simplex and Simulated Annealing methods on the path of Steepest Ascent, SAM. SAM was introduced to recommend preferable levels of ACO parameters via statistically significant regression analysis and Taguchi's signal to noise ratio. Other performance achievements include minimax and mean squared error measures. A series of computational experiments using each algorithm were conducted. Experimental results were analysed in terms of mean, design points and best so far solutions. It was found that results obtained from a hybridisation with stochastic procedures of Simulated Annealing method were better than that using Modified Simplex algorithm. However, the average execution time of experimental runs and number of design points using hybridisations were

  7. Multivariate optimization of production systems

    SciTech Connect

    Carroll, J.A.; Horne, R.N. )

    1992-07-01

    This paper reports that mathematically, optimization involves finding the extreme values of a function. Given a function of several variables, Z = {integral}({rvec x}{sub 1}, {rvec x}{sub 2},{rvec x}{sub 3},{yields}x{sub n}), an optimization scheme will find the combination of these variables that produces an extreme value in the function, whether it is a minimum or a maximum value. Many examples of optimization exist. For instance, if a function gives and investor's expected return on the basis of different investments, numerical optimization of the function will determine the mix of investments that will yield the maximum expected return. This is the basis of modern portfolio theory. If a function gives the difference between a set of data and a model of the data, numerical optimization of the function will produce the best fit of the model to the data. This is the basis for nonlinear parameter estimation. Similar examples can be given for network analysis, queuing theory, decision analysis, etc.

  8. A Phase I/II adaptive design to determine the optimal treatment regimen from a set of combination immunotherapies in high-risk melanoma.

    PubMed

    Wages, Nolan A; Slingluff, Craig L; Petroni, Gina R

    2015-03-01

    In oncology, vaccine-based immunotherapy often investigates regimens that demonstrate minimal toxicity overall and higher doses may not correlate with greater immune response. Rather than determining the maximum tolerated dose, the goal of the study becomes locating the optimal biological dose, which is defined as a safe dose demonstrating the greatest immunogenicity, based on some predefined measure of immune response. Incorporation of adjuvants, new or optimized peptide vaccines, and combining vaccines with immune modulators may enhance immune response, with the aim of improving clinical response. Innovative dose escalation strategies are needed to establish the safety and immunogenicity of new immunologic combinations. We describe the implementation of an adaptive design for identifying the optimal treatment strategy in a multi-site, FDA-approved, phase I/II trial of a novel vaccination approach using long-peptides plus TLR agonists for resected stage IIB-IV melanoma. Operating characteristics of the design are demonstrated under various possible true scenarios via simulation studies. Overall performance indicates that the design is a practical Phase I/II adaptive method for use with combined immunotherapy agents. The simulation results demonstrate the method's ability to effectively recommend optimal regimens in a high percentage of trials with manageable sample sizes. The numerical results presented in this work include the type of simulation information that aid review boards in understanding design performance, such as average sample size and frequency of early trial termination, which we hope will augment early-phase trial design in cancer immunotherapy. PMID:25638752

  9. Joint Task Force on Undergraduate Physics Programs (J-TUPP): What skills and knowledge are needed for a diverse set of careers and what's the basis for these recommendations?

    NASA Astrophysics Data System (ADS)

    Woolf, Lawrence

    2016-03-01

    A wide variety of reports have been issued recently concerning the skills, knowledge, and attitudes needed by employees to be successful. This talk will review findings from reports from the major science and engineering disciplines, from surveys of employers, and from interviews with recent undergraduate physics graduates. Also to be discussed is the correlation between these findings and the detailed J-TUPP recommendations for the skills and knowledge needed by the next generation of undergraduate physics degree holders to be prepared for a diverse set of careers.

  10. Tractable Pareto Optimization of Temporal Preferences

    NASA Technical Reports Server (NTRS)

    Morris, Robert; Morris, Paul; Khatib, Lina; Venable, Brent

    2003-01-01

    This paper focuses on temporal constraint problems where the objective is to optimize a set of local preferences for when events occur. In previous work, a subclass of these problems has been formalized as a generalization of Temporal CSPs, and a tractable strategy for optimization has been proposed, where global optimality is defined as maximizing the minimum of the component preference values. This criterion for optimality, which we call 'Weakest Link Optimization' (WLO), is known to have limited practical usefulness because solutions are compared only on the basis of their worst value; thus, there is no requirement to improve the other values. To address this limitation, we introduce a new algorithm that re-applies WLO iteratively in a way that leads to improvement of all the values. We show the value of this strategy by proving that, with suitable preference functions, the resulting solutions are Pareto Optimal.

  11. Detection of Gaseous Plumes using Basis Vectors

    SciTech Connect

    Chilton, Lawrence; Walsh, Stephen

    2009-05-01

    Detecting and identifying weak gaseous plumes using thermal imaging data is complicated by many factors. There are several methods currently being used to detect plumes. They can be grouped into two categories: those that use a chemical spectral library and those that don’t. The approaches that use chemical libraries include least squares methods and physics-based approaches. They are "optimal" only if the plume chemical is actually in the search set but risk missing chemicals not in the library. The methods that don’t use a chemical spectral library are based on a statistical or data analytical transformation applied to the data. These include principle components, independent components, entropy, Fourier transform, and others. These methods do not explicitly take advantage of the physics of the signal formulation process and therefore don’t exploit all available information in the data. This paper presents initial results of employing basis vectors as a tool for plume detection. It describes the standard generalized least squares approach using gas spectra, presents the detection approach using basis vectors, and compares detection images resulting from applying both methods to synthetic hyperspectral images.

  12. Dispositional Optimism

    PubMed Central

    Carver, Charles S.; Scheier, Michael F.

    2014-01-01

    Optimism is a cognitive construct (expectancies regarding future outcomes) that also relates to motivation: optimistic people exert effort, whereas pessimistic people disengage from effort. Study of optimism began largely in health contexts, finding positive associations between optimism and markers of better psychological and physical health. Physical health effects likely occur through differences in both health-promoting behaviors and physiological concomitants of coping. Recently, the scientific study of optimism has extended to the realm of social relations: new evidence indicates that optimists have better social connections, partly because they work harder at them. In this review, we examine the myriad ways this trait can benefit an individual, and our current understanding of the biological basis of optimism. PMID:24630971

  13. Fuzzy Sets in Dynamic Adaptation of Parameters of a Bee Colony Optimization for Controlling the Trajectory of an Autonomous Mobile Robot.

    PubMed

    Amador-Angulo, Leticia; Mendoza, Olivia; Castro, Juan R; Rodríguez-Díaz, Antonio; Melin, Patricia; Castillo, Oscar

    2016-01-01

    A hybrid approach composed by different types of fuzzy systems, such as the Type-1 Fuzzy Logic System (T1FLS), Interval Type-2 Fuzzy Logic System (IT2FLS) and Generalized Type-2 Fuzzy Logic System (GT2FLS) for the dynamic adaptation of the alpha and beta parameters of a Bee Colony Optimization (BCO) algorithm is presented. The objective of the work is to focus on the BCO technique to find the optimal distribution of the membership functions in the design of fuzzy controllers. We use BCO specifically for tuning membership functions of the fuzzy controller for trajectory stability in an autonomous mobile robot. We add two types of perturbations in the model for the Generalized Type-2 Fuzzy Logic System to better analyze its behavior under uncertainty and this shows better results when compared to the original BCO. We implemented various performance indices; ITAE, IAE, ISE, ITSE, RMSE and MSE to measure the performance of the controller. The experimental results show better performances using GT2FLS then by IT2FLS and T1FLS in the dynamic adaptation the parameters for the BCO algorithm. PMID:27618062

  14. Cost tradeoffs in consequence management at nuclear power plants: A risk based approach to setting optimal long-term interdiction limits for regulatory analyses

    SciTech Connect

    Mubayi, V.

    1995-05-01

    The consequences of severe accidents at nuclear power plants can be limited by various protective actions, including emergency responses and long-term measures, to reduce exposures of affected populations. Each of these protective actions involve costs to society. The costs of the long-term protective actions depend on the criterion adopted for the allowable level of long-term exposure. This criterion, called the ``long term interdiction limit,`` is expressed in terms of the projected dose to an individual over a certain time period from the long-term exposure pathways. The two measures of offsite consequences, latent cancers and costs, are inversely related and the choice of an interdiction limit is, in effect, a trade-off between these two measures. By monetizing the health effects (through ascribing a monetary value to life lost), the costs of the two consequence measures vary with the interdiction limit, the health effect costs increasing as the limit is relaxed and the protective action costs decreasing. The minimum of the total cost curve can be used to calculate an optimal long term interdiction limit. The calculation of such an optimal limit is presented for each of five US nuclear power plants which were analyzed for severe accident risk in the NUREG-1150 program by the Nuclear Regulatory Commission.

  15. Performance evaluation of the IBM RISC (reduced instruction set computer) System/6000: Comparison of an optimized scalar processor with two vector processors

    SciTech Connect

    Simmons, M.L.; Wasserman, H.J.

    1990-01-01

    RISC System/6000 computers are workstations with a reduced instruction set processor recently developed by IBM. This report details the performance of the 6000-series computers as measured using a set of portable, standard-Fortran, computationally-intensive benchmark codes that represent the scientific workload at the Los Alamos National Laboratory. On all but three of our benchmark codes, the 40-ns RISC System was able to perform as well as a single Convex C-240 processor, a vector processor that also has a 40-ns clock cycle, and on these same codes, it performed as well as the FPS-500, a vector processor with a 30-ns clock cycle. 17 refs., 2 figs., 6 tabs.

  16. Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets.

    PubMed

    Blanco, Luca; Mead, Jennifer A; Bessant, Conrad

    2009-04-01

    Decoy database searches are used to filter out false positive protein identifications derived from search engines, but there is no consensus about which decoy is "the best". We evaluate nine different decoy designs using public data sets from samples of known composition. Statistically significant performance differences were found, but no single decoy stood out among the best performers. Ultimately, we recommend peptide level reverse decoys searched independently from the target. PMID:19714810

  17. The Basis Code Development System

    Energy Science and Technology Software Center (ESTSC)

    1994-03-15

    BASIS9.4 is a system for developing interactive computer programs in Fortran, with some support for C and C++ as well. Using BASIS9.4 you can create a program that has a sophisticated programming language as its user interface so that the user can set, calculate with, and plot, all the major variables in the program. The program author writes only the scientific part of the program; BASIS9.4 supplies an environment in which to exercise that scientificmore » programming which includes an interactive language, an interpreter, graphics, terminal logs, error recovery, macros, saving and retrieving variables, formatted I/O, and online documentation.« less

  18. Optimization Method to Branch and Bound Large SBO State Spaces Under Dynamic Probabilistic Risk Assessment via use of LENDIT Scales and S2R2 Sets

    SciTech Connect

    Joseph W. Nielsen; Akira Tokurio; Robert Hiromoto; Jivan Khatry

    2014-06-01

    Traditional Probabilistic Risk Assessment (PRA) methods have been developed and are quite effective in evaluating risk associated with complex systems, but lack the capability to evaluate complex dynamic systems. These time and energy scales associated with the transient may vary as a function of transition time to a different physical state. Dynamic PRA (DPRA) methods provide a more rigorous analysis of complex dynamic systems, while complete, results in issues associated with combinatorial explosion. In order to address the combinatorial complexity arising from the number of possible state configurations and discretization of transition times, a characteristic scaling metric (LENDIT – length, energy, number, distribution, information and time) is proposed as a means to describe systems uniformly and thus provide means to describe relational constraints expected in the dynamics of a complex (coupled) systems. Thus when LENDIT is used to characterize four sets – ‘state, system, resource and response’ (S2R2) – describing reactor operations (normal and off-normal), LENDIT and S2R2 in combination have the potential to ‘branch and bound’ the state space investigated by DPRA. In this paper we introduce the concept of LENDIT scales and S2R2 sets applied to a branch-and-bound algorithm and apply the methods to a station black out transient (SBO).

  19. Direct Effective Dose Calculations in Pediatric Fluoroscopy-Guided Abdominal Interventions with Rando-Alderson Phantoms – Optimization of Preset Parameter Settings

    PubMed Central

    Wildgruber, Moritz; Müller-Wille, René; Goessmann, Holger; Uller, Wibke; Wohlgemuth, Walter A.

    2016-01-01

    Objective The aim of the study was to calculate the effective dose during fluoroscopy-guided pediatric interventional procedures of the liver in a phantom model before and after adjustment of preset parameters. Methods Organ doses were measured in three anthropomorphic Rando-Alderson phantoms representing children at various age and body weight (newborn 3.5kg, toddler 10kg, child 19kg). Collimation was performed focusing on the upper abdomen representing mock interventional radiology procedures such as percutaneous transhepatic cholangiography and drainage placement (PTCD). Fluoroscopy and digital subtraction angiography (DSA) acquisitions were performed in a posterior-anterior geometry using a state of the art flat-panel detector. Effective dose was directly measured from multiple incorporated thermoluminescent dosimeters (TLDs) using two different parameter settings. Results Effective dose values for each pediatric phantom were below 0.1mSv per minute fluoroscopy, and below 1mSv for a 1 minute DSA acquisition with a frame rate of 2 f/s. Lowering the values for the detector entrance dose enabled a reduction of the applied effective dose from 12 to 27% for fluoroscopy and 22 to 63% for DSA acquisitions. Similarly, organ doses of radiosensitive organs could be reduced by over 50%, especially when close to the primary x-ray beam. Conclusion Modification of preset parameter settings enabled to decrease the effective dose for pediatric interventional procedures, as determined by effective dose calculations using dedicated pediatric Rando-Alderson phantoms. PMID:27556584

  20. An accurate and efficient computational protocol for obtaining the complete basis set limits of the binding energies of water clusters at the MP2 and CCSD(T) levels of theory: Application to (H₂O)m, m=2-6, 8, 11, 16 and 17

    SciTech Connect

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-06-21

    We report MP2 and CCSD(T) binding energies with basis sets up to pentuple zeta quality for the m = 2-6, 8 clusters. Or best CCSD(T)/CBS estimates are -4.99 kcal/mol (dimer), -15.77 kcal/mol (trimer), -27.39 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer) and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (dimer) and BSSE-corrected (dimerCPe) binding energies recovered with respect to the CBS limit falls into a narrow range for each basis set for all clusters and in addition this range was found to decrease upon increasing the basis set. Relatively accurate estimates (within < 0.5%) of the CBS limits can be obtained when using the “ 2/3, 1/3” (for the AVDZ set) or the “½ , ½” (for the AVTZ, AVQZ and AV5Z sets) mixing ratio between dimere and dimerCPe. Based on those findings we propose an accurate and efficient computational protocol that can be used to estimate accurate binding energies of clusters at the MP2 (for up to 100 molecules) and CCSD(T) (for up to 30 molecules) levels of theory. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multi program national laboratory operated for DOE by Battelle. This research also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. AC02-05CH11231.