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

Jibben, Zechariah Joel; Herrmann, Marcus

Here, we present a Runge-Kutta discontinuous Galerkin method for solving conservative reinitialization in the context of the conservative level set method. This represents an extension of the method recently proposed by Owkes and Desjardins [21], by solving the level set equations on the refined level set grid and projecting all spatially-dependent variables into the full basis used by the discontinuous Galerkin discretization. By doing so, we achieve the full k+1 order convergence rate in the L1 norm of the level set field predicted for RKDG methods given kth degree basis functions when the level set profile thickness is held constantmore » with grid refinement. Shape and volume errors for the 0.5-contour of the level set, on the other hand, are found to converge between first and second order. We show a variety of test results, including the method of manufactured solutions, reinitialization of a circle and sphere, Zalesak's disk, and deforming columns and spheres, all showing substantial improvements over the high-order finite difference traditional level set method studied for example by Herrmann. We also demonstrate the need for kth order accurate normal vectors, as lower order normals are found to degrade the convergence rate of the method.« less

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

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

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

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

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

DOE PAGES

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

2017-01-27

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

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

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

An arbitrary-order Runge–Kutta discontinuous Galerkin approach to reinitialization for banded conservative level sets

DOE PAGES

Jibben, Zechariah Joel; Herrmann, Marcus

2017-08-24

Here, we present a Runge-Kutta discontinuous Galerkin method for solving conservative reinitialization in the context of the conservative level set method. This represents an extension of the method recently proposed by Owkes and Desjardins [21], by solving the level set equations on the refined level set grid and projecting all spatially-dependent variables into the full basis used by the discontinuous Galerkin discretization. By doing so, we achieve the full k+1 order convergence rate in the L1 norm of the level set field predicted for RKDG methods given kth degree basis functions when the level set profile thickness is held constantmore » with grid refinement. Shape and volume errors for the 0.5-contour of the level set, on the other hand, are found to converge between first and second order. We show a variety of test results, including the method of manufactured solutions, reinitialization of a circle and sphere, Zalesak's disk, and deforming columns and spheres, all showing substantial improvements over the high-order finite difference traditional level set method studied for example by Herrmann. We also demonstrate the need for kth order accurate normal vectors, as lower order normals are found to degrade the convergence rate of the method.« less

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

Papajak, Ewa; Truhlar, Donald G.

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

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

PubMed

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

2017-06-07

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

On the origin independence of the Verdet tensor†

NASA Astrophysics Data System (ADS)

Caputo, M. C.; Coriani, S.; Pelloni, S.; Lazzeretti, P.

2013-07-01

The condition for invariance under a translation of the coordinate system of the Verdet tensor and the Verdet constant, calculated via quantum chemical methods using gaugeless basis sets, is expressed by a vanishing sum rule involving a third-rank polar tensor. The sum rule is, in principle, satisfied only in the ideal case of optimal variational electronic wavefunctions. In general, it is not fulfilled in non-variational calculations and variational calculations allowing for the algebraic approximation, but it can be satisfied for reasons of molecular symmetry. Group-theoretical procedures have been used to determine (i) the total number of non-vanishing components and (ii) the unique components of both the polar tensor appearing in the sum rule and the axial Verdet tensor, for a series of symmetry groups. Test calculations at the random-phase approximation level of accuracy for water, hydrogen peroxide and ammonia molecules, using basis sets of increasing quality, show a smooth convergence to zero of the sum rule. Verdet tensor components calculated for the same molecules converge to limit values, estimated via large basis sets of gaugeless Gaussian functions and London orbitals.

Linear-scaling explicitly correlated treatment of solids: periodic local MP2-F12 method.

PubMed

Usvyat, Denis

2013-11-21

Theory and implementation of the periodic local MP2-F12 method in the 3*A fixed-amplitude ansatz is presented. The method is formulated in the direct space, employing local representation for the occupied, virtual, and auxiliary orbitals in the form of Wannier functions (WFs), projected atomic orbitals (PAOs), and atom-centered Gaussian-type orbitals, respectively. Local approximations are introduced, restricting the list of the explicitly correlated pairs, as well as occupied, virtual, and auxiliary spaces in the strong orthogonality projector to the pair-specific domains on the basis of spatial proximity of respective orbitals. The 4-index two-electron integrals appearing in the formalism are approximated via the direct-space density fitting technique. In this procedure, the fitting orbital spaces are also restricted to local fit-domains surrounding the fitted densities. The formulation of the method and its implementation exploits the translational symmetry and the site-group symmetries of the WFs. Test calculations are performed on LiH crystal. The results show that the periodic LMP2-F12 method substantially accelerates basis set convergence of the total correlation energy, and even more so the correlation energy differences. The resulting energies are quite insensitive to the resolution-of-the-identity domain sizes and the quality of the auxiliary basis sets. The convergence with the orbital domain size is somewhat slower, but still acceptable. Moreover, inclusion of slightly more diffuse functions, than those usually used in the periodic calculations, improves the convergence of the LMP2-F12 correlation energy with respect to both the size of the PAO-domains and the quality of the orbital basis set. At the same time, the essentially diffuse atomic orbitals from standard molecular basis sets, commonly utilized in molecular MP2-F12 calculations, but problematic in the periodic context, are not necessary for LMP2-F12 treatment of crystals.

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

PubMed

Varandas, A J C

2009-02-01

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

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

PubMed

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

2018-05-14

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

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

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

Alternative formulation of explicitly correlated third-order Møller-Plesset perturbation theory

NASA Astrophysics Data System (ADS)

Ohnishi, Yu-ya; Ten-no, Seiichiro

2013-09-01

The second-order wave operator in the explicitly correlated wave function theory has been newly defined as an extension of the conventional s- and p-wave (SP) ansatz (also referred to as the FIXED amplitude ansatz) based on the linked-diagram theorem. The newly defined second-order wave operator has been applied to the calculation of the F12 correction to the third-order many-body perturbation (MP3) energy. In addition to this new wave operator, the F12 correction with the conventional first-order wave operator has been derived and calculated. Among three components of the MP3 correlation energy, the particle ladder contribution, which has shown the slowest convergence with respect to the basis set size, is fairly ameliorated by employing these F12 corrections. Both the newly defined and conventional formalisms of the F12 corrections exhibit a similar recovery of over 90% of the complete basis set limit of the particle ladder contribution of the MP3 correlation energy with a triple-zeta quality basis set for the neon atom, while the amount is about 75% without the F12 correction. The corrections to the ring term are small but the corrected energy has shown similar recovery as the particle ladder term. The hole ladder term has shown a rapid convergence even without the F12 corrections. Owing to these balanced recoveries, the deviation of the total MP3 correlation energy from the complete basis set limit has been calculated to be about 1 kcal/mol with the triple-zeta quality basis set, which is more than five times smaller than the error without the F12 correction.

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

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.

Improved techniques for outgoing wave variational principle calculations of converged state-to-state transition probabilities for chemical reactions

NASA Technical Reports Server (NTRS)

Mielke, Steven L.; Truhlar, Donald G.; Schwenke, David W.

1991-01-01

Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.

Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal?

PubMed

Hu, Lianrui; Chen, Kejuan; Chen, Hui

2017-10-10

Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE ‡ ) and reaction energy (ΔE R ) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE ‡ quite accurately, which is not true for the ΔE R calculations. Using highest-level CCSD(T) results of ΔE ‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.

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

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

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

Explicitly correlated coupled-cluster theory using cusp conditions. II. Treatment of connected triple excitations.

PubMed

Köhn, Andreas

2010-11-07

The coupled-cluster singles and doubles method augmented with single Slater-type correlation factors (CCSD-F12) determined by the cusp conditions (also denoted as SP ansatz) yields results close to the basis set limit with only small overhead compared to conventional CCSD. Quantitative calculations on many-electron systems, however, require to include the effect of connected triple excitations at least. In this contribution, the recently proposed [A. Köhn, J. Chem. Phys. 130, 131101 (2009)] extended SP ansatz and its application to the noniterative triples correction CCSD(T) is reviewed. The approach allows to include explicit correlation into connected triple excitations without introducing additional unknown parameters. The explicit expressions are presented and analyzed, and possible simplifications to arrive at a computationally efficient scheme are suggested. Numerical tests based on an implementation obtained by an automated approach are presented. Using a partial wave expansion for the neon atom, we can show that the proposed ansatz indeed leads to the expected (L(max)+1)(-7) convergence of the noniterative triples correction, where L(max) is the maximum angular momentum in the orbital expansion. Further results are reported for a test set of 29 molecules, employing Peterson's F12-optimized basis sets. We find that the customary approach of using the conventional noniterative triples correction on top of a CCSD-F12 calculation leads to significant basis set errors. This, however, is not always directly visible for total CCSD(T) energies due to fortuitous error compensation. The new approach offers a thoroughly explicitly correlated CCSD(T)-F12 method with improved basis set convergence of the triples contributions to both total and relative energies.

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

PubMed

Hill, J Grant

2013-09-30

Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit. Copyright © 2013 Wiley Periodicals, Inc.

Non-perturbative calculation of orbital and spin effects in molecules subject to non-uniform magnetic fields

NASA Astrophysics Data System (ADS)

Sen, Sangita; Tellgren, Erik I.

2018-05-01

External non-uniform magnetic fields acting on molecules induce non-collinear spin densities and spin-symmetry breaking. This necessitates a general two-component Pauli spinor representation. In this paper, we report the implementation of a general Hartree-Fock method, without any spin constraints, for non-perturbative calculations with finite non-uniform fields. London atomic orbitals are used to ensure faster basis convergence as well as invariance under constant gauge shifts of the magnetic vector potential. The implementation has been applied to investigate the joint orbital and spin response to a field gradient—quantified through the anapole moments—of a set of small molecules. The relative contributions of orbital and spin-Zeeman interaction terms have been studied both theoretically and computationally. Spin effects are stronger and show a general paramagnetic behavior for closed shell molecules while orbital effects can have either direction. Basis set convergence and size effects of anapole susceptibility tensors have been reported. The relation of the mixed anapole susceptibility tensor to chirality is also demonstrated.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2.

PubMed

Solomonik, Victor G; Smirnov, Alexander N; Navarkin, Ilya S

2016-04-14

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2

NASA Astrophysics Data System (ADS)

Solomonik, Victor G.; Smirnov, Alexander N.; Navarkin, Ilya S.

2016-04-01

The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes.

PubMed

Colombo, Marco; Diepeveen, Eveline T; Muschick, Moritz; Santos, M Emilia; Indermaur, Adrian; Boileau, Nicolas; Barluenga, Marta; Salzburger, Walter

2013-02-01

The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, for example in the Central American Midas Cichlid assemblage. Here, we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of molluscs and invertebrates. We then used comparative Illumina RNA sequencing of thick vs. normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages. © 2012 Blackwell Publishing Ltd.

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.

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

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

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

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

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

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

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

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

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

2015-09-14

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

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.

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

DOE PAGES

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

2014-11-04

Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number L max = (l,m) max, while scattering matrices, which determine spectral properties, are truncated at L tr = (l,m) tr where phase shifts δl>l tr are negligible. Historically, L max is set equal to L tr, which is correct for large enough L max but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for L maxmore » > L tr with δl>l tr 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 [R 3 process with rank N(l tr + 1) 2] and includes higher-L contributions via linear algebra [R 2 process with rank N(l max +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 L1 0 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus L max for a given L tr.« less

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Agriculture, health, and wealth convergence: bridging traditional food systems and modern agribusiness solutions.

PubMed

Dubé, Laurette; Webb, Patrick; Arora, Narendra K; Pingali, Prabhu

2014-12-01

The causes of many vexing challenges facing 21st-century society are at the nexus of systems involved in agriculture, health and wealth production, consumption, and distribution. Using food as a test bed, and on the basis of emerging roadmaps that set achievable objectives over a 1- to 3-year horizon, we introduce this special feature with convergence thinking and practice at its core. Specifically, we discuss academic papers structured around four themes: (1) evidence for a need for convergence and underlying mechanisms at the individual and societal levels; (2) strategy for mainstreaming convergence as a driver of business engagement and innovation; (3) convergence in policy and governance; (4) convergence in metrics and methods. Academic papers under each theme are accompanied by a roadmap paper reporting on the current status of concrete transformative convergence-building projects associated with that theme. We believe that the insights provided by these papers have the potential to enable all actors throughout society to singly and collectively work to build supply and demand for nutritious food, in both traditional and modern food systems, while placing the burdens of malnutrition and ill health on their core strategic agendas. © 2014 New York Academy of Sciences.

Comparison of localized basis and plane-wave basis for density-functional calculations of organic molecules on metals

NASA Astrophysics Data System (ADS)

Lee, Kyuho; Yu, Jaejun; Morikawa, Yoshitada

2007-01-01

Localized pseudoatomic orbitals (PAOs) are mainly optimized and tested for the strong chemical bonds within molecules and solids with their proven accuracy and efficiency, but are prone to significant basis set superposition error (BSSE) for weakly interacting systems. Here we test the accuracy of PAO basis in comparison with the BSSE-free plane-wave basis for the physisorption of pentacene molecule on Au (001) by calculating the binding energy, adsorption height, and energy level alignment. We show that both the large cutoff radius for localized PAOs and the counter-poise correction for BSSE are necessary to obtain well-converged physical properties. Thereby obtained results are as accurate as the plane-wave basis results. The comparison with experiment is given as well.

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

NASA Astrophysics Data System (ADS)

Romero, Angel H.

2017-10-01

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

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES.

PubMed

Rand, Alexander; Gillette, Andrew; Bajaj, Chandrajit

2014-01-01

We introduce a finite element construction for use on the class of convex, planar polygons and show it obtains a quadratic error convergence estimate. On a convex n -gon, our construction produces 2 n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, by transforming and combining a set of n ( n + 1)/2 basis functions known to obtain quadratic convergence. The technique broadens the scope of the so-called 'serendipity' elements, previously studied only for quadrilateral and regular hexahedral meshes, by employing the theory of generalized barycentric coordinates. Uniform a priori error estimates are established over the class of convex quadrilaterals with bounded aspect ratio as well as over the class of convex planar polygons satisfying additional shape regularity conditions to exclude large interior angles and short edges. Numerical evidence is provided on a trapezoidal quadrilateral mesh, previously not amenable to serendipity constructions, and applications to adaptive meshing are discussed.

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

PubMed

Götz, Andreas W; Kollmar, Christian; Hess, Bernd A

2005-09-01

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods. (c) 2005 Wiley Periodicals, Inc.

Performance of local orbital basis sets in the self-consistent Sternheimer method for dielectric matrices of extended systems

NASA Astrophysics Data System (ADS)

Hübener, H.; Pérez-Osorio, M. A.; Ordejón, P.; Giustino, F.

2012-09-01

We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81, 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices of silicon and diamond calculated using our method fall within 1% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional ζ's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2001-08-01

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

Quartic scaling MP2 for solids: A highly parallelized algorithm in the plane wave basis

NASA Astrophysics Data System (ADS)

Schäfer, Tobias; Ramberger, Benjamin; Kresse, Georg

2017-03-01

We present a low-complexity algorithm to calculate the correlation energy of periodic systems in second-order Møller-Plesset (MP2) perturbation theory. In contrast to previous approximation-free MP2 codes, our implementation possesses a quartic scaling, O ( N 4 ) , with respect to the system size N and offers an almost ideal parallelization efficiency. The general issue that the correlation energy converges slowly with the number of basis functions is eased by an internal basis set extrapolation. The key concept to reduce the scaling is to eliminate all summations over virtual orbitals which can be elegantly achieved in the Laplace transformed MP2 formulation using plane wave basis sets and fast Fourier transforms. Analogously, this approach could allow us to calculate second order screened exchange as well as particle-hole ladder diagrams with a similar low complexity. Hence, the presented method can be considered as a step towards systematically improved correlation energies.

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

PubMed

Mackie, Iain D; DiLabio, Gino A

2011-10-07

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

Simulation of the Flow Through Porous Layers Composed of Converging-Diverging Capillary Fissures or Tubes

NASA Astrophysics Data System (ADS)

Walicka, A.

2018-02-01

In this paper, a porous medium is modelled by a network of converging-diverging capillaries which may be considered as fissures or tubes. This model makes it necessary to consider flows through capillary fissures or tubes. Therefore an analytical method for deriving the relationships between pressure drops, volumetric flow rates and velocities for the following fluids: Newtonian, polar, power-law, pseudoplastic (DeHaven and Sisko types) and Shulmanian, was developed. Next, considerations on the models of pore network for Newtonian and non-Newtonian fluids were presented. The models, similar to the schemes of central finite differences may provide a good basis for transforming the governing equations of a flow through the porous medium into a set of linear or quasi-linear algebraic equations. It was shown that the some coefficients in these algebraic equations depend on the kind of the capillary convergence.

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES

PubMed Central

RAND, ALEXANDER; GILLETTE, ANDREW; BAJAJ, CHANDRAJIT

2013-01-01

We introduce a finite element construction for use on the class of convex, planar polygons and show it obtains a quadratic error convergence estimate. On a convex n-gon, our construction produces 2n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, by transforming and combining a set of n(n + 1)/2 basis functions known to obtain quadratic convergence. The technique broadens the scope of the so-called ‘serendipity’ elements, previously studied only for quadrilateral and regular hexahedral meshes, by employing the theory of generalized barycentric coordinates. Uniform a priori error estimates are established over the class of convex quadrilaterals with bounded aspect ratio as well as over the class of convex planar polygons satisfying additional shape regularity conditions to exclude large interior angles and short edges. Numerical evidence is provided on a trapezoidal quadrilateral mesh, previously not amenable to serendipity constructions, and applications to adaptive meshing are discussed. PMID:25301974

Accurate wavelengths for X-ray spectroscopy and the NIST hydrogen-like ion database

NASA Astrophysics Data System (ADS)

Kotochigova, S. A.; Kirby, K. P.; Brickhouse, N. S.; Mohr, P. J.; Tupitsyn, I. I.

2005-06-01

We have developed an ab initio multi-configuration Dirac-Fock-Sturm method for the precise calculation of X-ray emission spectra, including energies, transition wavelengths and transition probabilities. The calculations are based on non-orthogonal basis sets, generated by solving the Dirac-Fock and Dirac-Fock-Sturm equations. Inclusion of Sturm functions into the basis set provides an efficient description of correlation effects in highly charged ions and fast convergence of the configuration interaction procedure. A second part of our study is devoted to developing a theoretical procedure and creating an interactive database to generate energies and transition frequencies for hydrogen-like ions. This procedure is highly accurate and based on current knowledge of the relevant theory, which includes relativistic, quantum electrodynamic, recoil, and nuclear size effects.

Cotton-Mouton effect and shielding polarizabilities of ethylene: An MCSCF study

NASA Astrophysics Data System (ADS)

Coriani, Sonia; Rizzo, Antonio; Ruud, Kenneth; Helgaker, Trygve

1997-03-01

The static hypermagnetizabilities and nuclear shielding polarizabilities of the carbon and hydrogen atoms of ethylene have been computed using multiconfigurational linear-response theory and a finite-field method, in a mixed analytical-numerical approach. Extended sets of magnetic-field-dependent basis functions have been employed in large MCSCF calculations, involving active spaces giving rise to a few million configurations in the finite-field perturbed symmetry. The convergence of the observables with respect to the extension of the basis set as well as the effect of electron correlation have been investigated. Whereas for the shielding polarizabilities we can compare with other published SCF results, the ab initio estimates for the static hypermagnetizabilities and the observable to which they are related - the Cotton-Mouton constant, - are presented for the first time.

Quantification provides a conceptual basis for convergent evolution.

PubMed

Speed, Michael P; Arbuckle, Kevin

2017-05-01

While much of evolutionary biology attempts to explain the processes of diversification, there is an important place for the study of phenotypic similarity across life forms. When similar phenotypes evolve independently in different lineages this is referred to as convergent evolution. Although long recognised, evolutionary convergence is receiving a resurgence of interest. This is in part because new genomic data sets allow detailed and tractable analysis of the genetic underpinnings of convergent phenotypes, and in part because of renewed recognition that convergence may reflect limitations in the diversification of life. In this review we propose that although convergent evolution itself does not require a new evolutionary framework, none the less there is room to generate a more systematic approach which will enable evaluation of the importance of convergent phenotypes in limiting the diversity of life's forms. We therefore propose that quantification of the frequency and strength of convergence, rather than simply identifying cases of convergence, should be considered central to its systematic comprehension. We provide a non-technical review of existing methods that could be used to measure evolutionary convergence, bringing together a wide range of methods. We then argue that quantification also requires clear specification of the level at which the phenotype is being considered, and argue that the most constrained examples of convergence show similarity both in function and in several layers of underlying form. Finally, we argue that the most important and impressive examples of convergence are those that pertain, in form and function, across a wide diversity of selective contexts as these persist in the likely presence of different selection pressures within the environment. © 2016 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

The interacting correlated fragments model for weak interactions, basis set superposition error, and the helium dimer potential

NASA Astrophysics Data System (ADS)

Liu, B.; McLean, A. D.

1989-08-01

We report the LM-2 helium dimer interaction potential, from helium separations of 1.6 Å to dissociation, obtained by careful convergence studies with respect to configuration space, through a sequence of interacting correlated fragment (ICF) wave functions, and with respect to the primitive Slater-type basis used for orbital expansion. Parameters of the LM-2 potential are re=2.969 Å, rm=2.642 Å, and De=10.94 K, in near complete agreement with those of the best experimental potential of Aziz, McCourt, and Wong [Mol. Phys. 61, 1487 (1987)], which are re=2.963 Å, rm=2.637 Å, and De=10.95 K. The computationally estimated accuracy of each point on the potential is given; at re it is 0.03 K. Extrapolation procedures used to produce the LM-2 potential make use of the orbital basis inconsistency (OBI) and configuration base inconsistency (CBI) adjustments to separated fragment energies when computing the interaction energy. These components of basis set superposition error (BSSE) are given a full discussion.

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

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

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 L max = (l,m) max, while scattering matrices, which determine spectral properties, are truncated at L tr = (l,m) tr where phase shifts δl>l tr are negligible. Historically, L max is set equal to L tr, which is correct for large enough L max but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for L maxmore » > L tr with δl>l tr 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 [R 3 process with rank N(l tr + 1) 2] and includes higher-L contributions via linear algebra [R 2 process with rank N(l max +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 L1 0 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus L max for a given L tr.« less

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.

Density by moduli and Wijsman lacunary statistical convergence of sequences of sets.

PubMed

Bhardwaj, Vinod K; Dhawan, Shweta

2017-01-01

The main object of this paper is to introduce and study a new concept of f -Wijsman lacunary statistical convergence of sequences of sets, where f is an unbounded modulus. The definition of Wijsman lacunary strong convergence of sequences of sets is extended to a definition of Wijsman lacunary strong convergence with respect to a modulus for sequences of sets and it is shown that, under certain conditions on a modulus f , the concepts of Wijsman lacunary strong convergence with respect to a modulus f and f -Wijsman lacunary statistical convergence are equivalent on bounded sequences. We further characterize those θ for which [Formula: see text], where [Formula: see text] and [Formula: see text] denote the sets of all f -Wijsman lacunary statistically convergent sequences and f -Wijsman statistically convergent sequences, respectively.

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

DOE PAGES

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol; ...

2017-04-07

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

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

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

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

Sparse-grid, reduced-basis Bayesian inversion: Nonaffine-parametric nonlinear equations

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

Chen, Peng, E-mail: peng@ices.utexas.edu; Schwab, Christoph, E-mail: christoph.schwab@sam.math.ethz.ch

2016-07-01

We extend the reduced basis (RB) accelerated Bayesian inversion methods for affine-parametric, linear operator equations which are considered in [16,17] to non-affine, nonlinear parametric operator equations. We generalize the analysis of sparsity of parametric forward solution maps in [20] and of Bayesian inversion in [48,49] to the fully discrete setting, including Petrov–Galerkin high-fidelity (“HiFi”) discretization of the forward maps. We develop adaptive, stochastic collocation based reduction methods for the efficient computation of reduced bases on the parametric solution manifold. The nonaffinity and nonlinearity with respect to (w.r.t.) the distributed, uncertain parameters and the unknown solution is collocated; specifically, by themore » so-called Empirical Interpolation Method (EIM). For the corresponding Bayesian inversion problems, computational efficiency is enhanced in two ways: first, expectations w.r.t. the posterior are computed by adaptive quadratures with dimension-independent convergence rates proposed in [49]; the present work generalizes [49] to account for the impact of the PG discretization in the forward maps on the convergence rates of the Quantities of Interest (QoI for short). Second, we propose to perform the Bayesian estimation only w.r.t. a parsimonious, RB approximation of the posterior density. Based on the approximation results in [49], the infinite-dimensional parametric, deterministic forward map and operator admit N-term RB and EIM approximations which converge at rates which depend only on the sparsity of the parametric forward map. In several numerical experiments, the proposed algorithms exhibit dimension-independent convergence rates which equal, at least, the currently known rate estimates for N-term approximation. We propose to accelerate Bayesian estimation by first offline construction of reduced basis surrogates of the Bayesian posterior density. The parsimonious surrogates can then be employed for online data assimilation and for Bayesian estimation. They also open a perspective for optimal experimental design.« less

Influence of single particle orbital sets and configuration selection on multideterminant wavefunctions in quantum Monte Carlo

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

Clay, Raymond C.; Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550; Morales, Miguel A., E-mail: moralessilva2@llnl.gov

2015-06-21

Multideterminant wavefunctions, while having a long history in quantum chemistry, are increasingly being used in highly accurate quantum Monte Carlo calculations. Since the accuracy of QMC is ultimately limited by the quality of the trial wavefunction, multi-Slater determinants wavefunctions offer an attractive alternative to Slater-Jastrow and more sophisticated wavefunction ansatz for several reasons. They can be efficiently calculated, straightforwardly optimized, and systematically improved by increasing the number of included determinants. In spite of their potential, however, the convergence properties of multi-Slater determinant wavefunctions with respect to orbital set choice and excited determinant selection are poorly understood, which hinders the applicationmore » of these wavefunctions to large systems and solids. In this paper, by performing QMC calculations on the equilibrium and stretched carbon dimer, we find that convergence of the recovered correlation energy with respect to number of determinants can depend quite strongly on basis set and determinant selection methods, especially where there is strong correlation. We demonstrate that properly chosen orbital sets and determinant selection techniques from quantum chemistry methods can dramatically reduce the required number of determinants (and thus the computational cost) to reach a given accuracy, which we argue shows clear need for an automatic QMC-only method for selecting determinants and generating optimal orbital sets.« less

An analysis of value function learning with piecewise linear control

NASA Astrophysics Data System (ADS)

Tutsoy, Onder; Brown, Martin

2016-05-01

Reinforcement learning (RL) algorithms attempt to learn optimal control actions by iteratively estimating a long-term measure of system performance, the so-called value function. For example, RL algorithms have been applied to walking robots to examine the connection between robot motion and the brain, which is known as embodied cognition. In this paper, RL algorithms are analysed using an exemplar test problem. A closed form solution for the value function is calculated and this is represented in terms of a set of basis functions and parameters, which is used to investigate parameter convergence. The value function expression is shown to have a polynomial form where the polynomial terms depend on the plant's parameters and the value function's discount factor. It is shown that the temporal difference error introduces a null space for the differenced higher order basis associated with the effects of controller switching (saturated to linear control or terminating an experiment) apart from the time of the switch. This leads to slow convergence in the relevant subspace. It is also shown that badly conditioned learning problems can occur, and this is a function of the value function discount factor and the controller switching points. Finally, a comparison is performed between the residual gradient and TD(0) learning algorithms, and it is shown that the former has a faster rate of convergence for this test problem.

Theoretical investigation of gas-surface interactions

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.

1990-01-01

A Dirac-Hartree-Fock code was developed for polyatomic molecules. The program uses integrals over symmetry-adapted real spherical harmonic Gaussian basis functions generated by a modification of the MOLECULE integrals program. A single Gaussian function is used for the nuclear charge distribution, to ensure proper boundary conditions at the nuclei. The Gaussian primitive functions are chosen to satisfy the kinetic balance condition. However, contracted functions which do not necessarily satisfy this condition may be used. The Fock matrix is constructed in the scalar basis and transformed to a jj-coupled 2-spinor basis before diagonalization. The program was tested against numerical results for atoms with a Gaussian nucleus and diatomic molecules with point nuclei. The energies converge on the numerical values as the basis set size is increased. Full use of molecular symmetry (restricted to D sub 2h and subgroups) is yet to be implemented.

The Convergence of European Business Cycles 1980--2004

NASA Astrophysics Data System (ADS)

Ormerod, P.

2005-09-01

The degree of convergence of the business cycles of the economies of the European Union is a key policy issue. In particular, a substantial degree of convergence is needed if the European Central Bank is to be capable of setting a monetary policy which is appropriate to the stage of the cycle of the Euro zone economies. I consider the annual rates of real GDP growth on a quarterly basis in the main economies of the EU (France, Germany, Italy, UK, Spain, Belgium and the Netherlands) over the period 1980Q1--2004Q4. An important empirical question is the degree to which the correlations between these growth rates contain true information rather than noise. The technique of random matrix theory is able to answer this question, and has been applied successfully in the physics journals to financial markets data. I find that the correlations between the growth rates of most of the core EU economies contain substantial amounts of true information, and exhibit considerable stability over time. Even in the late 1970s and early 1980s, these economies moved together closely over the course of the business cycle. There was a slight loosening at the time of German re-unification, but the economies have moved back into close synchronisation. The same result holds when Spain is added to the group of core EU countries. However, the problems of the German economy which arose from the early 1990s onwards has led to Germany becoming increasingly less synchronised with the rest of the core EU. Further, the results obtained with a data set of the converged EU core plus the UK show no real convergence between the UK and this group of economies.

H{sub 2} dissociation due to collisions with He

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

Ohlinger, L.; Forrey, R. C.; Lee, Teck-Ghee

2007-10-15

Cross sections for dissociation of H{sub 2} due to collision with He are calculated for highly excited rovibrational states using the quantum-mechanical coupled-states approximation. An L{sup 2} Sturmian basis set with multiple length scales is used to provide a discrete representation of the H{sub 2} continuum which includes orbiting resonances and a nonresonant background. Cross sections are given over a range of translational energies for both resonant and nonresonant dissociation together with the most important bound-state transitions for many different initial states. The results demonstrate that it is possible to compute converged quantum-mechanical cross sections using basis sets of modestmore » size. It is found that collision-induced dissociation competes with inelastic scattering as a depopulation mechanism for the highly excited states. The relevance of the present calculations to astrophysical models is discussed.« less

Calculation of smooth potential energy surfaces using local electron correlation methods

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

Mata, Ricardo A.; Werner, Hans-Joachim

2006-11-14

The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl{sup -} with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barriermore » heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.« less

First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.

PubMed

Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio

2015-07-15

The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

Genomic basis for the convergent evolution of electric organs

PubMed Central

Gallant, Jason R.; Traeger, Lindsay L.; Volkening, Jeremy D.; Moffett, Howell; Chen, Po-Hao; Novina, Carl D.; Phillips, George N.; Anand, Rene; Wells, Gregg B.; Pinch, Matthew; Güth, Robert; Unguez, Graciela A.; Albert, James S.; Zakon, Harold H.; Samanta, Manoj P.; Sussman, Michael R.

2017-01-01

Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins of these organs by assembling the genome of the electric eel (Electrophorus electricus) and sequencing electric organ and skeletal muscle transcriptomes from three lineages that have independently evolved electric organs. Our results indicate that, despite millions of years of evolution and large differences in the morphology of electric organ cells, independent lineages have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs. PMID:24970089

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

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

Peterson, Kirk A., E-mail: kipeters@wsu.edu

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. Bothmore » 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 value by ∼1 kcal/mol.« less

Training models of anatomic shape variability

PubMed Central

Merck, Derek; Tracton, Gregg; Saboo, Rohit; Levy, Joshua; Chaney, Edward; Pizer, Stephen; Joshi, Sarang

2008-01-01

Learning probability distributions of the shape of anatomic structures requires fitting shape representations to human expert segmentations from training sets of medical images. The quality of statistical segmentation and registration methods is directly related to the quality of this initial shape fitting, yet the subject is largely overlooked or described in an ad hoc way. This article presents a set of general principles to guide such training. Our novel method is to jointly estimate both the best geometric model for any given image and the shape distribution for the entire population of training images by iteratively relaxing purely geometric constraints in favor of the converging shape probabilities as the fitted objects converge to their target segmentations. The geometric constraints are carefully crafted both to obtain legal, nonself-interpenetrating shapes and to impose the model-to-model correspondences required for useful statistical analysis. The paper closes with example applications of the method to synthetic and real patient CT image sets, including same patient male pelvis and head and neck images, and cross patient kidney and brain images. Finally, we outline how this shape training serves as the basis for our approach to IGRT∕ART. PMID:18777919

Widespread neural oscillations in the delta band dissociate rule convergence from rule divergence during creative idea generation.

PubMed

Boot, Nathalie; Baas, Matthijs; Mühlfeld, Elisabeth; de Dreu, Carsten K W; van Gaal, Simon

2017-09-01

Critical to creative cognition and performance is both the generation of multiple alternative solutions in response to open-ended problems (divergent thinking) and a series of cognitive operations that converges on the correct or best possible answer (convergent thinking). Although the neural underpinnings of divergent and convergent thinking are still poorly understood, several electroencephalography (EEG) studies point to differences in alpha-band oscillations between these thinking modes. We reason that, because most previous studies employed typical block designs, these pioneering findings may mainly reflect the more sustained aspects of creative processes that extend over longer time periods, and that still much is unknown about the faster-acting neural mechanisms that dissociate divergent from convergent thinking during idea generation. To this end, we developed a new event-related paradigm, in which we measured participants' tendency to implicitly follow a rule set by examples, versus breaking that rule, during the generation of novel names for specific categories (e.g., pasta, planets). This approach allowed us to compare the oscillatory dynamics of rule convergent and rule divergent idea generation and at the same time enabled us to measure spontaneous switching between these thinking modes on a trial-to-trial basis. We found that, relative to more systematic, rule convergent thinking, rule divergent thinking was associated with widespread decreases in delta band activity. Therefore, this study contributes to advancing our understanding of the neural underpinnings of creativity by addressing some methodological challenges that neuroscientific creativity research faces. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estimation of Δ R/ R values by benchmark study of the Mössbauer Isomer shifts for Ru, Os complexes using relativistic DFT calculations

NASA Astrophysics Data System (ADS)

Kaneko, Masashi; Yasuhara, Hiroki; Miyashita, Sunao; Nakashima, Satoru

2017-11-01

The present study applies all-electron relativistic DFT calculation with Douglas-Kroll-Hess (DKH) Hamiltonian to each ten sets of Ru and Os compounds. We perform the benchmark investigation of three density functionals (BP86, B3LYP and B2PLYP) using segmented all-electron relativistically contracted (SARC) basis set with the experimental Mössbauer isomer shifts for 99Ru and 189Os nuclides. Geometry optimizations at BP86 theory of level locate the structure in a local minimum. We calculate the contact density to the wavefunction obtained by a single point calculation. All functionals show the good linear correlation with experimental isomer shifts for both 99Ru and 189Os. Especially, B3LYP functional gives a stronger correlation compared to BP86 and B2PLYP functionals. The comparison of contact density between SARC and well-tempered basis set (WTBS) indicated that the numerical convergence of contact density cannot be obtained, but the reproducibility is less sensitive to the choice of basis set. We also estimate the values of Δ R/ R, which is an important nuclear constant, for 99Ru and 189Os nuclides by using the benchmark results. The sign of the calculated Δ R/ R values is consistent with the predicted data for 99Ru and 189Os. We obtain computationally the Δ R/ R values of 99Ru and 189Os (36.2 keV) as 2.35×10-4 and -0.20×10-4, respectively, at B3LYP level for SARC basis set.

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

PubMed

Lemke, Kono H

2017-06-21

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

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

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

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

Ultrasound beam transmission using a discretely orthogonal Gaussian aperture basis

NASA Astrophysics Data System (ADS)

Roberts, R. A.

2018-04-01

Work is reported on development of a computational model for ultrasound beam transmission at an arbitrary geometry transmission interface for generally anisotropic materials. The work addresses problems encountered when the fundamental assumptions of ray theory do not hold, thereby introducing errors into ray-theory-based transmission models. Specifically, problems occur when the asymptotic integral analysis underlying ray theory encounters multiple stationary phase points in close proximity, due to focusing caused by concavity on either the entry surface or a material slowness surface. The approach presented here projects integrands over both the transducer aperture and the entry surface beam footprint onto a Gaussian-derived basis set, thereby distributing the integral over a summation of second-order phase integrals which are amenable to single stationary phase point analysis. Significantly, convergence is assured provided a sufficiently fine distribution of basis functions is used.

Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.; Knizia, Gerald; Werner, Hans-Joachim

2009-11-01

Accurate extrapolation to the complete basis set (CBS) limit of valence correlation energies calculated with explicitly correlated MP2-F12 and CCSD(T)-F12b methods have been investigated using a Schwenke-style approach for molecules containing both first and second row atoms. Extrapolation coefficients that are optimal for molecular systems containing first row elements differ from those optimized for second row analogs, hence values optimized for a combined set of first and second row systems are also presented. The new coefficients are shown to produce excellent results in both Schwenke-style and equivalent power-law-based two-point CBS extrapolations, with the MP2-F12/cc-pV(D,T)Z-F12 extrapolations producing an average error of just 0.17 mEh with a maximum error of 0.49 for a collection of 23 small molecules. The use of larger basis sets, i.e., cc-pV(T,Q)Z-F12 and aug-cc-pV(Q,5)Z, in extrapolations of the MP2-F12 correlation energy leads to average errors that are smaller than the degree of confidence in the reference data (˜0.1 mEh). The latter were obtained through use of very large basis sets in MP2-F12 calculations on small molecules containing both first and second row elements. CBS limits obtained from optimized coefficients for conventional MP2 are only comparable to the accuracy of the MP2-F12/cc-pV(D,T)Z-F12 extrapolation when the aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z basis sets are used. The CCSD(T)-F12b correlation energy is extrapolated as two distinct parts: CCSD-F12b and (T). While the CCSD-F12b extrapolations with smaller basis sets are statistically less accurate than those of the MP2-F12 correlation energies, this is presumably due to the slower basis set convergence of the CCSD-F12b method compared to MP2-F12. The use of larger basis sets in the CCSD-F12b extrapolations produces correlation energies with accuracies exceeding the confidence in the reference data (also obtained in large basis set F12 calculations). It is demonstrated that the use of the 3C(D) Ansatz is preferred for MP2-F12 CBS extrapolations. Optimal values of the geminal Slater exponent are presented for the diagonal, fixed amplitude Ansatz in MP2-F12 calculations, and these are also recommended for CCSD-F12b calculations.

Nonhuman genetics. Genomic basis for the convergent evolution of electric organs.

PubMed

Gallant, Jason R; Traeger, Lindsay L; Volkening, Jeremy D; Moffett, Howell; Chen, Po-Hao; Novina, Carl D; Phillips, George N; Anand, Rene; Wells, Gregg B; Pinch, Matthew; Güth, Robert; Unguez, Graciela A; Albert, James S; Zakon, Harold H; Samanta, Manoj P; Sussman, Michael R

2014-06-27

Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins of these organs by assembling the genome of the electric eel (Electrophorus electricus) and sequencing electric organ and skeletal muscle transcriptomes from three lineages that have independently evolved electric organs. Our results indicate that, despite millions of years of evolution and large differences in the morphology of electric organ cells, independent lineages have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs. Copyright © 2014, American Association for the Advancement of Science.

The fractal geometry of Hartree-Fock

NASA Astrophysics Data System (ADS)

Theel, Friethjof; Karamatskou, Antonia; Santra, Robin

2017-12-01

The Hartree-Fock method is an important approximation for the ground-state electronic wave function of atoms and molecules so that its usage is widespread in computational chemistry and physics. The Hartree-Fock method is an iterative procedure in which the electronic wave functions of the occupied orbitals are determined. The set of functions found in one step builds the basis for the next iteration step. In this work, we interpret the Hartree-Fock method as a dynamical system since dynamical systems are iterations where iteration steps represent the time development of the system, as encountered in the theory of fractals. The focus is put on the convergence behavior of the dynamical system as a function of a suitable control parameter. In our case, a complex parameter λ controls the strength of the electron-electron interaction. An investigation of the convergence behavior depending on the parameter λ is performed for helium, neon, and argon. We observe fractal structures in the complex λ-plane, which resemble the well-known Mandelbrot set, determine their fractal dimension, and find that with increasing nuclear charge, the fragmentation increases as well.

Relativistic theory of nuclear spin-rotation tensor with kinetically balanced rotational London orbitals

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

Xiao, Yunlong; Zhang, Yong; Liu, Wenjian, E-mail: liuwjbdf@gmail.com

2014-10-28

Both kinetically balanced (KB) and kinetically unbalanced (KU) rotational London orbitals (RLO) are proposed to resolve the slow basis set convergence in relativistic calculations of nuclear spin-rotation (NSR) coupling tensors of molecules containing heavy elements [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. While they perform rather similarly, the KB-RLO Ansatz is clearly preferred as it ensures the correct nonrelativistic limit even with a finite basis. Moreover, it gives rise to the same “direct relativistic mapping” between nuclear magnetic resonance shielding and NSR coupling tensors as that without using the London orbitals [Y. Xiao, Y. Zhang, andmore » W. Liu, J. Chem. Theory Comput. 10, 600 (2014)].« less

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

PubMed

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

2014-04-08

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

Analysis of sea ice dynamics

NASA Technical Reports Server (NTRS)

Zwally, J.

1988-01-01

The ongoing work has established the basis for using multiyear sea ice concentrations from SMMR passive microwave for studies of largescale advection and convergence/divergence of the Arctic sea ice pack. Comparisons were made with numerical model simulations and buoy data showing qualitative agreement on daily to interannual time scales. Analysis of the 7-year SMMR data set shows significant interannual variations in the total area of multiyear ice. The scientific objective is to investigate the dynamics, mass balance, and interannual variability of the Arctic sea ice pack. The research emphasizes the direct application of sea ice parameters derived from passive microwave data (SMMR and SSMI) and collaborative studies using a sea ice dynamics model. The possible causes of observed interannual variations in the multiyear ice area are being examined. The relative effects of variations in the large scale advection and convergence/divergence within the ice pack on a regional and seasonal basis are investigated. The effects of anomolous atmospheric forcings are being examined, including the long-lived effects of synoptic events and monthly variations in the mean geostrophic winds. Estimates to be made will include the amount of new ice production within the ice pack during winter and the amount of ice exported from the pack.

A combined semiempirical-DFT study of oligomers within the finite-chain approximation, evolution from oligomers to polymers.

PubMed

Derosa, Pedro A

2009-06-01

A computationally cheap approach combining time-independent density functional theory (TIDFT) and semiempirical methods with an appropriate extrapolation procedure is proposed to accurately estimate geometrical and electronic properties of conjugated polymers using just a small set of oligomers. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap (HLG) obtained at a TIDFT level (B3PW91) for two polymers, trans-polyacetylene--the simplest conjugated polymer, and a much larger poly(2-methoxy-5-(2,9-ethyl-hexyloxy)-1,4-phenylenevinylene (MEH-PPV) polymer converge to virtually the same asymptotic value than the excitation energy obtained with time-dependent DFT (TDDFT) calculations using the same functional. For TIDFT geometries, the HLG is found to converge to a value within the experimentally accepted range for the band gap of these polymers, when an exponential extrapolation is used; however if semiempirical geometries are used, a linear fit of the HLG versus 1/n is found to produce the best results. Geometrical parameters are observed to reach a saturation value in good agreement with experimental information, within the length of oligomers calculated here and no extrapolation was considered necessary. Finally, the performance of three different semiempirical methods (AM1, PM3, and MNDO) and for the TIDFT calculations, the performance of 7 different full electron basis sets (6-311+G**, 6-31+ +G**, 6-311+ +G**, 6-31+G**, 6-31G**, 6-31+G*, and 6-31G) is compared and it is determined that the choice of semiempirical method or the basis set does not significantly affect the results. 2008 Wiley Periodicals, Inc.

Illuminating the conceptual structure of the space of moral violations with searchlight representational similarity analysis.

PubMed

Wasserman, E A; Chakroff, A; Saxe, R; Young, L

2017-10-01

Characterizing how representations of moral violations are organized, cognitively and neurally, is central to understanding how people conceive and judge them. Past work has identified brain regions that represent morally relevant features and distinguish moral domains, but has not yet advanced a broader account of where and on what basis neural representations of moral violations are organized. With searchlight representational similarity analysis, we investigate where category membership drives similarity in neural patterns during moral judgment of violations from two key moral domains: Harm and Purity. Representations converge across domains in a network of regions resembling the mentalizing network. However, Harm and Purity violation representations respectively converge in different regions: precuneus (PC) and left inferior frontal gyrus (LIFG). Examining substructure within moral domains, Harm violations converge in PC regardless of subdomain (physical harms, psychological harms), while Purity subdomains (pathogen-related violations, sex-related violations) converge in distinct sets of regions - mirroring a dissociation observed in principal-component analysis of behavioral data. Further, we find initial evidence for representation of morally relevant features within these two domain-encoding regions. The present analyses offer a case study for understanding how organization within the complex conceptual space of moral violations is reflected in the organization of neural patterns across the cortex. Copyright © 2017 Elsevier Inc. All rights reserved.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Independent Molecular Basis of Convergent Highland Adaptation in Maize

PubMed Central

Takuno, Shohei; Ralph, Peter; Swarts, Kelly; Elshire, Rob J.; Glaubitz, Jeffrey C.; Buckler, Edward S.; Hufford, Matthew B.; Ross-Ibarra, Jeffrey

2015-01-01

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize. PMID:26078279

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

PubMed

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

2018-03-01

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

Critical Nuclear Charge for Two-electron Atoms

NASA Astrophysics Data System (ADS)

Estienne, C. S.; Drake, G. W. F.

2014-05-01

There has been a recent revival of interest in the critical nuclear charge Zc that is just sufficient to bind a nucleus of charge Z and two electrons in the 1s21 S ground state. It is conjectured that the inverse of critical charge is related to the radius of convergence 1 /Z* for a 1 / Z expansion of the energy of the form E (Z) =Z2 (E0 +E1 / Z +E2 /Z2 + ⋯) . We have performed high precision variational calculations in Hylleraas coordinates, using the double basis set method, for values of Z very close to Zc, with basis sets containing up to 2809 terms (Ω = 24). Our preliminary result is Zc = 0 . 911 028 224 077 260 (15) , corresponding to 1 /Zc = 1 . 097 660 833 738 555 (18) . Well-defined eigenvalues continue to appear for Z

Complex multireference configuration interaction calculations for the K-vacancy Auger states of N{sup q+} (q = 2-5) ions

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

Peng, Yi-Geng; Data Center for High Energy Density Physics, Institute of Applied Physics and Computational Mathematics, P.O. Box 8009, Beijing 100088; Wu, Yong, E-mail: wu-yong@iapcm.ac.cn

2016-02-07

K-vacancy Auger states of N{sup q+} (q = 2-5) ions are studied by using the complex multireference single- and double-excitation configuration interaction (CMRD-CI) method. The calculated resonance parameters are in good agreement with the available experimental and theoretical data. It shows that the resonance positions and widths converge quickly with the increase of the atomic basis sets in the CMRD-CI calculations; the standard atomic basis set can be employed to describe the atomic K-vacancy Auger states well. The strong correlations between the valence and core electrons play important roles in accurately determining those resonance parameters, Rydberg electrons contribute negligibly inmore » the calculations. Note that it is the first time that the complex scaling method has been successfully applied for the B-like nitrogen. CMRD-CI is readily extended to treat the resonance states of molecules in the near future.« less

On the error in the nucleus-centered multipolar expansion of molecular electron density and its topology: A direct-space computational study.

PubMed

Michael, J Robert; Koritsanszky, Tibor

2017-05-28

The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical harmonics at each center. The partial sums of this exact one-center expansion are compared with the corresponding Hansen-Coppens pseudoatom (HC-PA) formalism [Hansen, N. K. and Coppens, P., "Testing aspherical atom refinements on small-molecule data sets," Acta Crystallogr., Sect. A 34, 909-921 (1978)] commonly utilized in experimental electron density studies. It is found that the latter model, due to its inadequate radial part, lacks pointwise convergence and fails to reproduce the local topology of the target QC-ED even at a high-order expansion. The significance of the quantitative agreement often found between HC-PA-based (quadrupolar-level) experimental and extended-basis QC-EDs can thus be challenged.

On the error in the nucleus-centered multipolar expansion of molecular electron density and its topology: A direct-space computational study

NASA Astrophysics Data System (ADS)

Michael, J. Robert; Koritsanszky, Tibor

2017-05-01

The convergence of nucleus-centered multipolar expansion of the quantum-chemical electron density (QC-ED), gradient, and Laplacian is investigated in terms of numerical radial functions derived by projecting stockholder atoms onto real spherical harmonics at each center. The partial sums of this exact one-center expansion are compared with the corresponding Hansen-Coppens pseudoatom (HC-PA) formalism [Hansen, N. K. and Coppens, P., "Testing aspherical atom refinements on small-molecule data sets," Acta Crystallogr., Sect. A 34, 909-921 (1978)] commonly utilized in experimental electron density studies. It is found that the latter model, due to its inadequate radial part, lacks pointwise convergence and fails to reproduce the local topology of the target QC-ED even at a high-order expansion. The significance of the quantitative agreement often found between HC-PA-based (quadrupolar-level) experimental and extended-basis QC-EDs can thus be challenged.

Correlation consistent basis sets for lanthanides: The atoms La–Lu

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

Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

Convergence of the Light-Front Coupled-Cluster Method in Scalar Yukawa Theory

NASA Astrophysics Data System (ADS)

Usselman, Austin

We use Fock-state expansions and the Light-Front Coupled-Cluster (LFCC) method to study mass eigenvalue problems in quantum field theory. Specifically, we study convergence of the method in scalar Yukawa theory. In this theory, a single charged particle is surrounded by a cloud of neutral particles. The charged particle can create or annihilate neutral particles, causing the n-particle state to depend on the n + 1 and n - 1-particle state. Fock state expansion leads to an infinite set of coupled equations where truncation is required. The wave functions for the particle states are expanded in a basis of symmetric polynomials and a generalized eigenvalue problem is solved for the mass eigenvalue. The mass eigenvalue problem is solved for multiple values for the coupling strength while the number of particle states and polynomial basis order are increased. Convergence of the mass eigenvalue solutions is then obtained. Three mass ratios between the charged particle and neutral particles were studied. This includes a massive charged particle, equal masses and massive neutral particles. Relative probability between states can also be explored for more detailed understanding of the process of convergence with respect to the number of Fock sectors. The reliance on higher order particle states depended on how large the mass of the charge particle was. The higher the mass of the charged particle, the more the system depended on higher order particle states. The LFCC method solves this same mass eigenvalue problem using an exponential operator. This exponential operator can then be truncated instead to form a finite system of equations that can be solved using a built in system solver provided in most computational environments, such as MatLab and Mathematica. First approximation in the LFCC method allows for only one particle to be created by the new operator and proved to be not powerful enough to match the Fock state expansion. The second order approximation allowed one and two particles to be created by the new operator and converged to the Fock state expansion results. This showed the LFCC method to be a reliable replacement method for solving quantum field theory problems.

A combined representation method for use in band structure calculations. 1: Method

NASA Technical Reports Server (NTRS)

Friedli, C.; Ashcroft, N. W.

1975-01-01

A representation was described whose basis levels combine the important physical aspects of a finite set of plane waves with those of a set of Bloch tight-binding levels. The chosen combination has a particularly simple dependence on the wave vector within the Brillouin Zone, and its use in reducing the standard one-electron band structure problem to the usual secular equation has the advantage that the lattice sums involved in the calculation of the matrix elements are actually independent of the wave vector. For systems with complicated crystal structures, for which the Korringa-Kohn-Rostoker (KKR), Augmented-Plane Wave (APW) and Orthogonalized-Plane Wave (OPW) methods are difficult to apply, the present method leads to results with satisfactory accuracy and convergence.

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

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

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

2016-06-07

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

Laws of Large Numbers and Langevin Approximations for Stochastic Neural Field Equations

PubMed Central

2013-01-01

In this study, we consider limit theorems for microscopic stochastic models of neural fields. We show that the Wilson–Cowan equation can be obtained as the limit in uniform convergence on compacts in probability for a sequence of microscopic models when the number of neuron populations distributed in space and the number of neurons per population tend to infinity. This result also allows to obtain limits for qualitatively different stochastic convergence concepts, e.g., convergence in the mean. Further, we present a central limit theorem for the martingale part of the microscopic models which, suitably re-scaled, converges to a centred Gaussian process with independent increments. These two results provide the basis for presenting the neural field Langevin equation, a stochastic differential equation taking values in a Hilbert space, which is the infinite-dimensional analogue of the chemical Langevin equation in the present setting. On a technical level, we apply recently developed law of large numbers and central limit theorems for piecewise deterministic processes taking values in Hilbert spaces to a master equation formulation of stochastic neuronal network models. These theorems are valid for processes taking values in Hilbert spaces, and by this are able to incorporate spatial structures of the underlying model. Mathematics Subject Classification (2000): 60F05, 60J25, 60J75, 92C20. PMID:23343328

Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs.

PubMed

Liu, Kuan-Yu; Herbert, John M

2017-10-28

Papers I and II in this series [R. M. Richard et al., J. Chem. Phys. 141, 014108 (2014); K. U. Lao et al., ibid. 144, 164105 (2016)] have attempted to shed light on precision and accuracy issues affecting the many-body expansion (MBE), which only manifest in larger systems and thus have received scant attention in the literature. Many-body counterpoise (CP) corrections are shown to accelerate convergence of the MBE, which otherwise suffers from a mismatch between how basis-set superposition error affects subsystem versus supersystem calculations. In water clusters ranging in size up to (H 2 O) 37 , four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of tetramers makes the use of cutoff schemes essential. To predict relative energies of (H 2 O) 20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the appropriate MBE benchmark, namely, a CP-corrected supersystem calculation at the same level of theory. Results using an energy-based cutoff scheme suggest that if reasonable approximations to the subsystem energies are available (based on classical multipoles, say), then the number of requisite subsystem calculations can be reduced even more dramatically than when distance-based thresholds are employed. The end result is several accurate four-body methods that do not require charge embedding, and which are stable in large basis sets such as aug-cc-pVTZ that have sometimes proven problematic for fragment-based quantum chemistry methods. Even with aggressive thresholding, however, the four-body approach at the self-consistent field level still requires roughly ten times more processors to outmatch the performance of the corresponding supersystem calculation, in test cases involving 1500-1800 basis functions.

Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs

NASA Astrophysics Data System (ADS)

Liu, Kuan-Yu; Herbert, John M.

2017-10-01

Papers I and II in this series [R. M. Richard et al., J. Chem. Phys. 141, 014108 (2014); K. U. Lao et al., ibid. 144, 164105 (2016)] have attempted to shed light on precision and accuracy issues affecting the many-body expansion (MBE), which only manifest in larger systems and thus have received scant attention in the literature. Many-body counterpoise (CP) corrections are shown to accelerate convergence of the MBE, which otherwise suffers from a mismatch between how basis-set superposition error affects subsystem versus supersystem calculations. In water clusters ranging in size up to (H2O)37, four-body terms prove necessary to achieve accurate results for both total interaction energies and relative isomer energies, but the sheer number of tetramers makes the use of cutoff schemes essential. To predict relative energies of (H2O)20 isomers, two approximations based on a lower level of theory are introduced and an ONIOM-type procedure is found to be very well converged with respect to the appropriate MBE benchmark, namely, a CP-corrected supersystem calculation at the same level of theory. Results using an energy-based cutoff scheme suggest that if reasonable approximations to the subsystem energies are available (based on classical multipoles, say), then the number of requisite subsystem calculations can be reduced even more dramatically than when distance-based thresholds are employed. The end result is several accurate four-body methods that do not require charge embedding, and which are stable in large basis sets such as aug-cc-pVTZ that have sometimes proven problematic for fragment-based quantum chemistry methods. Even with aggressive thresholding, however, the four-body approach at the self-consistent field level still requires roughly ten times more processors to outmatch the performance of the corresponding supersystem calculation, in test cases involving 1500-1800 basis functions.

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

NASA Astrophysics Data System (ADS)

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

2005-03-01

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

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

Resolution of identity approximation for the Coulomb term in molecular and periodic systems.

PubMed

Burow, Asbjörn M; Sierka, Marek; Mohamed, Fawzi

2009-12-07

A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 muhartree per atom, for both molecular and periodic systems.

Resolution of identity approximation for the Coulomb term in molecular and periodic systems

NASA Astrophysics Data System (ADS)

Burow, Asbjörn M.; Sierka, Marek; Mohamed, Fawzi

2009-12-01

A new formulation of resolution of identity approximation for the Coulomb term is presented, which uses atom-centered basis and auxiliary basis functions and treats molecular and periodic systems of any dimensionality on an equal footing. It relies on the decomposition of an auxiliary charge density into charged and chargeless components. Applying the Coulomb metric under periodic boundary conditions constrains the explicit form of the charged part. The chargeless component is determined variationally and converged Coulomb lattice sums needed for its determination are obtained using chargeless linear combinations of auxiliary basis functions. The lattice sums are partitioned in near- and far-field portions which are treated through an analytical integration scheme employing two- and three-center electron repulsion integrals and multipole expansions, respectively, operating exclusively in real space. Our preliminary implementation within the TURBOMOLE program package demonstrates consistent accuracy of the method across molecular and periodic systems. Using common auxiliary basis sets the errors of the approximation are small, in average about 20 μhartree per atom, for both molecular and periodic systems.

Converged G W quasiparticle energies for transition metal oxide perovskites

NASA Astrophysics Data System (ADS)

Ergönenc, Zeynep; Kim, Bongjae; Liu, Peitao; Kresse, Georg; Franchini, Cesare

2018-02-01

The ab initio calculation of quasiparticle (QP) energies is a technically and computationally challenging problem. In condensed matter physics, the most widely used approach to determine QP energies is the G W approximation. Although the G W method has been widely applied to many typical semiconductors and insulators, its application to more complex compounds such as transition metal oxide perovskites has been comparatively rare, and its proper use is not well established from a technical point of view. In this work, we have applied the single-shot G0W0 method to a representative set of transition metal oxide perovskites including 3 d (SrTiO3, LaScO3, SrMnO3, LaTiO3, LaVO3, LaCrO3, LaMnO3, and LaFeO3), 4 d (SrZrO3, SrTcO3, and Ca2RuO4 ), and 5 d (SrHfO3, KTaO3, and NaOsO3) compounds with different electronic configurations, magnetic orderings, structural characteristics, and band gaps ranging from 0.1 to 6.1 eV. We discuss the proper procedure to obtain well-converged QP energies and accurate band gaps within single-shot G0W0 by comparing the conventional approach based on an incremental variation of a specific set of parameters (number of bands, energy cutoff for the plane-wave expansion and number of k points) and the basis-set extrapolation scheme [J. Klimeš et al., Phys. Rev. B 90, 075125 (2014), 10.1103/PhysRevB.90.075125]. Although the conventional scheme is not supported by a formal proof of convergence, for most cases it delivers QP energies in reasonably good agreement with those obtained by the basis-set correction procedure and it is by construction more useful for calculating band structures. In addition, we have inspected the difference between the adoption of norm-conserving and ultrasoft potentials in G W calculations and found that the norm violation for the d shell can lead to less accurate results in particular for charge-transfer systems and late transition metals. A minimal statistical analysis indicates that the correlation of the G W data with the density functional theory gap is more robust than the correlation with the experimental gaps; moreover, we identify the static dielectric constant as alternative useful parameter for the approximation of G W gap in high-throughput automatic procedures. Finally, we compute the QP band structure and spectra within the random phase approximation and compare the results with available experimental data.

Many-body-theory study of lithium photoionization

NASA Technical Reports Server (NTRS)

Chang, T. N.; Poe, R. T.

1975-01-01

A detailed theoretical calculation is carried out for the photoionization of lithium at low energies within the framework of Brueckner-Goldstone perturbational approach. In this calculation extensive use is made of the recently developed multiple-basis-set technique. Through this technique all second-order perturbation terms, plus a number of important classes of terms to infinite order, have been taken into account. Analysis of the results enables one to resolve the discrepancies between two previous works on this subject. The detailed calculation also serves as a test on the convergence of the many-body perturbation-expansion approach.

OpenMC In Situ Source Convergence Detection

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

Aldrich, Garrett Allen; Dutta, Soumya; Woodring, Jonathan Lee

2016-05-07

We designed and implemented an in situ version of particle source convergence for the OpenMC particle transport simulator. OpenMC is a Monte Carlo based-particle simulator for neutron criticality calculations. For the transport simulation to be accurate, source particles must converge on a spatial distribution. Typically, convergence is obtained by iterating the simulation by a user-settable, fixed number of steps, and it is assumed that convergence is achieved. We instead implement a method to detect convergence, using the stochastic oscillator for identifying convergence of source particles based on their accumulated Shannon Entropy. Using our in situ convergence detection, we are ablemore » to detect and begin tallying results for the full simulation once the proper source distribution has been confirmed. Our method ensures that the simulation is not started too early, by a user setting too optimistic parameters, or too late, by setting too conservative a parameter.« less

Effective field theory in the harmonic oscillator basis

DOE PAGES

Binder, S.; Ekström, Jan A.; Hagen, Gaute; ...

2016-04-25

In this paper, we develop interactions from chiral effective field theory (EFT) that are tailored to the harmonic oscillator basis. As a consequence, ultraviolet convergence with respect to the model space is implemented by construction and infrared convergence can be achieved by enlarging the model space for the kinetic energy. In oscillator EFT, matrix elements of EFTs formulated for continuous momenta are evaluated at the discrete momenta that stem from the diagonalization of the kinetic energy in the finite oscillator space. By fitting to realistic phase shifts and deuteron data we construct an effective interaction from chiral EFT at next-to-leadingmore » order. Finally, many-body coupled-cluster calculations of nuclei up to 132Sn converge fast for the ground-state energies and radii in feasible model spaces.« less

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

Tang, Zhoufei; Ouyang, Xiaolong; Gong, Zhihao

An extended hierarchy equation of motion (HEOM) is proposed and applied to study the dynamics of the spin-boson model. In this approach, a complete set of orthonormal functions are used to expand an arbitrary bath correlation function. As a result, a complete dynamic basis set is constructed by including the system reduced density matrix and auxiliary fields composed of these expansion functions, where the extended HEOM is derived for the time derivative of each element. The reliability of the extended HEOM is demonstrated by comparison with the stochastic Hamiltonian approach under room-temperature classical ohmic and sub-ohmic noises and the multilayermore » multiconfiguration time-dependent Hartree theory under zero-temperature quantum ohmic noise. Upon increasing the order in the hierarchical expansion, the result obtained from the extended HOEM systematically converges to the numerically exact answer.« less

Determination of Phobos' rotational parameters by an inertial frame bundle block adjustment

NASA Astrophysics Data System (ADS)

Burmeister, Steffi; Willner, Konrad; Schmidt, Valentina; Oberst, Jürgen

2018-01-01

A functional model for a bundle block adjustment in the inertial reference frame was developed, implemented and tested. This approach enables the determination of rotation parameters of planetary bodies on the basis of photogrammetric observations. Tests with a self-consistent synthetic data set showed that the implementation converges reliably toward the expected values of the introduced unknown parameters of the adjustment, e.g., spin pole orientation, and that it can cope with typical observational errors in the data. We applied the model to a data set of Phobos using images from the Mars Express and the Viking mission. With Phobos being in a locked rotation, we computed a forced libration amplitude of 1.14^circ ± 0.03^circ together with a control point network of 685 points.

Convergence of neural networks for programming problems via a nonsmooth Lojasiewicz inequality.

PubMed

Forti, Mauro; Nistri, Paolo; Quincampoix, Marc

2006-11-01

This paper considers a class of neural networks (NNs) for solving linear programming (LP) problems, convex quadratic programming (QP) problems, and nonconvex QP problems where an indefinite quadratic objective function is subject to a set of affine constraints. The NNs are characterized by constraint neurons modeled by ideal diodes with vertical segments in their characteristic, which enable to implement an exact penalty method. A new method is exploited to address convergence of trajectories, which is based on a nonsmooth Lojasiewicz inequality for the generalized gradient vector field describing the NN dynamics. The method permits to prove that each forward trajectory of the NN has finite length, and as a consequence it converges toward a singleton. Furthermore, by means of a quantitative evaluation of the Lojasiewicz exponent at the equilibrium points, the following results on convergence rate of trajectories are established: (1) for nonconvex QP problems, each trajectory is either exponentially convergent, or convergent in finite time, toward a singleton belonging to the set of constrained critical points; (2) for convex QP problems, the same result as in (1) holds; moreover, the singleton belongs to the set of global minimizers; and (3) for LP problems, each trajectory converges in finite time to a singleton belonging to the set of global minimizers. These results, which improve previous results obtained via the Lyapunov approach, are true independently of the nature of the set of equilibrium points, and in particular they hold even when the NN possesses infinitely many nonisolated equilibrium points.

A theoretical framework for convergence and continuous dependence of estimates in inverse problems for distributed parameter systems

NASA Technical Reports Server (NTRS)

Banks, H. T.; Ito, K.

1988-01-01

Numerical techniques for parameter identification in distributed-parameter systems are developed analytically. A general convergence and stability framework (for continuous dependence on observations) is derived for first-order systems on the basis of (1) a weak formulation in terms of sesquilinear forms and (2) the resolvent convergence form of the Trotter-Kato approximation. The extension of this framework to second-order systems is considered.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

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

PubMed

Gaspari, Roberto; Rapallo, Arnaldo

2008-06-28

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

GW100: Benchmarking G0W0 for Molecular Systems.

PubMed

van Setten, Michiel J; Caruso, Fabio; Sharifzadeh, Sahar; Ren, Xinguo; Scheffler, Matthias; Liu, Fang; Lischner, Johannes; Lin, Lin; Deslippe, Jack R; Louie, Steven G; Yang, Chao; Weigend, Florian; Neaton, Jeffrey B; Evers, Ferdinand; Rinke, Patrick

2015-12-08

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW. The use of these three codes allows for a quantitative comparison of the type of basis set (plane wave or local orbital) and handling of unoccupied states, the treatment of core and valence electrons (all electron or pseudopotentials), the treatment of the frequency dependence of the self-energy (full frequency or more approximate plasmon-pole models), and the algorithm for solving the quasi-particle equation. Primary results include reference values for future benchmarks, best practices for convergence within a particular approach, and average error bars for the most common approximations.

Subduction Orogeny and the Late Cenozoic Evolution of the Mediterranean Arcs

NASA Astrophysics Data System (ADS)

Royden, Leigh; Faccenna, Claudio

2018-05-01

The Late Cenozoic tectonic evolution of the Mediterranean region, which is sandwiched between the converging African and European continents, is dominated by the process of subduction orogeny. Subduction orogeny occurs where localized subduction, driven by negative slab buoyancy, is more rapid than the convergence rate of the bounding plates; it is commonly developed in zones of early or incomplete continental collision. Subduction orogens can be distinguished from collisional orogens on the basis of driving mechanism, tectonic setting, and geologic expression. Three distinct Late Cenozoic subduction orogens can be identified in the Mediterranean region, making up the Western Mediterranean (Apennine, external Betic, Maghebride, Rif), Central Mediterranean (Carpathian), and Eastern Mediterranean (southern Dinaride, external Hellenide, external Tauride) Arcs. The Late Cenozoic evolution of these orogens, described in this article, is best understood in light of the processes that govern subduction orogeny and depends strongly on the buoyancy of the locally subducting lithosphere; it is thus strongly related to paleogeography. Because the slow (4–10 mm/yr) convergence rate between Africa and Eurasia has preserved the early collisional environment, and associated tectonism, for tens of millions of years, the Mediterranean region provides an excellent opportunity to elucidate the dynamic and kinematic processes of subduction orogeny and to better understand how these processes operate in other orogenic systems.

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr

NASA Astrophysics Data System (ADS)

Feng, Rulin; Peterson, Kirk A.

2017-08-01

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO2 is predicted to be the 0 g +5Σ state.

Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr.

PubMed

Feng, Rulin; Peterson, Kirk A

2017-08-28

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO 2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP 0 for PuO 2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO 2 is predicted to be the Σ0g+5 state.

The theory of maximally and minimally even sets, the one- dimensional antiferromagnetic Ising model, and the continued fraction compromise of musical scales

NASA Astrophysics Data System (ADS)

Douthett, Elwood (Jack) Moser, Jr.

1999-10-01

Cyclic configurations of white and black sites, together with convex (concave) functions used to weight path length, are investigated. The weights of the white set and black set are the sums of the weights of the paths connecting the white sites and black sites, respectively, and the weight between sets is the sum of the weights of the paths that connect sites opposite in color. It is shown that when the weights of all configurations of a fixed number of white and a fixed number of black sites are compared, minimum (maximum) weight of a white set, minimum (maximum) weight of the a black set, and maximum (minimum) weight between sets occur simultaneously. Such configurations are called maximally even configurations. Similarly, the configurations whose weights are the opposite extremes occur simultaneously and are called minimally even configurations. Algorithms that generate these configurations are constructed and applied to the one- dimensional antiferromagnetic spin-1/2 Ising model. Next the goodness of continued fractions as applied to musical intervals (frequency ratios and their base 2 logarithms) is explored. It is shown that, for the intermediate convergents between two consecutive principal convergents of an irrational number, the first half of the intermediate convergents are poorer approximations than the preceding principal convergent while the second half are better approximations; the goodness of a middle intermediate convergent can only be determined by calculation. These convergents are used to determine what equal-tempered systems have intervals that most closely approximate the musical fifth (pn/ qn = log2(3/2)). The goodness of exponentiated convergents ( 2pn/qn~3/2 ) is also investigated. It is shown that, with the exception of a middle convergent, the goodness of the exponential form agrees with that of its logarithmic Counterpart As in the case of the logarithmic form, the goodness of a middle intermediate convergent in the exponential form can only be determined by calculation. A Desirability Function is constructed that simultaneously measures how well multiple intervals fit in a given equal-tempered system. These measurements are made for octave (base 2) and tritave systems (base 3). Combinatorial properties important to music modulation are considered. These considerations lead These considerations lead to the construction of maximally even scales as partitions of an equal-tempered system.

Numerical study of the shape parameter dependence of the local radial point interpolation method in linear elasticity.

PubMed

Moussaoui, Ahmed; Bouziane, Touria

2016-01-01

The method LRPIM is a Meshless method with properties of simple implementation of the essential boundary conditions and less costly than the moving least squares (MLS) methods. This method is proposed to overcome the singularity associated to polynomial basis by using radial basis functions. In this paper, we will present a study of a 2D problem of an elastic homogenous rectangular plate by using the method LRPIM. Our numerical investigations will concern the influence of different shape parameters on the domain of convergence,accuracy and using the radial basis function of the thin plate spline. It also will presents a comparison between numerical results for different materials and the convergence domain by precising maximum and minimum values as a function of distribution nodes number. The analytical solution of the deflection confirms the numerical results. The essential points in the method are: •The LRPIM is derived from the local weak form of the equilibrium equations for solving a thin elastic plate.•The convergence of the LRPIM method depends on number of parameters derived from local weak form and sub-domains.•The effect of distributions nodes number by varying nature of material and the radial basis function (TPS).

The survey of preconditioners used for accelerating the rate of convergence in the Gauss-Seidel method

NASA Astrophysics Data System (ADS)

Niki, Hiroshi; Harada, Kyouji; Morimoto, Munenori; Sakakihara, Michio

2004-03-01

Several preconditioned iterative methods reported in the literature have been used for improving the convergence rate of the Gauss-Seidel method. In this article, on the basis of nonnegative matrix, comparisons between some splittings for such preconditioned matrices are derived. Simple numerical examples are also given.

Super-convergence of Discontinuous Galerkin Method Applied to the Navier-Stokes Equations

NASA Technical Reports Server (NTRS)

Atkins, Harold L.

2009-01-01

The practical benefits of the hyper-accuracy properties of the discontinuous Galerkin method are examined. In particular, we demonstrate that some flow attributes exhibit super-convergence even in the absence of any post-processing technique. Theoretical analysis suggest that flow features that are dominated by global propagation speeds and decay or growth rates should be super-convergent. Several discrete forms of the discontinuous Galerkin method are applied to the simulation of unsteady viscous flow over a two-dimensional cylinder. Convergence of the period of the naturally occurring oscillation is examined and shown to converge at 2p+1, where p is the polynomial degree of the discontinuous Galerkin basis. Comparisons are made between the different discretizations and with theoretical analysis.

Analytic model of a multi-electron atom

NASA Astrophysics Data System (ADS)

Skoromnik, O. D.; Feranchuk, I. D.; Leonau, A. U.; Keitel, C. H.

2017-12-01

A fully analytical approximation for the observable characteristics of many-electron atoms is developed via a complete and orthonormal hydrogen-like basis with a single-effective charge parameter for all electrons of a given atom. The basis completeness allows us to employ the secondary-quantized representation for the construction of regular perturbation theory, which includes in a natural way correlation effects, converges fast and enables an effective calculation of the subsequent corrections. The hydrogen-like basis set provides a possibility to perform all summations over intermediate states in closed form, including both the discrete and continuous spectra. This is achieved with the help of the decomposition of the multi-particle Green function in a convolution of single-electronic Coulomb Green functions. We demonstrate that our fully analytical zeroth-order approximation describes the whole spectrum of the system, provides accuracy, which is independent of the number of electrons and is important for applications where the Thomas-Fermi model is still utilized. In addition already in second-order perturbation theory our results become comparable with those via a multi-configuration Hartree-Fock approach.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Application and development of the Schwinger multichannel scattering theory and the partial differential equation theory of electron-molecule scattering

NASA Technical Reports Server (NTRS)

Weatherford, Charles A.

1993-01-01

One version of the multichannel theory for electron-target scattering based on the Schwinger variational principle, the SMC method, requires the introduction of a projection parameter. The role of the projection parameter a is investigated and it is shown that the principal-value operator in the SMC equation is Hermitian regardless of the value of a as long as it is real and nonzero. In a basis that is properly orthonormalizable, the matrix representation of this operator is also Hermitian. The use of such basis is consistent with the Schwinger variational principle because the Lippmann-Schwinger equation automatically builds in the correct boundary conditions. Otherwise, an auxiliary condition needs to be introduced, and Takatsuka and McKoy's original value of a is one of the three possible ways to achieve Hermiticity. In all cases but one, a can be uncoupled from the Hermiticity condition and becomes a free parameter. An equation for a based on the variational stability of the scattering amplitude is derived; its solution has an interesting property that the scattering amplitude from a converged SMC calculation is independent of the choice of a even though the SMC operator itself is a-dependent. This property provides a sensitive test of the convergence of the calculation. For a static-exchange calculation, the convergence requirement only depends on the completeness of the one-electron basis, but for a general multichannel case, the a-invariance in the scattering amplitude requires both the one-electron basis and the N plus 1-electron basis to be complete. The role of a in the SMC equation and the convergence property are illustrated using two examples: e-CO elastic scattering in the static-exchange approximation, and a two-state treatment of the e-H2 Chi(sup 1)Sigma(sub g)(+) yields b(sup 3)Sigma(sub u)(+) excitation.

Magnitude of finite-nucleus-size effects in relativistic density functional computations of indirect NMR nuclear spin-spin coupling constants.

PubMed

Autschbach, Jochen

2009-09-14

A spherical Gaussian nuclear charge distribution model has been implemented for spin-free (scalar) and two-component (spin-orbit) relativistic density functional calculations of indirect NMR nuclear spin-spin coupling (J-coupling) constants. The finite nuclear volume effects on the hyperfine integrals are quite pronounced and as a consequence they noticeably alter coupling constants involving heavy NMR nuclei such as W, Pt, Hg, Tl, and Pb. Typically, the isotropic J-couplings are reduced in magnitude by about 10 to 15 % for couplings between one of the heaviest NMR nuclei and a light atomic ligand, and even more so for couplings between two heavy atoms. For a subset of the systems studied, viz. the Hg atom, Hg(2) (2+), and Tl--X where X=Br, I, the basis set convergence of the hyperfine integrals and the coupling constants was monitored. For the Hg atom, numerical and basis set calculations of the electron density and the 1s and 6s orbital hyperfine integrals are directly compared. The coupling anisotropies of TlBr and TlI increase by about 2 % due to finite-nucleus effects.

Communication: Density functional theory embedding with the orthogonality constrained basis set expansion procedure

NASA Astrophysics Data System (ADS)

Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon

2017-06-01

Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.

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

NASA Astrophysics Data System (ADS)

Jentschura, Ulrich; Noble, Jonathan

2014-03-01

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

The convergence of double Fourier-Haar series over homothetic copies of sets

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

Oniani, G. G., E-mail: oniani@atsu.edu.ge

The paper is concerned with the convergence of double Fourier- Haar series with partial sums taken over homothetic copies of a given bounded set W⊂R{sub +}{sup 2} containing the intersection of some neighbourhood of the origin with R{sub +}{sup 2}. It is proved that for a set W from a fairly broad class (in particular, for convex W) there are two alternatives: either the Fourier-Haar series of an arbitrary function f∈L([0,1]{sup 2}) converges almost everywhere or Lln{sup +} L([0,1]{sup 2}) is the best integral class in which the double Fourier-Haar series converges almost everywhere. Furthermore, a characteristic property is obtained, whichmore » distinguishes which of the two alternatives is realized for a given W. Bibliography: 12 titles. (paper)« less

The convergence of European business cycles 1978-2000

NASA Astrophysics Data System (ADS)

Ormerod, Paul; Mounfield, Craig

2002-05-01

The degree of convergence of the business cycles of the economies of the European Union (EU) is a key policy issue. In particular, a substantial degree of convergence is needed if the European Central Bank is to be capable of setting a monetary policy which is appropriate to the stage of the cycle of the Euro zone economies. We consider the annual rates of real GDP growth on a quarterly basis in the large core economies of the EU (France, Germany and Italy, plus The Netherlands) over the period 1978Q1-2000Q3. An important empirical question is the degree to which the correlations between these growth rates contain true information rather than noise. The technique of random matrix theory is able to answer this question, and has been recently applied successfully in the physics journals to financial markets data. We find that the correlations between the growth rates of the core EU economies contain substantial amounts of true information, and exhibit considerable stability over time. Even in the late 1970s and early 1980s, these economies moved together closely over the course of the business cycle. There was a slight loosening at the time of German re-unification, but the economies are now, if anything, even more closely correlated. As a benchmark for comparison, we add a series to the EU core data set which by construction is uncorrelated with these business cycles. We then analyse the EU core plus Spain, a country which has attached great importance to greater integration with Europe. In the early part of the period examined, the results are very similar to those obtained with the data set of the EU core plus the random series. However, there is a clear trend in the results, which provide strong evidence to support the view that the Spanish economy has now become closely converged with the core EU economies in terms of its movements over the business cycle. In contrast, the results obtained with a data set of the EU core plus the UK show no such trend. In the late 1970s and early 1980s, the UK economy did exhibit some degree of correlation with those of the core EU. However, there is no clear evidence to suggest that the UK business cycle has moved more closely into line with that of the core EU economies over the 1978-2000 period.

Quasi-measures on the group G{sup m}, Dirichlet sets, and uniqueness problems for multiple Walsh series

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

Plotnikov, Mikhail G

2011-02-11

Multiple Walsh series (S) on the group G{sup m} are studied. It is proved that every at most countable set is a uniqueness set for series (S) under convergence over cubes. The recovery problem is solved for the coefficients of series (S) that converge outside countable sets or outside sets of Dirichlet type. A number of analogues of the de la Vallee Poussin theorem are established for series (S). Bibliography: 28 titles.

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Sliding Mode Fault Tolerant Control with Adaptive Diagnosis for Aircraft Engines

NASA Astrophysics Data System (ADS)

Xiao, Lingfei; Du, Yanbin; Hu, Jixiang; Jiang, Bin

2018-03-01

In this paper, a novel sliding mode fault tolerant control method is presented for aircraft engine systems with uncertainties and disturbances on the basis of adaptive diagnostic observer. By taking both sensors faults and actuators faults into account, the general model of aircraft engine control systems which is subjected to uncertainties and disturbances, is considered. Then, the corresponding augmented dynamic model is established in order to facilitate the fault diagnosis and fault tolerant controller design. Next, a suitable detection observer is designed to detect the faults effectively. Through creating an adaptive diagnostic observer and based on sliding mode strategy, the sliding mode fault tolerant controller is constructed. Robust stabilization is discussed and the closed-loop system can be stabilized robustly. It is also proven that the adaptive diagnostic observer output errors and the estimations of faults converge to a set exponentially, and the converge rate greater than some value which can be adjusted by choosing designable parameters properly. The simulation on a twin-shaft aircraft engine verifies the applicability of the proposed fault tolerant control method.

Intelligent Control of a Sensor-Actuator System via Kernelized Least-Squares Policy Iteration

PubMed Central

Liu, Bo; Chen, Sanfeng; Li, Shuai; Liang, Yongsheng

2012-01-01

In this paper a new framework, called Compressive Kernelized Reinforcement Learning (CKRL), for computing near-optimal policies in sequential decision making with uncertainty is proposed via incorporating the non-adaptive data-independent Random Projections and nonparametric Kernelized Least-squares Policy Iteration (KLSPI). Random Projections are a fast, non-adaptive dimensionality reduction framework in which high-dimensionality data is projected onto a random lower-dimension subspace via spherically random rotation and coordination sampling. KLSPI introduce kernel trick into the LSPI framework for Reinforcement Learning, often achieving faster convergence and providing automatic feature selection via various kernel sparsification approaches. In this approach, policies are computed in a low-dimensional subspace generated by projecting the high-dimensional features onto a set of random basis. We first show how Random Projections constitute an efficient sparsification technique and how our method often converges faster than regular LSPI, while at lower computational costs. Theoretical foundation underlying this approach is a fast approximation of Singular Value Decomposition (SVD). Finally, simulation results are exhibited on benchmark MDP domains, which confirm gains both in computation time and in performance in large feature spaces. PMID:22736969

Instituting interaction: normative transformations in human communicative practices.

PubMed

Elias, John Z; Tylén, Kristian

2014-01-01

Recent experiments in semiotics and linguistics demonstrate that groups tend to converge on a common set of signs or terms in response to presented problems, experiments which potentially bear on the emergence and establishment of institutional interactions. Taken together, these studies indicate a spectrum, ranging from the spontaneous convergence of communicative practices to their eventual conventionalization, a process which might be described as an implicit institutionalization of those practices. However, the emergence of such convergence and conventionalization does not in itself constitute an institution, in the strict sense of a social organization partly created and governed by explicit rules. A further step toward institutions proper may occur when others are instructed about a task. That is, given task situations which select for successful practices, instructions about such situations make explicit what was tacit practice, instructions which can then be followed correctly or incorrectly. This transition gives rise to the normative distinction between conditions of success versus conditions of correctness, a distinction which will be explored and complicated in the course of this paper. Using these experiments as a basis, then, the emergence of institutions will be characterized in evolutionary and normative terms, beginning with our adaptive responses to the selective pressures of certain situational environments, and continuing with our capacity to then shape, constrain, and institute those environments to further refine and streamline our problem-solving activity.

Instituting interaction: normative transformations in human communicative practices

PubMed Central

Elias, John Z.; Tylén, Kristian

2014-01-01

Recent experiments in semiotics and linguistics demonstrate that groups tend to converge on a common set of signs or terms in response to presented problems, experiments which potentially bear on the emergence and establishment of institutional interactions. Taken together, these studies indicate a spectrum, ranging from the spontaneous convergence of communicative practices to their eventual conventionalization, a process which might be described as an implicit institutionalization of those practices. However, the emergence of such convergence and conventionalization does not in itself constitute an institution, in the strict sense of a social organization partly created and governed by explicit rules. A further step toward institutions proper may occur when others are instructed about a task. That is, given task situations which select for successful practices, instructions about such situations make explicit what was tacit practice, instructions which can then be followed correctly or incorrectly. This transition gives rise to the normative distinction between conditions of success versus conditions of correctness, a distinction which will be explored and complicated in the course of this paper. Using these experiments as a basis, then, the emergence of institutions will be characterized in evolutionary and normative terms, beginning with our adaptive responses to the selective pressures of certain situational environments, and continuing with our capacity to then shape, constrain, and institute those environments to further refine and streamline our problem-solving activity. PMID:25295020

First-principles calculations of Ti and O NMR chemical shift tensors in ferroelectric perovskites

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

Complementary chemical shift calculations were carried out with embedded clusters, using quantum chemistry methods, and with periodic boundary conditions, using the GIPAW approach within the Quantum Espresso package. Compared to oxygen chemical shifts, δ̂ (O), cluster calculations for δ̂ (Ti) were found to be more sensitive to size effects, termination, and choice of gaussian-type atomic basis set, while GIPAW results were found to be more sensitive to the pseudopotential construction. The two approaches complemented each other in optimizing these factors. We show that the two approaches yield comparable chemical shifts for suitably converged simulations, and results are compared with available experimental measurements. Supported by ONR.

LQR Control of Thin Shell Dynamics: Formulation and Numerical Implementation

NASA Technical Reports Server (NTRS)

delRosario, R. C. H.; Smith, R. C.

1997-01-01

A PDE-based feedback control method for thin cylindrical shells with surface-mounted piezoceramic actuators is presented. Donnell-Mushtari equations modified to incorporate both passive and active piezoceramic patch contributions are used to model the system dynamics. The well-posedness of this model and the associated LQR problem with an unbounded input operator are established through analytic semigroup theory. The model is discretized using a Galerkin expansion with basis functions constructed from Fourier polynomials tensored with cubic splines, and convergence criteria for the associated approximate LQR problem are established. The effectiveness of the method for attenuating the coupled longitudinal, circumferential and transverse shell displacements is illustrated through a set of numerical examples.

No genome-wide protein sequence convergence for echolocation.

PubMed

Zou, Zhengting; Zhang, Jianzhi

2015-05-01

Toothed whales and two groups of bats independently acquired echolocation, the ability to locate and identify objects by reflected sound. Echolocation requires physiologically complex and coordinated vocal, auditory, and neural functions, but the molecular basis of the capacity for echolocation is not well understood. A recent study suggested that convergent amino acid substitutions widespread in the proteins of echolocators underlay the convergent origins of mammalian echolocation. Here, we show that genomic signatures of molecular convergence between echolocating lineages are generally no stronger than those between echolocating and comparable nonecholocating lineages. The same is true for the group of 29 hearing-related proteins claimed to be enriched with molecular convergence. Reexamining the previous selection test reveals several flaws and invalidates the asserted evidence for adaptive convergence. Together, these findings indicate that the reported genomic signatures of convergence largely reflect the background level of sequence convergence unrelated to the origins of echolocation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A histogram-free multicanonical Monte Carlo algorithm for the construction of analytical density of states

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

Eisenbach, Markus; Li, Ying Wai

We report a new multicanonical Monte Carlo (MC) algorithm to obtain the density of states (DOS) for physical systems with continuous state variables in statistical mechanics. Our algorithm is able to obtain an analytical form for the DOS expressed in a chosen basis set, instead of a numerical array of finite resolution as in previous variants of this class of MC methods such as the multicanonical (MUCA) sampling and Wang-Landau (WL) sampling. This is enabled by storing the visited states directly in a data set and avoiding the explicit collection of a histogram. This practice also has the advantage ofmore » avoiding undesirable artificial errors caused by the discretization and binning of continuous state variables. Our results show that this scheme is capable of obtaining converged results with a much reduced number of Monte Carlo steps, leading to a significant speedup over existing algorithms.« less

Static internal performance including thrust vectoring and reversing of two-dimensional convergent-divergent nozzles

NASA Technical Reports Server (NTRS)

Re, R. J.; Leavitt, L. D.

1984-01-01

The effects of geometric design parameters on two dimensional convergent-divergent nozzles were investigated at nozzle pressure ratios up to 12 in the static test facility. Forward flight (dry and afterburning power settings), vectored-thrust (afterburning power setting), and reverse-thrust (dry power setting) nozzles were investigated. The nozzles had thrust vector angles from 0 deg to 20.26 deg, throat aspect ratios of 3.696 to 7.612, throat radii from sharp to 2.738 cm, expansion ratios from 1.089 to 1.797, and various sidewall lengths. The results indicate that unvectored two dimensional convergent-divergent nozzles have static internal performance comparable to axisymmetric nozzles with similar expansion ratios.

A radial basis function Galerkin method for inhomogeneous nonlocal diffusion

DOE PAGES

Lehoucq, Richard B.; Rowe, Stephen T.

2016-02-01

We introduce a discretization for a nonlocal diffusion problem using a localized basis of radial basis functions. The stiffness matrix entries are assembled by a special quadrature routine unique to the localized basis. Combining the quadrature method with the localized basis produces a well-conditioned, sparse, symmetric positive definite stiffness matrix. We demonstrate that both the continuum and discrete problems are well-posed and present numerical results for the convergence behavior of the radial basis function method. As a result, we explore approximating the solution to anisotropic differential equations by solving anisotropic nonlocal integral equations using the radial basis function method.

Persistent accommodative spasm nine years after head trauma.

PubMed

Bohlmann, B J; France, T D

1987-09-01

Spasm of the near reflex is most often seen on a functional basis in young adults with underlying emotional problems. In particular, when convergence spasm is associated with miosis on attempted lateral gaze, a functional basis for the disorder should be suspected. Patients who experience spasm of the near reflex following trauma commonly follow a benign course with spontaneous resolution of their ocular complaints within 1-2 years. Accommodative spasm, manifested by pseudomyopia, or spasm of convergence, alone, or in combination with miosis, may be found as isolated signs of spasm of the near reflex. We report a patient who continues to demonstrate accommodative spasm 9 years after a motor vehicle accident.

Limitations of the method of complex basis functions

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

Baumel, R.T.; Crocker, M.C.; Nuttall, J.

1975-08-01

The method of complex basis functions proposed by Rescigno and Reinhardt is applied to the calculation of the amplitude in a model problem which can be treated analytically. It is found for an important class of potentials, including some of infinite range and also the square well, that the method does not provide a converging sequence of approximations. However, in some cases, approximations of relatively low order might be close to the correct result. The method is also applied to S-wave e-H elastic scattering above the ionization threshold, and spurious ''convergence'' to the wrong result is found. A procedure whichmore » might overcome the difficulties of the method is proposed.« less

Strong convergence of an extragradient-type algorithm for the multiple-sets split equality problem.

PubMed

Zhao, Ying; Shi, Luoyi

2017-01-01

This paper introduces a new extragradient-type method to solve the multiple-sets split equality problem (MSSEP). Under some suitable conditions, the strong convergence of an algorithm can be verified in the infinite-dimensional Hilbert spaces. Moreover, several numerical results are given to show the effectiveness of our algorithm.

Least-Squares Adaptive Control Using Chebyshev Orthogonal Polynomials

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Burken, John; Ishihara, Abraham

2011-01-01

This paper presents a new adaptive control approach using Chebyshev orthogonal polynomials as basis functions in a least-squares functional approximation. The use of orthogonal basis functions improves the function approximation significantly and enables better convergence of parameter estimates. Flight control simulations demonstrate the effectiveness of the proposed adaptive control approach.

Entrepreneurial Creativity as a Convergent Basis for Teaching Business Communication

ERIC Educational Resources Information Center

Grenci, Richard T.

2012-01-01

Of the "21st Century" business skills of communication, collaboration, creativity, and critical thinking, creativity arguably receives among the least explicit attention in traditional business core curricula. With that in mind, the context of entrepreneurial creativity is put forth as a basis for teaching business communication. By…

Synthesis, thermogravimetric, spectroscopic and theoretical characterization of copper(II) complex with 4-chloro-2-nitrobenzenosulfonamide

NASA Astrophysics Data System (ADS)

Camí, G.; Chacón Villalba, E.; Di Santi, Y.; Colinas, P.; Estiu, G.; Soria, D. B.

2011-05-01

4-Chloro-2-nitrobenzenesulfonamide (ClNbsa) was purified and characterized. A new copper(II) complex, [Cu(ClNbsa) 2(NH 3) 2], has been prepared using the sulfonamide as ligand. The thermal behavior of both, the ligand and the Cu(II) complex, was investigated by thermogravimetric analyses (TG) and differential thermal analysis (DT), and the electronic characteristics analyzed by UV-VIS, FTIR, Raman and 1H NMR spectroscopies. The experimental IR, Raman and UV-VIS spectra have been assigned on the basis of DFT calculations at the B3LYP level of theory using the standard (6-31 + G ∗∗) basis set. The geometries have been fully optimized in vacuum and in modeled dimethylsulfoxide (DMSO) solvent, using for the latter a continuum solvation model that reproduced the experimental conditions of the UV-VIS spectroscopy. The theoretical results converged to stable conformations for the free sulfonamide and for the complex, suggesting for the latter a distorted square planar geometry in both environments.

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

Patent Network Analysis and Quadratic Assignment Procedures to Identify the Convergence of Robot Technologies

PubMed Central

Lee, Woo Jin; Lee, Won Kyung

2016-01-01

Because of the remarkable developments in robotics in recent years, technological convergence has been active in this area. We focused on finding patterns of convergence within robot technology using network analysis of patents in both the USPTO and KIPO. To identify the variables that affect convergence, we used quadratic assignment procedures (QAP). From our analysis, we observed the patent network ecology related to convergence and found technologies that have great potential to converge with other robotics technologies. The results of our study are expected to contribute to setting up convergence based R&D policies for robotics, which can lead new innovation. PMID:27764196

Trait and State Variance in Oppositional Defiant Disorder Symptoms: A Multi-Source Investigation with Spanish Children

PubMed Central

Preszler, Jonathan; Burns, G. Leonard; Litson, Kaylee; Geiser, Christian; Servera, Mateu

2016-01-01

The objective was to determine and compare the trait and state components of oppositional defiant disorder (ODD) symptom reports across multiple informants. Mothers, fathers, primary teachers, and secondary teachers rated the occurrence of the ODD symptoms in 810 Spanish children (55% boys) on two occasions (end first and second grades). Single source latent state-trait (LST) analyses revealed that ODD symptom ratings from all four sources showed more trait (M = 63%) than state residual (M = 37%) variance. A multiple source LST analysis revealed substantial convergent validity of mothers’ and fathers’ trait variance components (M = 68%) and modest convergent validity of state residual variance components (M = 35%). In contrast, primary and secondary teachers showed low convergent validity relative to mothers for trait variance (Ms = 31%, 32%, respectively) and essentially zero convergent validity relative to mothers for state residual variance (Ms = 1%, 3%, respectively). Although ODD symptom ratings reflected slightly more trait- than state-like constructs within each of the four sources separately across occasions, strong convergent validity for the trait variance only occurred within settings (i.e., mothers with fathers; primary with secondary teachers) with the convergent validity of the trait and state residual variance components being low to non-existent across settings. These results suggest that ODD symptom reports are trait-like across time for individual sources with this trait variance, however, only having convergent validity within settings. Implications for assessment of ODD are discussed. PMID:27148784

Continuous quality improvement and medical informatics: the convergent synergy.

PubMed

Werth, G R; Connelly, D P

1992-01-01

Continuous quality improvement (CQI) and medical informatics specialists need to converge their efforts to create synergy for improving health care. Health care CQI needs medical informatics' expertise and technology to build the information systems needed to manage health care organizations according to quality improvement principles. Medical informatics needs CQI's philosophy and methods to build health care information systems that can evolve to meet the changing needs of clinicians and other stakeholders. This paper explores the philosophical basis for convergence of CQI and medical informatics efforts, and then examines a clinical computer workstation development project that is applying a combined approach.

Ab initio study of excited state electronic circular dichroism. Two prototype cases: methyl oxirane and R-(+)-1,1'-bi(2-naphthol).

PubMed

Rizzo, Antonio; Vahtras, Olav

2011-06-28

A computational approach to the calculation of excited state electronic circular dichroism (ESECD) spectra of chiral molecules is discussed. Frequency dependent quadratic response theory is employed to compute the rotatory strength for transitions between excited electronic states, by employing both a magnetic gauge dependent and a (velocity-based) magnetic gauge independent approach. Application is made to the lowest excited states of two prototypical chiral molecules, propylene oxide, also known as 1,2-epoxypropane or methyl oxirane, and R-(+)-1,1'-bi(2-naphthol), or BINOL. The dependence of the rotatory strength for transitions between the lowest three excited states of methyl oxirane upon the quality and extension of the basis set is analyzed, by employing a hierarchy of correlation consistent basis sets. Once established that basis sets of at least triple zeta quality, and at least doubly augmented, are sufficient to ensure sufficiently converged results, at least at the Hartree-Fock self-consistent field (HF-SCF) level, the rotatory strengths for all transitions between the lowest excited electronic states of methyl oxirane are computed and analyzed, employing HF-SCF, and density functional theory (DFT) electronic structure models. For DFT, both the popular B3LYP and its recently highly successful CAM-B3LYP extension are exploited. The strong dependence of the spectra upon electron correlation is highlighted. A HF-SCF and DFT study is carried out also for BINOL, a system where excited states show the typical pairing structure arising from the interaction of the two monomeric moieties, and whose conformational changes following photoexcitation were studied recently with via time-resolved CD.

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

NASA Astrophysics Data System (ADS)

Lee, Hee-Seung; Tuckerman, Mark E.

2007-04-01

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

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

PubMed

Lee, Hee-Seung; Tuckerman, Mark E

2007-04-28

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

Third-order Douglas-Kroll Relativistic Coupled-Cluster Theory through Connected Single, Double, Triple, and Quadruple Substitutions: Applications to Diatomic and Triatomic Hydrides

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

Hirata, So; Yanai, Takeshi; De Jong, Wibe A.

Coupled-cluster methods including through and up to the connected single, double, triple, and quadruple substitutions (CCSD, CCSDT, and CCSDTQ) have been automatically derived and implemented for sequential and parallel executions for use in conjunction with a one-component third-order Douglas-Kroll (DK3) approximation for relativistic corrections. A combination of the converging electron-correlation methods, the accurate relativistic reference wave functions, and the use of systematic basis sets tailored to the relativistic approximation has been shown to predict the experimental singlet-triplet separations within 0.02 eV (0.5 kcal/mol) for five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+), the experimental bond lengths within 0.002 angstroms,more » rotational constants within 0.02 cm-1, vibration-rotation constants within 0.01 cm-1, centrifugal distortion constants within 2 %, harmonic vibration frequencies within 9 cm-1 (0.4 %), anharmonic vibrational constants within 2 cm-1, and dissociation energies within 0.03 eV (0.8 kcal/mol) for twenty diatomic hydrides (BH, CH, NH, OH, FH, AlH, SiH, PH, SH, ClH, GaH, GeH, AsH, SeH, BrH, InH, SnH, SbH, TeH, and IH) containing main-group elements across the second through fifth periods of the periodic table. In these calculations, spin-orbit effects on dissociation energies, which were assumed to be additive, were estimated from the measured spin-orbit coupling constants of atoms and diatomic molecules, and an electronic energy in the complete-basis-set, complete-electron-correlation limit has been extrapolated by the formula which was in turn based on the exponential-Gaussian extrapolation formula of the basis set dependence.« less

Novel approach for tomographic reconstruction of gas concentration distributions in air: Use of smooth basis functions and simulated annealing

NASA Astrophysics Data System (ADS)

Drescher, A. C.; Gadgil, A. J.; Price, P. N.; Nazaroff, W. W.

Optical remote sensing and iterative computed tomography (CT) can be applied to measure the spatial distribution of gaseous pollutant concentrations. We conducted chamber experiments to test this combination of techniques using an open path Fourier transform infrared spectrometer (OP-FTIR) and a standard algebraic reconstruction technique (ART). Although ART converged to solutions that showed excellent agreement with the measured ray-integral concentrations, the solutions were inconsistent with simultaneously gathered point-sample concentration measurements. A new CT method was developed that combines (1) the superposition of bivariate Gaussians to represent the concentration distribution and (2) a simulated annealing minimization routine to find the parameters of the Gaussian basis functions that result in the best fit to the ray-integral concentration data. This method, named smooth basis function minimization (SBFM), generated reconstructions that agreed well, both qualitatively and quantitatively, with the concentration profiles generated from point sampling. We present an analysis of two sets of experimental data that compares the performance of ART and SBFM. We conclude that SBFM is a superior CT reconstruction method for practical indoor and outdoor air monitoring applications.

Morphological Diversity and the Roles of Contingency, Chance and Determinism in African Cichlid Radiations

PubMed Central

Young, Kyle A.; Snoeks, Jos; Seehausen, Ole

2009-01-01

Background Deterministic evolution, phylogenetic contingency and evolutionary chance each can influence patterns of morphological diversification during adaptive radiation. In comparative studies of replicate radiations, convergence in a common morphospace implicates determinism, whereas non-convergence suggests the importance of contingency or chance. Methodology/Principal Findings The endemic cichlid fish assemblages of the three African great lakes have evolved similar sets of ecomorphs but show evidence of non-convergence when compared in a common morphospace, suggesting the importance of contingency and/or chance. We then analyzed the morphological diversity of each assemblage independently and compared their axes of diversification in the unconstrained global morphospace. We find that despite differences in phylogenetic composition, invasion history, and ecological setting, the three assemblages are diversifying along parallel axes through morphospace and have nearly identical variance-covariance structures among morphological elements. Conclusions/Significance By demonstrating that replicate adaptive radiations are diverging along parallel axes, we have shown that non-convergence in the common morphospace is associated with convergence in the global morphospace. Applying these complimentary analyses to future comparative studies will improve our understanding of the relationship between morphological convergence and non-convergence, and the roles of contingency, chance and determinism in driving morphological diversification. PMID:19270732

Multiple data sets converge on a geologic structural model for Glass Buttes, Oregon geothermal prospect, Patrick Walsh, et al, 2010 American Geophysical Union Poster Session

DOE Data Explorer

Ezra Zemach

2010-01-01

Multiple data sets converge on a geologic structural model for Glass Buttes, Oregon geothermal prospect, Patrick Walsh, Brigette Martini, Chet Lide, Darrick Boschmann, John DIlles, Andrew Meigs, 2010 Ormat Nevada, Zonge Geophysical, Oregon State University American Geophysical Union, Poster Session

Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: Where it is shown how finite oligomer chains tend to the infinite periodic polymer

NASA Astrophysics Data System (ADS)

Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

2012-03-01

The longitudinal polarizability, αxx, and second hyperpolarizability, γxxxx, of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γxxxx, that is, very sensitive to the number of k points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C2H2)m-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on αxx and γxxxx of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for αxx and 1010 for γxxxx). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable.

Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

A metallic isolated band in the middle of the band gap of several III-V semiconductors has been predicted as photovoltaic materials with the possibility of providing substantially enhanced efficiencies. We have investigated the electronic band structures and lattice constants of GanAsmM and GanPmM with M=Sc, Ti, V, and Cr, to identify whether this isolated band is likely to exist by means of accurate calculations. For this task, we use the SIESTA program, an ab initio periodic density-functional method, fully self consistent in the local-density approximation. Norm-conserving, nonlocal pseudopotentials and confined linear combination of atomic orbitals have been used. We have carried out a case study of GanAsmTi and GanPmTi energy-band structure including analyses of the effect of the basis set, fine k-point mesh to ensure numerical convergence, structural parameters, and generalized gradient approximation for exchange and correlation corrections. We find the isolated intermediate band when one Ti atom replaces the position of one As (or P) atom in the crystal structure. For this kind of compound we show that the intermediate band relative position inside the band gap and width are sensitive to the dynamic relaxation of the crystal and the size of the basis set.

Convergent Evidence Scaling for Multiple Assessment Indicators: Conceptual Issues, Applications, and Technical Challenges

ERIC Educational Resources Information Center

Busse, R. T.; Elliott, Stephen N.; Kratochwill, Thomas R.

2010-01-01

The purpose of this article is to present Convergent Evidence Scaling (CES) as an emergent method for combining data from multiple assessment indicators. The CES method combines single-case assessment data by converging data gathered across multiple persons, settings, or measures, thereby providing an overall criterion-referenced outcome on which…

Spectral iterative method and convergence analysis for solving nonlinear fractional differential equation

NASA Astrophysics Data System (ADS)

Yarmohammadi, M.; Javadi, S.; Babolian, E.

2018-04-01

In this study a new spectral iterative method (SIM) based on fractional interpolation is presented for solving nonlinear fractional differential equations (FDEs) involving Caputo derivative. This method is equipped with a pre-algorithm to find the singularity index of solution of the problem. This pre-algorithm gives us a real parameter as the index of the fractional interpolation basis, for which the SIM achieves the highest order of convergence. In comparison with some recent results about the error estimates for fractional approximations, a more accurate convergence rate has been attained. We have also proposed the order of convergence for fractional interpolation error under the L2-norm. Finally, general error analysis of SIM has been considered. The numerical results clearly demonstrate the capability of the proposed method.

Autism As a Disorder of High Intelligence

PubMed Central

Crespi, Bernard J.

2016-01-01

A suite of recent studies has reported positive genetic correlations between autism risk and measures of mental ability. These findings indicate that alleles for autism overlap broadly with alleles for high intelligence, which appears paradoxical given that autism is characterized, overall, by below-average IQ. This paradox can be resolved under the hypothesis that autism etiology commonly involves enhanced, but imbalanced, components of intelligence. This hypothesis is supported by convergent evidence showing that autism and high IQ share a diverse set of convergent correlates, including large brain size, fast brain growth, increased sensory and visual-spatial abilities, enhanced synaptic functions, increased attentional focus, high socioeconomic status, more deliberative decision-making, profession and occupational interests in engineering and physical sciences, and high levels of positive assortative mating. These findings help to provide an evolutionary basis to understanding autism risk as underlain in part by dysregulation of intelligence, a core human-specific adaptation. In turn, integration of studies on intelligence with studies of autism should provide novel insights into the neurological and genetic causes of high mental abilities, with important implications for cognitive enhancement, artificial intelligence, the relationship of autism with schizophrenia, and the treatment of both autism and intellectual disability. PMID:27445671

Autism As a Disorder of High Intelligence.

PubMed

Crespi, Bernard J

2016-01-01

A suite of recent studies has reported positive genetic correlations between autism risk and measures of mental ability. These findings indicate that alleles for autism overlap broadly with alleles for high intelligence, which appears paradoxical given that autism is characterized, overall, by below-average IQ. This paradox can be resolved under the hypothesis that autism etiology commonly involves enhanced, but imbalanced, components of intelligence. This hypothesis is supported by convergent evidence showing that autism and high IQ share a diverse set of convergent correlates, including large brain size, fast brain growth, increased sensory and visual-spatial abilities, enhanced synaptic functions, increased attentional focus, high socioeconomic status, more deliberative decision-making, profession and occupational interests in engineering and physical sciences, and high levels of positive assortative mating. These findings help to provide an evolutionary basis to understanding autism risk as underlain in part by dysregulation of intelligence, a core human-specific adaptation. In turn, integration of studies on intelligence with studies of autism should provide novel insights into the neurological and genetic causes of high mental abilities, with important implications for cognitive enhancement, artificial intelligence, the relationship of autism with schizophrenia, and the treatment of both autism and intellectual disability.

Examining the Level of Convergence among Self-Regulated Learning Microanalytic Processes, Achievement, and a Self-Report Questionnaire

ERIC Educational Resources Information Center

Cleary, Timothy J.; Callan, Gregory L.; Malatesta, Jaime; Adams, Tanya

2015-01-01

This study examined the convergent and predictive validity of self-regulated learning (SRL) microanalytic measures. Specifically, theoretically based relations among a set of self-reflection processes, self-efficacy, and achievement were examined as was the level of convergence between a microanalytic strategy measure and a SRL self-report…

A note on convergence of solutions of total variation regularized linear inverse problems

NASA Astrophysics Data System (ADS)

Iglesias, José A.; Mercier, Gwenael; Scherzer, Otmar

2018-05-01

In a recent paper by Chambolle et al (2017 Inverse Problems 33 015002) it was proven that if the subgradient of the total variation at the noise free data is not empty, the level-sets of the total variation denoised solutions converge to the level-sets of the noise free data with respect to the Hausdorff distance. The condition on the subgradient corresponds to the source condition introduced by Burger and Osher (2007 Multiscale Model. Simul. 6 365–95), who proved convergence rates results with respect to the Bregman distance under this condition. We generalize the result of Chambolle et al to total variation regularization of general linear inverse problems under such a source condition. As particular applications we present denoising in bounded and unbounded, convex and non convex domains, deblurring and inversion of the circular Radon transform. In all these examples the convergence result applies. Moreover, we illustrate the convergence behavior through numerical examples.

Genetic identification of brain cell types underlying schizophrenia.

PubMed

Skene, Nathan G; Bryois, Julien; Bakken, Trygve E; Breen, Gerome; Crowley, James J; Gaspar, Héléna A; Giusti-Rodriguez, Paola; Hodge, Rebecca D; Miller, Jeremy A; Muñoz-Manchado, Ana B; O'Donovan, Michael C; Owen, Michael J; Pardiñas, Antonio F; Ryge, Jesper; Walters, James T R; Linnarsson, Sten; Lein, Ed S; Sullivan, Patrick F; Hjerling-Leffler, Jens

2018-06-01

With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells. These enrichments were due to sets of genes that were specifically expressed in each of these cell types. We also found that many of the diverse gene sets previously associated with schizophrenia (genes involved in synaptic function, those encoding mRNAs that interact with FMRP, antipsychotic targets, etc.) generally implicated the same brain cell types. Our results suggest a parsimonious explanation: the common-variant genetic results for schizophrenia point at a limited set of neurons, and the gene sets point to the same cells. The genetic risk associated with MSNs did not overlap with that of glutamatergic pyramidal cells and interneurons, suggesting that different cell types have biologically distinct roles in schizophrenia.

On the Hilbert-Huang Transform Theoretical Developments

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Blank, Karin; Flatley, Thomas; Huang, Norden E.; Patrick, David; Hestnes, Phyllis

2005-01-01

One of the main heritage tools used in scientific and engineering data spectrum analysis is the Fourier Integral Transform and its high performance digital equivalent - the Fast Fourier Transform (FFT). Both carry strong a-priori assumptions about the source data, such as linearity, of being stationary, and of satisfying the Dirichlet conditions. A recent development at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC), known as the Hilbert-Huang Transform (HHT), proposes a novel approach to the solution for the nonlinear class of spectrum analysis problems. Using a-posteriori data processing based on the Empirical Mode Decomposition (EMD) sifting process (algorithm), followed by the normalized Hilbert Transform of the decomposition data, the HHT allows spectrum analysis of nonlinear and nonstationary data. The EMD sifting process results in a non-constrained decomposition of a source real value data vector into a finite set of Intrinsic Mode Functions (IMF). These functions form a near orthogonal adaptive basis, a basis that is derived from the data. The IMFs can be further analyzed for spectrum interpretation by the classical Hilbert Transform. A new engineering spectrum analysis tool using HHT has been developed at NASA GSFC, the HHT Data Processing System (HHT-DPS). As the HHT-DPS has been successfully used and commercialized, new applications post additional questions about the theoretical basis behind the HHT and EMD algorithms. Why is the fastest changing component of a composite signal being sifted out first in the EMD sifting process? Why does the EMD sifting process seemingly converge and why does it converge rapidly? Does an IMF have a distinctive structure? Why are the IMFs near orthogonal? We address these questions and develop the initial theoretical background for the HHT. This will contribute to the developments of new HHT processing options, such as real-time and 2-D processing using Field Programmable Array (FPGA) computational resources, enhanced HHT synthesis, and broaden the scope of HHT applications for signal processing.

Achieving accuracy in first-principles calculations for EOS: basis completeness at high temperatures

NASA Astrophysics Data System (ADS)

Wills, John; Mattsson, Ann

2013-06-01

First-principles electronic structure calculations can provide EOS data in regimes of pressure and temperature where accurate experimental data is difficult or impossible to obtain. This lack, however, also precludes validation of calculations in those regimes. Factors that influence the accuracy of first-principles data include (1) theoretical approximations and (2) computational approximations used in implementing and solving the underlying equations. In the first category are the approximate exchange/correlation functionals and approximate wave equations approximating the Dirac equation; in the second are basis completeness, series convergence, and truncation errors. We are using two rather different electronic structure methods (VASP and RSPt) to make definitive the requirements for accuracy of the second type, common to both. In this talk, we discuss requirements for converged calculation at high temperature and moderated pressure. At convergence we show that both methods give identical results. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Method for implementation of recursive hierarchical segmentation on parallel computers

NASA Technical Reports Server (NTRS)

Tilton, James C. (Inventor)

2005-01-01

A method, computer readable storage, and apparatus for implementing a recursive hierarchical segmentation algorithm on a parallel computing platform. The method includes setting a bottom level of recursion that defines where a recursive division of an image into sections stops dividing, and setting an intermediate level of recursion where the recursive division changes from a parallel implementation into a serial implementation. The segmentation algorithm is implemented according to the set levels. The method can also include setting a convergence check level of recursion with which the first level of recursion communicates with when performing a convergence check.

From plane waves to local Gaussians for the simulation of correlated periodic systems

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

Booth, George H., E-mail: george.booth@kcl.ac.uk; Tsatsoulis, Theodoros; Grüneis, Andreas, E-mail: a.grueneis@fkf.mpg.de

2016-08-28

We present a simple, robust, and black-box approach to the implementation and use of local, periodic, atom-centered Gaussian basis functions within a plane wave code, in a computationally efficient manner. The procedure outlined is based on the representation of the Gaussians within a finite bandwidth by their underlying plane wave coefficients. The core region is handled within the projected augment wave framework, by pseudizing the Gaussian functions within a cutoff radius around each nucleus, smoothing the functions so that they are faithfully represented by a plane wave basis with only moderate kinetic energy cutoff. To mitigate the effects of themore » basis set superposition error and incompleteness at the mean-field level introduced by the Gaussian basis, we also propose a hybrid approach, whereby the complete occupied space is first converged within a large plane wave basis, and the Gaussian basis used to construct a complementary virtual space for the application of correlated methods. We demonstrate that these pseudized Gaussians yield compact and systematically improvable spaces with an accuracy comparable to their non-pseudized Gaussian counterparts. A key advantage of the described method is its ability to efficiently capture and describe electronic correlation effects of weakly bound and low-dimensional systems, where plane waves are not sufficiently compact or able to be truncated without unphysical artifacts. We investigate the accuracy of the pseudized Gaussians for the water dimer interaction, neon solid, and water adsorption on a LiH surface, at the level of second-order Møller–Plesset perturbation theory.« less

Permitted and forbidden sets in symmetric threshold-linear networks.

PubMed

Hahnloser, Richard H R; Seung, H Sebastian; Slotine, Jean-Jacques

2003-03-01

The richness and complexity of recurrent cortical circuits is an inexhaustible source of inspiration for thinking about high-level biological computation. In past theoretical studies, constraints on the synaptic connection patterns of threshold-linear networks were found that guaranteed bounded network dynamics, convergence to attractive fixed points, and multistability, all fundamental aspects of cortical information processing. However, these conditions were only sufficient, and it remained unclear which were the minimal (necessary) conditions for convergence and multistability. We show that symmetric threshold-linear networks converge to a set of attractive fixed points if and only if the network matrix is copositive. Furthermore, the set of attractive fixed points is nonconnected (the network is multiattractive) if and only if the network matrix is not positive semidefinite. There are permitted sets of neurons that can be coactive at a stable steady state and forbidden sets that cannot. Permitted sets are clustered in the sense that subsets of permitted sets are permitted and supersets of forbidden sets are forbidden. By viewing permitted sets as memories stored in the synaptic connections, we provide a formulation of long-term memory that is more general than the traditional perspective of fixed-point attractor networks. There is a close correspondence between threshold-linear networks and networks defined by the generalized Lotka-Volterra equations.

The Last of the Gem Elixir (Research).

ERIC Educational Resources Information Center

Otto, Wayne

1988-01-01

Draws a humorous analogy between the Harmonic Convergence ushering in the dawn of the New Age and the convergence of a whole set of different views of reading instruction with established views and practices. (RS)

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

PubMed

Ferenczy, György G

2013-04-05

The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. Copyright © 2013 Wiley Periodicals, Inc.

Reverse engineering of machine-tool settings with modified roll for spiral bevel pinions

NASA Astrophysics Data System (ADS)

Liu, Guanglei; Chang, Kai; Liu, Zeliang

2013-05-01

Although a great deal of research has been dedicated to the synthesis of spiral bevel gears, little related to reverse engineering can be found. An approach is proposed to reverse the machine-tool settings of the pinion of a spiral bevel gear drive on the basis of the blank and tooth surface data obtained by a coordinate measuring machine(CMM). Real tooth contact analysis(RTCA) is performed to preliminary ascertain the contact pattern, the motion curve, as well as the position of the mean contact point. And then the tangent to the contact path and the motion curve are interpolated in the sense of the least square method to extract the initial values of the bias angle and the higher order coefficients(HOC) in modified roll motion. A trial tooth surface is generated by machine-tool settings derived from the local synthesis relating to the initial meshing performances and modified roll motion. An optimization objective is formed which equals the tooth surface deviation between the real tooth surface and the trial tooth surface. The design variables are the parameters describing the meshing performances at the mean contact point in addition to the HOC. When the objective is optimized within an arbitrarily given convergence tolerance, the machine-tool settings together with the HOC are obtained. The proposed approach is verified by a spiral bevel pinion used in the accessory gear box of an aviation engine. The trial tooth surfaces approach to the real tooth surface on the whole in the example. The results show that the convergent tooth surface deviation for the concave side on the average is less than 0.5 μm, and is less than 1.3 μm for the convex side. The biggest tooth surface deviation is 6.7 μm which is located at the corner of the grid on the convex side. Those nodes with relative bigger tooth surface deviations are all located at the boundary of the grid. An approach is proposed to figure out the machine-tool settings of a spiral bevel pinion by way of reverse engineering without having known the theoretical tooth surfaces and the corresponding machine-tool settings.

Slab interactions in 3-D subduction settings: The Philippine Sea Plate region

NASA Astrophysics Data System (ADS)

Holt, Adam F.; Royden, Leigh H.; Becker, Thorsten W.; Faccenna, Claudio

2018-05-01

The importance of slab-slab interactions is manifested in the kinematics and geometry of the Philippine Sea Plate and western Pacific subduction zones, and such interactions offer a dynamic basis for the first-order observations in this complex subduction setting. The westward subduction of the Pacific Sea Plate changes, along-strike, from single slab subduction beneath Japan, to a double-subduction setting where Pacific subduction beneath the Philippine Sea Plate occurs in tandem with westward subduction of the Philippine Sea Plate beneath Eurasia. Our 3-D numerical models show that there are fundamental differences between single slab systems and double slab systems where both subduction systems have the same vergence. We find that the observed kinematics and slab geometry of the Pacific-Philippine subduction can be understood by considering an along-strike transition from single to double subduction, and is largely independent from the detailed geometry of the Philippine Sea Plate. Important first order features include the relatively shallow slab dip, retreating/stationary trenches, and rapid subduction for single slab systems (Pacific Plate subducting under Japan), and front slabs within a double slab system (Philippine Sea Plate subducting at Ryukyu). In contrast, steep to overturned slab dips, advancing trench motion, and slower subduction occurs for rear slabs in a double slab setting (Pacific subducting at the Izu-Bonin-Mariana). This happens because of a relative build-up of pressure in the asthenosphere beneath the Philippine Sea Plate, where the asthenosphere is constrained between the converging Ryukyu and Izu-Bonin-Mariana slabs. When weak back-arc regions are included, slab-slab convergence rates slow and the middle (Philippine) plate extends, which leads to reduced pressure build up and reduced slab-slab coupling. Models without back-arcs, or with back-arc viscosities that are reduced by a factor of five, produce kinematics compatible with present-day observations.

Convergent evolution of the genomes of marine mammals

USGS Publications Warehouse

Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

2015-01-01

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Convergent evolution of the genomes of marine mammals

PubMed Central

Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret E.; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

2015-01-01

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

Convoluted Quasi Sturmian basis for the two-electron continuum

NASA Astrophysics Data System (ADS)

Ancarani, Lorenzo Ugo; Zaytsev, A. S.; Zaytsev, S. A.

2016-09-01

In the construction of solutions for the Coulomb three-body scattering problem one encounters a series of mathematical and numerical difficulties, one of which are the cumbersome boundary conditions the wave function should obey. We propose to describe a Coulomb three-body system continuum with a set of two-particle functions, named Convoluted Quasi Sturmian (CQS) in. They are built using recently introduced Quasi Sturmian (QS) functions which have the merit of possessing a closed form. Unlike a simple product of two one-particle functions, by construction, the CQS functions look asymptotically like a six-dimensional outgoing spherical wave. The proposed CQS basis is tested through the study of the double ionization of helium by high-energy electron impact in the framework of the Temkin-Poet model. An adequate logarithmic-like phase factor is further included in order to take into account the Coulomb interelectronic interaction and formally build the correct asymptotic behavior when all interparticle distances are large. With such a phase-factor (that can be easily extended to take into account higher partial waves) rapid convergence of the expansion can be obtained.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Self-similar dynamic converging shocks - I. An isothermal gas sphere with self-gravity

NASA Astrophysics Data System (ADS)

Lou, Yu-Qing; Shi, Chun-Hui

2014-07-01

We explore novel self-similar dynamic evolution of converging spherical shocks in a self-gravitating isothermal gas under conceivable astrophysical situations. The construction of such converging shocks involves a time-reversal operation on feasible flow profiles in self-similar expansion with a proper care for the increasing direction of the specific entropy. Pioneered by Guderley since 1942 but without self-gravity so far, self-similar converging shocks are important for implosion processes in aerodynamics, combustion, and inertial fusion. Self-gravity necessarily plays a key role for grossly spherical structures in very broad contexts of astrophysics and cosmology, such as planets, stars, molecular clouds (cores), compact objects, planetary nebulae, supernovae, gamma-ray bursts, supernova remnants, globular clusters, galactic bulges, elliptical galaxies, clusters of galaxies as well as relatively hollow cavity or bubble structures on diverse spatial and temporal scales. Large-scale dynamic flows associated with such quasi-spherical systems (including collapses, accretions, fall-backs, winds and outflows, explosions, etc.) in their initiation, formation, and evolution are likely encounter converging spherical shocks at times. Our formalism lays an important theoretical basis for pertinent astrophysical and cosmological applications of various converging shock solutions and for developing and calibrating numerical codes. As examples, we describe converging shock triggered star formation, supernova explosions, and void collapses.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Fourier phase retrieval with a single mask by Douglas-Rachford algorithms.

PubMed

Chen, Pengwen; Fannjiang, Albert

2018-05-01

The Fourier-domain Douglas-Rachford (FDR) algorithm is analyzed for phase retrieval with a single random mask. Since the uniqueness of phase retrieval solution requires more than a single oversampled coded diffraction pattern, the extra information is imposed in either of the following forms: 1) the sector condition on the object; 2) another oversampled diffraction pattern, coded or uncoded. For both settings, the uniqueness of projected fixed point is proved and for setting 2) the local, geometric convergence is derived with a rate given by a spectral gap condition. Numerical experiments demonstrate global, power-law convergence of FDR from arbitrary initialization for both settings as well as for 3 or more coded diffraction patterns without oversampling. In practice, the geometric convergence can be recovered from the power-law regime by a simple projection trick, resulting in highly accurate reconstruction from generic initialization.

Assessment of higher order correlation effects with the help of Moller-Plesset perturbation theory up to sixth order

NASA Astrophysics Data System (ADS)

He, Yuan; Cremer, Dieter

For 30 molecules and two atoms, MP n correlation energies up to n = 6 are computed and used to analyse higher order correlation effects and the initial convergence behaviour of the MP n series. Particularly useful is the analysis of correlation contributions E(n)XY ...( n = 4,5,6; X , Y ,... = S, D, T, Q denoting single, double, triple, and quadruple excitations) in the form of correlation energy spectra. Two classes of system are distinguished, namely class A systems possessing well separated electron pairs and class B systems which are characterized by electron clustering in certain regions of atomic and molecular space. For class A systems, electron pair correlation effects as described by D, Q, DD, DQ, QQ, DDD, etc., contributions are most important, which are stepwise included at MP n with n = 2,... ,6. Class A systems are reasonably described by MP n theory, which is reflected by the fact that convergence of the MP n series is monotonic (but relatively slow) for class A systems. The description of class B systems is difficult since three- and four-electron correlation effects and couplings between two-, three-, and four-electron correlation effects missing for lower order perturbation theory are significant. MP n methods, which do not cover these effects, simulate higher order with lower order correlation effects thus exaggerating the latter, which has to be corrected with increasing n. Consequently, the MP n series oscillates for class B systems at low orders. A possible divergence of the MP n series is mostly a consequence of an unbalanced basis set. For example, diffuse functions added to an unsaturated sp basis lead to an exaggeration of higher order correlation effects, which can cause enhanced oscillations and divergence of the MP n series.

An Efficient Method Coupling Kernel Principal Component Analysis with Adjoint-Based Optimal Control and Its Goal-Oriented Extensions

NASA Astrophysics Data System (ADS)

Thimmisetty, C.; Talbot, C.; Tong, C. H.; Chen, X.

2016-12-01

The representativeness of available data poses a significant fundamental challenge to the quantification of uncertainty in geophysical systems. Furthermore, the successful application of machine learning methods to geophysical problems involving data assimilation is inherently constrained by the extent to which obtainable data represent the problem considered. We show how the adjoint method, coupled with optimization based on methods of machine learning, can facilitate the minimization of an objective function defined on a space of significantly reduced dimension. By considering uncertain parameters as constituting a stochastic process, the Karhunen-Loeve expansion and its nonlinear extensions furnish an optimal basis with respect to which optimization using L-BFGS can be carried out. In particular, we demonstrate that kernel PCA can be coupled with adjoint-based optimal control methods to successfully determine the distribution of material parameter values for problems in the context of channelized deformable media governed by the equations of linear elasticity. Since certain subsets of the original data are characterized by different features, the convergence rate of the method in part depends on, and may be limited by, the observations used to furnish the kernel principal component basis. By determining appropriate weights for realizations of the stochastic random field, then, one may accelerate the convergence of the method. To this end, we present a formulation of Weighted PCA combined with a gradient-based means using automatic differentiation to iteratively re-weight observations concurrent with the determination of an optimal reduced set control variables in the feature space. We demonstrate how improvements in the accuracy and computational efficiency of the weighted linear method can be achieved over existing unweighted kernel methods, and discuss nonlinear extensions of the algorithm.

Standard Setting Methods for Pass/Fail Decisions on High-Stakes Objective Structured Clinical Examinations: A Validity Study.

PubMed

Yousuf, Naveed; Violato, Claudio; Zuberi, Rukhsana W

2015-01-01

CONSTRUCT: Authentic standard setting methods will demonstrate high convergent validity evidence of their outcomes, that is, cutoff scores and pass/fail decisions, with most other methods when compared with each other. The objective structured clinical examination (OSCE) was established for valid, reliable, and objective assessment of clinical skills in health professions education. Various standard setting methods have been proposed to identify objective, reliable, and valid cutoff scores on OSCEs. These methods may identify different cutoff scores for the same examinations. Identification of valid and reliable cutoff scores for OSCEs remains an important issue and a challenge. Thirty OSCE stations administered at least twice in the years 2010-2012 to 393 medical students in Years 2 and 3 at Aga Khan University are included. Psychometric properties of the scores are determined. Cutoff scores and pass/fail decisions of Wijnen, Cohen, Mean-1.5SD, Mean-1SD, Angoff, borderline group and borderline regression (BL-R) methods are compared with each other and with three variants of cluster analysis using repeated measures analysis of variance and Cohen's kappa. The mean psychometric indices on the 30 OSCE stations are reliability coefficient = 0.76 (SD = 0.12); standard error of measurement = 5.66 (SD = 1.38); coefficient of determination = 0.47 (SD = 0.19), and intergrade discrimination = 7.19 (SD = 1.89). BL-R and Wijnen methods show the highest convergent validity evidence among other methods on the defined criteria. Angoff and Mean-1.5SD demonstrated least convergent validity evidence. The three cluster variants showed substantial convergent validity with borderline methods. Although there was a high level of convergent validity of Wijnen method, it lacks the theoretical strength to be used for competency-based assessments. The BL-R method is found to show the highest convergent validity evidences for OSCEs with other standard setting methods used in the present study. We also found that cluster analysis using mean method can be used for quality assurance of borderline methods. These findings should be further confirmed by studies in other settings.

Convergence in Reports of Adolescents' Psychopathology: A Focus on Disorganized Attachment and Reflective Functioning.

PubMed

Borelli, Jessica L; Palmer, Alexandra; Vanwoerden, Salome; Sharp, Carla

2017-12-13

Although convergence in parent-youth reports of adolescent psychopathology is critical for treatment planning, research documents a pervasive lack of agreement in ratings of adolescents' symptoms. Attachment insecurity (particularly disorganized attachment) and impoverished reflective functioning (RF) are 2 theoretically implicated predictors of low convergence that have not been examined in the literature. In a cross-sectional investigation of adolescents receiving inpatient psychiatric treatment, we examined whether disorganized attachment and low (adolescent and parent) RF were associated with patterns of convergence in adolescent internalizing and externalizing symptoms. Compared with organized adolescents, disorganized adolescents had lower parent-youth convergence in reports of their internalizing symptoms and higher convergence in reports of their externalizing symptoms; low adolescent self-focused RF was associated with low convergence in parent-adolescent reports of internalizing symptoms, whereas low adolescent global RF was associated with high convergence in parent-adolescent reports of externalizing symptoms. Among adolescents receiving inpatient psychiatric treatment, disorganized attachment and lower RF were associated with weaker internalizing symptom convergence and greater externalizing symptom convergence, which if replicated, could inform assessment strategies and treatment planning in this setting.

Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: where it is shown how finite oligomer chains tend to the infinite periodic polymer.

PubMed

Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto

2012-03-21

The longitudinal polarizability, α(xx), and second hyperpolarizability, γ(xxxx), of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γ(xxxx), that is, very sensitive to the number of k(->) points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k(->) points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C(2)H(2))(m)-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on α(xx) and γ(xxxx) of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for α(xx) and 10(10) for γ(xxxx)). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable. © 2012 American Institute of Physics

Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life.

PubMed

Agrawal, Anurag A

2017-08-01

A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles. Although naturalists have long made inferences about convergent evolution and its importance, there has been confusion in the interpretation of the pattern of convergence. Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles? In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution.

A class of convergent neural network dynamics

NASA Astrophysics Data System (ADS)

Fiedler, Bernold; Gedeon, Tomáš

1998-01-01

We consider a class of systems of differential equations in Rn which exhibits convergent dynamics. We find a Lyapunov function and show that every bounded trajectory converges to the set of equilibria. Our result generalizes the results of Cohen and Grossberg (1983) for convergent neural networks. It replaces the symmetry assumption on the matrix of weights by the assumption on the structure of the connections in the neural network. We prove the convergence result also for a large class of Lotka-Volterra systems. These are naturally defined on the closed positive orthant. We show that there are no heteroclinic cycles on the boundary of the positive orthant for the systems in this class.

Shaping mobile belts by small-scale convection.

PubMed

Faccenna, Claudio; Becker, Thorsten W

2010-06-03

Mobile belts are long-lived deformation zones composed of an ensemble of crustal fragments, distributed over hundreds of kilometres inside continental convergent margins. The Mediterranean represents a remarkable example of this tectonic setting: the region hosts a diffuse boundary between the Nubia and Eurasia plates comprised of a mosaic of microplates that move and deform independently from the overall plate convergence. Surface expressions of Mediterranean tectonics include deep, subsiding backarc basins, intraplate plateaux and uplifting orogenic belts. Although the kinematics of the area are now fairly well defined, the dynamical origins of many of these active features are controversial and usually attributed to crustal and lithospheric interactions. However, the effects of mantle convection, well established for continental interiors, should be particularly relevant in a mobile belt, and modelling may constrain important parameters such as slab coherence and lithospheric strength. Here we compute global mantle flow on the basis of recent, high-resolution seismic tomography to investigate the role of buoyancy-driven and plate-motion-induced mantle circulation for the Mediterranean. We show that mantle flow provides an explanation for much of the observed dynamic topography and microplate motion in the region. More generally, vigorous small-scale convection in the uppermost mantle may also underpin other complex mobile belts such as the North American Cordillera or the Himalayan-Tibetan collision zone.

Evidence for attractors in English intonation.

PubMed

Braun, Bettina; Kochanski, Greg; Grabe, Esther; Rosner, Burton S

2006-06-01

Although the pitch of the human voice is continuously variable, some linguists contend that intonation in speech is restricted to a small, limited set of patterns. This claim is tested by asking subjects to mimic a block of 100 randomly generated intonation contours and then to imitate themselves in several successive sessions. The produced f0 contours gradually converge towards a limited set of distinct, previously recognized basic English intonation patterns. These patterns are "attractors" in the space of possible intonation English contours. The convergence does not occur immediately. Seven of the ten participants show continued convergence toward their attractors after the first iteration. Subjects retain and use information beyond phonological contrasts, suggesting that intonational phonology is not a complete description of their mental representation of intonation.

Societal response to nanotechnology: converging technologies-converging societal response research?

NASA Astrophysics Data System (ADS)

Ronteltap, Amber; Fischer, Arnout R. H.; Tobi, Hilde

2011-10-01

Nanotechnology is an emerging technology particularly vulnerable to societal unrest, which may hinder its further development. With the increasing convergence of several technological domains in the field of nanotechnology, so too could convergence of social science methods help to anticipate societal response. This paper systematically reviews the current state of convergence in societal response research by first sketching the predominant approaches to previous new technologies, followed by an analysis of current research into societal response to nanotechnology. A set of 107 papers on previous new technologies shows that rational actor models have played an important role in the study of societal response to technology, in particular in the field of information technology and the geographic region of Asia. Biotechnology and nuclear power have, in contrast, more often been investigated through risk perception and other affective determinants, particularly in Europe and the USA. A set of 42 papers on societal response to nanotechnology shows similarities to research in biotechnology, as it also builds on affective variables such as risk perception. Although there is a tendency to extend the rational models with affective variables, convergence in social science approaches to response to new technologies still has a long way to go. The challenge for researchers of societal response to technologies is to converge to some shared principles by taking up the best parts from the rational actor models dominant in information technology, whilst integrating non-rational constructs from biotechnology research. The introduction of nanotechnology gives a unique opportunity to do so.

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

PubMed

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

2018-02-21

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

Eye vergence responses during a visual memory task.

PubMed

Solé Puig, Maria; Romeo, August; Cañete Crespillo, Jose; Supèr, Hans

2017-02-08

In a previous report it was shown that covertly attending visual stimuli produce small convergence of the eyes, and that visual stimuli can give rise to different modulations of the angle of eye vergence, depending on their power to capture attention. Working memory is highly dependent on attention. Therefore, in this study we assessed vergence responses in a memory task. Participants scanned a set of 8 or 12 images for 10 s, and thereafter were presented with a series of single images. One half were repeat images - that is, they belonged to the initial set - and the other half were novel images. Participants were asked to indicate whether or not the images were included in the initial image set. We observed that eyes converge during scanning the set of images and during the presentation of the single images. The convergence was stronger for remembered images compared with the vergence for nonremembered images. Modulation in pupil size did not correspond to behavioural responses. The correspondence between vergence and coding/retrieval processes of memory strengthen the idea of a role for vergence in attention processing of visual information.

A coherent discrete variable representation method on a sphere

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

Yu, Hua -Gen

Here, the coherent discrete variable representation (ZDVR) has been extended for construct- ing a multidimensional potential-optimized DVR basis on a sphere. In order to deal with the non-constant Jacobian in spherical angles, two direct product primitive basis methods are proposed so that the original ZDVR technique can be properly implemented. The method has been demonstrated by computing the lowest states of a two dimensional (2D) vibrational model. Results show that the extended ZDVR method gives accurate eigenval- ues and exponential convergence with increasing ZDVR basis size.

A coherent discrete variable representation method on a sphere

DOE PAGES

Yu, Hua -Gen

2017-09-05

Here, the coherent discrete variable representation (ZDVR) has been extended for construct- ing a multidimensional potential-optimized DVR basis on a sphere. In order to deal with the non-constant Jacobian in spherical angles, two direct product primitive basis methods are proposed so that the original ZDVR technique can be properly implemented. The method has been demonstrated by computing the lowest states of a two dimensional (2D) vibrational model. Results show that the extended ZDVR method gives accurate eigenval- ues and exponential convergence with increasing ZDVR basis size.

Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution.

PubMed

Zou, Zhengting; Zhang, Jianzhi

2017-07-01

Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here, we demonstrate in a genome-wide data set from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD. Similar results are observed in a comparable data set of 12 fruit flies in some but not all of these tests. We conclude that, at least in some cases, the temporal decline of convergence is genuine, reflecting an impact of epistasis on protein evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

SU-E-T-422: Fast Analytical Beamlet Optimization for Volumetric Intensity-Modulated Arc Therapy

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

Chan, Kenny S K; Lee, Louis K Y; Xing, L

2015-06-15

Purpose: To implement a fast optimization algorithm on CPU/GPU heterogeneous computing platform and to obtain an optimal fluence for a given target dose distribution from the pre-calculated beamlets in an analytical approach. Methods: The 2D target dose distribution was modeled as an n-dimensional vector and estimated by a linear combination of independent basis vectors. The basis set was composed of the pre-calculated beamlet dose distributions at every 6 degrees of gantry angle and the cost function was set as the magnitude square of the vector difference between the target and the estimated dose distribution. The optimal weighting of the basis,more » which corresponds to the optimal fluence, was obtained analytically by the least square method. Those basis vectors with a positive weighting were selected for entering into the next level of optimization. Totally, 7 levels of optimization were implemented in the study.Ten head-and-neck and ten prostate carcinoma cases were selected for the study and mapped to a round water phantom with a diameter of 20cm. The Matlab computation was performed in a heterogeneous programming environment with Intel i7 CPU and NVIDIA Geforce 840M GPU. Results: In all selected cases, the estimated dose distribution was in a good agreement with the given target dose distribution and their correlation coefficients were found to be in the range of 0.9992 to 0.9997. Their root-mean-square error was monotonically decreasing and converging after 7 cycles of optimization. The computation took only about 10 seconds and the optimal fluence maps at each gantry angle throughout an arc were quickly obtained. Conclusion: An analytical approach is derived for finding the optimal fluence for a given target dose distribution and a fast optimization algorithm implemented on the CPU/GPU heterogeneous computing environment greatly reduces the optimization time.« less

Composite thermochemistry of gas phase U(VI)-containing molecules

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

Bross, David H.; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Reaction energies have been calculated for a series of reactions involving UF{sub 6}, UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2} using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with themore » accurately known heat of formation of UF{sub 6} to determine the enthalpies of formation of UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2}. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO{sub 2}F{sub 2} was in excellent agreement with experiment, while the two results obtained for UO{sub 3} were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO{sub 2}(OH){sub 2} is predicted from this work to be −288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of −292.7 ± 6 kcal/mol.« less

Range-Separated Brueckner Coupled Cluster Doubles Theory

NASA Astrophysics Data System (ADS)

Shepherd, James J.; Henderson, Thomas M.; Scuseria, Gustavo E.

2014-04-01

We introduce a range-separation approximation to coupled cluster doubles (CCD) theory that successfully overcomes limitations of regular CCD when applied to the uniform electron gas. We combine the short-range ladder channel with the long-range ring channel in the presence of a Bruckner renormalized one-body interaction and obtain ground-state energies with an accuracy of 0.001 a.u./electron across a wide range of density regimes. Our scheme is particularly useful in the low-density and strongly correlated regimes, where regular CCD has serious drawbacks. Moreover, we cure the infamous overcorrelation of approaches based on ring diagrams (i.e., the particle-hole random phase approximation). Our energies are further shown to have appropriate basis set and thermodynamic limit convergence, and overall this scheme promises energetic properties for realistic periodic and extended systems which existing methods do not possess.

Application of the exact exchange potential method for half metallic intermediate band alloy semiconductor.

PubMed

Fernández, J J; Tablero, C; Wahnón, P

2004-06-08

In this paper we present an analysis of the convergence of the band structure properties, particularly the influence on the modification of the bandgap and bandwidth values in half metallic compounds by the use of the exact exchange formalism. This formalism for general solids has been implemented using a localized basis set of numerical functions to represent the exchange density. The implementation has been carried out using a code which uses a linear combination of confined numerical pseudoatomic functions to represent the Kohn-Sham orbitals. The application of this exact exchange scheme to a half-metallic semiconductor compound, in particular to Ga(4)P(3)Ti, a promising material in the field of high efficiency solar cells, confirms the existence of the isolated intermediate band in this compound. (c) 2004 American Institute of Physics.

A Regularizer Approach for RBF Networks Under the Concurrent Weight Failure Situation.

PubMed

Leung, Chi-Sing; Wan, Wai Yan; Feng, Ruibin

2017-06-01

Many existing results on fault-tolerant algorithms focus on the single fault source situation, where a trained network is affected by one kind of weight failure. In fact, a trained network may be affected by multiple kinds of weight failure. This paper first studies how the open weight fault and the multiplicative weight noise degrade the performance of radial basis function (RBF) networks. Afterward, we define the objective function for training fault-tolerant RBF networks. Based on the objective function, we then develop two learning algorithms, one batch mode and one online mode. Besides, the convergent conditions of our online algorithm are investigated. Finally, we develop a formula to estimate the test set error of faulty networks trained from our approach. This formula helps us to optimize some tuning parameters, such as RBF width.

A new BP Fourier algorithm and its application in English teaching evaluation

NASA Astrophysics Data System (ADS)

Pei, Xuehui; Pei, Guixin

2017-08-01

BP neural network algorithm has wide adaptability and accuracy when used in complicated system evaluation, but its calculation defects such as slow convergence have limited its practical application. The paper tries to speed up the calculation convergence of BP neural network algorithm with Fourier basis functions and presents a new BP Fourier algorithm for complicated system evaluation. First, shortages and working principle of BP algorithm are analyzed for subsequent targeted improvement; Second, the presented BP Fourier algorithm adopts Fourier basis functions to simplify calculation structure, designs new calculation transfer function between input and output layers, and conducts theoretical analysis to prove the efficiency of the presented algorithm; Finally, the presented algorithm is used in evaluating university English teaching and the application results shows that the presented BP Fourier algorithm has better performance in calculation efficiency and evaluation accuracy and can be used in evaluating complicated system practically.

Quantized kernel least mean square algorithm.

PubMed

Chen, Badong; Zhao, Songlin; Zhu, Pingping; Príncipe, José C

2012-01-01

In this paper, we propose a quantization approach, as an alternative of sparsification, to curb the growth of the radial basis function structure in kernel adaptive filtering. The basic idea behind this method is to quantize and hence compress the input (or feature) space. Different from sparsification, the new approach uses the "redundant" data to update the coefficient of the closest center. In particular, a quantized kernel least mean square (QKLMS) algorithm is developed, which is based on a simple online vector quantization method. The analytical study of the mean square convergence has been carried out. The energy conservation relation for QKLMS is established, and on this basis we arrive at a sufficient condition for mean square convergence, and a lower and upper bound on the theoretical value of the steady-state excess mean square error. Static function estimation and short-term chaotic time-series prediction examples are presented to demonstrate the excellent performance.

Eigenmodes of Multilayer Slit Structures

NASA Astrophysics Data System (ADS)

Kovalenko, A. N.

2017-12-01

We generalize the high-efficiency numerical-analytical method of calculating the eigenmodes of a microstrip line, which was proposed in [1], to multilayer slit structures. The obtained relationships make it possible to allow for the multilayer nature of the medium on the basis of solving the electrodynamic problem for a two-layer structure. The algebraic models of a single line and coupled slit lines in a multilayer dielectric medium are constructed. The matrix elements of the system of linear algebraic equations, which is used to determine the expansion coefficients of the electric field inside the slits in a Chebyshev basis, are converted to rapidly convergent series. The constructed models allow one to use computer simulation to obtain numerical results with high speed and accuracy, regardless of the number of dielectric layers. The presented results of a numerical study of the method convergence confirm high efficiency of the method.

Application of Improved APO Algorithm in Vulnerability Assessment and Reconstruction of Microgrid

NASA Astrophysics Data System (ADS)

Xie, Jili; Ma, Hailing

2018-01-01

Artificial Physics Optimization (APO) has good global search ability and can avoid the premature convergence phenomenon in PSO algorithm, which has good stability of fast convergence and robustness. On the basis of APO of the vector model, a reactive power optimization algorithm based on improved APO algorithm is proposed for the static structure and dynamic operation characteristics of microgrid. The simulation test is carried out through the IEEE 30-bus system and the result shows that the algorithm has better efficiency and accuracy compared with other optimization algorithms.

Characteristics of Perforated Diffusers at Free-stream Mach Number 1.90

NASA Technical Reports Server (NTRS)

Hunczak, Henry R; Kremzier, Emil J

1950-01-01

An investigation was conducted at Mach number 1.90 to determine pressure recovery and mass-flow characteristics of series of perforated convergent-divergent supersonic diffusers. Pressure recoveries as high as 96 percent were obtained, but at reduced mass flows through the diffuser. Theoretical considerations of effect of perforation distribution on shock stability in converging section of diffuser are presented and correlated with experimental data. A method of estimating relative importance of pressure recovery and mass flow on internal thrust coefficient basis is given and a comparison of various diffusers investigated is made.

Framework for three-dimensional coherent diffraction imaging by focused beam x-ray Bragg ptychography.

PubMed

Hruszkewycz, Stephan O; Holt, Martin V; Tripathi, Ash; Maser, Jörg; Fuoss, Paul H

2011-06-15

We present the framework for convergent beam Bragg ptychography, and, using simulations, we demonstrate that nanocrystals can be ptychographically reconstructed from highly convergent x-ray Bragg diffraction. The ptychographic iterative engine is extended to three dimensions and shown to successfully reconstruct a simulated nanocrystal using overlapping raster scans with a defocused curved beam, the diameter of which matches the crystal size. This object reconstruction strategy can serve as the basis for coherent diffraction imaging experiments at coherent scanning nanoprobe x-ray sources.

Best Intentions: Using Convergent Practices Divergently

ERIC Educational Resources Information Center

Whyte, Barbara; Deane, Penny

2017-01-01

Summative assessment and explicit teaching are on the increase in New Zealand primary and intermediate learning spaces; either, or both, frequently used by teachers to assist with requirements for National Standards. Combined use means learning destinations are set by teachers within convergent practice, allowing little room for student…

Convergence analysis of sliding mode trajectories in multi-objective neural networks learning.

PubMed

Costa, Marcelo Azevedo; Braga, Antonio Padua; de Menezes, Benjamin Rodrigues

2012-09-01

The Pareto-optimality concept is used in this paper in order to represent a constrained set of solutions that are able to trade-off the two main objective functions involved in neural networks supervised learning: data-set error and network complexity. The neural network is described as a dynamic system having error and complexity as its state variables and learning is presented as a process of controlling a learning trajectory in the resulting state space. In order to control the trajectories, sliding mode dynamics is imposed to the network. It is shown that arbitrary learning trajectories can be achieved by maintaining the sliding mode gains within their convergence intervals. Formal proofs of convergence conditions are therefore presented. The concept of trajectory learning presented in this paper goes further beyond the selection of a final state in the Pareto set, since it can be reached through different trajectories and states in the trajectory can be assessed individually against an additional objective function. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mathematical model and coordination algorithms for ensuring complex security of an organization

NASA Astrophysics Data System (ADS)

Novoseltsev, V. I.; Orlova, D. E.; Dubrovin, A. S.; Irkhin, V. P.

2018-03-01

The mathematical model of coordination when ensuring complex security of the organization is considered. On the basis of use of a method of casual search three types of algorithms of effective coordination adequate to mismatch level concerning security are developed: a coordination algorithm at domination of instructions of the coordinator; a coordination algorithm at domination of decisions of performers; a coordination algorithm at parity of interests of the coordinator and performers. Assessment of convergence of the algorithms considered above it was made by carrying out a computing experiment. The described algorithms of coordination have property of convergence in the sense stated above. And, the following regularity is revealed: than more simply in the structural relation the algorithm, for the smaller number of iterations is provided to those its convergence.

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

PubMed

Jiang, Wei; Roux, Benoît

2010-07-01

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

Parametric adaptive filtering and data validation in the bar GW detector AURIGA

NASA Astrophysics Data System (ADS)

Ortolan, A.; Baggio, L.; Cerdonio, M.; Prodi, G. A.; Vedovato, G.; Vitale, S.

2002-04-01

We report on our experience gained in the signal processing of the resonant GW detector AURIGA. Signal amplitude and arrival time are estimated by means of a matched-adaptive Wiener filter. The detector noise, entering in the filter set-up, is modelled as a parametric ARMA process; to account for slow non-stationarity of the noise, the ARMA parameters are estimated on an hourly basis. A requirement of the set-up of an unbiased Wiener filter is the separation of time spans with 'almost Gaussian' noise from non-Gaussian and/or strongly non-stationary time spans. The separation algorithm consists basically of a variance estimate with the Chauvenet convergence method and a threshold on the Curtosis index. The subsequent validation of data is strictly connected with the separation procedure: in fact, by injecting a large number of artificial GW signals into the 'almost Gaussian' part of the AURIGA data stream, we have demonstrated that the effective probability distributions of the signal-to-noise ratio χ2 and the time of arrival are those that are expected.

Convergent and Divergent Validity of the Learning Transfer System Inventory

ERIC Educational Resources Information Center

Holton, Elwood F., III; Bates, Reid A.; Bookter, Annette I.; Yamkovenko, V. Bogdan

2007-01-01

The Learning Transfer System Inventory (LTSI) was developed to identify a select set of factors with the potential to substantially enhance or inhibit transfer of learning to the work environment. It has undergone a variety of validation studies, including construct, criterion, and crosscultural studies. However, the convergent and divergent…

Sensitivity of Optimal Solutions to Control Problems for Second Order Evolution Subdifferential Inclusions.

PubMed

Bartosz, Krzysztof; Denkowski, Zdzisław; Kalita, Piotr

In this paper the sensitivity of optimal solutions to control problems described by second order evolution subdifferential inclusions under perturbations of state relations and of cost functionals is investigated. First we establish a new existence result for a class of such inclusions. Then, based on the theory of sequential [Formula: see text]-convergence we recall the abstract scheme concerning convergence of minimal values and minimizers. The abstract scheme works provided we can establish two properties: the Kuratowski convergence of solution sets for the state relations and some complementary [Formula: see text]-convergence of the cost functionals. Then these two properties are implemented in the considered case.

Efficient Controls for Finitely Convergent Sequential Algorithms

PubMed Central

Chen, Wei; Herman, Gabor T.

2010-01-01

Finding a feasible point that satisfies a set of constraints is a common task in scientific computing: examples are the linear feasibility problem and the convex feasibility problem. Finitely convergent sequential algorithms can be used for solving such problems; an example of such an algorithm is ART3, which is defined in such a way that its control is cyclic in the sense that during its execution it repeatedly cycles through the given constraints. Previously we found a variant of ART3 whose control is no longer cyclic, but which is still finitely convergent and in practice it usually converges faster than ART3 does. In this paper we propose a general methodology for automatic transformation of finitely convergent sequential algorithms in such a way that (i) finite convergence is retained and (ii) the speed of convergence is improved. The first of these two properties is proven by mathematical theorems, the second is illustrated by applying the algorithms to a practical problem. PMID:20953327

Acceleration of Convergence to Equilibrium in Markov Chains by Breaking Detailed Balance

NASA Astrophysics Data System (ADS)

Kaiser, Marcus; Jack, Robert L.; Zimmer, Johannes

2017-07-01

We analyse and interpret the effects of breaking detailed balance on the convergence to equilibrium of conservative interacting particle systems and their hydrodynamic scaling limits. For finite systems of interacting particles, we review existing results showing that irreversible processes converge faster to their steady state than reversible ones. We show how this behaviour appears in the hydrodynamic limit of such processes, as described by macroscopic fluctuation theory, and we provide a quantitative expression for the acceleration of convergence in this setting. We give a geometrical interpretation of this acceleration, in terms of currents that are antisymmetric under time-reversal and orthogonal to the free energy gradient, which act to drive the system away from states where (reversible) gradient-descent dynamics result in slow convergence to equilibrium.

Numerical Optimization of converging diverging miniature cavitating nozzles

NASA Astrophysics Data System (ADS)

Chavan, Kanchan; Bhingole, B.; Raut, J.; Pandit, A. B.

2015-12-01

The work focuses on the numerical optimization of converging diverging cavitating nozzles through nozzle dimensions and wall shape. The objective is to develop design rules for the geometry of cavitating nozzles for desired end-use. Two main aspects of nozzle design which affects the cavitation have been studied i.e. end dimensions of the geometry (i.e. angle and/or curvature of the inlet, outlet and the throat and the lengths of the converging and diverging sections) and wall curvatures(concave or convex). Angle of convergence at the inlet was found to control the cavity growth whereas angle of divergence of the exit controls the collapse of cavity. CFD simulations were carried out for the straight line converging and diverging sections by varying converging and diverging angles to study its effect on the collapse pressure generated by the cavity. Optimized geometry configurations were obtained on the basis of maximum Cavitational Efficacy Ratio (CER)i.e. cavity collapse pressure generated for a given permanent pressure drop across the system. With increasing capabilities in machining and fabrication, it is possible to exploit the effect of wall curvature to create nozzles with further increase in the CER. Effect of wall curvature has been studied for the straight, concave and convex shapes. Curvature has been varied and effect of concave and convex wall curvatures vis-à-vis straight walls studied for fixed converging and diverging angles.It is concluded that concave converging-diverging nozzles with converging angle of 20° and diverging angle of 5° with the radius of curvature 0.03 m and 0.1530 m respectively gives maximum CER. Preliminary experiments using optimized geometry are indicating similar trends and are currently being carried out. Refinements of the CFD technique using two phase flow simulations are planned.

A simple scheme for magnetic balance in four-component relativistic Kohn-Sham calculations of nuclear magnetic resonance shielding constants in a Gaussian basis.

PubMed

Olejniczak, Małgorzata; Bast, Radovan; Saue, Trond; Pecul, Magdalena

2012-01-07

We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn-Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms.

Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages

PubMed Central

Rao, Xiaolan; Lu, Nan; Li, Guifen; Nakashima, Jin; Tang, Yuhong; Dixon, Richard A.

2016-01-01

Almost all C4 plants require the co-ordination of the adjacent and fully differentiated cell types, mesophyll (M) and bundle sheath (BS). The C4 photosynthetic pathway operates through two distinct subtypes based on how malate is decarboxylated in BS cells; through NAD-malic enzyme (NAD-ME) or NADP-malic enzyme (NADP-ME). The diverse or unique cell-specific molecular features of M and BS cells from separate C4 subtypes of independent lineages remain to be determined. We here provide an M/BS cell type-specific transcriptome data set from the monocot NAD-ME subtype switchgrass (Panicum virgatum). A comparative transcriptomics approach was then applied to compare the M/BS mRNA profiles of switchgrass, monocot NADP-ME subtype C4 plants maize and Setaria viridis, and dicot NAD-ME subtype Cleome gynandra. We evaluated the convergence in the transcript abundance of core components in C4 photosynthesis and transcription factors to establish Kranz anatomy, as well as gene distribution of biological functions, in these four independent C4 lineages. We also estimated the divergence between NAD-ME and NADP-ME subtypes of C4 photosynthesis in the two cell types within C4 species, including differences in genes encoding decarboxylating enzymes, aminotransferases, and metabolite transporters, and differences in the cell-specific functional enrichment of RNA regulation and protein biogenesis/homeostasis. We suggest that C4 plants of independent lineages in both monocots and dicots underwent convergent evolution to establish C4 photosynthesis, while distinct C4 subtypes also underwent divergent processes for the optimization of M and BS cell co-ordination. The comprehensive data sets in our study provide a basis for further research on evolution of C4 species. PMID:26896851

Exponentially convergent state estimation for delayed switched recurrent neural networks.

PubMed

Ahn, Choon Ki

2011-11-01

This paper deals with the delay-dependent exponentially convergent state estimation problem for delayed switched neural networks. A set of delay-dependent criteria is derived under which the resulting estimation error system is exponentially stable. It is shown that the gain matrix of the proposed state estimator is characterised in terms of the solution to a set of linear matrix inequalities (LMIs), which can be checked readily by using some standard numerical packages. An illustrative example is given to demonstrate the effectiveness of the proposed state estimator.

A symmetric version of the generalized alternating direction method of multipliers for two-block separable convex programming.

PubMed

Liu, Jing; Duan, Yongrui; Sun, Min

2017-01-01

This paper introduces a symmetric version of the generalized alternating direction method of multipliers for two-block separable convex programming with linear equality constraints, which inherits the superiorities of the classical alternating direction method of multipliers (ADMM), and which extends the feasible set of the relaxation factor α of the generalized ADMM to the infinite interval [Formula: see text]. Under the conditions that the objective function is convex and the solution set is nonempty, we establish the convergence results of the proposed method, including the global convergence, the worst-case [Formula: see text] convergence rate in both the ergodic and the non-ergodic senses, where k denotes the iteration counter. Numerical experiments to decode a sparse signal arising in compressed sensing are included to illustrate the efficiency of the new method.

Set Convergences In Nonlinear Analysis and Optimization (Abstracts) (Convergences en Analyse Multivoque et Unilaterale (Resumes de Conferences),

DTIC Science & Technology

1992-06-01

Anal. Appl. 102 (1984), 399-414. 43 On B-subgradients and applications Alejandro Jofre Departamento de Ingenieria Matemrtica, Universidad de Chile...Universitd de Provence51)2S Catania Italic 3, place Victor Hugo 13331 Marseille Cedex Steve Robinson Michel Th~raDepartment of Industrial Engineering

Has the Elite Foundation Agenda Spread beyond the Gates? An Organizational Network Analysis of Nonmajor Philanthropic Giving in K-12 Education

ERIC Educational Resources Information Center

Ferrare, Joseph J.; Reynolds, Katherine

2016-01-01

Previous research focusing on major philanthropic foundations suggests that these actors have collectively converged around a set of jurisdictional challengers promoting market-based education reforms. Using correspondence analysis, network analysis, and geographic information science, this article empirically tests whether this convergence has…

Algorithm for computing descriptive statistics for very large data sets and the exa-scale era

NASA Astrophysics Data System (ADS)

Beekman, Izaak

2017-11-01

An algorithm for Single-point, Parallel, Online, Converging Statistics (SPOCS) is presented. It is suited for in situ analysis that traditionally would be relegated to post-processing, and can be used to monitor the statistical convergence and estimate the error/residual in the quantity-useful for uncertainty quantification too. Today, data may be generated at an overwhelming rate by numerical simulations and proliferating sensing apparatuses in experiments and engineering applications. Monitoring descriptive statistics in real time lets costly computations and experiments be gracefully aborted if an error has occurred, and monitoring the level of statistical convergence allows them to be run for the shortest amount of time required to obtain good results. This algorithm extends work by Pébay (Sandia Report SAND2008-6212). Pébay's algorithms are recast into a converging delta formulation, with provably favorable properties. The mean, variance, covariances and arbitrary higher order statistical moments are computed in one pass. The algorithm is tested using Sillero, Jiménez, & Moser's (2013, 2014) publicly available UPM high Reynolds number turbulent boundary layer data set, demonstrating numerical robustness, efficiency and other favorable properties.

Resolvent estimates in homogenisation of periodic problems of fractional elasticity

NASA Astrophysics Data System (ADS)

Cherednichenko, Kirill; Waurick, Marcus

2018-03-01

We provide operator-norm convergence estimates for solutions to a time-dependent equation of fractional elasticity in one spatial dimension, with rapidly oscillating coefficients that represent the material properties of a viscoelastic composite medium. Assuming periodicity in the coefficients, we prove operator-norm convergence estimates for an operator fibre decomposition obtained by applying to the original fractional elasticity problem the Fourier-Laplace transform in time and Gelfand transform in space. We obtain estimates on each fibre that are uniform in the quasimomentum of the decomposition and in the period of oscillations of the coefficients as well as quadratic with respect to the spectral variable. On the basis of these uniform estimates we derive operator-norm-type convergence estimates for the original fractional elasticity problem, for a class of sufficiently smooth densities of applied forces.

Robust non-rigid registration algorithm based on local affine registration

NASA Astrophysics Data System (ADS)

Wu, Liyang; Xiong, Lei; Du, Shaoyi; Bi, Duyan; Fang, Ting; Liu, Kun; Wu, Dongpeng

2018-04-01

Aiming at the problem that the traditional point set non-rigid registration algorithm has low precision and slow convergence speed for complex local deformation data, this paper proposes a robust non-rigid registration algorithm based on local affine registration. The algorithm uses a hierarchical iterative method to complete the point set non-rigid registration from coarse to fine. In each iteration, the sub data point sets and sub model point sets are divided and the shape control points of each sub point set are updated. Then we use the control point guided affine ICP algorithm to solve the local affine transformation between the corresponding sub point sets. Next, the local affine transformation obtained by the previous step is used to update the sub data point sets and their shape control point sets. When the algorithm reaches the maximum iteration layer K, the loop ends and outputs the updated sub data point sets. Experimental results demonstrate that the accuracy and convergence of our algorithm are greatly improved compared with the traditional point set non-rigid registration algorithms.

Wheat forecast economics effect study. [value of improved information on crop inventories, production, imports and exports

NASA Technical Reports Server (NTRS)

Mehra, R. K.; Rouhani, R.; Jones, S.; Schick, I.

1980-01-01

A model to assess the value of improved information regarding the inventories, productions, exports, and imports of crop on a worldwide basis is discussed. A previously proposed model is interpreted in a stochastic control setting and the underlying assumptions of the model are revealed. In solving the stochastic optimization problem, the Markov programming approach is much more powerful and exact as compared to the dynamic programming-simulation approach of the original model. The convergence of a dual variable Markov programming algorithm is shown to be fast and efficient. A computer program for the general model of multicountry-multiperiod is developed. As an example, the case of one country-two periods is treated and the results are presented in detail. A comparison with the original model results reveals certain interesting aspects of the algorithms and the dependence of the value of information on the incremental cost function.

Communication: Nuclear quadrupole moment-induced Cotton-Mouton effect in noble gas atoms

NASA Astrophysics Data System (ADS)

Fu, Li-juan; Rizzo, Antonio; Vaara, Juha

2013-11-01

New, high-sensitivity and high-resolution spectroscopic and imaging methods may be developed by exploiting nuclear magneto-optic effects. A first-principles electronic structure formulation of nuclear electric quadrupole moment-induced Cotton-Mouton effect (NQCME) is presented for closed-shell atoms. In NQCME, aligned quadrupole moments alter the index of refraction of the medium along with and perpendicular to the direction of nuclear alignment. The roles of basis-set convergence, electron correlation, and relativistic effects are investigated for three quadrupolar noble gas isotopes: 21Ne, 83Kr, and 131Xe. The magnitude of the resulting ellipticities is predicted to be 10-4-10-6 rad/(M cm) for fully spin-polarized nuclei. These should be detectable in the Voigt setup. Particularly interesting is the case of 131Xe, in which a high degree of spin polarization can be achieved via spin-exchange optical hyperpolarization.

Composite Intelligent Learning Control of Strict-Feedback Systems With Disturbance.

PubMed

Xu, Bin; Sun, Fuchun

2018-02-01

This paper addresses the dynamic surface control of uncertain nonlinear systems on the basis of composite intelligent learning and disturbance observer in presence of unknown system nonlinearity and time-varying disturbance. The serial-parallel estimation model with intelligent approximation and disturbance estimation is built to obtain the prediction error and in this way the composite law for weights updating is constructed. The nonlinear disturbance observer is developed using intelligent approximation information while the disturbance estimation is guaranteed to converge to a bounded compact set. The highlight is that different from previous work directly toward asymptotic stability, the transparency of the intelligent approximation and disturbance estimation is included in the control scheme. The uniformly ultimate boundedness stability is analyzed via Lyapunov method. Through simulation verification, the composite intelligent learning with disturbance observer can efficiently estimate the effect caused by system nonlinearity and disturbance while the proposed approach obtains better performance with higher accuracy.

Accurate complex scaling of three dimensional numerical potentials

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

Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan

2013-05-28

The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scalingmore » of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.« less

Adaptive NN control for discrete-time pure-feedback systems with unknown control direction under amplitude and rate actuator constraints.

PubMed

Chen, Weisheng

2009-07-01

This paper focuses on the problem of adaptive neural network tracking control for a class of discrete-time pure-feedback systems with unknown control direction under amplitude and rate actuator constraints. Two novel state-feedback and output-feedback dynamic control laws are established where the function tanh(.) is employed to solve the saturation constraint problem. Implicit function theorem and mean value theorem are exploited to deal with non-affine variables that are used as actual control. Radial basis function neural networks are used to approximate the desired input function. Discrete Nussbaum gain is used to estimate the unknown sign of control gain. The uniform boundedness of all closed-loop signals is guaranteed. The tracking error is proved to converge to a small residual set around the origin. A simulation example is provided to illustrate the effectiveness of control schemes proposed in this paper.

Seismic behaviour of mountain belts controlled by plate convergence rate

NASA Astrophysics Data System (ADS)

Dal Zilio, Luca; van Dinther, Ylona; Gerya, Taras V.; Pranger, Casper C.

2018-01-01

The relative contribution of tectonic and kinematic processes to seismic behaviour of mountain belts is still controversial. To understand the partitioning between these processes we developed a model that simulates both tectonic and seismic processes in a continental collision setting. These 2D seismo-thermo-mechanical (STM) models obtain a Gutenberg-Richter frequency-magnitude distribution due to spontaneous events occurring throughout the orogen. Our simulations suggest that both the corresponding slope (b value) and maximum earthquake magnitude (MWmax) correlate linearly with plate convergence rate. By analyzing 1D rheological profiles and isotherm depths we demonstrate that plate convergence rate controls the brittle strength through a rheological feedback with temperature and strain rate. Faster convergence leads to cooler temperatures and also results in more larger seismogenic domains, thereby increasing both MWmax and the relative number of large earthquakes (decreasing b value). This mechanism also predicts a more seismogenic lower crust, which is confirmed by a transition from uni- to bi-modal hypocentre depth distributions in our models. This transition and a linear relation between convergence rate and b value and MWmax is supported by our comparison of earthquakes recorded across the Alps, Apennines, Zagros and Himalaya. These results imply that deformation in the Alps occurs in a more ductile manner compared to the Himalayas, thereby reducing its seismic hazard. Furthermore, a second set of experiments with higher temperature and different orogenic architecture shows the same linear relation with convergence rate, suggesting that large-scale tectonic structure plays a subordinate role. We thus propose that plate convergence rate, which also controls the average differential stress of the orogen and its linear relation to the b value, is the first-order parameter controlling seismic hazard of mountain belts.

Stereoscopic camera and viewing systems with undistorted depth presentation and reduced or eliminated erroneous acceleration and deceleration perceptions, or with perceptions produced or enhanced for special effects

NASA Technical Reports Server (NTRS)

Diner, Daniel B. (Inventor)

1991-01-01

Methods for providing stereoscopic image presentation and stereoscopic configurations using stereoscopic viewing systems having converged or parallel cameras may be set up to reduce or eliminate erroneously perceived accelerations and decelerations by proper selection of parameters, such as an image magnification factor, q, and intercamera distance, 2w. For converged cameras, q is selected to be equal to Ve - qwl = 0, where V is the camera distance, e is half the interocular distance of an observer, w is half the intercamera distance, and l is the actual distance from the first nodal point of each camera to the convergence point, and for parallel cameras, q is selected to be equal to e/w. While converged cameras cannot be set up to provide fully undistorted three-dimensional views, they can be set up to provide a linear relationship between real and apparent depth and thus minimize erroneously perceived accelerations and decelerations for three sagittal planes, x = -w, x = 0, and x = +w which are indicated to the observer. Parallel cameras can be set up to provide fully undistorted three-dimensional views by controlling the location of the observer and by magnification and shifting of left and right images. In addition, the teachings of this disclosure can be used to provide methods of stereoscopic image presentation and stereoscopic camera configurations to produce a nonlinear relation between perceived and real depth, and erroneously produce or enhance perceived accelerations and decelerations in order to provide special effects for entertainment, training, or educational purposes.

Convergent evolution at the pathway level: predictable regulatory changes during flower color transitions.

PubMed

Larter, Maximilian; Dunbar-Wallis, Amy; Berardi, Andrea E; Smith, Stacey D

2018-06-07

The predictability of evolution, or whether lineages repeatedly follow the same evolutionary trajectories during phenotypic convergence remains an open question of evolutionary biology. In this study, we investigate evolutionary convergence at the biochemical pathway level and test the predictability of evolution using floral anthocyanin pigmentation, a trait with a well-understood genetic and regulatory basis. We reconstructed the evolution of floral anthocyanin content across 28 species of the Andean clade Iochrominae (Solanaceae) and investigated how shifts in pigmentation are related to changes in expression of 7 key anthocyanin pathway genes. We used phylogenetic multivariate analysis of gene expression to test for phenotypic and developmental convergence at a macroevolutionary scale. Our results show that the four independent losses of the ancestral pigment delphinidin involved convergent losses of expression of the three late pathway genes (F3'5'h, Dfr and Ans). Transitions between pigment types affecting floral hue (e.g. blue to red) involve changes to the expression of branching genes F3'h and F3'5'h, while the expression levels of early steps of the pathway are strongly conserved in all species. These patterns support the idea that the macroevolution of floral pigmentation follows predictable evolutionary trajectories to reach convergent phenotype space, repeatedly involving regulatory changes. This is likely driven by constraints at the pathway level, such as pleiotropy and regulatory structure.

Tackling creativity at its roots: Evidence for different patterns of EEG alpha activity related to convergent and divergent modes of task processing

PubMed Central

Jauk, Emanuel; Benedek, Mathias; Neubauer, Aljoscha C.

2012-01-01

The distinction between convergent and divergent cognitive processes given by Guilford (1956) had a strong influence on the empirical research on creative thinking. Neuroscientific studies typically find higher event-related synchronization in the EEG alpha rhythm for individuals engaged in creative ideation tasks compared to intelligence-related tasks. This study examined, whether these neurophysiological effects can also be found when both cognitive processing modes (convergent vs. divergent) are assessed by means of the same task employing a simple variation of instruction. A sample of 55 participants performed the alternate uses task as well as a more basic word association task while EEG was recorded. On a trial-by-trial basis, participants were either instructed to find a most common solution (convergent condition) or a most uncommon solution (divergent condition). The answers given in the divergent condition were in both tasks significantly more original than those in the convergent condition. Moreover, divergent processing was found to involve higher task-related EEG alpha power than convergent processing in both the alternate uses task and the word association task. EEG alpha synchronization can hence explicitly be associated with divergent cognitive processing rather than with general task characteristics of creative ideation tasks. Further results point to a differential involvement of frontal and parietal cortical areas by individuals of lower versus higher trait creativity. PMID:22390860

An efficient method for solving the steady Euler equations

NASA Technical Reports Server (NTRS)

Liou, M. S.

1986-01-01

An efficient numerical procedure for solving a set of nonlinear partial differential equations is given, specifically for the steady Euler equations. Solutions of the equations were obtained by Newton's linearization procedure, commonly used to solve the roots of nonlinear algebraic equations. In application of the same procedure for solving a set of differential equations we give a theorem showing that a quadratic convergence rate can be achieved. While the domain of quadratic convergence depends on the problems studied and is unknown a priori, we show that firstand second-order derivatives of flux vectors determine whether the condition for quadratic convergence is satisfied. The first derivatives enter as an implicit operator for yielding new iterates and the second derivatives indicates smoothness of the flows considered. Consequently flows involving shocks are expected to require larger number of iterations. First-order upwind discretization in conjunction with the Steger-Warming flux-vector splitting is employed on the implicit operator and a diagonal dominant matrix results. However the explicit operator is represented by first- and seond-order upwind differencings, using both Steger-Warming's and van Leer's splittings. We discuss treatment of boundary conditions and solution procedures for solving the resulting block matrix system. With a set of test problems for one- and two-dimensional flows, we show detailed study as to the efficiency, accuracy, and convergence of the present method.

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

Marana, Naiara L.; Albuquerque, Anderson R.; La Porta, Felipe A.

Periodic density functional theory calculations with the B3LYP hybrid functional and all-electron Gaussian basis set were performed to simulate the structural and electronic properties as well as the strain and formation energies of single-walled ZnO nanotubes (SWZnONTs) and Carbon nanotubes (SWCNTs) with different chiralities as functions of their diameters. For all SWZnONTs, the band gap, strain energy, and formation energy converge to ~4.5 eV, 0.0 eV/atom, and 0.40 eV/atom, respectively. This result suggests that the nanotubes are formed more easily from the surface than from the bulk. For SWCNTs, the strain energy is always positive, while the formation energy ismore » negative for armchair and zigzag nanotubes, therefore suggesting that these types of nanotubes can be preferentially formed from the bulk. The electronic properties of SWCNTs depend on the chirality; all armchair nanotubes are metallic, while zigzag and chiral nanotubes can be metallic or semiconducting, depending on the n and m vectors. - Graphical abstract: DFT/B3LYP were performed to simulate the structural and electronic properties as well as the strain and formation energies of SWZnONTs and SWCNTs with different chiralities as functions of their diameters. - Highlights: • The energies of SWZnONTs converge for chirality with diameters up 20 Å. • SWCNTs electronic properties depend on the chirality. • The properties of SWZnONTs are very similar to those of monolayer surface.« less

How hot? Systematic convergence of the replica exchange method using multiple reservoirs.

PubMed

Ruscio, Jory Z; Fawzi, Nicolas L; Head-Gordon, Teresa

2010-02-01

We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high-temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Abeta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. Copyright 2009 Wiley Periodicals, Inc.

Cosmic Reionization On Computers: Numerical and Physical Convergence

DOE PAGES

Gnedin, Nickolay Y.

2016-04-01

In this paper I show that simulations of reionization performed under the Cosmic Reionization On Computers (CROC) project do converge in space and mass, albeit rather slowly. A fully converged solution (for a given star formation and feedback model) can be determined at a level of precision of about 20%, but such a solution is useless in practice, since achieving it in production-grade simulations would require a large set of runs at various mass and spatial resolutions, and computational resources for such an undertaking are not yet readily available. In order to make progress in the interim, I introduce amore » weak convergence correction factor in the star formation recipe, which allows one to approximate the fully converged solution with finite resolution simulations. The accuracy of weakly converged simulations approaches a comparable, ~20% level of precision for star formation histories of individual galactic halos and other galactic properties that are directly related to star formation rates, like stellar masses and metallicities. Yet other properties of model galaxies, for example, their HI masses, are recovered in the weakly converged runs only within a factor of two.« less

Cosmic Reionization On Computers: Numerical and Physical Convergence

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

Gnedin, Nickolay Y.

In this paper I show that simulations of reionization performed under the Cosmic Reionization On Computers (CROC) project do converge in space and mass, albeit rather slowly. A fully converged solution (for a given star formation and feedback model) can be determined at a level of precision of about 20%, but such a solution is useless in practice, since achieving it in production-grade simulations would require a large set of runs at various mass and spatial resolutions, and computational resources for such an undertaking are not yet readily available. In order to make progress in the interim, I introduce amore » weak convergence correction factor in the star formation recipe, which allows one to approximate the fully converged solution with finite resolution simulations. The accuracy of weakly converged simulations approaches a comparable, ~20% level of precision for star formation histories of individual galactic halos and other galactic properties that are directly related to star formation rates, like stellar masses and metallicities. Yet other properties of model galaxies, for example, their HI masses, are recovered in the weakly converged runs only within a factor of two.« less

Error detection and data smoothing based on local procedures

NASA Technical Reports Server (NTRS)

Guerra, V. M.

1974-01-01

An algorithm is presented which is able to locate isolated bad points and correct them without contaminating the rest of the good data. This work has been greatly influenced and motivated by what is currently done in the manual loft. It is not within the scope of this work to handle small random errors characteristic of a noisy system, and it is therefore assumed that the bad points are isolated and relatively few when compared with the total number of points. Motivated by the desire to imitate the loftsman a visual experiment was conducted to determine what is considered smooth data. This criterion is used to determine how much the data should be smoothed and to prove that this method produces such data. The method utimately converges to a set of points that lies on the polynomial that interpolates the first and last points; however convergence to such a set is definitely not the purpose of our algorithm. The proof of convergence is necessary to demonstrate that oscillation does not take place and that in a finite number of steps the method produces a set as smooth as desired.

Convergent evolution as natural experiment: the tape of life reconsidered

PubMed Central

Powell, Russell; Mariscal, Carlos

2015-01-01

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. PMID:26640647

Convergent evolution as natural experiment: the tape of life reconsidered.

PubMed

Powell, Russell; Mariscal, Carlos

2015-12-06

Stephen Jay Gould argued that replaying the 'tape of life' would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution-the independent origination of similar biological forms and functions-which many interpret as evidence against Gould's thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the 'critique from convergent evolution' fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life.

"Response to Loomis et al.:" Convergence and Uniformity in Teacher Production--A Catalyst to Create Individualistic Teacher Education Programs

ERIC Educational Resources Information Center

Nagel, Nancy G.

2008-01-01

In the essay, "The logic of convergence and uniformity in teacher production", Loomis et al. advocate that teachers are experiencing a shift from individualistic programs that prepare them toward uniform, common teacher preparation resulting from top-down agenda-setting and mandated regulations. In their theoretical stance, the knowledge…

Converging Higher Education Systems in a Global Setting: The Example of France and India

ERIC Educational Resources Information Center

Pilkington, Marc

2014-01-01

We present a comparative survey between the French and Indian higher education systems. In spite of their respective idiosyncratic features, we show that the two countries have both evolved comprehensively toward a knowledge-based society, in order to ensure the prosperity of their citizens. Secondly, we single out a threefold convergence between…

Computation of indirect nuclear spin-spin couplings with reduced complexity in pure and hybrid density functional approximations.

PubMed

Luenser, Arne; Kussmann, Jörg; Ochsenfeld, Christian

2016-09-28

We present a (sub)linear-scaling algorithm to determine indirect nuclear spin-spin coupling constants at the Hartree-Fock and Kohn-Sham density functional levels of theory. Employing efficient integral algorithms and sparse algebra routines, an overall (sub)linear scaling behavior can be obtained for systems with a non-vanishing HOMO-LUMO gap. Calculations on systems with over 1000 atoms and 20 000 basis functions illustrate the performance and accuracy of our reference implementation. Specifically, we demonstrate that linear algebra dominates the runtime of conventional algorithms for 10 000 basis functions and above. Attainable speedups of our method exceed 6 × in total runtime and 10 × in the linear algebra steps for the tested systems. Furthermore, a convergence study of spin-spin couplings of an aminopyrazole peptide upon inclusion of the water environment is presented: using the new method it is shown that large solvent spheres are necessary to converge spin-spin coupling values.

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

Liu, L; Han, Y; Jin, M

Purpose: To develop an iterative reconstruction method for X-ray CT, in which the reconstruction can quickly converge to the desired solution with much reduced projection views. Methods: The reconstruction is formulated as a convex feasibility problem, i.e. the solution is an intersection of three convex sets: 1) data fidelity (DF) set – the L2 norm of the difference of observed projections and those from the reconstructed image is no greater than an error bound; 2) non-negativity of image voxels (NN) set; and 3) piecewise constant (PC) set - the total variation (TV) of the reconstructed image is no greater thanmore » an upper bound. The solution can be found by applying projection onto convex sets (POCS) sequentially for these three convex sets. Specifically, the algebraic reconstruction technique and setting negative voxels as zero are used for projection onto the DF and NN sets, respectively, while the projection onto the PC set is achieved by solving a standard Rudin, Osher, and Fatemi (ROF) model. The proposed method is named as full sequential POCS (FS-POCS), which is tested using the Shepp-Logan phantom and the Catphan600 phantom and compared with two similar algorithms, TV-POCS and CP-TV. Results: Using the Shepp-Logan phantom, the root mean square error (RMSE) of reconstructed images changing along with the number of iterations is used as the convergence measurement. In general, FS- POCS converges faster than TV-POCS and CP-TV, especially with fewer projection views. FS-POCS can also achieve accurate reconstruction of cone-beam CT of the Catphan600 phantom using only 54 views, comparable to that of FDK using 364 views. Conclusion: We developed an efficient iterative reconstruction for sparse-view CT using full sequential POCS. The simulation and physical phantom data demonstrated the computational efficiency and effectiveness of FS-POCS.« less

Internal performance of a hybrid axisymmetric/nonaxisymmetric convergent-divergent nozzle

NASA Technical Reports Server (NTRS)

Taylor, John G.

1991-01-01

An investigation was conducted in the static test facility of the Langley 16-foot transonic tunnel to determine the internal performance of a hybrid axisymmetric/nonaxisymmetric nozzle in forward-thrust mode. Nozzle cross-sections in the spherical convergent section were axisymmetric whereas cross-sections in the divergent flap area nonaxisymmetric (two-dimensional). Nozzle concepts simulating dry and afterburning power settings were investigated. Both subsonic cruise and supersonic cruise expansion ratios were tested for the dry power nozzle concepts. Afterburning power configurations were tested at an expansion ratio typical for subsonic acceleration. The spherical convergent flaps were designed in such a way that the transition from axisymmetric to nonaxisymmetric cross-section occurred in the region of the nozzle throat. Three different nozzle throat geometries were tested for each nozzle power setting. High-pressure air was used to simulate jet exhaust at nozzle pressure ratios up to 12.0.

Advanced ab initio relativistic calculations of transition probabilities for some O I and O III emission lines

NASA Astrophysics Data System (ADS)

Nguyen, T. V. B.; Chantler, C. T.; Lowe, J. A.; Grant, I. P.

2014-06-01

This work presents new ab initio relativistic calculations using the multiconfiguration Dirac-Hartree-Fock method of some O I and O III transition lines detected in B-type and Wolf-Rayet stars. Our results are the first able to be presented in both the length and velocity gauges, with excellent gauge convergence. Compared to previous experimental and theoretical uncertainties of up to 50 per cent, our accuracies appear to be in the range of 0.33-5.60 per cent, with gauge convergence up to 0.6 per cent. Similar impressive convergence of the calculated energies is also shown. Two sets of theoretical computations are compared with earlier tabulated measurements. Excellent agreement is obtained with one set of transitions but an interesting and consistent discrepancy exists between the current work and the prior literature, deserving of future experimental studies.

Stochastic Leader Gravitational Search Algorithm for Enhanced Adaptive Beamforming Technique

PubMed Central

Darzi, Soodabeh; Islam, Mohammad Tariqul; Tiong, Sieh Kiong; Kibria, Salehin; Singh, Mandeep

2015-01-01

In this paper, stochastic leader gravitational search algorithm (SL-GSA) based on randomized k is proposed. Standard GSA (SGSA) utilizes the best agents without any randomization, thus it is more prone to converge at suboptimal results. Initially, the new approach randomly choses k agents from the set of all agents to improve the global search ability. Gradually, the set of agents is reduced by eliminating the agents with the poorest performances to allow rapid convergence. The performance of the SL-GSA was analyzed for six well-known benchmark functions, and the results are compared with SGSA and some of its variants. Furthermore, the SL-GSA is applied to minimum variance distortionless response (MVDR) beamforming technique to ensure compatibility with real world optimization problems. The proposed algorithm demonstrates superior convergence rate and quality of solution for both real world problems and benchmark functions compared to original algorithm and other recent variants of SGSA. PMID:26552032

Expression profiling associates blood and brain glucocorticoid receptor signaling with trauma-related individual differences in both sexes.

PubMed

Daskalakis, Nikolaos P; Cohen, Hagit; Cai, Guiqing; Buxbaum, Joseph D; Yehuda, Rachel

2014-09-16

Delineating the molecular basis of individual differences in the stress response is critical to understanding the pathophysiology and treatment of posttraumatic stress disorder (PTSD). In this study, 7 d after predator-scent-stress (PSS) exposure, male and female rats were classified into vulnerable (i.e., "PTSD-like") and resilient (i.e., minimally affected) phenotypes on the basis of their performance on a variety of behavioral measures. Genome-wide expression profiling in blood and two limbic brain regions (amygdala and hippocampus), followed by quantitative PCR validation, was performed in these two groups of animals, as well as in an unexposed control group. Differentially expressed genes were identified in blood and brain associated with PSS-exposure and with distinct behavioral profiles postexposure. There was a small but significant between-tissue overlap (4-21%) for the genes associated with exposure-related individual differences, indicating convergent gene expression in both sexes. To uncover convergent signaling pathways across tissue and sex, upstream activated/deactivated transcription factors were first predicted for each tissue and then the respective pathways were identified. Glucocorticoid receptor (GR) signaling was the only convergent pathway associated with individual differences when using the most stringent statistical threshold. Corticosterone treatment 1 h after PSS-exposure prevented anxiety and hyperarousal 7 d later in both sexes, confirming the GR involvement in the PSS behavioral response. In conclusion, genes and pathways associated with extreme differences in the traumatic stress behavioral response can be distinguished from those associated with trauma exposure. Blood-based biomarkers can predict aspects of brain signaling. GR signaling is a convergent signaling pathway, associated with trauma-related individual differences in both sexes.

Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals

PubMed Central

Liu, Zhen; Wang, Wei; Zhang, Tong-Zuo; Li, Gong-Hua; He, Kai; Huang, Jing-Fei; Jiang, Xue-Long; Murphy, Robert W.; Shi, Peng

2014-01-01

Hibernating mammals need to be insensitive to acid in order to cope with conditions of high CO2; however, the molecular basis of acid tolerance remains largely unknown. The African naked mole-rat (Heterocephalus glaber) and hibernating mammals share similar environments and physiological features. In the naked mole-rat, acid insensitivity has been shown to be conferred by the functional motif of the sodium ion channel NaV1.7. There is now an opportunity to evaluate acid insensitivity in other taxa. In this study, we tested for functional convergence of NaV1.7 in 71 species of mammals, including 22 species that hibernate. Our analyses revealed a functional convergence of amino acid sequences, which occurred at least six times independently in mammals that hibernate. Evolutionary analyses determined that the convergence results from both parallel and divergent evolution of residues in the functional motif. Our findings not only identify the functional molecules responsible for acid insensitivity in hibernating mammals, but also open new avenues to elucidate the molecular underpinnings of acid insensitivity in mammals. PMID:24352952

Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals.

PubMed

Liu, Zhen; Wang, Wei; Zhang, Tong-Zuo; Li, Gong-Hua; He, Kai; Huang, Jing-Fei; Jiang, Xue-Long; Murphy, Robert W; Shi, Peng

2014-02-07

Hibernating mammals need to be insensitive to acid in order to cope with conditions of high CO2; however, the molecular basis of acid tolerance remains largely unknown. The African naked mole-rat (Heterocephalus glaber) and hibernating mammals share similar environments and physiological features. In the naked mole-rat, acid insensitivity has been shown to be conferred by the functional motif of the sodium ion channel NaV1.7. There is now an opportunity to evaluate acid insensitivity in other taxa. In this study, we tested for functional convergence of NaV1.7 in 71 species of mammals, including 22 species that hibernate. Our analyses revealed a functional convergence of amino acid sequences, which occurred at least six times independently in mammals that hibernate. Evolutionary analyses determined that the convergence results from both parallel and divergent evolution of residues in the functional motif. Our findings not only identify the functional molecules responsible for acid insensitivity in hibernating mammals, but also open new avenues to elucidate the molecular underpinnings of acid insensitivity in mammals.

Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

PubMed Central

Ellis, Nicholas A.; Glazer, Andrew M.; Donde, Nikunj N.; Cleves, Phillip A.; Agoglia, Rachel M.; Miller, Craig T.

2015-01-01

Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms. PMID:26062935

CONVERGENT TRANSCRIPTOMICS AND PROTEOMICS OF ENVIRONMENTAL ENRICHMENT AND COCAINE IDENTIFIES NOVEL THERAPEUTIC STRATEGIES FOR ADDICTION

PubMed Central

ZHANG, YAFANG; CROFTON, ELIZABETH J.; FAN, XIUZHEN; LI, DINGGE; KONG, FANPING; SINHA, MALA; LUXON, BRUCE A.; SPRATT, HEIDI M.; LICHTI, CHERYL F.; GREEN, THOMAS A.

2016-01-01

Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs. isolation and cocaine self-administration vs. saline. Multiple bioinformatics approaches (e.g. Gene Ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA)) were used to interrogate these rich data sets. Although there was little correspondence between mRNA vs. protein at the individual target level, good correspondence was found at the level of gene/protein sets, particularly for the environmental enrichment manipulation. These data identify gene sets where there is a positive relationship between changes in mRNA and protein (e.g. glycolysis, ATP synthesis, translation elongation factor activity, etc.) and gene sets where there is an inverse relationship (e.g. ribosomes, Rho GTPase signaling, protein ubiquitination, etc.). Overall environmental enrichment produced better correspondence than cocaine self-administration. The individual targets contributing to mRNA and protein effects were largely not overlapping. As a whole, these results confirm that robust transcriptomic and proteomic data sets can provide similar results at the gene/protein set level even when there is little correspondence at the individual target level and little overlap in the targets contributing to the effects. PMID:27717806

Convergence or divergence of male and female physicians' hours of work and income.

PubMed

Dedobbeleer, N; Contandriopoulos, A P; Desjardins, S

1995-08-01

This article verifies if the increase in the percentage of women in the medical profession led to the convergence of male and female physicians' hours of work as well as income. Active physicians in Quebec in 1978 were compared to the ones in 1988. Data were obtained from the computerized files of the Quebec Corporation of Physicians and the Régie d'assurance-maladie du Quebec. Despite the increasing representation of women in the medical profession, gender differences in hours worked and income remained. However, results also showed a tendency toward a convergence in total hours of work, more behavioral variation among women physicians and some behavioral change among men. The experience of the past should thus not be used as the basis for projections of future physician productivity or for medical manpower planning purposes without a careful analysis of trends in behavioral changes.

On Certain Theoretical Developments Underlying the Hilbert-Huang Transform

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Blank, Karin; Flatley, Thomas; Huang, Norden E.; Petrick, David; Hestness, Phyllis

2006-01-01

One of the main traditional tools used in scientific and engineering data spectral analysis is the Fourier Integral Transform and its high performance digital equivalent - the Fast Fourier Transform (FFT). Both carry strong a-priori assumptions about the source data, such as being linear and stationary, and of satisfying the Dirichlet conditions. A recent development at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC), known as the Hilbert-Huang Transform (HHT), proposes a novel approach to the solution for the nonlinear class of spectral analysis problems. Using a-posteriori data processing based on the Empirical Mode Decomposition (EMD) sifting process (algorithm), followed by the normalized Hilbert Transform of the decomposed data, the HHT allows spectral analysis of nonlinear and nonstationary data. The EMD sifting process results in a non-constrained decomposition of a source real-value data vector into a finite set of Intrinsic Mode Functions (IMF). These functions form a nearly orthogonal derived from the data (adaptive) basis. The IMFs can be further analyzed for spectrum content by using the classical Hilbert Transform. A new engineering spectral analysis tool using HHT has been developed at NASA GSFC, the HHT Data Processing System (HHT-DPS). As the HHT-DPS has been successfully used and commercialized, new applications pose additional questions about the theoretical basis behind the HHT and EMD algorithms. Why is the fastest changing component of a composite signal being sifted out first in the EMD sifting process? Why does the EMD sifting process seemingly converge and why does it converge rapidly? Does an IMF have a distinctive structure? Why are the IMFs nearly orthogonal? We address these questions and develop the initial theoretical background for the HHT. This will contribute to the development of new HHT processing options, such as real-time and 2-D processing using Field Programmable Gate Array (FPGA) computational resources,

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting.

PubMed

Naden, Levi N; Shirts, Michael R

2016-04-12

We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the computational cost to estimate thermodynamic properties from molecular simulations for over 130,000 tested parameter combinations from over 1000 CPU years to tens of CPU days. This speed increase is achieved primarily by computing the potential energy as a linear combination of basis functions, computed from either modified simulation code or as the difference of energy between two reference states, which can be done without any simulation code modification. The thermodynamic properties are then estimated with the Multistate Bennett Acceptance Ratio (MBAR) as a function of multiple model parameters without the need to define a priori how the states are connected by a pathway. Instead, we adaptively sample a set of points in parameter space to create mutual configuration space overlap. The existence of regions of poor configuration space overlap are detected by analyzing the eigenvalues of the sampled states' overlap matrix. The configuration space overlap to sampled states is monitored alongside the mean and maximum uncertainty to determine convergence, as neither the uncertainty or the configuration space overlap alone is a sufficient metric of convergence. This adaptive sampling scheme is demonstrated by estimating with high precision the solvation free energies of charged particles of Lennard-Jones plus Coulomb functional form with charges between -2 and +2 and generally physical values of σij and ϵij in TIP3P water. We also compute entropy, enthalpy, and radial distribution functions of arbitrary unsampled parameter combinations using only the data from these sampled states and use the estimates of free energies over the entire space to examine the deviation of atomistic simulations from the Born approximation to the solvation free energy.

A stable second order method for training back propagation networks

NASA Technical Reports Server (NTRS)

Nachtsheim, Philip R.

1993-01-01

A simple method for improving the learning rate of the back-propagation algorithm is described. The basis of the method is that approximate second order corrections can be incorporated in the output units. The extended method leads to significant improvements in the convergence rate.

Conceptualising Secondary Aurality and Its Impact on Possibility for Engagement of Children and Adolescents within School Music Settings

ERIC Educational Resources Information Center

Carlisle, Katie

2011-01-01

This paper explores the convergence of technology and the arts within the context of aurality in the twenty-first century. Jenkins argued this is taking place within a cultural convergence, whereby a vernacular culture focused upon participation, creation, performance, and migratory behaviour of media audiences has emerged. The developing changes…

Localized basis functions and other computational improvements in variational nonorthogonal basis function methods for quantum mechanical scattering problems involving chemical reactions

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Truhlar, Donald G.

1990-01-01

The Generalized Newton Variational Principle for 3D quantum mechanical reactive scattering is briefly reviewed. Then three techniques are described which improve the efficiency of the computations. First, the fact that the Hamiltonian is Hermitian is used to reduce the number of integrals computed, and then the properties of localized basis functions are exploited in order to eliminate redundant work in the integral evaluation. A new type of localized basis function with desirable properties is suggested. It is shown how partitioned matrices can be used with localized basis functions to reduce the amount of work required to handle the complex boundary conditions. The new techniques do not introduce any approximations into the calculations, so they may be used to obtain converged solutions of the Schroedinger equation.

Convergence in parameters and predictions using computational experimental design.

PubMed

Hagen, David R; White, Jacob K; Tidor, Bruce

2013-08-06

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

Multilevel filtering elliptic preconditioners

NASA Technical Reports Server (NTRS)

Kuo, C. C. Jay; Chan, Tony F.; Tong, Charles

1989-01-01

A class of preconditioners is presented for elliptic problems built on ideas borrowed from the digital filtering theory and implemented on a multilevel grid structure. They are designed to be both rapidly convergent and highly parallelizable. The digital filtering viewpoint allows the use of filter design techniques for constructing elliptic preconditioners and also provides an alternative framework for understanding several other recently proposed multilevel preconditioners. Numerical results are presented to assess the convergence behavior of the new methods and to compare them with other preconditioners of multilevel type, including the usual multigrid method as preconditioner, the hierarchical basis method and a recent method proposed by Bramble-Pasciak-Xu.

Vibrational excitation and vibrationally resolved electronic excitation cross sections of positron-H2 scattering

NASA Astrophysics Data System (ADS)

Zammit, Mark; Fursa, Dmitry; Savage, Jeremy; Bray, Igor

2016-09-01

Vibrational excitation and vibrationally resolved electronic excitation cross sections of positron-H2 scattering have been calculated using the single-centre molecular convergent close-coupling (CCC) method. The adiabatic-nuclei approximation was utilized to model the above scattering processes and obtain the vibrationally resolved positron-H2 scattering length. As previously demonstrated, the CCC results are converged and accurately account for virtual and physical positronium formation by coupling basis functions with large orbital angular momentum. Here vibrationally resolved integrated and differential cross sections are presented over a wide energy range and compared with previous calculations and available experiments. Los Alamos National Laboratory and Curtin University.

Generalized Bregman distances and convergence rates for non-convex regularization methods

NASA Astrophysics Data System (ADS)

Grasmair, Markus

2010-11-01

We generalize the notion of Bregman distance using concepts from abstract convexity in order to derive convergence rates for Tikhonov regularization with non-convex regularization terms. In particular, we study the non-convex regularization of linear operator equations on Hilbert spaces, showing that the conditions required for the application of the convergence rates results are strongly related to the standard range conditions from the convex case. Moreover, we consider the setting of sparse regularization, where we show that a rate of order δ1/p holds, if the regularization term has a slightly faster growth at zero than |t|p.

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

PubMed

Viñes, Francesc; Illas, Francesc

2017-03-30

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

Non-adiabatic dynamics around a conical intersection with surface-hopping coupled coherent states

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

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

A surface-hopping extension of the coupled coherent states-method [D. Shalashilin and M. Child, Chem. Phys. 304, 103-120 (2004)] for simulating non-adiabatic dynamics with quantum effects of the nuclei is put forward. The time-dependent Schrödinger equation for the motion of the nuclei is solved in a moving basis set. The basis set is guided by classical trajectories, which can hop stochastically between different electronic potential energy surfaces. The non-adiabatic transitions are modelled by a modified version of Tully’s fewest switches algorithm. The trajectories consist of Gaussians in the phase space of the nuclei (coherent states) combined with amplitudes for an electronicmore » wave function. The time-dependent matrix elements between different coherent states determine the amplitude of each trajectory in the total multistate wave function; the diagonal matrix elements determine the hopping probabilities and gradients. In this way, both interference effects and non-adiabatic transitions can be described in a very compact fashion, leading to the exact solution if convergence with respect to the number of trajectories is achieved and the potential energy surfaces are known globally. The method is tested on a 2D model for a conical intersection [A. Ferretti, J. Chem. Phys. 104, 5517 (1996)], where a nuclear wavepacket encircles the point of degeneracy between two potential energy surfaces and interferes with itself. These interference effects are absent in classical trajectory-based molecular dynamics but can be fully incorpo rated if trajectories are replaced by surface hopping coupled coherent states.« less

An Information Processing Perspective on Divergence and Convergence in Collaborative Learning

ERIC Educational Resources Information Center

Jorczak, Robert L.

2011-01-01

This paper presents a model of collaborative learning that takes an information processing perspective of learning by social interaction. The collaborative information processing model provides a theoretical basis for understanding learning principles associated with social interaction and explains why peer-to-peer discussion is potentially more…

Community Psychology in Australia and Aotearoa/New Zealand

ERIC Educational Resources Information Center

Fisher, Adrian T.; Gridley, Heather; Thomas, David R.; Bishop, Brian

2008-01-01

Community psychology in Australia and Aotearoa/New Zealand reflect interesting parallels and convergences. While both have a strong educational basis influenced by North American publications, they have developed foci and forms of practice reflecting the cultural, political, and historic underpinnings of these two countries. In New Zealand,…

The Vertical Structure of Urban Soils and Their Convergence Across Cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

The vertical geography of urban soils and its convergence across cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

Weight of evidence evaluation of adverse outcome pathways converging at impaired vitellogenin synthesis leading to reproductive impairment

EPA Science Inventory

Adverse outcome pathways (AOPs) provide a framework that supports greater use of mechanistic data measured at lower levels of biological organization as a basis for regulatory decision-making. However, it is recognized that different types of regulatory applications and decisions...

Optimization of selected molecular orbitals in group basis sets.

PubMed

Ferenczy, György G; Adams, William H

2009-04-07

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

COSMIC REIONIZATION ON COMPUTERS: NUMERICAL AND PHYSICAL CONVERGENCE

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

Gnedin, Nickolay Y., E-mail: gnedin@fnal.gov; Kavli Institute for Cosmological Physics, University of Chicago, Chicago, IL 60637; Department of Astronomy and Astrophysics, University of Chicago, Chicago, IL 60637

In this paper I show that simulations of reionization performed under the Cosmic Reionization On Computers project do converge in space and mass, albeit rather slowly. A fully converged solution (for a given star formation and feedback model) can be determined at a level of precision of about 20%, but such a solution is useless in practice, since achieving it in production-grade simulations would require a large set of runs at various mass and spatial resolutions, and computational resources for such an undertaking are not yet readily available. In order to make progress in the interim, I introduce a weakmore » convergence correction factor in the star formation recipe, which allows one to approximate the fully converged solution with finite-resolution simulations. The accuracy of weakly converged simulations approaches a comparable, ∼20% level of precision for star formation histories of individual galactic halos and other galactic properties that are directly related to star formation rates, such as stellar masses and metallicities. Yet other properties of model galaxies, for example, their H i masses, are recovered in the weakly converged runs only within a factor of 2.« less

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

PubMed

Kevorkyants, Ruslan; Eshuis, Henk; Pavanello, Michele

2014-07-28

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

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

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

Kevorkyants, Ruslan; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Eshuis, Henk

2014-07-28

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

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

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

Indirect addressing and load balancing for faster solution to Mandelbrot Set on SIMD architectures

NASA Technical Reports Server (NTRS)

Tomboulian, Sherryl

1989-01-01

SIMD computers with local indirect addressing allow programs to have queues and buffers, making certain kinds of problems much more efficient. Examined here are a class of problems characterized by computations on data points where the computation is identical, but the convergence rate is data dependent. Normally, in this situation, the algorithm time is governed by the maximum number of iterations required by each point. Using indirect addressing allows a processor to proceed to the next data point when it is done, reducing the overall number of iterations required to approach the mean convergence rate when a sufficiently large problem set is solved. Load balancing techniques can be applied for additional performance improvement. Simulations of this technique applied to solving Mandelbrot Sets indicate significant performance gains.

Equilibria Configurations for Epitaxial Crystal Growth with Adatoms

NASA Astrophysics Data System (ADS)

Caroccia, Marco; Cristoferi, Riccardo; Dietrich, Laurent

2018-05-01

The behavior of a surface energy F}(E,u)} , where E is a set of finite perimeter and u\\in L^1(partial^{*} E, R_+) , is studied. These energies have been recently considered in the context of materials science to derive a new model in crystal growth that takes into account the effect of atoms, the freely diffusing on the surface (called adatoms), which are responsible for morphological evolution through an attachment and detachment process. Regular critical points, the existence and uniqueness of minimizers are discussed and the relaxation of F in a general setting under the L 1 convergence of sets and the vague convergence of measures is characterized. This is part of an ongoing project aimed at an analytical study of diffuse interface approximations of the associated evolution equations.

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

PubMed

Brown, James; Carrington, Tucker

2016-10-14

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

Convergence and attractivity of memristor-based cellular neural networks with time delays.

PubMed

Qin, Sitian; Wang, Jun; Xue, Xiaoping

2015-03-01

This paper presents theoretical results on the convergence and attractivity of memristor-based cellular neural networks (MCNNs) with time delays. Based on a realistic memristor model, an MCNN is modeled using a differential inclusion. The essential boundedness of its global solutions is proven. The state of MCNNs is further proven to be convergent to a critical-point set located in saturated region of the activation function, when the initial state locates in a saturated region. It is shown that the state convergence time period is finite and can be quantitatively estimated using given parameters. Furthermore, the positive invariance and attractivity of state in non-saturated regions are also proven. The simulation results of several numerical examples are provided to substantiate the results. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

2011-06-07

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

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

PubMed

Feller, David; Peterson, Kirk A

2013-08-28

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 E(h)) 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.

Adaptive polynomial chaos techniques for uncertainty quantification of a gas cooled fast reactor transient

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

Perko, Z.; Gilli, L.; Lathouwers, D.

2013-07-01

Uncertainty quantification plays an increasingly important role in the nuclear community, especially with the rise of Best Estimate Plus Uncertainty methodologies. Sensitivity analysis, surrogate models, Monte Carlo sampling and several other techniques can be used to propagate input uncertainties. In recent years however polynomial chaos expansion has become a popular alternative providing high accuracy at affordable computational cost. This paper presents such polynomial chaos (PC) methods using adaptive sparse grids and adaptive basis set construction, together with an application to a Gas Cooled Fast Reactor transient. Comparison is made between a new sparse grid algorithm and the traditionally used techniquemore » proposed by Gerstner. An adaptive basis construction method is also introduced and is proved to be advantageous both from an accuracy and a computational point of view. As a demonstration the uncertainty quantification of a 50% loss of flow transient in the GFR2400 Gas Cooled Fast Reactor design was performed using the CATHARE code system. The results are compared to direct Monte Carlo sampling and show the superior convergence and high accuracy of the polynomial chaos expansion. Since PC techniques are easy to implement, they can offer an attractive alternative to traditional techniques for the uncertainty quantification of large scale problems. (authors)« less

Application of p-Multigrid to Discontinuous Galerkin Formulations of the Poisson Equation

NASA Technical Reports Server (NTRS)

Helenbrook, B. T.; Atkins, H. L.

2006-01-01

We investigate p-multigrid as a solution method for several different discontinuous Galerkin (DG) formulations of the Poisson equation. Different combinations of relaxation schemes and basis sets have been combined with the DG formulations to find the best performing combination. The damping factors of the schemes have been determined using Fourier analysis for both one and two-dimensional problems. One important finding is that when using DG formulations, the standard approach of forming the coarse p matrices separately for each level of multigrid is often unstable. To ensure stability the coarse p matrices must be constructed from the fine grid matrices using algebraic multigrid techniques. Of the relaxation schemes, we find that the combination of Jacobi relaxation with the spectral element basis is fairly effective. The results using this combination are p sensitive in both one and two dimensions, but reasonable convergence rates can still be achieved for moderate values of p and isotropic meshes. A competitive alternative is a block Gauss-Seidel relaxation. This actually out performs a more expensive line relaxation when the mesh is isotropic. When the mesh becomes highly anisotropic, the implicit line method and the Gauss-Seidel implicit line method are the only effective schemes. Adding the Gauss-Seidel terms to the implicit line method gives a significant improvement over the line relaxation method.

Uniform electron gases. III. Low-density gases on three-dimensional spheres.

PubMed

Agboola, Davids; Knol, Anneke L; Gill, Peter M W; Loos, Pierre-François

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGF centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids - the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) - and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.

Aviation and healthcare: a comparative review with implications for patient safety.

PubMed

Kapur, Narinder; Parand, Anam; Soukup, Tayana; Reader, Tom; Sevdalis, Nick

2016-01-01

Safety in aviation has often been compared with safety in healthcare. Following a recent article in this journal, the UK government set up an Independent Patient Safety Investigation Service, to emulate a similar well-established body in aviation. On the basis of a detailed review of relevant publications that examine patient safety in the context of aviation practice, we have drawn up a table of comparative features and a conceptual framework for patient safety. Convergence and divergence of safety-related behaviours across aviation and healthcare were derived and documented. Key safety-related domains that emerged included Checklists, Training, Crew Resource Management, Sterile Cockpit, Investigation and Reporting of Incidents and Organisational Culture. We conclude that whilst healthcare has much to learn from aviation in certain key domains, the transfer of lessons from aviation to healthcare needs to be nuanced, with the specific characteristics and needs of healthcare borne in mind. On the basis of this review, it is recommended that healthcare should emulate aviation in its resourcing of staff who specialise in human factors and related psychological aspects of patient safety and staff wellbeing. Professional and post-qualification staff training could specifically include Cognitive Bias Avoidance Training, as this appears to play a key part in many errors relating to patient safety and staff wellbeing.

Aviation and healthcare: a comparative review with implications for patient safety

PubMed Central

Parand, Anam; Soukup, Tayana; Reader, Tom; Sevdalis, Nick

2015-01-01

Safety in aviation has often been compared with safety in healthcare. Following a recent article in this journal, the UK government set up an Independent Patient Safety Investigation Service, to emulate a similar well-established body in aviation. On the basis of a detailed review of relevant publications that examine patient safety in the context of aviation practice, we have drawn up a table of comparative features and a conceptual framework for patient safety. Convergence and divergence of safety-related behaviours across aviation and healthcare were derived and documented. Key safety-related domains that emerged included Checklists, Training, Crew Resource Management, Sterile Cockpit, Investigation and Reporting of Incidents and Organisational Culture. We conclude that whilst healthcare has much to learn from aviation in certain key domains, the transfer of lessons from aviation to healthcare needs to be nuanced, with the specific characteristics and needs of healthcare borne in mind. On the basis of this review, it is recommended that healthcare should emulate aviation in its resourcing of staff who specialise in human factors and related psychological aspects of patient safety and staff wellbeing. Professional and post-qualification staff training could specifically include Cognitive Bias Avoidance Training, as this appears to play a key part in many errors relating to patient safety and staff wellbeing. PMID:26770817

Robust and fast-converging level set method for side-scan sonar image segmentation

NASA Astrophysics Data System (ADS)

Liu, Yan; Li, Qingwu; Huo, Guanying

2017-11-01

A robust and fast-converging level set method is proposed for side-scan sonar (SSS) image segmentation. First, the noise in each sonar image is removed using the adaptive nonlinear complex diffusion filter. Second, k-means clustering is used to obtain the initial presegmentation image from the denoised image, and then the distance maps of the initial contours are reinitialized to guarantee the accuracy of the numerical calculation used in the level set evolution. Finally, the satisfactory segmentation is achieved using a robust variational level set model, where the evolution control parameters are generated by the presegmentation. The proposed method is successfully applied to both synthetic image with speckle noise and real SSS images. Experimental results show that the proposed method needs much less iteration and therefore is much faster than the fuzzy local information c-means clustering method, the level set method using a gamma observation model, and the enhanced region-scalable fitting method. Moreover, the proposed method can usually obtain more accurate segmentation results compared with other methods.

TWO CRITERIA FOR WEAK GENERALIZED LOCALIZATION FOR MULTIPLE TRIGONOMETRIC FOURIER SERIES OF FUNCTIONS IN L_p, p \\ge 1

NASA Astrophysics Data System (ADS)

Bloshanskiĭ, I. L.

1986-04-01

The concept of weak generalized localization almost everywhere is introduced. For the multiple Fourier series of a function f, weak generalized localization almost everywhere holds on the set E (E is an arbitrary set of positive measure E \\subset T^N = \\lbrack- \\pi, \\pi\\rbrack^N) if the condition f(x) \\in L_p(T^N), p \\ge 1, f = 0 on E implies that the indicated series converges almost everywhere on some subset E_1 \\subset E of positive measure. For a large class of sets \\{ E \\}, E \\subset T^N, a number of propositions are proved showing that weak localization of rectangular sums holds on the set E in the classes L_p, p \\ge 1, if and only if the set E has certain specific properties. In the course of the proof the precise geometry and structure of the subset E_1 of E on which the multiple Fourier series converges almost everywhere to zero are determined. Bibliography: 13 titles.

Logic, passion and the problem of convergence

PubMed Central

2017-01-01

Our estimate of the likelihood of convergence on human-style intelligence depends on how we understand our various mental capacities. Here I revive David Hume's theory of motivation and action to argue that the most common understanding of the two conventionally recognized components of intelligence—reason and emotion—is confused. We say things like, ‘Reason can overcome emotion’, but to make this statement meaningful, we are forced to treat reason as a compound notion, as a forced and unhappy mixture of concepts that are incommensurate. An alternative is to parse intelligence in a different way, into two sets of capacities: (i) non-affective capacities, including logic, calculation and problem-solving; (ii) affective capacities, including wants, preferences and cares, along with the emotions. Thus, the question of convergence becomes two questions, one having to do with affective and one with non-affective capacities. What is the likelihood of convergence of these in non-human lineages, in other ecologies, on other worlds? Given certain assumptions, convergence of the non-affective capacities in thinking species seems likely, I argue, while convergence of the affective capacities seems much less likely. PMID:28479982

Quasi Sturmian basis for the two-electon continuum

NASA Astrophysics Data System (ADS)

Zaytsev, A. S.; Ancarani, L. U.; Zaytsev, S. A.

2016-02-01

A new type of basis functions is proposed to describe a two-electron continuum which arises as a final state in electron-impact ionization and double photoionization of atomic systems. We name these functions, which are calculated in terms of the recently introduced quasi Sturmian functions, Convoluted Quasi Sturmian functions (CQS); by construction, they look asymptotically like a six-dimensional spherical wave. The driven equation describing an ( e, 3 e) process on helium in the framework of the Temkin-Poet model is solved numerically in the entire space (rather than in a finite region of space) using expansions on CQS basis functions. We show that quite rapid convergence of the solution expansion can be achieved by multiplying the basis functions by the logarithmic phase factor corresponding to the Coulomb electron-electron interaction.

Computerized multiple image analysis on mammograms: performance improvement of nipple identification for registration of multiple views using texture convergence analyses

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Chan, Heang-Ping; Sahiner, Berkman; Hadjiiski, Lubomir M.; Paramagul, Chintana

2004-05-01

Automated registration of multiple mammograms for CAD depends on accurate nipple identification. We developed two new image analysis techniques based on geometric and texture convergence analyses to improve the performance of our previously developed nipple identification method. A gradient-based algorithm is used to automatically track the breast boundary. The nipple search region along the boundary is then defined by geometric convergence analysis of the breast shape. Three nipple candidates are identified by detecting the changes along the gray level profiles inside and outside the boundary and the changes in the boundary direction. A texture orientation-field analysis method is developed to estimate the fourth nipple candidate based on the convergence of the tissue texture pattern towards the nipple. The final nipple location is determined from the four nipple candidates by a confidence analysis. Our training and test data sets consisted of 419 and 368 randomly selected mammograms, respectively. The nipple location identified on each image by an experienced radiologist was used as the ground truth. For 118 of the training and 70 of the test images, the radiologist could not positively identify the nipple, but provided an estimate of its location. These were referred to as invisible nipple images. In the training data set, 89.37% (269/301) of the visible nipples and 81.36% (96/118) of the invisible nipples could be detected within 1 cm of the truth. In the test data set, 92.28% (275/298) of the visible nipples and 67.14% (47/70) of the invisible nipples were identified within 1 cm of the truth. In comparison, our previous nipple identification method without using the two convergence analysis techniques detected 82.39% (248/301), 77.12% (91/118), 89.93% (268/298) and 54.29% (38/70) of the nipples within 1 cm of the truth for the visible and invisible nipples in the training and test sets, respectively. The results indicate that the nipple on mammograms can be detected accurately. This will be an important step towards automatic multiple image analysis for CAD techniques.

An analysis of the convergence of Newton iterations for solving elliptic Kepler's equation

NASA Astrophysics Data System (ADS)

Elipe, A.; Montijano, J. I.; Rández, L.; Calvo, M.

2017-12-01

In this note a study of the convergence properties of some starters E_0 = E_0(e,M) in the eccentricity-mean anomaly variables for solving the elliptic Kepler's equation (KE) by Newton's method is presented. By using a Wang Xinghua's theorem (Xinghua in Math Comput 68(225):169-186, 1999) on best possible error bounds in the solution of nonlinear equations by Newton's method, we obtain for each starter E_0(e,M) a set of values (e,M) \\in [0, 1) × [0, π ] that lead to the q-convergence in the sense that Newton's sequence (E_n)_{n ≥ 0} generated from E_0 = E_0(e,M) is well defined, converges to the exact solution E^* = E^*(e,M) of KE and further \\vert E_n - E^* \\vert ≤ q^{2^n -1} \\vert E_0 - E^* \\vert holds for all n ≥ 0. This study completes in some sense the results derived by Avendaño et al. (Celest Mech Dyn Astron 119:27-44, 2014) by using Smale's α -test with q=1/2. Also since in KE the convergence rate of Newton's method tends to zero as e → 0, we show that the error estimates given in the Wang Xinghua's theorem for KE can also be used to determine sets of q-convergence with q = e^k \\widetilde{q} for all e \\in [0,1) and a fixed \\widetilde{q} ≤ 1. Some remarks on the use of this theorem to derive a priori estimates of the error \\vert E_n - E^* \\vert after n Kepler's iterations are given. Finally, a posteriori bounds of this error that can be used to a dynamical estimation of the error are also obtained.

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

NASA Astrophysics Data System (ADS)

Chmela, Jiří; Harding, Michael E.

2018-06-01

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

RNA Polymerase Collision versus DNA Structural Distortion: Twists and Turns Can Cause Break Failure

PubMed Central

Pannunzio, Nicholas R.; Lieber, Michael R.

2016-01-01

Summary The twisting of DNA due to the movement of RNA polymerases is the basis of numerous classic experiments in molecular biology. Recent mouse genetic models indicate that chromosomal breakage is common at sites of transcriptional turbulence. Two key studies on this point mapped breakpoints to sites of either convergent or divergent transcription, but arrived at different conclusions as to which is more detrimental and why. The issue turns on whether DNA strand separation is the basis for the chromosomal instability or collision of RNA polymerases? PMID:27153532

A weak Galerkin generalized multiscale finite element method

DOE PAGES

Mu, Lin; Wang, Junping; Ye, Xiu

2016-03-31

In this study, we propose a general framework for weak Galerkin generalized multiscale (WG-GMS) finite element method for the elliptic problems with rapidly oscillating or high contrast coefficients. This general WG-GMS method features in high order accuracy on general meshes and can work with multiscale basis derived by different numerical schemes. A special case is studied under this WG-GMS framework in which the multiscale basis functions are obtained by solving local problem with the weak Galerkin finite element method. Convergence analysis and numerical experiments are obtained for the special case.

A weak Galerkin generalized multiscale finite element method

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

Mu, Lin; Wang, Junping; Ye, Xiu

In this study, we propose a general framework for weak Galerkin generalized multiscale (WG-GMS) finite element method for the elliptic problems with rapidly oscillating or high contrast coefficients. This general WG-GMS method features in high order accuracy on general meshes and can work with multiscale basis derived by different numerical schemes. A special case is studied under this WG-GMS framework in which the multiscale basis functions are obtained by solving local problem with the weak Galerkin finite element method. Convergence analysis and numerical experiments are obtained for the special case.

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

PubMed

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

2009-06-09

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

Let's dance: Organization studies, medical sociology and health policy.

PubMed

Currie, Graeme; Dingwall, Robert; Kitchener, Martin; Waring, Justin

2012-02-01

This Special Issue of Social Science & Medicine investigates the potential for positive inter-disciplinary interaction, a 'generative dance', between organization studies (OS), and two of the journal's traditional disciplinary foundations: health policy and medical sociology. This is both necessary and timely because of the extent to which organizations have become a neglected topic within medical sociology and health policy analysis. We argue there is need for further and more sustained theoretical and conceptual synergy between OS, medical sociology and health policy, which provides, on the one-hand a cutting-edge and thought-provoking basis for the analysis of contemporary health reforms, and on the other hand, enables the development and elaboration of theory. We emphasize that sociologists and policy analysts in healthcare have been leading contributors to our understanding of organizations in modern society, that OS enhances our understanding of medical settings, and that organizations remain one of the most influential actors of our time. As a starting point to discussion, we outline the genealogy of OS and its application to healthcare settings. We then consider how medical sociology and health policy converge or diverge with the concerns of OS in the study of healthcare settings. Following this, we focus upon the material environment, specifically the position of business schools, which frames the generative dance between OS, medical sociology and health policy. This sets the context for introducing the thirteen articles that constitute the Special Issue of Social Science & Medicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Spatial and Temporal Patterns in Carbon Emissions to the Atmosphere

NASA Astrophysics Data System (ADS)

Broniak, C. T.; Blasing, T. J.; Marland, G.

2003-12-01

Data on global fossil-fuel emissions of CO2 to the atmosphere for year 2000 show that the range of national average per capita emissions, in metric tons of carbon per person, includes values of 5.40 for the United States, 2.61 for Germany, 0.29 for India and 0.04 for Liberia. This range is more than two orders of magnitude. Similar data on national fossil-fuel emissions for the United States vary by more than an order of magnitude, from 34.18 metric tons of carbon per person for Wyoming to 2.70 for California. The state data also show differing patterns of change over time. The Kyoto Protocol would require ratifying developed countries to reduce greenhouse gas emissions to quantified negotiated targets. The concept of contraction and convergence (C&C) has been widely touted as a possible basis for ultimate, more strict limits on greenhouse gas emissions. The idea of C&C is that per-capita emissions of CO2 for all countries would converge toward some common value that is consistent with stabilization of global climate. The U.S., on the other hand, has proposed intensity-based emissions targets whereby goals would be defined in terms of emissions per unit of gross domestic product, or perhaps emissions per unit of output for specific activities. This paper describes the data set on U.S. CO2 emissions by state, and begins to explore the patterns between states and over time.

Measure Once, Cut Twice – Adding Patient-Reported Outcome Measures to the Electronic Health Record for Comparative Effectiveness Research

PubMed Central

Wu, Albert W.; Kharrazi, Hadi; Boulware, L. Ebony; Snyder, Claire F.

2013-01-01

Objective This paper presents the current state of patient-reported outcome measures, and explains new opportunities for leveraging the recent adoption of electronic health records to expand the application of patient-reported outcomes in both clinical care and comparative effectiveness research. Study Design and Setting Historic developments of patient-reported outcome, electronic health record, and comparative effectiveness research are analyzed in two dimensions: patient-centeredness and digitization. We pose the question: “What needs to be standardized around the collection of patient-reported outcomes in electronic health records for comparative effectiveness research?” Results We identified three converging trends: the progression of patient-reported outcomes toward greater patient centeredness and electronic adaptation; the evolution of electronic health records into personalized and fully digitized solutions; the shift toward patient-oriented comparative effectiveness research. Related to this convergence, we propose an architecture for patient-reported outcome standardization that could serve as a first step toward a more comprehensive integration of patient-reported outcomes with electronic health record for both practice and research. Conclusion The science of patient-reported outcome measurement has matured sufficiently to be integrated routinely into electronic health records and other e-health solutions to collect data on an ongoing basis for clinical care and comparative effectiveness research. Further efforts and ideally coordinated efforts from various stakeholders are needed to refine the details of the proposed framework for standardization. PMID:23849145

Convergent evolution in mechanical design of lamnid sharks and tunas.

PubMed

Donley, Jeanine M; Sepulveda, Chugey A; Konstantinidis, Peter; Gemballa, Sven; Shadwick, Robert E

2004-05-06

The evolution of 'thunniform' body shapes in several different groups of vertebrates, including whales, ichthyosaurs and several species of large pelagic fishes supports the view that physical and hydromechanical demands provided important selection pressures to optimize body design for locomotion during vertebrate evolution. Recognition of morphological similarities between lamnid sharks (the most well known being the great white and the mako) and tunas has led to a general expectation that they also have converged in their functional design; however, no quantitative data exist on the mechanical performance of the locomotor system in lamnid sharks. Here we examine the swimming kinematics, in vivo muscle dynamics and functional morphology of the force-transmission system in a lamnid shark, and show that the evolutionary convergence in body shape and mechanical design between the distantly related lamnids and tunas is much more than skin deep; it extends to the depths of the myotendinous architecture and the mechanical basis for propulsive movements. We demonstrate that not only have lamnids and tunas converged to a much greater extent than previously known, but they have also developed morphological and functional adaptations in their locomotor systems that are unlike virtually all other fishes.

Short-term Time Step Convergence in a Climate Model

DOE PAGES

Wan, Hui; Rasch, Philip J.; Taylor, Mark; ...

2015-02-11

A testing procedure is designed to assess the convergence property of a global climate model with respect to time step size, based on evaluation of the root-mean-square temperature difference at the end of very short (1 h) simulations with time step sizes ranging from 1 s to 1800 s. A set of validation tests conducted without sub-grid scale parameterizations confirmed that the method was able to correctly assess the convergence rate of the dynamical core under various configurations. The testing procedure was then applied to the full model, and revealed a slow convergence of order 0.4 in contrast to themore » expected first-order convergence. Sensitivity experiments showed without ambiguity that the time stepping errors in the model were dominated by those from the stratiform cloud parameterizations, in particular the cloud microphysics. This provides a clear guidance for future work on the design of more accurate numerical methods for time stepping and process coupling in the model.« less

Moisture convergence using satellite-derived wind fields - A severe local storm case study

NASA Technical Reports Server (NTRS)

Negri, A. J.; Vonder Haar, T. H.

1980-01-01

Five-minute interval 1-km resolution SMS visible channel data were used to derive low-level wind fields by tracking small cumulus clouds on NASA's Atmospheric and Oceanographic Information Processing System. The satellite-derived wind fields were combined with surface mixing ratios to derive horizontal moisture convergence in the prestorm environment of April 24, 1975. Storms began developing in an area extending from southwest Oklahoma to eastern Tennessee 2 h subsequent to the time of the derived fields. The maximum moisture convergence was computed to be 0.0022 g/kg per sec and areas of low-level convergence of moisture were in general indicative of regions of severe storm genesis. The resultant moisture convergence fields derived from two wind sets 20 min apart were spatially consistent and reflected the mesoscale forcing of ensuing storm development. Results are discussed with regard to possible limitations in quantifying the relationship between low-level flow and between low-level flow and satellite-derived cumulus motion in an antecedent storm environment.

A linear recurrent kernel online learning algorithm with sparse updates.

PubMed

Fan, Haijin; Song, Qing

2014-02-01

In this paper, we propose a recurrent kernel algorithm with selectively sparse updates for online learning. The algorithm introduces a linear recurrent term in the estimation of the current output. This makes the past information reusable for updating of the algorithm in the form of a recurrent gradient term. To ensure that the reuse of this recurrent gradient indeed accelerates the convergence speed, a novel hybrid recurrent training is proposed to switch on or off learning the recurrent information according to the magnitude of the current training error. Furthermore, the algorithm includes a data-dependent adaptive learning rate which can provide guaranteed system weight convergence at each training iteration. The learning rate is set as zero when the training violates the derived convergence conditions, which makes the algorithm updating process sparse. Theoretical analyses of the weight convergence are presented and experimental results show the good performance of the proposed algorithm in terms of convergence speed and estimation accuracy. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Disappointing Gift: Dispositional and Situational Moderators of Emotional Expressions

ERIC Educational Resources Information Center

Tobin, Renee M.; Graziano, William G.

2011-01-01

Inferences about emotions in children are limited by studies that rely on only one research method. Convergence across methods provides a stronger basis for inference by identifying method variance. This multimethod study of 116 children (mean age = 8.21 years) examined emotional displays during social exchange. Each child received a desirable…

Nature and Resolution of a Model Application: The Collaborative Intensive Community Treatment Program

ERIC Educational Resources Information Center

Amendola, A. Mark; Oliver, Robert W.

2003-01-01

The success of any program for youth relies on program integrity. This requires that the program is delivered as planned on a daily basis. Many factors converge on this equation. This article outlines initial development and components of a comprehensive treatment program grounded in the principles of Aggression Replacement Training.

Exploring Higher Education Governance in Poland and Romania: Re-Convergence after Divergence?

ERIC Educational Resources Information Center

Dobbins, Michael

2017-01-01

This analysis focuses on changes in higher education governance in Poland and Romania in the post-communist era. The author applies a theoretical framework based on institutional isomorphism and historical institutionalism and maps the policy trajectories of both systems on the basis of three governance ideal-types. The public higher education…

Putting newborn hearing screening on the political agenda in Belgium: local initiatives toward a community programme – a qualitative study

PubMed Central

2014-01-01

Background The Kingdon model, based on the convergence of three streams (problem, policy, and politics) and the opening of a policy window, analyses the process by which a health issue is placed on the political agenda. We used this model to document the political agenda-setting process of the newborn hearing screening programme in Belgium. Methods A qualitative study based on a document review and on semi-directed interviews was carried out. The interviews were conducted with nine people who had played a role in putting the issue in question on the political agenda, and the documents reviewed included scientific literature and internal reports and publications from the newborn hearing screening programme. The thematic analysis of the data collected was carried out on the basis of the Kingdon model’s three streams. Results The political agenda-setting of this screening programme was based on many factors. The problem stream included factors external to the context under study, such as the technological developments and the contribution of the scientific literature which led to the recommendation to provide newborn hearing screening. The two other streams (policy and politics) covered factors internal to the Belgian context. The fact that it was locally feasible with financial support, the network of doctors convinced of the need for newborn hearing screening, the drafting of various proposals, and the search for financing were all part of the policy stream. The Belgian political context and the policy opportunities concerning preventive medicine were identified as significant factors in the third stream. When these three streams converged, a policy window opened, allowing newborn hearing screening onto the political agenda and enabling the policy decision for its introduction. Conclusions The advantage of applying the Kingdon model in our approach was the ability to demonstrate the political agenda-setting process, using the three streams. This made it possible to identify the many factors involved in the process. However, the roles of the stakeholders and of the context were somewhat inexplicit in this model. PMID:24986647

Putting newborn hearing screening on the political agenda in Belgium: local initiatives toward a community programme - a qualitative study.

PubMed

Vos, Bénédicte; Lagasse, Raphaël; Levêque, Alain

2014-07-01

The Kingdon model, based on the convergence of three streams (problem, policy, and politics) and the opening of a policy window, analyses the process by which a health issue is placed on the political agenda. We used this model to document the political agenda-setting process of the newborn hearing screening programme in Belgium. A qualitative study based on a document review and on semi-directed interviews was carried out. The interviews were conducted with nine people who had played a role in putting the issue in question on the political agenda, and the documents reviewed included scientific literature and internal reports and publications from the newborn hearing screening programme. The thematic analysis of the data collected was carried out on the basis of the Kingdon model's three streams. The political agenda-setting of this screening programme was based on many factors. The problem stream included factors external to the context under study, such as the technological developments and the contribution of the scientific literature which led to the recommendation to provide newborn hearing screening. The two other streams (policy and politics) covered factors internal to the Belgian context. The fact that it was locally feasible with financial support, the network of doctors convinced of the need for newborn hearing screening, the drafting of various proposals, and the search for financing were all part of the policy stream. The Belgian political context and the policy opportunities concerning preventive medicine were identified as significant factors in the third stream. When these three streams converged, a policy window opened, allowing newborn hearing screening onto the political agenda and enabling the policy decision for its introduction. The advantage of applying the Kingdon model in our approach was the ability to demonstrate the political agenda-setting process, using the three streams. This made it possible to identify the many factors involved in the process. However, the roles of the stakeholders and of the context were somewhat inexplicit in this model.

Pattern and Process in the Comparative Study of Convergent Evolution.

PubMed

Mahler, D Luke; Weber, Marjorie G; Wagner, Catherine E; Ingram, Travis

2017-08-01

Understanding processes that have shaped broad-scale biodiversity patterns is a fundamental goal in evolutionary biology. The development of phylogenetic comparative methods has yielded a tool kit for analyzing contemporary patterns by explicitly modeling processes of change in the past, providing neontologists tools for asking questions previously accessible only for select taxa via the fossil record or laboratory experimentation. The comparative approach, however, differs operationally from alternative approaches to studying convergence in that, for studies of only extant species, convergence must be inferred using evolutionary process models rather than being directly measured. As a result, investigation of evolutionary pattern and process cannot be decoupled in comparative studies of convergence, even though such a decoupling could in theory guard against adaptationist bias. Assumptions about evolutionary process underlying comparative tools can shape the inference of convergent pattern in sometimes profound ways and can color interpretation of such patterns. We discuss these issues and other limitations common to most phylogenetic comparative approaches and suggest ways that they can be avoided in practice. We conclude by promoting a multipronged approach to studying convergence that integrates comparative methods with complementary tests of evolutionary mechanisms and includes ecological and biogeographical perspectives. Carefully employed, the comparative method remains a powerful tool for enriching our understanding of convergence in macroevolution, especially for investigation of why convergence occurs in some settings but not others.

Measuring Renyi entanglement entropy in quantum Monte Carlo simulations.

PubMed

Hastings, Matthew B; González, Iván; Kallin, Ann B; Melko, Roger G

2010-04-16

We develop a quantum Monte Carlo procedure, in the valence bond basis, to measure the Renyi entanglement entropy of a many-body ground state as the expectation value of a unitary Swap operator acting on two copies of the system. An improved estimator involving the ratio of Swap operators for different subregions enables convergence of the entropy in a simulation time polynomial in the system size. We demonstrate convergence of the Renyi entropy to exact results for a Heisenberg chain. Finally, we calculate the scaling of the Renyi entropy in the two-dimensional Heisenberg model and confirm that the Néel ground state obeys the expected area law for systems up to linear size L=32.

Smoothing and the second law

NASA Technical Reports Server (NTRS)

Merriam, Marshal L.

1987-01-01

The technique of obtaining second-order oscillation-free total -variation-diminishing (TVD), scalar difference schemes by adding a limited diffusive flux ('smoothing') to a second-order centered scheme is explored. It is shown that such schemes do not always converge to the correct physical answer. The approach presented here is to construct schemes that numerically satisfy the second law of thermodynamics on a cell-by-cell basis. Such schemes can only converge to the correct physical solution and in some cases can be shown to be TVD. An explicit scheme with this property and second-order spatial accuracy was found to have extremely restrictive time-step limitation. Switching to an implicit scheme removed the time-step limitation.

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

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

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

Identifying all moiety conservation laws in genome-scale metabolic networks.

PubMed

De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea

2014-01-01

The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

Methodological aspects of an adaptive multidirectional pattern search to optimize speech perception using three hearing-aid algorithms

NASA Astrophysics Data System (ADS)

Franck, Bas A. M.; Dreschler, Wouter A.; Lyzenga, Johannes

2004-12-01

In this study we investigated the reliability and convergence characteristics of an adaptive multidirectional pattern search procedure, relative to a nonadaptive multidirectional pattern search procedure. The procedure was designed to optimize three speech-processing strategies. These comprise noise reduction, spectral enhancement, and spectral lift. The search is based on a paired-comparison paradigm, in which subjects evaluated the listening comfort of speech-in-noise fragments. The procedural and nonprocedural factors that influence the reliability and convergence of the procedure are studied using various test conditions. The test conditions combine different tests, initial settings, background noise types, and step size configurations. Seven normal hearing subjects participated in this study. The results indicate that the reliability of the optimization strategy may benefit from the use of an adaptive step size. Decreasing the step size increases accuracy, while increasing the step size can be beneficial to create clear perceptual differences in the comparisons. The reliability also depends on starting point, stop criterion, step size constraints, background noise, algorithms used, as well as the presence of drifting cues and suboptimal settings. There appears to be a trade-off between reliability and convergence, i.e., when the step size is enlarged the reliability improves, but the convergence deteriorates. .

Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas.

PubMed

Ciezarek, Adam G; Dunning, Luke T; Jones, Catherine S; Noble, Leslie R; Humble, Emily; Stefanni, Sergio S; Savolainen, Vincent

2016-10-05

Despite 400-450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior. Here, we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel, and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

Yang, Bo; Jiang, Yunchun; Yang, Jiayan

Taking advantage of the high spatiotemporal resolution observations from the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we present rare observations of the rapid formation of a filament caused by magnetic reconnection between two sets of dark threadlike structures. The two sets of dark threadlike structures belong to distinct flux systems with their adjacent ends anchored in an opposite-polarity magnetic field region, where the calculated photospheric velocity field shows that converging flows dominate there. Due to the converging flows, opposite-polarity magnetic flux converged and then canceled, leading to the formation ofmore » extreme ultraviolet (EUV) brightening that spread in opposite directions along the spine of the dark threadlike structures. Meanwhile, very weak remote brightening in the other terminals of the dark threadlike structures, as well as EUV loops, which rooted in the opposite-polarity magnetic field region, appeared. In addition, all of the AIA Fe line observations reveal that a flux rope was formed and underwent a rolling motion during the fadeaway of the EUV brightening. Soon after, as the EUV brightening disappeared, a filament that is very likely composed of two sets of intertwined dark threadlike structures was formed. Via differential emission measure (EM) analysis, it is found that both the EM and temperature of the plasma around the flux-canceling site increased during the brightening, implying that there, magnetic reconnection may occur to heat the plasma. These observations provide evidence that the filament is formed by magnetic reconnection associated with flux convergence and cancellation, and the magnetic structure of the filament is most likely a flux rope.« less

Exponential parameter and tracking error convergence guarantees for adaptive controllers without persistency of excitation

NASA Astrophysics Data System (ADS)

Chowdhary, Girish; Mühlegg, Maximilian; Johnson, Eric

2014-08-01

In model reference adaptive control (MRAC) the modelling uncertainty is often assumed to be parameterised with time-invariant unknown ideal parameters. The convergence of parameters of the adaptive element to these ideal parameters is beneficial, as it guarantees exponential stability, and makes an online learned model of the system available. Most MRAC methods, however, require persistent excitation of the states to guarantee that the adaptive parameters converge to the ideal values. Enforcing PE may be resource intensive and often infeasible in practice. This paper presents theoretical analysis and illustrative examples of an adaptive control method that leverages the increasing ability to record and process data online by using specifically selected and online recorded data concurrently with instantaneous data for adaptation. It is shown that when the system uncertainty can be modelled as a combination of known nonlinear bases, simultaneous exponential tracking and parameter error convergence can be guaranteed if the system states are exciting over finite intervals such that rich data can be recorded online; PE is not required. Furthermore, the rate of convergence is directly proportional to the minimum singular value of the matrix containing online recorded data. Consequently, an online algorithm to record and forget data is presented and its effects on the resulting switched closed-loop dynamics are analysed. It is also shown that when radial basis function neural networks (NNs) are used as adaptive elements, the method guarantees exponential convergence of the NN parameters to a compact neighbourhood of their ideal values without requiring PE. Flight test results on a fixed-wing unmanned aerial vehicle demonstrate the effectiveness of the method.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

An alternative extragradient projection method for quasi-equilibrium problems.

PubMed

Chen, Haibin; Wang, Yiju; Xu, Yi

2018-01-01

For the quasi-equilibrium problem where the players' costs and their strategies both depend on the rival's decisions, an alternative extragradient projection method for solving it is designed. Different from the classical extragradient projection method whose generated sequence has the contraction property with respect to the solution set, the newly designed method possesses an expansion property with respect to a given initial point. The global convergence of the method is established under the assumptions of pseudomonotonicity of the equilibrium function and of continuity of the underlying multi-valued mapping. Furthermore, we show that the generated sequence converges to the nearest point in the solution set to the initial point. Numerical experiments show the efficiency of the method.

Convergent evolution of mechanically optimal locomotion in aquatic invertebrates and vertebrates.

PubMed

Bale, Rahul; Neveln, Izaak D; Bhalla, Amneet Pal Singh; MacIver, Malcolm A; Patankar, Neelesh A

2015-04-01

Examples of animals evolving similar traits despite the absence of that trait in the last common ancestor, such as the wing and camera-type lens eye in vertebrates and invertebrates, are called cases of convergent evolution. Instances of convergent evolution of locomotory patterns that quantitatively agree with the mechanically optimal solution are very rare. Here, we show that, with respect to a very diverse group of aquatic animals, a mechanically optimal method of swimming with elongated fins has evolved independently at least eight times in both vertebrate and invertebrate swimmers across three different phyla. Specifically, if we take the length of an undulation along an animal's fin during swimming and divide it by the mean amplitude of undulations along the fin length, the result is consistently around twenty. We call this value the optimal specific wavelength (OSW). We show that the OSW maximizes the force generated by the body, which also maximizes swimming speed. We hypothesize a mechanical basis for this optimality and suggest reasons for its repeated emergence through evolution.

Molar tooth carbonates and benthic methane fluxes in Proterozoic oceans.

PubMed

Shen, Bing; Dong, Lin; Xiao, Shuhai; Lang, Xianguo; Huang, Kangjun; Peng, Yongbo; Zhou, Chuanming; Ke, Shan; Liu, Pengju

2016-01-07

Molar tooth structures are ptygmatically folded and microspar-filled structures common in early- and mid-Proterozoic (∼2,500-750 million years ago, Ma) subtidal successions, but extremely rare in rocks <750 Ma. Here, on the basis of Mg and S isotopes, we show that molar tooth structures may have formed within sediments where microbial sulphate reduction and methanogenesis converged. The convergence was driven by the abundant production of methyl sulphides (dimethyl sulphide and methanethiol) in euxinic or H2S-rich seawaters that were widespread in Proterozoic continental margins. In this convergence zone, methyl sulphides served as a non-competitive substrate supporting methane generation and methanethiol inhibited anaerobic oxidation of methane, resulting in the buildup of CH4, formation of degassing cracks in sediments and an increase in the benthic methane flux from sediments. Precipitation of crack-filling microspar was driven by methanogenesis-related alkalinity accumulation. Deep ocean ventilation and oxygenation around 750 Ma brought molar tooth structures to an end.

A high order accurate finite element algorithm for high Reynolds number flow prediction

NASA Technical Reports Server (NTRS)

Baker, A. J.

1978-01-01

A Galerkin-weighted residuals formulation is employed to establish an implicit finite element solution algorithm for generally nonlinear initial-boundary value problems. Solution accuracy, and convergence rate with discretization refinement, are quantized in several error norms, by a systematic study of numerical solutions to several nonlinear parabolic and a hyperbolic partial differential equation characteristic of the equations governing fluid flows. Solutions are generated using selective linear, quadratic and cubic basis functions. Richardson extrapolation is employed to generate a higher-order accurate solution to facilitate isolation of truncation error in all norms. Extension of the mathematical theory underlying accuracy and convergence concepts for linear elliptic equations is predicted for equations characteristic of laminar and turbulent fluid flows at nonmodest Reynolds number. The nondiagonal initial-value matrix structure introduced by the finite element theory is determined intrinsic to improved solution accuracy and convergence. A factored Jacobian iteration algorithm is derived and evaluated to yield a consequential reduction in both computer storage and execution CPU requirements while retaining solution accuracy.

Molar tooth carbonates and benthic methane fluxes in Proterozoic oceans

PubMed Central

Shen, Bing; Dong, Lin; Xiao, Shuhai; Lang, Xianguo; Huang, Kangjun; Peng, Yongbo; Zhou, Chuanming; Ke, Shan; Liu, Pengju

2016-01-01

Molar tooth structures are ptygmatically folded and microspar-filled structures common in early- and mid-Proterozoic (∼2,500–750 million years ago, Ma) subtidal successions, but extremely rare in rocks <750 Ma. Here, on the basis of Mg and S isotopes, we show that molar tooth structures may have formed within sediments where microbial sulphate reduction and methanogenesis converged. The convergence was driven by the abundant production of methyl sulphides (dimethyl sulphide and methanethiol) in euxinic or H2S-rich seawaters that were widespread in Proterozoic continental margins. In this convergence zone, methyl sulphides served as a non-competitive substrate supporting methane generation and methanethiol inhibited anaerobic oxidation of methane, resulting in the buildup of CH4, formation of degassing cracks in sediments and an increase in the benthic methane flux from sediments. Precipitation of crack-filling microspar was driven by methanogenesis-related alkalinity accumulation. Deep ocean ventilation and oxygenation around 750 Ma brought molar tooth structures to an end. PMID:26739600

Learning free energy landscapes using artificial neural networks.

PubMed

Sidky, Hythem; Whitmer, Jonathan K

2018-03-14

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

Quantitative molecular orbital energies within a G0W0 approximation

NASA Astrophysics Data System (ADS)

Sharifzadeh, S.; Tamblyn, I.; Doak, P.; Darancet, P. T.; Neaton, J. B.

2012-09-01

Using many-body perturbation theory within a G 0 W 0 approximation, with a plane wave basis set and using a starting point based on density functional theory within the generalized gradient approximation, we explore routes for computing the ionization potential (IP), electron affinity (EA), and fundamental gap of three gas-phase molecules — benzene, thiophene, and (1,4) diamino-benzene — and compare with experiments. We examine the dependence of the IP and fundamental gap on the number of unoccupied states used to represent the dielectric function and the self energy, as well as the dielectric function plane-wave cutoff. We find that with an effective completion strategy for approximating the unoccupied subspace, and a well converged dielectric function kinetic energy cutoff, the computed IPs and EAs are in excellent quantitative agreement with available experiment (within 0.2 eV), indicating that a one-shot G 0 W 0 approach can be very accurate for calculating addition/removal energies of small organic molecules.

Fuzzy regression modeling for tool performance prediction and degradation detection.

PubMed

Li, X; Er, M J; Lim, B S; Zhou, J H; Gan, O P; Rutkowski, L

2010-10-01

In this paper, the viability of using Fuzzy-Rule-Based Regression Modeling (FRM) algorithm for tool performance and degradation detection is investigated. The FRM is developed based on a multi-layered fuzzy-rule-based hybrid system with Multiple Regression Models (MRM) embedded into a fuzzy logic inference engine that employs Self Organizing Maps (SOM) for clustering. The FRM converts a complex nonlinear problem to a simplified linear format in order to further increase the accuracy in prediction and rate of convergence. The efficacy of the proposed FRM is tested through a case study - namely to predict the remaining useful life of a ball nose milling cutter during a dry machining process of hardened tool steel with a hardness of 52-54 HRc. A comparative study is further made between four predictive models using the same set of experimental data. It is shown that the FRM is superior as compared with conventional MRM, Back Propagation Neural Networks (BPNN) and Radial Basis Function Networks (RBFN) in terms of prediction accuracy and learning speed.

AUCTION MECHANISMS FOR IMPLEMENTING TRADABLE NETWORK PERMIT MARKETS

NASA Astrophysics Data System (ADS)

Wada, Kentaro; Akamatsu, Takashi

This paper proposes a new auction mechanism for implementing the tradable network permit markets. Assuming that each user makes a trip from an origin to a destination along a path in a specific time period, we design an auction mechanism that enables each user to purchase a bundle of permits corresponding to a set of links in the user's preferred path. The objective of the proposed mechanism is to achieve a socially optimal state with minimal revelation of users' private information. In order to achieve this, the mechanism employs an evolutionary approach that has an auction phase and a path capacity adjustment phase, which are repeated on a day-to-day basis. We prove that the proposed mechanism has the following desirable properties: (1) truthful bidding is the dominant strategy for each user and (2) the proposed mechanism converges to an approximate socially optimal state in the sense that the achieved value of the social surplus reaches its maximum value when the number of users is large.

Outstanding performance of configuration interaction singles and doubles using exact exchange Kohn-Sham orbitals in real-space numerical grid method

NASA Astrophysics Data System (ADS)

Lim, Jaechang; Choi, Sunghwan; Kim, Jaewook; Kim, Woo Youn

2016-12-01

To assess the performance of multi-configuration methods using exact exchange Kohn-Sham (KS) orbitals, we implemented configuration interaction singles and doubles (CISD) in a real-space numerical grid code. We obtained KS orbitals with the exchange-only optimized effective potential under the Krieger-Li-Iafrate (KLI) approximation. Thanks to the distinctive features of KLI orbitals against Hartree-Fock (HF), such as bound virtual orbitals with compact shapes and orbital energy gaps similar to excitation energies; KLI-CISD for small molecules shows much faster convergence as a function of simulation box size and active space (i.e., the number of virtual orbitals) than HF-CISD. The former also gives more accurate excitation energies with a few dominant configurations than the latter, even with many more configurations. The systematic control of basis set errors is straightforward in grid bases. Therefore, grid-based multi-configuration methods using exact exchange KS orbitals provide a promising new way to make accurate electronic structure calculations.

Measurement of tracer gas distributions using an open-path FTIR system coupled with computed tomography

NASA Astrophysics Data System (ADS)

Drescher, Anushka C.; Yost, Michael G.; Park, Doo Y.; Levine, Steven P.; Gadgil, Ashok J.; Fischer, Marc L.; Nazaroff, William W.

1995-05-01

Optical remote sensing and iterative computed tomography (CT) can be combined to measure the spatial distribution of gaseous pollutant concentrations in a plane. We have conducted chamber experiments to test this combination of techniques using an Open Path Fourier Transform Infrared Spectrometer (OP-FTIR) and a standard algebraic reconstruction technique (ART). ART was found to converge to solutions that showed excellent agreement with the ray integral concentrations measured by the FTIR but were inconsistent with simultaneously gathered point sample concentration measurements. A new CT method was developed based on (a) the superposition of bivariate Gaussians to model the concentration distribution and (b) a simulated annealing minimization routine to find the parameters of the Gaussians that resulted in the best fit to the ray integral concentration data. This new method, named smooth basis function minimization (SBFM) generated reconstructions that agreed well, both qualitatively and quantitatively, with the concentration profiles generated from point sampling. We present one set of illustrative experimental data to compare the performance of ART and SBFM.

Communication: Nuclear quadrupole moment-induced Cotton-Mouton effect in noble gas atoms

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

Fu, Li-juan; Vaara, Juha, E-mail: juha.vaara@iki.fi; Rizzo, Antonio

New, high-sensitivity and high-resolution spectroscopic and imaging methods may be developed by exploiting nuclear magneto-optic effects. A first-principles electronic structure formulation of nuclear electric quadrupole moment-induced Cotton-Mouton effect (NQCME) is presented for closed-shell atoms. In NQCME, aligned quadrupole moments alter the index of refraction of the medium along with and perpendicular to the direction of nuclear alignment. The roles of basis-set convergence, electron correlation, and relativistic effects are investigated for three quadrupolar noble gas isotopes: {sup 21}Ne, {sup 83}Kr, and {sup 131}Xe. The magnitude of the resulting ellipticities is predicted to be 10{sup −4}–10{sup −6} rad/(M cm) for fully spin-polarized nuclei.more » These should be detectable in the Voigt setup. Particularly interesting is the case of {sup 131}Xe, in which a high degree of spin polarization can be achieved via spin-exchange optical hyperpolarization.« less

Learning free energy landscapes using artificial neural networks

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Whitmer, Jonathan K.

2018-03-01

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

Robust Joint Graph Sparse Coding for Unsupervised Spectral Feature Selection.

PubMed

Zhu, Xiaofeng; Li, Xuelong; Zhang, Shichao; Ju, Chunhua; Wu, Xindong

2017-06-01

In this paper, we propose a new unsupervised spectral feature selection model by embedding a graph regularizer into the framework of joint sparse regression for preserving the local structures of data. To do this, we first extract the bases of training data by previous dictionary learning methods and, then, map original data into the basis space to generate their new representations, by proposing a novel joint graph sparse coding (JGSC) model. In JGSC, we first formulate its objective function by simultaneously taking subspace learning and joint sparse regression into account, then, design a new optimization solution to solve the resulting objective function, and further prove the convergence of the proposed solution. Furthermore, we extend JGSC to a robust JGSC (RJGSC) via replacing the least square loss function with a robust loss function, for achieving the same goals and also avoiding the impact of outliers. Finally, experimental results on real data sets showed that both JGSC and RJGSC outperformed the state-of-the-art algorithms in terms of k -nearest neighbor classification performance.

An IPSO-SVM algorithm for security state prediction of mine production logistics system

NASA Astrophysics Data System (ADS)

Zhang, Yanliang; Lei, Junhui; Ma, Qiuli; Chen, Xin; Bi, Runfang

2017-06-01

A theoretical basis for the regulation of corporate security warning and resources was provided in order to reveal the laws behind the security state in mine production logistics. Considering complex mine production logistics system and the variable is difficult to acquire, a superior security status predicting model of mine production logistics system based on the improved particle swarm optimization and support vector machine (IPSO-SVM) is proposed in this paper. Firstly, through the linear adjustments of inertia weight and learning weights, the convergence speed and search accuracy are enhanced with the aim to deal with situations associated with the changeable complexity and the data acquisition difficulty. The improved particle swarm optimization (IPSO) is then introduced to resolve the problem of parameter settings in traditional support vector machines (SVM). At the same time, security status index system is built to determine the classification standards of safety status. The feasibility and effectiveness of this method is finally verified using the experimental results.

Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase

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

Huerta, Carlos; Borek, Dominika; Machius, Mischa

2009-12-01

Flavin mononucleotide adenylyltransferase (FMNAT) catalyzes the formation of the essential flavocoenzyme flavin adenine dinucleotide (FAD) and plays an important role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different sets of active-site residues to accomplish the same chemistry. Here we report the first structural characterization of a eukaryotic FMNAT from the pathogenic yeast Candida glabrata. Four crystal structures of C. glabrata FMNAT in different complexed forms were determined at 1.20-1.95 A resolutions, capturing the enzyme active-site states prior to and after catalysis. These structures reveal a novelmore » flavin-binding mode and a unique enzyme-bound FAD conformation. Comparison of the bacterial and eukaryotic FMNATs provides a structural basis for understanding the convergent evolution of the same FMNAT activity from different protein ancestors. Structure-based investigation of the kinetic properties of FMNAT should offer insights into the regulatory mechanisms of FAD homeostasis by FMNAT in eukaryotic organisms.« less

Electron scattering on molecules: search for semi-empirical indications

NASA Astrophysics Data System (ADS)

Fedus, Kamil; Karwasz, Grzegorz P.

2017-06-01

Reliable cross-sections for electron-molecule collisions are urgently needed for numerical modeling of various processes important from technological point of view. Unfortunately, a significant progress in theory and experiment over the last decade is not usually accompanied by the convergence of cross-sections measured at different laboratories and calculated with different methods. Moreover the most advanced contemporary theories involve such large basis sets and complicated equations that they are not easily applied to each specific molecule for which data are needed. For these reasons the search for semi-empirical indications in angular and energy dependencies of scattering cross-section becomes important. In this paper we make a brief review of the applicability of the Born-dipole approximation for elastic, rotational, vibrational and ionization processes that can occur during electron-molecule collisions. We take into account the most recent experimental findings as the reference points. Contribution to the Topical Issue "Atomic and Molecular Data and Their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

Stability of Hydrocarbons of the Polyhedrane Family: Convergence of ab Initio Calculations and Corresponding Assessment of DFT Main Approximations.

PubMed

Sancho-García, J C

2011-09-13

Highly accurate coupled-cluster (CC) calculations with large basis sets have been performed to study the binding energy of the (CH)12, (CH)16, (CH)20, and (CH)24 polyhedral hydrocarbons in two, cage-like and planar, forms. We also considered the effect of other minor contributions: core-correlation, relativistic corrections, and extrapolations to the limit of the full CC expansion. Thus, chemically accurate values could be obtained for these complicated systems. These nearly exact results are used to evaluate next the performance of main approximations (i.e., pure, hybrid, and double-hybrid methods) within density functional theory (DFT) in a systematic fashion. Some commonly used functionals, including the B3LYP model, are affected by large errors, and only those having reduced self-interaction error (SIE), which includes the last family of conjectured expressions (double hybrids), are able to achieve reasonable low deviations of 1-2 kcal/mol especially when an estimate for dispersion interactions is also added.

A Discrete Constraint for Entropy Conservation and Sound Waves in Cloud-Resolving Modeling

NASA Technical Reports Server (NTRS)

Zeng, Xi-Ping; Tao, Wei-Kuo; Simpson, Joanne

2003-01-01

Ideal cloud-resolving models contain little-accumulative errors. When their domain is so large that synoptic large-scale circulations are accommodated, they can be used for the simulation of the interaction between convective clouds and the large-scale circulations. This paper sets up a framework for the models, using moist entropy as a prognostic variable and employing conservative numerical schemes. The models possess no accumulative errors of thermodynamic variables when they comply with a discrete constraint on entropy conservation and sound waves. Alternatively speaking, the discrete constraint is related to the correct representation of the large-scale convergence and advection of moist entropy. Since air density is involved in entropy conservation and sound waves, the challenge is how to compute sound waves efficiently under the constraint. To address the challenge, a compensation method is introduced on the basis of a reference isothermal atmosphere whose governing equations are solved analytically. Stability analysis and numerical experiments show that the method allows the models to integrate efficiently with a large time step.

Is Implicit Theory of Mind a Real and Robust Phenomenon? Results From a Systematic Replication Study.

PubMed

Kulke, Louisa; von Duhn, Britta; Schneider, Dana; Rakoczy, Hannes

2018-06-01

Recently, theory-of-mind research has been revolutionized by findings from novel implicit tasks suggesting that at least some aspects of false-belief reasoning develop earlier in ontogeny than previously assumed and operate automatically throughout adulthood. Although these findings are the empirical basis for far-reaching theories, systematic replications are still missing. This article reports a preregistered large-scale attempt to replicate four influential anticipatory-looking implicit theory-of-mind tasks using original stimuli and procedures. Results showed that only one of the four paradigms was reliably replicated. A second set of studies revealed, further, that this one paradigm was no longer replicated once confounds were removed, which calls its validity into question. There were also no correlations between paradigms, and thus, no evidence for their convergent validity. In conclusion, findings from anticipatory-looking false-belief paradigms seem less reliable and valid than previously assumed, thus limiting the conclusions that can be drawn from them.

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration

NASA Astrophysics Data System (ADS)

Eshuis, Henk; Yarkony, Julian; Furche, Filipp

2010-06-01

The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N4 log N) operations and O(N3) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield μH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration.

PubMed

Eshuis, Henk; Yarkony, Julian; Furche, Filipp

2010-06-21

The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration techniques. We show that the RI approximation to four-index electron repulsion integrals leads to a variational upper bound to the exact RPA correlation energy if the Coulomb metric is used. Auxiliary basis sets optimized for second-order Møller-Plesset (MP2) calculations are well suitable for RPA, as is demonstrated for the HEAT [A. Tajti et al., J. Chem. Phys. 121, 11599 (2004)] and MOLEKEL [F. Weigend et al., Chem. Phys. Lett. 294, 143 (1998)] benchmark sets. Using imaginary frequency integration rather than diagonalization to compute the matrix square root necessary for RPA, evaluation of the RPA correlation energy requires O(N(4) log N) operations and O(N(3)) storage only; the price for this dramatic improvement over existing algorithms is a numerical quadrature. We propose a numerical integration scheme that is exact in the two-orbital case and converges exponentially with the number of grid points. For most systems, 30-40 grid points yield muH accuracy in triple zeta basis sets, but much larger grids are necessary for small gap systems. The lowest-order approximation to the present method is a post-Kohn-Sham frequency-domain version of opposite-spin Laplace-transform RI-MP2 [J. Jung et al., Phys. Rev. B 70, 205107 (2004)]. Timings for polyacenes with up to 30 atoms show speed-ups of two orders of magnitude over previous implementations. The present approach makes it possible to routinely compute RPA correlation energies of systems well beyond 100 atoms, as is demonstrated for the octapeptide angiotensin II.

Progressive Sampling Technique for Efficient and Robust Uncertainty and Sensitivity Analysis of Environmental Systems Models: Stability and Convergence

NASA Astrophysics Data System (ADS)

Sheikholeslami, R.; Hosseini, N.; Razavi, S.

2016-12-01

Modern earth and environmental models are usually characterized by a large parameter space and high computational cost. These two features prevent effective implementation of sampling-based analysis such as sensitivity and uncertainty analysis, which require running these computationally expensive models several times to adequately explore the parameter/problem space. Therefore, developing efficient sampling techniques that scale with the size of the problem, computational budget, and users' needs is essential. In this presentation, we propose an efficient sequential sampling strategy, called Progressive Latin Hypercube Sampling (PLHS), which provides an increasingly improved coverage of the parameter space, while satisfying pre-defined requirements. The original Latin hypercube sampling (LHS) approach generates the entire sample set in one stage; on the contrary, PLHS generates a series of smaller sub-sets (also called `slices') while: (1) each sub-set is Latin hypercube and achieves maximum stratification in any one dimensional projection; (2) the progressive addition of sub-sets remains Latin hypercube; and thus (3) the entire sample set is Latin hypercube. Therefore, it has the capability to preserve the intended sampling properties throughout the sampling procedure. PLHS is deemed advantageous over the existing methods, particularly because it nearly avoids over- or under-sampling. Through different case studies, we show that PHLS has multiple advantages over the one-stage sampling approaches, including improved convergence and stability of the analysis results with fewer model runs. In addition, PLHS can help to minimize the total simulation time by only running the simulations necessary to achieve the desired level of quality (e.g., accuracy, and convergence rate).

Statistical characterization of planar two-dimensional Rayleigh-Taylor mixing layers

NASA Astrophysics Data System (ADS)

Sendersky, Dmitry

2000-10-01

The statistical evolution of a planar, randomly perturbed fluid interface subject to Rayleigh-Taylor instability is explored through numerical simulation in two space dimensions. The data set, generated by the front-tracking code FronTier, is highly resolved and covers a large ensemble of initial perturbations, allowing a more refined analysis of closure issues pertinent to the stochastic modeling of chaotic fluid mixing. We closely approach a two-fold convergence of the mean two-phase flow: convergence of the numerical solution under computational mesh refinement, and statistical convergence under increasing ensemble size. Quantities that appear in the two-phase averaged Euler equations are computed directly and analyzed for numerical and statistical convergence. Bulk averages show a high degree of convergence, while interfacial averages are convergent only in the outer portions of the mixing zone, where there is a coherent array of bubble and spike tips. Comparison with the familiar bubble/spike penetration law h = alphaAgt 2 is complicated by the lack of scale invariance, inability to carry the simulations to late time, the increasing Mach numbers of the bubble/spike tips, and sensitivity to the method of data analysis. Finally, we use the simulation data to analyze some constitutive properties of the mixing process.

Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets.

PubMed

Saller, Maximilian A C; Habershon, Scott

2017-07-11

Methods for solving the time-dependent Schrödinger equation via basis set expansion of the wave function can generally be categorized as having either static (time-independent) or dynamic (time-dependent) basis functions. We have recently introduced an alternative simulation approach which represents a middle road between these two extremes, employing dynamic (classical-like) trajectories to create a static basis set of Gaussian wavepackets in regions of phase-space relevant to future propagation of the wave function [J. Chem. Theory Comput., 11, 8 (2015)]. Here, we propose and test a modification of our methodology which aims to reduce the size of basis sets generated in our original scheme. In particular, we employ short-time classical trajectories to continuously generate new basis functions for short-time quantum propagation of the wave function; to avoid the continued growth of the basis set describing the time-dependent wave function, we employ Matching Pursuit to periodically minimize the number of basis functions required to accurately describe the wave function. Overall, this approach generates a basis set which is adapted to evolution of the wave function while also being as small as possible. In applications to challenging benchmark problems, namely a 4-dimensional model of photoexcited pyrazine and three different double-well tunnelling problems, we find that our new scheme enables accurate wave function propagation with basis sets which are around an order-of-magnitude smaller than our original trajectory-guided basis set methodology, highlighting the benefits of adaptive strategies for wave function propagation.

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

PubMed

Mitin, Alexander V

2013-09-05

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

Isotropy analyses of the Planck convergence map

NASA Astrophysics Data System (ADS)

Marques, G. A.; Novaes, C. P.; Bernui, A.; Ferreira, I. S.

2018-01-01

The presence of matter in the path of relic photons causes distortions in the angular pattern of the cosmic microwave background (CMB) temperature fluctuations, modifying their properties in a slight but measurable way. Recently, the Planck Collaboration released the estimated convergence map, an integrated measure of the large-scale matter distribution that produced the weak gravitational lensing (WL) phenomenon observed in Planck CMB data. We perform exhaustive analyses of this convergence map calculating the variance in small and large regions of the sky, but excluding the area masked due to Galactic contaminations, and compare them with the features expected in the set of simulated convergence maps, also released by the Planck Collaboration. Our goal is to search for sky directions or regions where the WL imprints anomalous signatures to the variance estimator revealed through a χ2 analyses at a statistically significant level. In the local analysis of the Planck convergence map, we identified eight patches of the sky in disagreement, in more than 2σ, with what is observed in the average of the simulations. In contrast, in the large regions analysis we found no statistically significant discrepancies, but, interestingly, the regions with the highest χ2 values are surrounding the ecliptic poles. Thus, our results show a good agreement with the features expected by the Λ cold dark matter concordance model, as given by the simulations. Yet, the outliers regions found here could suggest that the data still contain residual contamination, like noise, due to over- or underestimation of systematic effects in the simulation data set.

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ab initio anharmonic vibrational frequency predictions for linear proton-bound complexes OC-H(+)-CO and N(2)-H(+)-N(2).

PubMed

Terrill, Kasia; Nesbitt, David J

2010-08-01

Ab initio anharmonic transition frequencies are calculated for strongly coupled (i) asymmetric and (ii) symmetric proton stretching modes in the X-H(+)-X linear ionic hydrogen bonded complexes for OCHCO(+) and N(2)HN(2)(+). The optimized potential surface is calculated in these two coordinates for each molecular ion at CCSD(T)/aug-cc-pVnZ (n = 2-4) levels and extrapolated to the complete-basis-set limit (CBS). Slices through both 2D surfaces reveal a relatively soft potential in the asymmetric proton stretching coordinate at near equilibrium geometries, which rapidly becomes a double minimum potential with increasing symmetric proton acceptor center of mass separation. Eigenvalues are obtained by solution of the 2D Schrödinger equation with potential/kinetic energy coupling explicity taken into account, converged in a distributed Gaussian basis set as a function of grid density. The asymmetric proton stretch fundamental frequency for N(2)HN(2)(+) is predicted at 848 cm(-1), with strong negative anharmonicity in the progression characteristic of a shallow "particle in a box" potential. The corresponding proton stretch fundamental for OCHCO(+) is anomalously low at 386 cm(-1), but with a strong alternation in the vibrational spacing due to the presence of a shallow D(infinityh) transition state barrier (Delta = 398 cm(-1)) between the two equivalent minimum geometries. Calculation of a 2D dipole moment surface and transition matrix elements reveals surprisingly strong combination and difference bands with appreciable intensity throughout the 300-1500 cm(-1) region. Corrected for zero point (DeltaZPE) and thermal vibrational excitation (DeltaE(vib)) at 300 K, the single and double dissociation energies in these complexes are in excellent agreement with thermochemical gas phase ion data.

The cellular basis of the convergence and extension of the Xenopus neural plate.

PubMed

Keller, R; Shih, J; Sater, A

1992-03-01

There is great interest in the patterning and morphogenesis of the vertebrate nervous system, but the morphogenetic movements involved in early neural development and their underlying cellular mechanisms are poorly understood. This paper describes the cellular basis of the early neural morphogenesis of Xenopus laevis. The results have important implications for neural induction. Mapping the fate map of the midneurula (Eagleson and Harris: J. Neurobiol. 21:427-440, 1990) back to the early gastrula with time-lapse video recording demonstrates that the prospective hindbrain and spinal cord are initially very wide and very short, and thus at the beginning of gastrulation all their precursor cells lie within a few cell diameters of the inducing mesoderm. In the midgastrula, the prospective hindbrain and spinal cord undergo very strong convergence and extension movements in two phases: In the first phase they primarily undergo thinning in the radial direction and lengthening (extension) in the animal-vegetal direction, and the second phase is characterized primarily by mediolateral narrowing (convergence) and anterior-posterior lengthening (extension). These movements also occur in sandwich explants of the gastrula, thus demonstrating the local autonomy of the forces producing them. Tracing cell movements with fluorescein dextran-labeled cells in embryos or explants shows that the initial thinning and extension occurs by radial intercalation of deep cells to form fewer layers of greater area, all of which is expressed as increased length. The subsequent convergence and extension occurs by mediolateral intercalation of deep cells to form a longer, narrower array. These results establish that a similar if not identical sequence of radial and mediolateral cell intercalations underlie convergence and extension of the neural and the mesoderm tissues (Wilson and Keller: Development, 112:289-300, 1991). Moreover, these results establish that radial and mediolateral intercalation are the principal neural cell behaviors induced by the planar signals emanating from the dorsal involuting marginal zone (the Spemann organizer) in the early gastrula (Keller et al: Develop. Dynamics, 193: 218-234, 1992). Radial and mediolateral intercalation are induced among the 5 to 7 rows of cells comprising the prospective hindbrain and spinal cord, thus producing the massive convergence and extension movements that narrow and elongate these regions of the nervous system in the late gastrula. A more general significance of these results is that neural induction is best analyzed and understood in terms of the dynamics of the morphogenetic processes involved.

Using a Multitrait-Multimethod Analysis to Examine Conceptual Similarities of Three Self-Regulated Learning Inventories

ERIC Educational Resources Information Center

Muis, Krista R.; Winne, Philip H.; Jamieson-Noel, Dianne

2007-01-01

Background: A programme of construct validity research is necessary to clarify previous research on self-regulation and to provide a stronger basis for future research. Aim: A multitrait-multimethod (MTMM) analysis was conducted to assess convergent and discriminant validity of three self-regulation measures: the Learning and Study Strategies…

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

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

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

2016-07-28

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

Computational Investigations in Rectangular Convergent and Divergent Ribbed Channels

NASA Astrophysics Data System (ADS)

Sivakumar, Karthikeyan; Kulasekharan, N.; Natarajan, E.

2018-05-01

Computational investigations on the rib turbulated flow inside a convergent and divergent rectangular channel with square ribs of different rib heights and different Reynolds numbers (Re=20,000, 40,000 and 60,000). The ribs were arranged in a staggered fashion between the upper and lower surfaces of the test section. Computational investigations are carried out using computational fluid dynamic software ANSYS Fluent 14.0. Suitable solver settings like turbulence models were identified from the literature and the boundary conditions for the simulations on a solution of independent grid. Computations were carried out for both convergent and divergent channels with 0 (smooth duct), 1.5, 3, 6, 9 and 12 mm rib heights, to identify the ribbed channel with optimal performance, assessed using a thermo hydraulic performance parameter. The convergent and divergent rectangular channels show higher Nu values than the standard correlation values.

A Multistrategy Optimization Improved Artificial Bee Colony Algorithm

PubMed Central

Liu, Wen

2014-01-01

Being prone to the shortcomings of premature and slow convergence rate of artificial bee colony algorithm, an improved algorithm was proposed. Chaotic reverse learning strategies were used to initialize swarm in order to improve the global search ability of the algorithm and keep the diversity of the algorithm; the similarity degree of individuals of the population was used to characterize the diversity of population; population diversity measure was set as an indicator to dynamically and adaptively adjust the nectar position; the premature and local convergence were avoided effectively; dual population search mechanism was introduced to the search stage of algorithm; the parallel search of dual population considerably improved the convergence rate. Through simulation experiments of 10 standard testing functions and compared with other algorithms, the results showed that the improved algorithm had faster convergence rate and the capacity of jumping out of local optimum faster. PMID:24982924

Convergence studies in meshfree peridynamic simulations

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

Seleson, Pablo; Littlewood, David J.

2016-04-15

Meshfree methods are commonly applied to discretize peridynamic models, particularly in numerical simulations of engineering problems. Such methods discretize peridynamic bodies using a set of nodes with characteristic volume, leading to particle-based descriptions of systems. In this article, we perform convergence studies of static peridynamic problems. We show that commonly used meshfree methods in peridynamics suffer from accuracy and convergence issues, due to a rough approximation of the contribution to the internal force density of nodes near the boundary of the neighborhood of a given node. We propose two methods to improve meshfree peridynamic simulations. The first method uses accuratemore » computations of volumes of intersections between neighbor cells and the neighborhood of a given node, referred to as partial volumes. The second method employs smooth influence functions with a finite support within peridynamic kernels. Numerical results demonstrate great improvements in accuracy and convergence of peridynamic numerical solutions, when using the proposed methods.« less

A study of the utility of convergent characters for phylogeny reconstruction: do ecomorphological characters track evolutionary history in Anolis lizards?

PubMed

Poe, Steven

2005-01-01

The reconstruction of phylogeny requires homologous similarities across species. Characters that have been shown to evolve quickly or convergently in some species are often considered to be poor phylogenetic markers. Here I evaluate the phylogenetic utility of a set of morphological characters that are correlated with ecology and have been shown to evolve convergently in Anolis lizards in the Greater Antilles. Results of randomization tests suggest that these "ecomorph" characters are adequate phylogenetic markers, both for Anolis in general and for the Greater Antillean species for which ecomorphological convergence was originally documented. Explanations for this result include the presence of ecomorphologically similar species within evolutionary radiations within islands, some monophyly of ecomorphs across islands, and the existence of several species that defy ecomorphological characterization but share phylogenetic similarity in some ecomorph characters.

A globally convergent MC algorithm with an adaptive learning rate.

PubMed

Peng, Dezhong; Yi, Zhang; Xiang, Yong; Zhang, Haixian

2012-02-01

This brief deals with the problem of minor component analysis (MCA). Artificial neural networks can be exploited to achieve the task of MCA. Recent research works show that convergence of neural networks based MCA algorithms can be guaranteed if the learning rates are less than certain thresholds. However, the computation of these thresholds needs information about the eigenvalues of the autocorrelation matrix of data set, which is unavailable in online extraction of minor component from input data stream. In this correspondence, we introduce an adaptive learning rate into the OJAn MCA algorithm, such that its convergence condition does not depend on any unobtainable information, and can be easily satisfied in practical applications.

An improved VSS NLMS algorithm for active noise cancellation

NASA Astrophysics Data System (ADS)

Sun, Yunzhuo; Wang, Mingjiang; Han, Yufei; Zhang, Congyan

2017-08-01

In this paper, an improved variable step size NLMS algorithm is proposed. NLMS has fast convergence rate and low steady state error compared to other traditional adaptive filtering algorithm. But there is a contradiction between the convergence speed and steady state error that affect the performance of the NLMS algorithm. Now, we propose a new variable step size NLMS algorithm. It dynamically changes the step size according to current error and iteration times. The proposed algorithm has simple formulation and easily setting parameters, and effectively solves the contradiction in NLMS. The simulation results show that the proposed algorithm has a good tracking ability, fast convergence rate and low steady state error simultaneously.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

PubMed

Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

2018-06-27

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

NASA Astrophysics Data System (ADS)

Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

2018-06-01

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Convergence to equilibrium under a random Hamiltonian.

PubMed

Brandão, Fernando G S L; Ćwikliński, Piotr; Horodecki, Michał; Horodecki, Paweł; Korbicz, Jarosław K; Mozrzymas, Marek

2012-09-01

We analyze equilibration times of subsystems of a larger system under a random total Hamiltonian, in which the basis of the Hamiltonian is drawn from the Haar measure. We obtain that the time of equilibration is of the order of the inverse of the arithmetic average of the Bohr frequencies. To compute the average over a random basis, we compute the inverse of a matrix of overlaps of operators which permute four systems. We first obtain results on such a matrix for a representation of an arbitrary finite group and then apply it to the particular representation of the permutation group under consideration.

Convergence to equilibrium under a random Hamiltonian

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Ćwikliński, Piotr; Horodecki, Michał; Horodecki, Paweł; Korbicz, Jarosław K.; Mozrzymas, Marek

2012-09-01

We analyze equilibration times of subsystems of a larger system under a random total Hamiltonian, in which the basis of the Hamiltonian is drawn from the Haar measure. We obtain that the time of equilibration is of the order of the inverse of the arithmetic average of the Bohr frequencies. To compute the average over a random basis, we compute the inverse of a matrix of overlaps of operators which permute four systems. We first obtain results on such a matrix for a representation of an arbitrary finite group and then apply it to the particular representation of the permutation group under consideration.

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models

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

Haraldsdóttir, Hulda S.; Cousins, Ben; Thiele, Ines

In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. Wemore » apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks.« less

Correlates of the MMPI-2-RF in a college setting.

PubMed

Forbey, Johnathan D; Lee, Tayla T C; Handel, Richard W

2010-12-01

The current study examined empirical correlates of scores on Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; A. Tellegen & Y. S. Ben-Porath, 2008; Y. S. Ben-Porath & A. Tellegen, 2008) scales in a college setting. The MMPI-2-RF and six criterion measures (assessing anger, assertiveness, sex roles, cognitive failures, social avoidance, and social fear) were administered to 846 college students (nmen = 264, nwomen = 582) to examine the convergent and discriminant validity of scores on the MMPI-2-RF Specific Problems and Interest scales. Results demonstrated evidence of generally good convergent score validity for the selected MMPI-2-RF scales, reflected in large effect size correlations with criterion measure scores. Further, MMPI-2-RF scale scores demonstrated adequate discriminant validity, reflected in relatively low comparative median correlations between scores on MMPI-2-RF substantive scale sets and criterion measures. Limitations and future directions are discussed.

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models

DOE PAGES

Haraldsdóttir, Hulda S.; Cousins, Ben; Thiele, Ines; ...

2017-01-31

In constraint-based metabolic modelling, physical and biochemical constraints define a polyhedral convex set of feasible flux vectors. Uniform sampling of this set provides an unbiased characterization of the metabolic capabilities of a biochemical network. However, reliable uniform sampling of genome-scale biochemical networks is challenging due to their high dimensionality and inherent anisotropy. Here, we present an implementation of a new sampling algorithm, coordinate hit-and-run with rounding (CHRR). This algorithm is based on the provably efficient hit-and-run random walk and crucially uses a preprocessing step to round the anisotropic flux set. CHRR provably converges to a uniform stationary sampling distribution. Wemore » apply it to metabolic networks of increasing dimensionality. We show that it converges several times faster than a popular artificial centering hit-and-run algorithm, enabling reliable and tractable sampling of genome-scale biochemical networks.« less

Extrapolating subsurface geometry by surface expressions in transpressional strike slip fault, deduced from analogue experiments with settings of rheology and convergence angle

NASA Astrophysics Data System (ADS)

Hsieh, Shang Yu; Neubauer, Franz

2015-04-01

The internal structure of major strike-slip faults is still poorly understood, particularly how to extrapolate subsurface structures by surface expressions. Series of brittle analogue experiments by Leever et al., 2011 resulted the convergence angle is the most influential factor for surface structures. Further analogue models with different ductile settings allow a better understanding in extrapolating surface structures to the subsurface geometry of strike-slip faults. Fifteen analogue experiments were constructed to represent strike-slip faults in nature in different geological settings. As key parameters investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressional system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a thin and rheologically weaker layer in the middle of the brittle layer, deformation is distributed over more faults and the geometry of the fault zone below and above the weak zone shows significant differences, suggesting that the correlation of structures across a weak layer has to be supported by geophysical data, which help constraining the geometry of the deep part. This latter experiment has significantly similar phenomena in reality, such as few pressure ridges along Altyn fault. The experimental results underline the need to understand the role of the convergence angle and the influence of rheology on fault evolution, in order to connect between surface deformation and subsurface geometry.

Smoothing and the second law

NASA Technical Reports Server (NTRS)

Merriam, Marshal L.

1986-01-01

The technique of obtaining second order, oscillation free, total variation diminishing (TVD), scalar difference schemes by adding a limited diffusion flux (smoothing) to a second order centered scheme is explored. It is shown that such schemes do not always converge to the correct physical answer. The approach presented here is to construct schemes that numerically satisfy the second law of thermodynamics on a cell by cell basis. Such schemes can only converge to the correct physical solution and in some cases can be shown to be TVD. An explicit scheme with this property and second order spatial accuracy was found to have an extremely restrictive time step limitation (Delta t less than Delta x squared). Switching to an implicit scheme removed the time step limitation.

Approximate Joint Diagonalization and Geometric Mean of Symmetric Positive Definite Matrices

PubMed Central

Congedo, Marco; Afsari, Bijan; Barachant, Alexandre; Moakher, Maher

2015-01-01

We explore the connection between two problems that have arisen independently in the signal processing and related fields: the estimation of the geometric mean of a set of symmetric positive definite (SPD) matrices and their approximate joint diagonalization (AJD). Today there is a considerable interest in estimating the geometric mean of a SPD matrix set in the manifold of SPD matrices endowed with the Fisher information metric. The resulting mean has several important invariance properties and has proven very useful in diverse engineering applications such as biomedical and image data processing. While for two SPD matrices the mean has an algebraic closed form solution, for a set of more than two SPD matrices it can only be estimated by iterative algorithms. However, none of the existing iterative algorithms feature at the same time fast convergence, low computational complexity per iteration and guarantee of convergence. For this reason, recently other definitions of geometric mean based on symmetric divergence measures, such as the Bhattacharyya divergence, have been considered. The resulting means, although possibly useful in practice, do not satisfy all desirable invariance properties. In this paper we consider geometric means of covariance matrices estimated on high-dimensional time-series, assuming that the data is generated according to an instantaneous mixing model, which is very common in signal processing. We show that in these circumstances we can approximate the Fisher information geometric mean by employing an efficient AJD algorithm. Our approximation is in general much closer to the Fisher information geometric mean as compared to its competitors and verifies many invariance properties. Furthermore, convergence is guaranteed, the computational complexity is low and the convergence rate is quadratic. The accuracy of this new geometric mean approximation is demonstrated by means of simulations. PMID:25919667

Fast alternating projection methods for constrained tomographic reconstruction

PubMed Central

Liu, Li; Han, Yongxin

2017-01-01

The alternating projection algorithms are easy to implement and effective for large-scale complex optimization problems, such as constrained reconstruction of X-ray computed tomography (CT). A typical method is to use projection onto convex sets (POCS) for data fidelity, nonnegative constraints combined with total variation (TV) minimization (so called TV-POCS) for sparse-view CT reconstruction. However, this type of method relies on empirically selected parameters for satisfactory reconstruction and is generally slow and lack of convergence analysis. In this work, we use a convex feasibility set approach to address the problems associated with TV-POCS and propose a framework using full sequential alternating projections or POCS (FS-POCS) to find the solution in the intersection of convex constraints of bounded TV function, bounded data fidelity error and non-negativity. The rationale behind FS-POCS is that the mathematically optimal solution of the constrained objective function may not be the physically optimal solution. The breakdown of constrained reconstruction into an intersection of several feasible sets can lead to faster convergence and better quantification of reconstruction parameters in a physical meaningful way than that in an empirical way of trial-and-error. In addition, for large-scale optimization problems, first order methods are usually used. Not only is the condition for convergence of gradient-based methods derived, but also a primal-dual hybrid gradient (PDHG) method is used for fast convergence of bounded TV. The newly proposed FS-POCS is evaluated and compared with TV-POCS and another convex feasibility projection method (CPTV) using both digital phantom and pseudo-real CT data to show its superior performance on reconstruction speed, image quality and quantification. PMID:28253298

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

Pilot study: evaluation of the use of the convergent interview technique in understanding the perception of surgical design and simulation.

PubMed

Logan, Heather; Wolfaardt, Johan; Boulanger, Pierre; Hodgetts, Bill; Seikaly, Hadi

2013-06-19

It is important to understand the perceived value of surgical design and simulation (SDS) amongst surgeons, as this will influence its implementation in clinical settings. The purpose of the present study was to examine the application of the convergent interview technique in the field of surgical design and simulation and evaluate whether the technique would uncover new perceptions of virtual surgical planning (VSP) and medical models not discovered by other qualitative case-based techniques. Five surgeons were asked to participate in the study. Each participant was interviewed following the convergent interview technique. After each interview, the interviewer interpreted the information by seeking agreements and disagreements among the interviewees in order to understand the key concepts in the field of SDS. Fifteen important issues were extracted from the convergent interviews. In general, the convergent interview was an effective technique in collecting information about the perception of clinicians. The study identified three areas where the technique could be improved upon for future studies in the SDS field.

Pilot study: evaluation of the use of the convergent interview technique in understanding the perception of surgical design and simulation

PubMed Central

2013-01-01

Background It is important to understand the perceived value of surgical design and simulation (SDS) amongst surgeons, as this will influence its implementation in clinical settings. The purpose of the present study was to examine the application of the convergent interview technique in the field of surgical design and simulation and evaluate whether the technique would uncover new perceptions of virtual surgical planning (VSP) and medical models not discovered by other qualitative case-based techniques. Methods Five surgeons were asked to participate in the study. Each participant was interviewed following the convergent interview technique. After each interview, the interviewer interpreted the information by seeking agreements and disagreements among the interviewees in order to understand the key concepts in the field of SDS. Results Fifteen important issues were extracted from the convergent interviews. Conclusion In general, the convergent interview was an effective technique in collecting information about the perception of clinicians. The study identified three areas where the technique could be improved upon for future studies in the SDS field. PMID:23782771

Genetic Convergence in the Adaptation of Dogs and Humans to the High-Altitude Environment of the Tibetan Plateau

PubMed Central

Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

2014-01-01

The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. PMID:25091388

On a variational approach to some parameter estimation problems

NASA Technical Reports Server (NTRS)

Banks, H. T.

1985-01-01

Examples (1-D seismic, large flexible structures, bioturbation, nonlinear population dispersal) in which a variation setting can provide a convenient framework for convergence and stability arguments in parameter estimation problems are considered. Some of these examples are 1-D seismic, large flexible structures, bioturbation, and nonlinear population dispersal. Arguments for convergence and stability via a variational approach of least squares formulations of parameter estimation problems for partial differential equations is one aspect of the problem considered.

A Two-Dimensional Helmholtz Equation Solution for the Multiple Cavity Scattering Problem

DTIC Science & Technology

2013-02-01

obtained by using the block Gauss – Seidel iterative meth- od. To show the convergence of the iterative method, we define the error between two...models to the general multiple cavity setting. Numerical examples indicate that the convergence of the Gauss – Seidel iterative method depends on the...variational approach. A block Gauss – Seidel iterative method is introduced to solve the cou- pled system of the multiple cavity scattering problem, where

Davidenko’s Method for the Solution of Nonlinear Operator Equations.

DTIC Science & Technology

NONLINEAR DIFFERENTIAL EQUATIONS, NUMERICAL INTEGRATION), OPERATORS(MATHEMATICS), BANACH SPACE , MAPPING (TRANSFORMATIONS), NUMERICAL METHODS AND PROCEDURES, INTEGRALS, SET THEORY, CONVERGENCE, MATRICES(MATHEMATICS)

Developing one-dimensional implosions for inertial confinement fusion science

DOE PAGES

Kline, John L.; Yi, Sunghwan A.; Simakov, Andrei Nikolaevich; ...

2016-12-12

Experiments on the National Ignition Facility show that multi-dimensional effects currently dominate the implosion performance. Low mode implosion symmetry and hydrodynamic instabilities seeded by capsule mounting features appear to be two key limiting factors for implosion performance. One reason these factors have a large impact on the performance of inertial confinement fusion implosions is the high convergence required to achieve high fusion gains. To tackle these problems, a predictable implosion platform is needed meaning experiments must trade-off high gain for performance. LANL has adopted three main approaches to develop a one-dimensional (1D) implosion platform where 1D means measured yield overmore » the 1D clean calculation. A high adiabat, low convergence platform is being developed using beryllium capsules enabling larger case-to-capsule ratios to improve symmetry. The second approach is liquid fuel layers using wetted foam targets. With liquid fuel layers, the implosion convergence can be controlled via the initial vapor pressure set by the target fielding temperature. The last method is double shell targets. For double shells, the smaller inner shell houses the DT fuel and the convergence of this cavity is relatively small compared to hot spot ignition. However, double shell targets have a different set of trade-off versus advantages. As a result, details for each of these approaches are described.« less

Convergent and discriminant validity of alternative measures of maladaptive personality traits.

PubMed

Crego, Cristina; Widiger, Thomas A

2016-12-01

The purpose of the current study was to test empirically the convergent and discriminant validity of 3 recently developed, alternative measures of maladaptive personality traits: the Personality Inventory for Diagnostic and Statistical Manual for Mental Disorders-Fifth Edition (DSM-5, PID-5; Krueger, Derringer, Markon, Watson, & Skodol, 2012), the Computerized Adaptive Test-Personality Disorder Static Form (CAT-PD-SF; Simms et al., 2011), and Five Factor Model Personality Disorder scales (FFMPD; Widiger, Lynam, Miller, & Oltmanns, 2012). These measures were constructed with different rationales and methods, yet the result was highly congruent. The PID-5 and CAT-PD-SF were administered to 286 community adults with current or a history of mental health treatment; the CAT-PD-SF and FFMPD scales to 262 such adults; and the PID-5 and FFMPD scales to 266. The results indicated good to excellent internal consistency, as well as good to excellent convergent and discriminant validity for most scales with a few notable exceptions. Suggestions for future research are provided, including the potential benefits of scales that are unique to a respective instrument, replication of a dependency factor, and exploration as to the basis for instances of questionable convergent or discriminant validity. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Comparative Analysis of Gene Expression for Convergent Evolution of Camera Eye Between Octopus and Human

PubMed Central

Ogura, Atsushi; Ikeo, Kazuho; Gojobori, Takashi

2004-01-01

Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been known as a typical example of convergent evolution. To study the molecular basis of convergent evolution of camera eyes, we conducted a comparative analysis of gene expression in octopus and human camera eyes. We sequenced 16,432 ESTs of the octopus eye, leading to 1052 nonredundant genes that have matches in the protein database. Comparing these 1052 genes with 13,303 already-known ESTs of the human eye, 729 (69.3%) genes were commonly expressed between the human and octopus eyes. On the contrary, when we compared octopus eye ESTs with human connective tissue ESTs, the expression similarity was quite low. To trace the evolutionary changes that are potentially responsible for camera eye formation, we also compared octopus-eye ESTs with the completed genome sequences of other organisms. We found that 1019 out of the 1052 genes had already existed at the common ancestor of bilateria, and 875 genes were conserved between humans and octopuses. It suggests that a larger number of conserved genes and their similar gene expression may be responsible for the convergent evolution of the camera eye. PMID:15289475

Electric dipole (hyper)polarizabilities of selected X2Y2 and X3Y3 (X = Al, Ga, In and Y = P, As): III-V semiconductor clusters. An ab initio comparative study.

PubMed

Karamanis, Panaghiotis; Pouchan, Claude; Leszczynski, Jerzy

2008-12-25

A systematic ab initio comparative study of the (hyper)polarizabilities of selected III-V stoichiometric semiconductor clusters has been carried out. Our investigation focuses on the ground state structures of the dimers and on two dissimilar trimer configurations of aluminum, gallium, indium phosphide and arsenide. The basis set effect on both the polarizabilities and hyperpolarizabilities of the studied systems has been explicitly taken into account relying on the augmented correlation consistent aug-cc-pVnZ (n = D, T, Q, and 5) basis sets series. In addition, a rough estimation of the effects of the relativistic effects on the investigated properties is provided by extension of the study to include calculations performed with relativistic electron core potentials (or pseudopotentials). Electron correlation effects have been estimated utilizing methods of increasing predictive reliability, e.g., the Møller-Plesset many body perturbation theory and the couple cluster approach. Our results reveal that in the considered semiconductor species the Group III elements (Al, Ga, In) play a vital role on the values of their relative (hyper)polarizability. At all levels of theory employed the most hyperpolarizable clusters are the indium derivatives while the aluminum arsenide clusters also exhibit high, comparable hyperpolarizabilities. The less hyperpolarizable species are those composed of gallium and this is associated with the strong influence of the nuclear charge on the valence electrons of Ga due to the poor shielding that is provided by the semicore d electrons. In addition, the analysis of the electronic structure and the hyperpolarizability magnitudes reveals that clusters, in which their bonding is characterized by strong electron transfer from the electropositive to the electronegative atoms, are less hyperpolarizable than species in which the corresponding electron transfer is weaker. Lastly, from the methodological point of view our results point out that the hyperpolarizabilities of those species converge when an augmented triple-zeta quality basis set is used and, also, that the second order Møller-Plesset approximation (MP2) overestimates considerably their second hyperpolarizabilities with respect to the highest level of coupled cluster theory applied in this study (CCSD(T)).

1-RAAP: An Efficient 1-Round Anonymous Authentication Protocol for Wireless Body Area Networks

PubMed Central

Liu, Jingwei; Zhang, Lihuan; Sun, Rong

2016-01-01

Thanks to the rapid technological convergence of wireless communications, medical sensors and cloud computing, Wireless Body Area Networks (WBANs) have emerged as a novel networking paradigm enabling ubiquitous Internet services, allowing people to receive medical care, monitor health status in real-time, analyze sports data and even enjoy online entertainment remotely. However, because of the mobility and openness of wireless communications, WBANs are inevitably exposed to a large set of potential attacks, significantly undermining their utility and impeding their widespread deployment. To prevent attackers from threatening legitimate WBAN users or abusing WBAN services, an efficient and secure authentication protocol termed 1-Round Anonymous Authentication Protocol (1-RAAP) is proposed in this paper. In particular, 1-RAAP preserves anonymity, mutual authentication, non-repudiation and some other desirable security properties, while only requiring users to perform several low cost computational operations. More importantly, 1-RAAP is provably secure thanks to its design basis, which is resistant to the anonymous in the random oracle model. To validate the computational efficiency of 1-RAAP, a set of comprehensive comparative studies between 1-RAAP and other authentication protocols is conducted, and the results clearly show that 1-RAAP achieves the best performance in terms of computational overhead. PMID:27213384

Prediction of pKa Values for Neutral and Basic Drugs based on Hybrid Artificial Intelligence Methods.

PubMed

Li, Mengshan; Zhang, Huaijing; Chen, Bingsheng; Wu, Yan; Guan, Lixin

2018-03-05

The pKa value of drugs is an important parameter in drug design and pharmacology. In this paper, an improved particle swarm optimization (PSO) algorithm was proposed based on the population entropy diversity. In the improved algorithm, when the population entropy was higher than the set maximum threshold, the convergence strategy was adopted; when the population entropy was lower than the set minimum threshold the divergence strategy was adopted; when the population entropy was between the maximum and minimum threshold, the self-adaptive adjustment strategy was maintained. The improved PSO algorithm was applied in the training of radial basis function artificial neural network (RBF ANN) model and the selection of molecular descriptors. A quantitative structure-activity relationship model based on RBF ANN trained by the improved PSO algorithm was proposed to predict the pKa values of 74 kinds of neutral and basic drugs and then validated by another database containing 20 molecules. The validation results showed that the model had a good prediction performance. The absolute average relative error, root mean square error, and squared correlation coefficient were 0.3105, 0.0411, and 0.9685, respectively. The model can be used as a reference for exploring other quantitative structure-activity relationships.

1-RAAP: An Efficient 1-Round Anonymous Authentication Protocol for Wireless Body Area Networks.

PubMed

Liu, Jingwei; Zhang, Lihuan; Sun, Rong

2016-05-19

Thanks to the rapid technological convergence of wireless communications, medical sensors and cloud computing, Wireless Body Area Networks (WBANs) have emerged as a novel networking paradigm enabling ubiquitous Internet services, allowing people to receive medical care, monitor health status in real-time, analyze sports data and even enjoy online entertainment remotely. However, because of the mobility and openness of wireless communications, WBANs are inevitably exposed to a large set of potential attacks, significantly undermining their utility and impeding their widespread deployment. To prevent attackers from threatening legitimate WBAN users or abusing WBAN services, an efficient and secure authentication protocol termed 1-Round Anonymous Authentication Protocol (1-RAAP) is proposed in this paper. In particular, 1-RAAP preserves anonymity, mutual authentication, non-repudiation and some other desirable security properties, while only requiring users to perform several low cost computational operations. More importantly, 1-RAAP is provably secure thanks to its design basis, which is resistant to the anonymous in the random oracle model. To validate the computational efficiency of 1-RAAP, a set of comprehensive comparative studies between 1-RAAP and other authentication protocols is conducted, and the results clearly show that 1-RAAP achieves the best performance in terms of computational overhead.

Geomagnetic field modeling by optimal recursive filtering

NASA Technical Reports Server (NTRS)

1980-01-01

Data sets selected for mini-batches and the software modifications required for processing these sets are described. Initial analysis was performed on minibatch field model recovery. Studies are being performed to examine the convergence of the solutions and the maximum expansion order the data will support in the constant and secular terms.

Uniform electron gases. III. Low-density gases on three-dimensional spheres

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

Agboola, Davids; Knol, Anneke L.; Gill, Peter M. W., E-mail: peter.gill@anu.edu.au

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGFmore » centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids — the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) — and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.« less

A new single-particle basis for nuclear many-body calculations

NASA Astrophysics Data System (ADS)

Puddu, G.

2017-10-01

Predominantly, harmonic oscillator single-particle wave functions are the preferred choice for a basis in ab initio nuclear many-body calculations. These wave-functions, although very convenient in order to evaluate the matrix elements of the interaction in the laboratory frame, have too fast a fall-off at large distances. In the past, as an alternative to the harmonic oscillator, other single-particle wave functions have been proposed. In this work, we propose a new single-particle basis, directly linked to nucleon-nucleon interaction. This new basis is orthonormal and complete, has the proper asymptotic behavior at large distances and does not contain the continuum which would pose severe convergence problems in nuclear many body calculations. We consider the newly proposed NNLO-opt nucleon-nucleon interaction, without any renormalization. We show that, unlike other bases, this single-particle representation has a computational cost similar to the harmonic oscillator basis with the same space truncation and it gives lower energies for 6He and 6Li.

Murine glomerulotropic monoclonal antibodies are highly oligoclonal and exhibit distinctive molecular features.

PubMed

Lefkowith, J B; Di Valerio, R; Norris, J; Glick, G D; Alexander, A L; Jackson, L; Gilkeson, G S

1996-08-01

We recently produced a panel of seven glomerular-binding mAbs from a nephritic MRL-lpr mouse that bind to histones/nucleosomes (group I) or DNA (group II) adherent to glomerular basement membrane. To elucidate the molecular basis of their binding and ontogeny, we sequenced their variable (V) regions, analyzed the apparent somatic mutations, and predicted their three-dimensional structures. There were two clonally related sets (3 of 4 in group I, 3 of 3 in group II) both of the VHJ1558 family, and one mAb of the VH 7183 family. V region somatic mutations within clonally related sets had little effect on glomerular binding and did not appear to be selected for based on glomerular binding. The VH regions were most homologous with those from autoantibodies to histones, DNA, or IgG (i.e., rheumatoid factors), the Vkappa regions, with those from autoantibodies to small nuclear ribonucleoproteins (snRNP). The VH regions also exhibited an unusual VD junction (in the group I clonally related set) and an overall high content of charged amino acids (arginine, aspartic acid) in complementarity-determining regions (CDRs), particularly in CDR3. Molecular modeling studies suggested that the Fv regions of these mAbs converge to form a flat, open surface with a net positive charge. The CDR arginines in group I mAbs; appear to be located in Ag contact regions of the binding cleft. In sum, these data suggest that glomerulotropic mAbs are a highly restricted set of Abs with distinctive molecular features that may mediate their binding to glomeruli.

Convergent Polishing: A Simple, Rapid, Full Aperture Polishing Process of High Quality Optical Flats & Spheres

PubMed Central

Suratwala, Tayyab; Steele, Rusty; Feit, Michael; Dylla-Spears, Rebecca; Desjardin, Richard; Mason, Dan; Wong, Lana; Geraghty, Paul; Miller, Phil; Shen, Nan

2014-01-01

Convergent Polishing is a novel polishing system and method for finishing flat and spherical glass optics in which a workpiece, independent of its initial shape (i.e., surface figure), will converge to final surface figure with excellent surface quality under a fixed, unchanging set of polishing parameters in a single polishing iteration. In contrast, conventional full aperture polishing methods require multiple, often long, iterative cycles involving polishing, metrology and process changes to achieve the desired surface figure. The Convergent Polishing process is based on the concept of workpiece-lap height mismatch resulting in pressure differential that decreases with removal and results in the workpiece converging to the shape of the lap. The successful implementation of the Convergent Polishing process is a result of the combination of a number of technologies to remove all sources of non-uniform spatial material removal (except for workpiece-lap mismatch) for surface figure convergence and to reduce the number of rogue particles in the system for low scratch densities and low roughness. The Convergent Polishing process has been demonstrated for the fabrication of both flats and spheres of various shapes, sizes, and aspect ratios on various glass materials. The practical impact is that high quality optical components can be fabricated more rapidly, more repeatedly, with less metrology, and with less labor, resulting in lower unit costs. In this study, the Convergent Polishing protocol is specifically described for fabricating 26.5 cm square fused silica flats from a fine ground surface to a polished ~λ/2 surface figure after polishing 4 hr per surface on a 81 cm diameter polisher. PMID:25489745

Frequency of convergence and accommodative disorders in a clinical population of Mashhad, Iran.

PubMed

Hoseini-Yazdi, Seyed Hosein; Yekta, AbbasAli; Nouri, Hosein; Heravian, Javad; Ostadimoghaddam, Hadi; Khabazkhoob, Mehdi

2015-01-01

To investigate the frequency of convergence and accommodation anomalies in an optometric clinical setting in Mashhad, Iran, and to determine tests with highest accuracy in diagnosing these anomalies. From 261 patients who came to the optometric clinics of Mashhad University of Medical Sciences during a month, 83 of them were included in the study based on the inclusion criteria. Near point of convergence (NPC), near and distance heterophoria, monocular and binocular accommodative facility (MAF and BAF, respectively), lag of accommodation, positive and negative fusional vergences (PFV and NFV, respectively), AC/A ratio, relative accommodation, and amplitude of accommodation (AA) were measured to diagnose the convergence and accommodation anomalies. The results were also compared between symptomatic and asymptomatic patients. The accuracy of these tests was explored using sensitivity (S), specificity (Sp), and positive and negative likelihood ratios (LR+, LR-). Mean age of the patients was 21.3 ± 3.5 years and 14.5% of them had specific binocular and accommodative symptoms. Convergence and accommodative anomalies were found in 19.3% of the patients; accommodative excess (4.8%) and convergence insufficiency (3.6%) were the most common accommodative and convergence disorders, respectively. Symptomatic patients showed lower values for BAF (p = .003), MAF (p = .001), as well as AA (p = .001) compared with asymptomatic patients. Moreover, BAF (S = 75%, Sp = 62%) and MAF (S = 62%, Sp = 89%) were the most accurate tests for detecting accommodative and convergence disorders in terms of both sensitivity and specificity. Convergence and accommodative anomalies are the most common binocular disorders in optometric patients. Including tests of monocular and binocular accommodative facility in routine eye examinations as accurate tests to diagnose these anomalies requires further investigation.

Density-based cluster algorithms for the identification of core sets

NASA Astrophysics Data System (ADS)

Lemke, Oliver; Keller, Bettina G.

2016-10-01

The core-set approach is a discretization method for Markov state models of complex molecular dynamics. Core sets are disjoint metastable regions in the conformational space, which need to be known prior to the construction of the core-set model. We propose to use density-based cluster algorithms to identify the cores. We compare three different density-based cluster algorithms: the CNN, the DBSCAN, and the Jarvis-Patrick algorithm. While the core-set models based on the CNN and DBSCAN clustering are well-converged, constructing core-set models based on the Jarvis-Patrick clustering cannot be recommended. In a well-converged core-set model, the number of core sets is up to an order of magnitude smaller than the number of states in a conventional Markov state model with comparable approximation error. Moreover, using the density-based clustering one can extend the core-set method to systems which are not strongly metastable. This is important for the practical application of the core-set method because most biologically interesting systems are only marginally metastable. The key point is to perform a hierarchical density-based clustering while monitoring the structure of the metric matrix which appears in the core-set method. We test this approach on a molecular-dynamics simulation of a highly flexible 14-residue peptide. The resulting core-set models have a high spatial resolution and can distinguish between conformationally similar yet chemically different structures, such as register-shifted hairpin structures.

What relates newspaper, definite, and clothing? An article describing deficits in convergent problem solving and creativity following hippocampal damage

PubMed Central

Warren, David E.; Kurczek, Jake; Duff, Melissa C.

2016-01-01

Creativity relies on a diverse set of cognitive processes associated with distinct neural correlates, and one important aspect of creativity, divergent thinking, has been associated with the hippocampus. However, hippocampal contributions to another important aspect of creativity, convergent problem solving, have not been investigated. We tested the necessity of hippocampus for convergent problem solving using a neuropsychological method. Participants with amnesia due to hippocampal damage (N=5) and healthy normal comparison participants (N=5) were tested using a task that promoted solutions based on existing knowledge (Bowden and Jung-Beeman, 2003). During each trial, participants were given a list of three words (e.g., fly, man, place) and asked to respond with a word that could be combined with each of the three words (e.g., fire). The amnesic group produced significantly fewer correct responses than the healthy comparison group. These findings indicate that the hippocampus is necessary for normal convergent problem solving and that changes in the status of the hippocampus should affect convergent problem solving in the context of creative problem-solving across short intervals. This proposed contribution of the hippocampus to convergent problem solving is consistent with an expanded perspective on hippocampal function that acknowledges its role in cognitive processes beyond declarative memory. PMID:27010751

Convergence in the Bilingual Lexicon: A Pre-registered Replication of Previous Studies.

PubMed

White, Anne; Malt, Barbara C; Storms, Gert

2016-01-01

Naming patterns of bilinguals have been found to converge and form a new intermediate language system from elements of both the bilinguals' languages. This converged naming pattern differs from the monolingual naming patterns of both a bilingual's languages. We conducted a pre-registered replication study of experiments addressing the question whether there is a convergence between a bilingual's both lexicons. The replication used an enlarged set of stimuli of common household containers, providing generalizability, and more reliable representations of the semantic domain. Both an analysis at the group-level and at the individual level of the correlations between naming patterns reject the two-pattern hypothesis that poses that bilinguals use two monolingual-like naming patterns, one for each of their two languages. However, the results of the original study and the replication comply with the one-pattern hypothesis, which poses that bilinguals converge the naming patterns of their two languages and form a compromise. Since this convergence is only partial the naming pattern in bilinguals corresponds to a moderate version of the one-pattern hypothesis. These findings are further confirmed by a representation of the semantic domain in a multidimensional space and the finding of shorter distances between bilingual category centers than monolingual category centers in this multidimensional space both in the original and in the replication study.

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

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Sundermann, Andreas

2001-02-01

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

Chandrasekhar equations and computational algorithms for distributed parameter systems

NASA Technical Reports Server (NTRS)

Burns, J. A.; Ito, K.; Powers, R. K.

1984-01-01

The Chandrasekhar equations arising in optimal control problems for linear distributed parameter systems are considered. The equations are derived via approximation theory. This approach is used to obtain existence, uniqueness, and strong differentiability of the solutions and provides the basis for a convergent computation scheme for approximating feedback gain operators. A numerical example is presented to illustrate these ideas.

Functional Data Approximation on Bounded Domains using Polygonal Finite Elements.

PubMed

Cao, Juan; Xiao, Yanyang; Chen, Zhonggui; Wang, Wenping; Bajaj, Chandrajit

2018-07-01

We construct and analyze piecewise approximations of functional data on arbitrary 2D bounded domains using generalized barycentric finite elements, and particularly quadratic serendipity elements for planar polygons. We compare approximation qualities (precision/convergence) of these partition-of-unity finite elements through numerical experiments, using Wachspress coordinates, natural neighbor coordinates, Poisson coordinates, mean value coordinates, and quadratic serendipity bases over polygonal meshes on the domain. For a convex n -sided polygon, the quadratic serendipity elements have 2 n basis functions, associated in a Lagrange-like fashion to each vertex and each edge midpoint, rather than the usual n ( n + 1)/2 basis functions to achieve quadratic convergence. Two greedy algorithms are proposed to generate Voronoi meshes for adaptive functional/scattered data approximations. Experimental results show space/accuracy advantages for these quadratic serendipity finite elements on polygonal domains versus traditional finite elements over simplicial meshes. Polygonal meshes and parameter coefficients of the quadratic serendipity finite elements obtained by our greedy algorithms can be further refined using an L 2 -optimization to improve the piecewise functional approximation. We conduct several experiments to demonstrate the efficacy of our algorithm for modeling features/discontinuities in functional data/image approximation.

The dynamical control of subduction parameters on surface topography

NASA Astrophysics Data System (ADS)

Crameri, F.; Lithgow-Bertelloni, C. R.; Tackley, P. J.

2017-04-01

The long-wavelength surface deflection of Earth's outermost rocky shell is mainly controlled by large-scale dynamic processes like isostasy or mantle flow. The largest topographic amplitudes are therefore observed at plate boundaries due to the presence of large thermal heterogeneities and strong tectonic forces. Distinct vertical surface deflections are particularly apparent at convergent plate boundaries mostly due to the convergence and asymmetric sinking of the plates. Having a mantle convection model with a free surface that is able to reproduce both realistic single-sided subduction and long-wavelength surface topography self-consistently, we are now able to better investigate this interaction. We separate the topographic signal into distinct features and quantify the individual topographic contribution of several controlling subduction parameters. Results are diagnosed by splitting the topographic signal into isostatic and residual components, and by considering various physical aspects like viscous dissipation during plate bending. Performing several systematic suites of experiments, we are then able to quantify the topographic impact of the buoyancy, rheology, and geometry of the subduction-zone system to each and every topographic feature at a subduction zone and to provide corresponding scaling laws. We identify slab dip and, slightly less importantly, slab buoyancy as the major agents controlling surface topography at subduction zones on Earth. Only the island-arc high and the back-arc depression extent are mainly controlled by plate strength. Overall, his modeling study sets the basis to better constrain deep-seated mantle structures and their physical properties via the observed surface topography on present-day Earth and back through time.

On the Optimization of Aerospace Plane Ascent Trajectory

NASA Astrophysics Data System (ADS)

Al-Garni, Ahmed; Kassem, Ayman Hamdy

A hybrid heuristic optimization technique based on genetic algorithms and particle swarm optimization has been developed and tested for trajectory optimization problems with multi-constraints and a multi-objective cost function. The technique is used to calculate control settings for two types for ascending trajectories (constant dynamic pressure and minimum-fuel-minimum-heat) for a two-dimensional model of an aerospace plane. A thorough statistical analysis is done on the hybrid technique to make comparisons with both basic genetic algorithms and particle swarm optimization techniques with respect to convergence and execution time. Genetic algorithm optimization showed better execution time performance while particle swarm optimization showed better convergence performance. The hybrid optimization technique, benefiting from both techniques, showed superior robust performance compromising convergence trends and execution time.

Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

NASA Astrophysics Data System (ADS)

Stoudenmire, Edwin Miles; White, Steven

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

Numerical algorithms for scatter-to-attenuation reconstruction in PET: empirical comparison of convergence, acceleration, and the effect of subsets.

PubMed

Berker, Yannick; Karp, Joel S; Schulz, Volkmar

2017-09-01

The use of scattered coincidences for attenuation correction of positron emission tomography (PET) data has recently been proposed. For practical applications, convergence speeds require further improvement, yet there exists a trade-off between convergence speed and the risk of non-convergence. In this respect, a maximum-likelihood gradient-ascent (MLGA) algorithm and a two-branch back-projection (2BP), which was previously proposed, were evaluated. MLGA was combined with the Armijo step size rule; and accelerated using conjugate gradients, Nesterov's momentum method, and data subsets of different sizes. In 2BP, we varied the subset size, an important determinant of convergence speed and computational burden. We used three sets of simulation data to evaluate the impact of a spatial scale factor. The Armijo step size allowed 10-fold increased step sizes compared to native MLGA. Conjugate gradients and Nesterov momentum lead to slightly faster, yet non-uniform convergence; improvements were mostly confined to later iterations, possibly due to the non-linearity of the problem. MLGA with data subsets achieved faster, uniform, and predictable convergence, with a speed-up factor equivalent to the number of subsets and no increase in computational burden. By contrast, 2BP computational burden increased linearly with the number of subsets due to repeated evaluation of the objective function, and convergence was limited to the case of many (and therefore small) subsets, which resulted in high computational burden. Possibilities of improving 2BP appear limited. While general-purpose acceleration methods appear insufficient for MLGA, results suggest that data subsets are a promising way of improving MLGA performance.

Neural Encoding and Integration of Learned Probabilistic Sequences in Avian Sensory-Motor Circuitry

PubMed Central

Brainard, Michael S.

2013-01-01

Many complex behaviors, such as human speech and birdsong, reflect a set of categorical actions that can be flexibly organized into variable sequences. However, little is known about how the brain encodes the probabilities of such sequences. Behavioral sequences are typically characterized by the probability of transitioning from a given action to any subsequent action (which we term “divergence probability”). In contrast, we hypothesized that neural circuits might encode the probability of transitioning to a given action from any preceding action (which we term “convergence probability”). The convergence probability of repeatedly experienced sequences could naturally become encoded by Hebbian plasticity operating on the patterns of neural activity associated with those sequences. To determine whether convergence probability is encoded in the nervous system, we investigated how auditory-motor neurons in vocal premotor nucleus HVC of songbirds encode different probabilistic characterizations of produced syllable sequences. We recorded responses to auditory playback of pseudorandomly sequenced syllables from the bird's repertoire, and found that variations in responses to a given syllable could be explained by a positive linear dependence on the convergence probability of preceding sequences. Furthermore, convergence probability accounted for more response variation than other probabilistic characterizations, including divergence probability. Finally, we found that responses integrated over >7–10 syllables (∼700–1000 ms) with the sign, gain, and temporal extent of integration depending on convergence probability. Our results demonstrate that convergence probability is encoded in sensory-motor circuitry of the song-system, and suggest that encoding of convergence probability is a general feature of sensory-motor circuits. PMID:24198363

The new world of discovery, invention, and innovation: convergence of knowledge, technology, and society

NASA Astrophysics Data System (ADS)

Roco, Mihail C.; Bainbridge, William S.

2013-09-01

Convergence of knowledge and technology for the benefit of society (CKTS) is the core opportunity for progress in the twenty-first century. CKTS is defined as the escalating and transformative interactions among seemingly different disciplines, technologies, communities, and domains of human activity to achieve mutual compatibility, synergism, and integration, and through this process to create added value and branch out to meet shared goals. Convergence has been progressing by stages over the past several decades, beginning with nanotechnology for the material world, followed by convergence of nanotechnology, biotechnology, information, and cognitive science (NBIC) for emerging technologies. CKTS is the third level of convergence. It suggests a general process to advance creativity, innovation, and societal progress based on five general purpose principles: (1) the interdependence of all components of nature and society, (2) decision analysis for research, development, and applications based on dynamic system-logic deduction, (3) enhancement of creativity and innovation through evolutionary processes of convergence that combines existing principles and divergence that generates new ones, (4) the utility of higher-level cross-domain languages to generate new solutions and support transfer of new knowledge, and (5) the value of vision-inspired basic research embodied in grand challenges. CKTS is a general purpose approach in knowledge society. It allows society to answer questions and resolve problems that isolated capabilities cannot, as well as to create new competencies, knowledge, and technologies on this basis. Possible solutions are outlined for key societal challenges in the next decade, including support for foundational emerging technologies NBIC to penetrate essential platforms of human activity and create new industries and jobs, improve lifelong wellness and human potential, achieve personalized and integrated healthcare and education, and secure a sustainable quality of life for all. This paper provides a 10-year "NBIC2" vision within a longer-term framework for converging technology and human progress outlined in a previous study of unifying principles across "NBIC" fields that began with nanotechnology, biotechnology, information technology, and technologies based on and enabling cognitive science (Roco and Bainbridge, Converging technologies for improving human performance: nanotechnology, biotechnology, information technology and cognitive sciences, 2003).

Collaborating on convergent technologies: education and practice.

PubMed

Gorman, Michael E

2004-05-01

Converging technologies will require collaboration across disciplines. A good metaphor for such collaborations is the kind of trading zone that emerges whenever human beings from different cultures interact. NBIC must avoid trading zones that are dominated by one discipline or set of interests and instead encourage multiple stakeholders to form a shared mental model of what needs to be accomplished. An example is drawn from current work on societal dimensions of nanotechnology. Students need to gain experience working in such trading zones, in addition to acquiring disciplinary depth.

Solution of elliptic partial differential equations by fast Poisson solvers using a local relaxation factor. 2: Two-step method

NASA Technical Reports Server (NTRS)

Chang, S. C.

1986-01-01

A two-step semidirect procedure is developed to accelerate the one-step procedure described in NASA TP-2529. For a set of constant coefficient model problems, the acceleration factor increases from 1 to 2 as the one-step procedure convergence rate decreases from + infinity to 0. It is also shown numerically that the two-step procedure can substantially accelerate the convergence of the numerical solution of many partial differential equations (PDE's) with variable coefficients.

Aerothermodynamics and Propulsion Integration for Hypersonic Vehicles (L’Integration de la Propusion et de l’aerodynnamique pour les vehicules hypersoniques).

DTIC Science & Technology

1996-10-01

aerothermoelasticity, temperature gradients and internal heat gies, belong fully resuable SSTO and TSTO sytems, protection. The demand of extreme light...supersonic conditions, convergent and convergent-divergent nozzles matching the cold cage internal diameter will be fixed on the end plate. A set of five...in hypersonic flow. AIAA Paper93- des Fluides, Avril 1996. 5111, 5th International Aerospace Planes and 16. Morrisette, E.L., Creel, T.R., Chen, F.J

Physical condition for elimination of ambiguity in conditionally convergent lattice sums

NASA Astrophysics Data System (ADS)

Young, K.

1987-02-01

The conditional convergence of the lattice sum defining the Madelung constant gives rise to an ambiguity in its value. It is shown that this ambiguity is related, through a simple and universal integral, to the average charge density on the crystal surface. The physically correct value is obtained by setting the charge density to zero. A simple and universally applicable formula for the Madelung constant is derived as a consequence. It consists of adding up dipole-dipole energies together with a nontrivial correction term.

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

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

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

Genes involved in convergent evolution of eusociality in bees

PubMed Central

Woodard, S. Hollis; Fischman, Brielle J.; Venkat, Aarti; Hudson, Matt E.; Varala, Kranthi; Cameron, Sydney A.; Clark, Andrew G.; Robinson, Gene E.

2011-01-01

Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality. PMID:21482769

The "covariation method" for estimating the parameters of the standard Dynamic Energy Budget model II: Properties and preliminary patterns

NASA Astrophysics Data System (ADS)

Lika, Konstadia; Kearney, Michael R.; Kooijman, Sebastiaan A. L. M.

2011-11-01

The covariation method for estimating the parameters of the standard Dynamic Energy Budget (DEB) model provides a single-step method of accessing all the core DEB parameters from commonly available empirical data. In this study, we assess the robustness of this parameter estimation procedure and analyse the role of pseudo-data using elasticity coefficients. In particular, we compare the performance of Maximum Likelihood (ML) vs. Weighted Least Squares (WLS) approaches and find that the two approaches tend to converge in performance as the number of uni-variate data sets increases, but that WLS is more robust when data sets comprise single points (zero-variate data). The efficiency of the approach is shown to be high, and the prior parameter estimates (pseudo-data) have very little influence if the real data contain information about the parameter values. For instance, the effects of the pseudo-value for the allocation fraction κ is reduced when there is information for both growth and reproduction, that for the energy conductance is reduced when information on age at birth and puberty is given, and the effects of the pseudo-value for the maturity maintenance rate coefficient are insignificant. The estimation of some parameters (e.g., the zoom factor and the shape coefficient) requires little information, while that of others (e.g., maturity maintenance rate, puberty threshold and reproduction efficiency) require data at several food levels. The generality of the standard DEB model, in combination with the estimation of all of its parameters, allows comparison of species on the basis of parameter values. We discuss a number of preliminary patterns emerging from the present collection of parameter estimates across a wide variety of taxa. We make the observation that the estimated value of the fraction κ of mobilised reserve that is allocated to soma is far away from the value that maximises reproduction. We recognise this as the reason why two very different parameter sets must exist that fit most data set reasonably well, and give arguments why, in most cases, the set with the large value of κ should be preferred. The continued development of a parameter database through the estimation procedures described here will provide a strong basis for understanding evolutionary patterns in metabolic organisation across the diversity of life.

Testing Convergence Versus History: Convergence Dominates Phenotypic Evolution for over 150 Million Years in Frogs.

PubMed

Moen, Daniel S; Morlon, Hélène; Wiens, John J

2016-01-01

Striking evolutionary convergence can lead to similar sets of species in different locations, such as in cichlid fishes and Anolis lizards, and suggests that evolution can be repeatable and predictable across clades. Yet, most examples of convergence involve relatively small temporal and/or spatial scales. Some authors have speculated that at larger scales (e.g., across continents), differing evolutionary histories will prevent convergence. However, few studies have compared the contrasting roles of convergence and history, and none have done so at large scales. Here we develop a two-part approach to test the scale over which convergence can occur, comparing the relative importance of convergence and history in macroevolution using phylogenetic models of adaptive evolution. We apply this approach to data from morphology, ecology, and phylogeny from 167 species of anuran amphibians (frogs) from 10 local sites across the world, spanning ~160 myr of evolution. Mapping ecology on the phylogeny revealed that similar microhabitat specialists (e.g., aquatic, arboreal) have evolved repeatedly across clades and regions, producing many evolutionary replicates for testing for morphological convergence. By comparing morphological optima for clades and microhabitat types (our first test), we find that convergence associated with microhabitat use dominates frog morphological evolution, producing recurrent ecomorphs that together encompass all sampled species in each community in each region. However, our second test, which examines whether and how much species differ from their inferred optima, shows that convergence is incomplete: that is, phenotypes of most species are still somewhat distant from the estimated optimum for each microhabitat, seemingly because of insufficient time for more complete adaptation (an effect of history). Yet, these effects of history are related to past ecologies, and not clade membership. Overall, our study elucidates the dominant drivers of morphological evolution across a major vertebrate clade and shows that evolution can be repeatable at much greater temporal and spatial scales than commonly thought. It also provides an analytical framework for testing other potential examples of large-scale convergence. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Decentralized finite-time attitude synchronization for multiple rigid spacecraft via a novel disturbance observer.

PubMed

Zong, Qun; Shao, Shikai

2016-11-01

This paper investigates decentralized finite-time attitude synchronization for a group of rigid spacecraft by using quaternion with the consideration of environmental disturbances, inertia uncertainties and actuator saturation. Nonsingular terminal sliding mode (TSM) is used for controller design. Firstly, a theorem is proven that there always exists a kind of TSM that converges faster than fast terminal sliding mode (FTSM) for quaternion-descripted attitude control system. Controller with this kind of TSM has faster convergence and reduced computation than FTSM controller. Then, combining with an adaptive parameter estimation strategy, a novel terminal sliding mode disturbance observer is proposed. The proposed disturbance observer needs no upper bound information of the lumped uncertainties or their derivatives. On the basis of undirected topology and the disturbance observer, decentralized attitude synchronization control laws are designed and all attitude errors are ensured to converge to small regions in finite time. As for actuator saturation problem, an auxiliary variable is introduced and accommodated by the disturbance observer. Finally, simulation results are given and the effectiveness of the proposed control scheme is testified. Copyright © 2016. Published by Elsevier Ltd.

Convergent Evolution of Mechanically Optimal Locomotion in Aquatic Invertebrates and Vertebrates

PubMed Central

Bale, Rahul; Neveln, Izaak D.; Bhalla, Amneet Pal Singh

2015-01-01

Examples of animals evolving similar traits despite the absence of that trait in the last common ancestor, such as the wing and camera-type lens eye in vertebrates and invertebrates, are called cases of convergent evolution. Instances of convergent evolution of locomotory patterns that quantitatively agree with the mechanically optimal solution are very rare. Here, we show that, with respect to a very diverse group of aquatic animals, a mechanically optimal method of swimming with elongated fins has evolved independently at least eight times in both vertebrate and invertebrate swimmers across three different phyla. Specifically, if we take the length of an undulation along an animal’s fin during swimming and divide it by the mean amplitude of undulations along the fin length, the result is consistently around twenty. We call this value the optimal specific wavelength (OSW). We show that the OSW maximizes the force generated by the body, which also maximizes swimming speed. We hypothesize a mechanical basis for this optimality and suggest reasons for its repeated emergence through evolution. PMID:25919026

Finite-time containment control of perturbed multi-agent systems based on sliding-mode control

NASA Astrophysics Data System (ADS)

Yu, Di; Ji, Xiang Yang

2018-01-01

Aimed at faster convergence rate, this paper investigates finite-time containment control problem for second-order multi-agent systems with norm-bounded non-linear perturbation. When topology between the followers are strongly connected, the nonsingular fast terminal sliding-mode error is defined, corresponding discontinuous control protocol is designed and the appropriate value range of control parameter is obtained by applying finite-time stability analysis, so that the followers converge to and move along the desired trajectories within the convex hull formed by the leaders in finite time. Furthermore, on the basis of the sliding-mode error defined, the corresponding distributed continuous control protocols are investigated with fast exponential reaching law and double exponential reaching law, so as to make the followers move to the small neighbourhoods of their desired locations and keep within the dynamic convex hull formed by the leaders in finite time to achieve practical finite-time containment control. Meanwhile, we develop the faster control scheme according to comparison of the convergence rate of these two different reaching laws. Simulation examples are given to verify the correctness of theoretical results.

Localized basis sets for unbound electrons in nanoelectronics.

PubMed

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

2008-02-21

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

Second-order asymptotics for quantum hypothesis testing in settings beyond i.i.d. - quantum lattice systems and more

NASA Astrophysics Data System (ADS)

Datta, Nilanjana; Pautrat, Yan; Rouzé, Cambyse

2016-06-01

Quantum Stein's lemma is a cornerstone of quantum statistics and concerns the problem of correctly identifying a quantum state, given the knowledge that it is one of two specific states (ρ or σ). It was originally derived in the asymptotic i.i.d. setting, in which arbitrarily many (say, n) identical copies of the state (ρ⊗n or σ⊗n) are considered to be available. In this setting, the lemma states that, for any given upper bound on the probability αn of erroneously inferring the state to be σ, the probability βn of erroneously inferring the state to be ρ decays exponentially in n, with the rate of decay converging to the relative entropy of the two states. The second order asymptotics for quantum hypothesis testing, which establishes the speed of convergence of this rate of decay to its limiting value, was derived in the i.i.d. setting independently by Tomamichel and Hayashi, and Li. We extend this result to settings beyond i.i.d. Examples of these include Gibbs states of quantum spin systems (with finite-range, translation-invariant interactions) at high temperatures, and quasi-free states of fermionic lattice gases.

Clinical test responses to different orthoptic exercise regimes in typical young adults

PubMed Central

Horwood, Anna; Toor, Sonia

2014-01-01

Purpose The relative efficiency of different eye exercise regimes is unclear, and in particular the influences of practice, placebo and the amount of effort required are rarely considered. This study measured conventional clinical measures following different regimes in typical young adults. Methods A total of 156 asymptomatic young adults were directed to carry out eye exercises three times daily for 2 weeks. Exercises were directed at improving blur responses (accommodation), disparity responses (convergence), both in a naturalistic relationship, convergence in excess of accommodation, accommodation in excess of convergence, and a placebo regime. They were compared to two control groups, neither of which were given exercises, but the second of which were asked to make maximum effort during the second testing. Results Instruction set and participant effort were more effective than many exercises. Convergence exercises independent of accommodation were the most effective treatment, followed by accommodation exercises, and both regimes resulted in changes in both vergence and accommodation test responses. Exercises targeting convergence and accommodation working together were less effective than those where they were separated. Accommodation measures were prone to large instruction/effort effects and monocular accommodation facility was subject to large practice effects. Conclusions Separating convergence and accommodation exercises seemed more effective than exercising both systems concurrently and suggests that stimulation of accommodation and convergence may act in an additive fashion to aid responses. Instruction/effort effects are large and should be carefully controlled if claims for the efficacy of any exercise regime are to be made. PMID:24471739

Rapid computation of directional wellbore drawdown in a confined aquifer via Poisson resummation

NASA Astrophysics Data System (ADS)

Blumenthal, Benjamin J.; Zhan, Hongbin

2016-08-01

We have derived a rapidly computed analytical solution for drawdown caused by a partially or fully penetrating directional wellbore (vertical, horizontal, or slant) via Green's function method. The mathematical model assumes an anisotropic, homogeneous, confined, box-shaped aquifer. Any dimension of the box can have one of six possible boundary conditions: 1) both sides no-flux; 2) one side no-flux - one side constant-head; 3) both sides constant-head; 4) one side no-flux; 5) one side constant-head; 6) free boundary conditions. The solution has been optimized for rapid computation via Poisson Resummation, derivation of convergence rates, and numerical optimization of integration techniques. Upon application of the Poisson Resummation method, we were able to derive two sets of solutions with inverse convergence rates, namely an early-time rapidly convergent series (solution-A) and a late-time rapidly convergent series (solution-B). From this work we were able to link Green's function method (solution-B) back to image well theory (solution-A). We then derived an equation defining when the convergence rate between solution-A and solution-B is the same, which we termed the switch time. Utilizing the more rapidly convergent solution at the appropriate time, we obtained rapid convergence at all times. We have also shown that one may simplify each of the three infinite series for the three-dimensional solution to 11 terms and still maintain a maximum relative error of less than 10-14.

Working set selection using functional gain for LS-SVM.

PubMed

Bo, Liefeng; Jiao, Licheng; Wang, Ling

2007-09-01

The efficiency of sequential minimal optimization (SMO) depends strongly on the working set selection. This letter shows how the improvement of SMO in each iteration, named the functional gain (FG), is used to select the working set for least squares support vector machine (LS-SVM). We prove the convergence of the proposed method and give some theoretical support for its performance. Empirical comparisons demonstrate that our method is superior to the maximum violating pair (MVP) working set selection.

Intonational meaning in institutional settings: the role of syntagmatic relations

NASA Astrophysics Data System (ADS)

Wichmann, Anne

2010-12-01

This paper addresses the power of intonation to convey interpersonal or attitudinal meaning. Speakers have been shown to accommodate to each other in the course of conversation, and this convergence may be perceived as a sign of empathy. Accommodation often involves paradigmatic choices—choosing the same words, gestures, regional accent or melodic pattern, but this paper suggests that affective meaning can also be conveyed syntagmatically through the relationship between prosodic features in successive utterances. The paper also addresses the use of prosody in situations of conflict, particularly in institutional settings. The requirement of the more powerful participant to exercise control may conflict with the expression of empathy. Situations are described where divergent rather than convergent behaviour is more successful both in keeping control and in maintaining rapport.

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.

Recombinatorial biases and convergent recombination determine interindividual TCRβ sharing in murine thymocytes.

PubMed

Li, Hanjie; Ye, Congting; Ji, Guoli; Wu, Xiaohui; Xiang, Zhe; Li, Yuanyue; Cao, Yonghao; Liu, Xiaolong; Douek, Daniel C; Price, David A; Han, Jiahuai

2012-09-01

Overlap of TCR repertoires among individuals provides the molecular basis for public T cell responses. By deep-sequencing the TCRβ repertoires of CD4+CD8+ thymocytes from three individual mice, we observed that a substantial degree of TCRβ overlap, comprising ∼10-15% of all unique amino acid sequences and ∼5-10% of all unique nucleotide sequences across any two individuals, is already present at this early stage of T cell development. The majority of TCRβ sharing between individual thymocyte repertoires could be attributed to the process of convergent recombination, with additional contributions likely arising from recombinatorial biases; the role of selection during intrathymic development was negligible. These results indicate that the process of TCR gene recombination is the major determinant of clonotype sharing between individuals.

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

PubMed

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

2017-03-14

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

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

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

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

NBIC-Convergence of Machinery and Basic Technologies as the Ecological Factor of Wellbeing

NASA Astrophysics Data System (ADS)

Zhironkin, S. A.; Kolotov, K. A.; Genin, A. E.; Agafonov, F. V.; Kovalevsky, S. A.

2017-01-01

The development of science and technology in the XXI century is on the way of the extensive use of natural resources. As a result, the scientific and technical progress does not initiate the reduction of environmental damage but encourages its cumulative growth. So the environmental problems have become a serious threat to social wellbeing of all mankind. The development of the core technologies doesn’t allow creating the situation in which the new knowledge would generate positive changes in the environment. Therefore, among the issues that define the future of advanced environmental technologies, and potentially significant for the understanding of the humanities, there is the phenomenon of technological convergence and, in particular, the predicted convergence of the nano-, bio-, information and cognitive technologies (NBIC). The consequence of NBIC-convergence may be the transformation of the humanity into a single global mind, which can be linked into a solid set of technologies, establishing united standards for social wellbeing and environmental technologies.

Convergence of damped inertial dynamics governed by regularized maximally monotone operators

NASA Astrophysics Data System (ADS)

Attouch, Hedy; Cabot, Alexandre

2018-06-01

In a Hilbert space setting, we study the asymptotic behavior, as time t goes to infinity, of the trajectories of a second-order differential equation governed by the Yosida regularization of a maximally monotone operator with time-varying positive index λ (t). The dissipative and convergence properties are attached to the presence of a viscous damping term with positive coefficient γ (t). A suitable tuning of the parameters γ (t) and λ (t) makes it possible to prove the weak convergence of the trajectories towards zeros of the operator. When the operator is the subdifferential of a closed convex proper function, we estimate the rate of convergence of the values. These results are in line with the recent articles by Attouch-Cabot [3], and Attouch-Peypouquet [8]. In this last paper, the authors considered the case γ (t) = α/t, which is naturally linked to Nesterov's accelerated method. We unify, and often improve the results already present in the literature.

Monte Carlo criticality source convergence in a loosely coupled fuel storage system.

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

Blomquist, R. N.; Gelbard, E. M.

2003-06-10

The fission source convergence of a very loosely coupled array of 36 fuel subassemblies with slightly non-symmetric reflection is studied. The fission source converges very slowly from a uniform guess to the fundamental mode in which about 40% of the fissions occur in one corner subassembly. Eigenvalue and fission source estimates are analyzed using a set of statistical tests similar to those used in MCNP, including the ''drift-in-mean'' test and a new drift-in-mean test using a linear fit to the cumulative estimate drift, the Shapiro-Wilk test for normality, the relative error test, and the ''1/N'' test. The normality test doesmore » not detect a drifting eigenvalue or fission source. Applied to eigenvalue estimates, the other tests generally fail to detect an unconverged solution, but they are sometimes effective when evaluating fission source distributions. None of the test provides completely reliable indication of convergence, although they can detect nonconvergence.« less

Designing the future: NBIC technologies and human performance enhancement.

PubMed

Canton, James

2004-05-01

Never before has any civilization had the unique opportunity to enhance human performance on the scale that we will face in the near future. The convergence of nanotechnology, biotechnology, information technology, and cognitive science (NBIC) is creating a set of powerful tools that have the potential to significantly enhance human performance as well as transform society, science, economics, and human evolution. As the NBIC convergence becomes more understood, the possibility that we may be able to enhance human performance in the three domains of therapy, augmentation, and designed evolution will become anticipated and even expected. In addition, NBIC convergence represents entirely new challenges for scientists, policymakers, and business leaders who will have, for the first time, vast new and powerful tools to shape markets, societies, and lifestyles. The emergence of NBIC convergence will challenge us in new ways to balance risk and return, threat and opportunity, and social responsibility and competitive advantage as we step into the 21st century.

Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm.

PubMed

Yang, Zhang; Shufan, Ye; Li, Guo; Weifeng, Ding

2016-01-01

The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method.

Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm

PubMed Central

Yang, Zhang; Li, Guo; Weifeng, Ding

2016-01-01

The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method. PMID:27403428

Nonlinear recurrent neural networks for finite-time solution of general time-varying linear matrix equations.

PubMed

Xiao, Lin; Liao, Bolin; Li, Shuai; Chen, Ke

2018-02-01

In order to solve general time-varying linear matrix equations (LMEs) more efficiently, this paper proposes two nonlinear recurrent neural networks based on two nonlinear activation functions. According to Lyapunov theory, such two nonlinear recurrent neural networks are proved to be convergent within finite-time. Besides, by solving differential equation, the upper bounds of the finite convergence time are determined analytically. Compared with existing recurrent neural networks, the proposed two nonlinear recurrent neural networks have a better convergence property (i.e., the upper bound is lower), and thus the accurate solutions of general time-varying LMEs can be obtained with less time. At last, various different situations have been considered by setting different coefficient matrices of general time-varying LMEs and a great variety of computer simulations (including the application to robot manipulators) have been conducted to validate the better finite-time convergence of the proposed two nonlinear recurrent neural networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the efficiency of treating singularities in triatomic variational vibrational computations. The vibrational states of H(+)3 up to dissociation.

PubMed

Szidarovszky, Tamás; Császár, Attila G; Czakó, Gábor

2010-08-01

Several techniques of varying efficiency are investigated, which treat all singularities present in the triatomic vibrational kinetic energy operator given in orthogonal internal coordinates of the two distances-one angle type. The strategies are based on the use of a direct-product basis built from one-dimensional discrete variable representation (DVR) bases corresponding to the two distances and orthogonal Legendre polynomials, or the corresponding Legendre-DVR basis, corresponding to the angle. The use of Legendre functions ensures the efficient treatment of the angular singularity. Matrix elements of the singular radial operators are calculated employing DVRs using the quadrature approximation as well as special DVRs satisfying the boundary conditions and thus allowing for the use of exact DVR expressions. Potential optimized (PO) radial DVRs, based on one-dimensional Hamiltonians with potentials obtained by fixing or relaxing the two non-active coordinates, are also studied. The numerical calculations employed Hermite-DVR, spherical-oscillator-DVR, and Bessel-DVR bases as the primitive radial functions. A new analytical formula is given for the determination of the matrix elements of the singular radial operator using the Bessel-DVR basis. The usually claimed failure of the quadrature approximation in certain singular integrals is revisited in one and three dimensions. It is shown that as long as no potential optimization is carried out the quadrature approximation works almost as well as the exact DVR expressions. If wave functions with finite amplitude at the boundary are to be computed, the basis sets need to meet the required boundary conditions. The present numerical results also confirm that PO-DVRs should be constructed employing relaxed potentials and PO-DVRs can be useful for optimizing quadrature points for calculations applying large coordinate intervals and describing large-amplitude motions. The utility and efficiency of the different algorithms is demonstrated by the computation of converged near-dissociation vibrational energy levels for the H molecular ion.

CPTAC Announces New PTRCs, PCCs, and PGDACs | Office of Cancer Clinical Proteomics Research

Cancer.gov

This week, the Office of Cancer Clinical Proteomics Research (OCCPR) at the National Cancer Institute (NCI), part of the National Institutes of Health, announced its aim to further the convergence of proteomics with genomics – “proteogenomics,” to better understand the molecular basis of cancer and accelerate research in these areas by disseminating research resources to the scientific community.

Determination of elastic constants of a generally orthotropic plate by modal analysis

NASA Astrophysics Data System (ADS)

Lai, T. C.; Lau, T. C.

1993-01-01

This paper describes a method of finding the elastic constants of a generally orthotropic composite thin plate through modal analysis based on a Rayleigh-Ritz formulation. The natural frequencies and mode shapes for a plate with free-free boundary conditions are obtained with chirp excitation. Based on the eigenvalue equation and the constitutive equations of the plate, an iteration scheme is derived using the experimentally determined natural frequencies to arrive at a set of converged values for the elastic constants. Four sets of experimental data are required for the four independent constants: namely the two Young's moduli E1 and E2, the in-plane shear modulus G12, and one Poisson's ratio nu12. The other Poisson's ratio nu21 can then be determined from the relationship among the constants. Comparison with static test results indicate good agreement. Choosing the right combinations of natural modes together with a set of reasonable initial estimates for the constants to start the iteration has been found to be crucial in achieving convergence.

Fitting a Point Cloud to a 3d Polyhedral Surface

NASA Astrophysics Data System (ADS)

Popov, E. V.; Rotkov, S. I.

2017-05-01

The ability to measure parameters of large-scale objects in a contactless fashion has a tremendous potential in a number of industrial applications. However, this problem is usually associated with an ambiguous task to compare two data sets specified in two different co-ordinate systems. This paper deals with the study of fitting a set of unorganized points to a polyhedral surface. The developed approach uses Principal Component Analysis (PCA) and Stretched grid method (SGM) to substitute a non-linear problem solution with several linear steps. The squared distance (SD) is a general criterion to control the process of convergence of a set of points to a target surface. The described numerical experiment concerns the remote measurement of a large-scale aerial in the form of a frame with a parabolic shape. The experiment shows that the fitting process of a point cloud to a target surface converges in several linear steps. The method is applicable to the geometry remote measurement of large-scale objects in a contactless fashion.

Velocity-free attitude coordinated tracking control for spacecraft formation flying.

PubMed

Hu, Qinglei; Zhang, Jian; Zhang, Youmin

2018-02-01

This article investigates the velocity-free attitude coordinated tracking control scheme for a group of spacecraft with the assumption that the angular velocities of the formation members are not available in control feedback. Initially, an angular velocity observer is constructed based on each individual's attitude quarternion. Then, the distributed attitude coordinated control law is designed by using the observed states, in which adaptive control method is adopted to handle the external disturbances. Stability of the overall closed-loop system is analyzed theoretically, which shows the system trajectory converges to a small set around origin with fast convergence rate. Numerical simulations are performed to demonstrate fast convergence and improved tracking performance of the proposed control strategy. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

An efficient method for solving the steady Euler equations

NASA Technical Reports Server (NTRS)

Liou, M.-S.

1986-01-01

An efficient numerical procedure for solving a set of nonlinear partial differential equations, the steady Euler equations, using Newton's linearization procedure is presented. A theorem indicating quadratic convergence for the case of differential equations is demonstrated. A condition for the domain of quadratic convergence Omega(2) is obtained which indicates that whether an approximation lies in Omega(2) depends on the rate of change and the smoothness of the flow vectors, and hence is problem-dependent. The choice of spatial differencing, of particular importance for the present method, is discussed. The treatment of boundary conditions is addressed, and the system of equations resulting from the foregoing analysis is summarized and solution strategies are discussed. The convergence of calculated solutions is demonstrated by comparing them with exact solutions to one and two-dimensional problems.

Convergence Toward Common Standards in Machine-Readable Cataloging *

PubMed Central

Gull, C. D.

1969-01-01

The adoption of the MARC II format for the communication of bibliographic information by the three National Libraries of the U.S.A. makes it possible for those libraries to converge on the remaining necessary common standards for machine-readable cataloging. Three levels of standards are identified: fundamental, the character set; intermediate, MARC II; and detailed, the codes for identifying data elements. The convergence on these standards implies that the National Libraries can create and operate a Joint Bibliographic Data Bank requiring standard book numbers and universal serial numbers for identifying monographs and serials and that the system will thoroughly process contributed catalog entries before adding them to the Data Bank. There is reason to hope that the use of the MARC II format will facilitate catalogers' decision processes. PMID:5782261

Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau.

PubMed

Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

2014-08-01

The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Convergent and invariant object representations for sight, sound, and touch.

PubMed

Man, Kingson; Damasio, Antonio; Meyer, Kaspar; Kaplan, Jonas T

2015-09-01

We continuously perceive objects in the world through multiple sensory channels. In this study, we investigated the convergence of information from different sensory streams within the cerebral cortex. We presented volunteers with three common objects via three different modalities-sight, sound, and touch-and used multivariate pattern analysis of functional magnetic resonance imaging data to map the cortical regions containing information about the identity of the objects. We could reliably predict which of the three stimuli a subject had seen, heard, or touched from the pattern of neural activity in the corresponding early sensory cortices. Intramodal classification was also successful in large portions of the cerebral cortex beyond the primary areas, with multiple regions showing convergence of information from two or all three modalities. Using crossmodal classification, we also searched for brain regions that would represent objects in a similar fashion across different modalities of presentation. We trained a classifier to distinguish objects presented in one modality and then tested it on the same objects presented in a different modality. We detected audiovisual invariance in the right temporo-occipital junction, audiotactile invariance in the left postcentral gyrus and parietal operculum, and visuotactile invariance in the right postcentral and supramarginal gyri. Our maps of multisensory convergence and crossmodal generalization reveal the underlying organization of the association cortices, and may be related to the neural basis for mental concepts. © 2015 Wiley Periodicals, Inc.

Olfactory identification and Stroop interference converge in schizophrenia.

PubMed Central

Purdon, S E

1998-01-01

OBJECTIVE: To test the discriminant validity of a model predicting a dissociation between measures of right and left frontal lobe function in people with schizophrenia. PARTICIPANTS: Twenty-one clinically stable outpatients with schizophrenia. INTERVENTIONS: Patients were administered the University of Pennsylvania Smell Identification Test (UPSIT), the Stroop Color-Word Test (Stroop), and the Positive and Negative Syndrome Scale (PANSS). OUTCOME MEASURES: Scores on these tests and relation among scores. RESULTS: There was a convergence of UPSII and Stroop interference scores consistent with a common cerebral basis for limitations in olfactory identification and inhibition of distraction. There was also a divergence of UPSIT and Stroop reading scores suggesting that the olfactory identification limitation is distinct from a general limitation of attention or a dysfunction of the left dorsolateral prefrontal cortex. Most notable was the 81% classification convergence between the UPSIT and Stroop incongruous colour naming scores compared with the near-random 57% classification convergence of the UPSIT and Stroop reading scores. CONCLUSIONS: These data are consistent with a right orbitofrontal dysfunction in a subgroup of patients with schizophrenia, although the involvement of mesial temporal structures in both tasks must be ruled out with further study. A multifactorial model depicting contributions from diverse cerebral structures is required to describe the pathophysiology of schizophrenia. Valid behavioural methods for classifying suspected subgroups of patients with particular cerebral dysfunction would be of value in the construction of this model. PMID:9595890

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

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

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

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

Exploring service delivery in occupational therapy: The use of convergent interviewing.

PubMed

van Biljon, Hester; du Toit, Sanetta H J; Masango, July; Casteleijn, Daleen

2017-01-01

Occupational therapy clinicians working in South Africa's public healthcare had views on what patients thought about their vocational rehabilitation services that were based on anecdotal evidence. However evidence-based practice requires more than that. Reliable information is important in patient-centred practice and in the assessment of service quality. Clinical occupational therapists used the convergent interviewing technique to explore patients' views of the vocational rehabilitation services on offer in public hospitals. An Action Learning Action Research (ALAR) approach was used to explore the vocational rehabilitation services occupational therapy clinicians provided over a two week period in three settings. The majority (96%) of patients interviewed were not aware that occupational therapists offered vocational rehabilitation services. The convergent interview technique allowed continued unrestricted discussion of their vocational rehabilitation concerns and provided evidence that patients had significant concerns about work. Critical reflection on the interview experience and technique indicated that therapists were in favour of using convergent interviewing to obtain their patients views about the services offered. Therapists found the convergent interview technique easy to apply in clinical practice. Establishing patients' views of a clinical service have multiple values. However it is meaningless unless clinicians use the knowledge to improve service delivery to the patients who provided the views. Convergent interviewing was a valuable technique for occupational therapy clinicians to incorporate patients' views of their services into service development.

What relates newspaper, definite, and clothing? An article describing deficits in convergent problem solving and creativity following hippocampal damage.

PubMed

Warren, David E; Kurczek, Jake; Duff, Melissa C

2016-07-01

Creativity relies on a diverse set of cognitive processes associated with distinct neural correlates, and one important aspect of creativity, divergent thinking, has been associated with the hippocampus. However, hippocampal contributions to another important aspect of creativity, convergent problem solving, have not been investigated. We tested the necessity of hippocampus for convergent problem solving using a neuropsychological method. Participants with amnesia due to hippocampal damage (N = 5) and healthy normal comparison participants (N = 5) were tested using a task that promoted solutions based on existing knowledge (Bowden and Jung-Beeman, 2003). During each trial, participants were given a list of three words (e.g., fly, man, place) and asked to respond with a word that could be combined with each of the three words (e.g., fire). The amnesic group produced significantly fewer correct responses than the healthy comparison group. These findings indicate that the hippocampus is necessary for normal convergent problem solving and that changes in the status of the hippocampus should affect convergent problem solving in the context of creative problem-solving across short intervals. This proposed contribution of the hippocampus to convergent problem solving is consistent with an expanded perspective on hippocampal function that acknowledges its role in cognitive processes beyond declarative memory. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Convergence

NASA Astrophysics Data System (ADS)

Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

2005-02-01

Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and long-haul services. These trends have many consequences for consumers, vendors, and carriers. Faced with large volumes of low-margin data traffic mixed with traditional voice services, the need for capital conservation and operational efficiency drives carriers away from today's separate overlay networks for each service and towards "converged" platforms. For example, cable operators require transport of multiple services over both hybrid fiber coax (HFC) and DWDM transport technologies. Local carriers seek an economical architecture to deliver integrated services on optically enabled broadband-access networks. Services over wireless-access networks must coexist with those from wired networks. In each case, convergence of networks and services inspires an important set of questions and challenges, driven by the need for low cost, operational efficiency, service performance requirements, and optical transport technology options. This Feature Issue explores the various interpretations and implications of network convergence pertinent to optical networking. How does convergence affect the evolution of optical transport-layer and control approaches? Are the implied directions consistent with research vision for optical networks? Substantial challenges remain. Papers are solicited across the broad spectrum of interests. These include, but are not limited to:

Convergence

NASA Astrophysics Data System (ADS)

Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

2005-03-01

Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and long-haul services. These trends have many consequences for consumers, vendors, and carriers. Faced with large volumes of low-margin data traffic mixed with traditional voice services, the need for capital conservation and operational efficiency drives carriers away from today's separate overlay networks for each service and towards "converged" platforms. For example, cable operators require transport of multiple services over both hybrid fiber coax (HFC) and DWDM transport technologies. Local carriers seek an economical architecture to deliver integrated services on optically enabled broadband-access networks. Services over wireless-access networks must coexist with those from wired networks. In each case, convergence of networks and services inspires an important set of questions and challenges, driven by the need for low cost, operational efficiency, service performance requirements, and optical transport technology options. This Feature Issue explores the various interpretations and implications of network convergence pertinent to optical networking. How does convergence affect the evolution of optical transport-layer and control approaches? Are the implied directions consistent with research vision for optical networks? Substantial challenges remain. Papers are solicited across the broad spectrum of interests. These include, but are not limited to:

A Separable Insertion Method to Calculate Atomic and Molecular Resonances on a FE-DVR Grid using Exterior Complex Scaling

NASA Astrophysics Data System (ADS)

Abeln, Brant Anthony

The study of metastable electronic resonances, anion or neutral states of finite lifetime, in molecules is an important area of research where currently no theoretical technique is generally applicable. The role of theory is to calculate both the position and width, which is proportional to the inverse of the lifetime, of these resonances and how they vary with respect to nuclear geometry in order to generate potential energy surfaces. These surfaces are the basis of time-dependent models of the molecular dynamics where the system moves towards vibrational excitation or fragmentation. Three fundamental electronic processes that can be modeled this way are dissociative electronic attachment, vibrational excitation through electronic impact and autoionization. Currently, experimental investigation into these processes is being preformed on polyatomic molecules while theoreticians continue their fifty-year-old search for robust methods to calculate them. The separable insertion method, investigated in this thesis, seeks to tackle the problem of calculating metastable resonances by using existing quantum chemistry tools along with a grid-based method employing exterior complex scaling (ECS). Modern quantum chemistry methods are extremely efficient at calculating ground and (bound) excited electronic states of atoms and molecules by utilizing Gaussian basis functions. These functions provide both a numerically fast and analytic solution to the necessary two-electron, six-dimensional integrals required in structure calculations. However, these computer programs, based on analytic Gaussian basis sets, cannot construct solutions that are not square-integrable, such as resonance wavefunctions. ECS, on the other hand, can formally calculate resonance solutions by rotating the asymptotic electronic coordinates into the complex plane. The complex Siegert energies for resonances, Eres = ER - iGamma/2 where ER is the real-valued position of the resonance and Gamma is the width of the resonance, can be found directly as an isolated pole in the complex energy plane. Unlike the straight complex scaling, ECS on the electronic coordinates overcomes the non-analytic behavior of the nuclear attraction potential, as a function of complex [special characters omitted] where the sum is over each nucleus in a molecular system. Discouragingly, the Gaussian basis functions, which are computationally well-suited for bound electronic structure, fail at forming an effective basis set for ECS due to the derivative discontinuity generated by the complex coordinate rotation and the piecewise defined contour. This thesis seeks to explore methods for implementing ECS indirectly without losing the numerical simplicity and power of Gaussian basis sets. The separable insertion method takes advantage of existing software by constructing a N2-term separable potential of the target system using Gaussian functions to be inserted into a finite-element discrete variable representation (FE-DVR) grid that implements ECS. This work reports an exhaustive investigation into this approach for calculating resonances. This thesis shows that this technique is successful at describing an anion shape resonance of a closed-shell atom or molecule in the static-exchange approximation. This method is applied to the 2P Be-, 2pig N2- and 2pi u CO2- shape resonances to calculate their complex Seigert energies. Additionally, many details on the exact construction of the separable potential and of the expansion basis are explored. The future work considers methods for faster convergence of the resonance energy, moving beyond the static-exchange approximation and applying this technique to polyatomic systems of interest.

Generalized seniority on a deformed single-particle basis

NASA Astrophysics Data System (ADS)

Jia, L. Y.

2017-09-01

Recently, I proposed a fast computing scheme for generalized seniority on a spherical single-particle basis [J. Phys. G: Nucl. Part. Phys. 42, 115105 (2015), 10.1088/0954-3899/42/11/115105]. This work redesigns the scheme to make it applicable to deformed single-particle basis. The algorithm is applied to the rare-earth-metal nucleus 94 64 158Gd for intrinsic (body-fixed frame) neutron excitations under the low-momentum NN interaction Vlow -k. By allowing as many as four broken pairs, I compute the lowest 300 intrinsic states of several multipolarities. These states converge well to the exact ones, showing generalized seniority is very effective in truncating the deformed shell model. Under realistic interactions, the picture remains approximately valid: The ground state is a coherent pair condensate and the pairs gradually break up as excitation energy increases.

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.

Relativistic well-tempered Gaussian basis sets for helium through mercury

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

Okada, S.; Matsuoka, O.

1989-10-01

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

A Comparison of EQ-5D-3L Index Scores Using Malaysian, Singaporean, Thai, and UK Value Sets in Indonesian Cervical Cancer Patients.

PubMed

Endarti, Dwi; Riewpaiboon, Arthorn; Thavorncharoensap, Montarat; Praditsitthikorn, Naiyana; Hutubessy, Raymond; Kristina, Susi Ari

2018-05-01

To gain insight into the most suitable foreign value set among Malaysian, Singaporean, Thai, and UK value sets for calculating the EuroQol five-dimensional questionnaire index score (utility) among patients with cervical cancer in Indonesia. Data from 87 patients with cervical cancer recruited from a referral hospital in Yogyakarta province, Indonesia, from an earlier study of health-related quality of life were used in this study. The differences among the utility scores derived from the four value sets were determined using the Friedman test. Performance of the psychometric properties of the four value sets versus visual analogue scale (VAS) was assessed. Intraclass correlation coefficients and Bland-Altman plots were used to test the agreement among the utility scores. Spearman ρ correlation coefficients were used to assess convergent validity between utility scores and patients' sociodemographic and clinical characteristics. With respect to known-group validity, the Kruskal-Wallis test was used to examine the differences in utility according to the stages of cancer. There was significant difference among utility scores derived from the four value sets, among which the Malaysian value set yielded higher utility than the other three value sets. Utility obtained from the Malaysian value set had more agreements with VAS than the other value sets versus VAS (intraclass correlation coefficients and Bland-Altman plot tests results). As for the validity, the four value sets showed equivalent psychometric properties as those that resulted from convergent and known-group validity tests. In the absence of an Indonesian value set, the Malaysian value set was more preferable to be used compared with the other value sets. Further studies on the development of an Indonesian value set need to be conducted. Copyright © 2018. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

Wang, Feng; Pang, Wenning; Duffy, Patrick

2012-12-01

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

A Comparison of the Behavior of Functional/Basis Set Combinations for Hydrogen-Bonding in the Water Dimer with Emphasis on Basis Set Superposition Error

PubMed Central

Plumley, Joshua A.; Dannenberg, J. J.

2011-01-01

We evaluate the performance of nine functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-DFT molecular orbital calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise corrected PES. The calculated ΔE's with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, due to error compensation, the smaller basis sets gave the best results (in comparison to experimental and high level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. Since many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: 1) D95(d,p) with B3LYP, B97D, M06 or MPWB1k; 2) 6-311G(d,p) with B3LYP; 3) D95++(d,p) with B3LYP, B97D or MPWB1K; 4)6-311++G(d,p) with B3LYP or B97D; and 5) aug-cc-pVDZ with M05-2X, M06-2X or X3LYP. PMID:21328398

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error.

PubMed

Plumley, Joshua A; Dannenberg, J J

2011-06-01

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP. Copyright © 2011 Wiley Periodicals, Inc.

Neuroanatomical correlates of personality in chimpanzees (Pan troglodytes): Associations between personality and frontal cortex.

PubMed

Latzman, Robert D; Hecht, Lisa K; Freeman, Hani D; Schapiro, Steven J; Hopkins, William D

2015-12-01

Converging empirical data suggests that a set of largely consistent personality traits exist in both human and nonhuman primates; despite these similarities, almost nothing is known concerning the neurobiological basis of these traits in nonhuman primates. The current study examined associations between chimpanzee personality traits and the grey matter volume and asymmetry of various frontal cortex regions in 107 captive chimpanzees. Chimpanzees rated as higher on Openness and Extraversion had greater bilateral grey matter volumes in the anterior cingulate cortex. Further, chimpanzee rated as higher on Dominance had larger grey volumes in the left anterior cingulate cortex and right Prefrontal Cortex (PFC). Finally, apes rated higher on Reactivity/Unpredictability had higher grey matter volumes in the right mesial PFC. All associations survived after applying False Discovery Rate (FDR) thresholds. Results are discussed in terms of current neuroscientific models of personality which suggest that the frontal cortex, and asymmetries in this region, play an important role in the neurobiological foundation of broad dispositional traits. Copyright © 2015 Elsevier Inc. All rights reserved.

Ab initio quantum chemical calculations of the interaction between radioactive elements and imidazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Saravanan, A. V. Sai; Abishek, B.; Anantharaj, R.

2018-04-01

The fundamental natures of the molecular level interaction and charge transfer between specific radioactive elements and ionic liquids of 1-butyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide ([BMIM]+[NTf2]-), 1-Butyl-3-methylimidazolium ethylsulfate ([BMIM]+[ES]-) and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]+[BF4]-) were investigated utilising HF theory and B3LYP hybrid DFT. The ambiguity in reaction mechanism of the interacting species dictates to employ Effective Core Potential (ECP) basis sets such as UGBS, SDD, and SDDAll to account for the relativistic effects of deep core electrons in the system involving potential, heavy and hazardous radioactive elements present in nuclear waste. The SCF energy convergence of each system validates the characterisation of the molecular orbitals as a linear combination of atomic orbitals utilising fixed MO coefficients and the optimized geometry of each system is visualised based on which Mulliken partial charge analysis is carried out to account for the polarising behaviour of the radioactive element and charge transfer between the IL phase by comparison with the bare IL species.

A pair natural orbital based implementation of CCSD excitation energies within the framework of linear response theory

NASA Astrophysics Data System (ADS)

Frank, Marius S.; Hättig, Christof

2018-04-01

We present a pair natural orbital (PNO)-based implementation of coupled cluster singles and doubles (CCSD) excitation energies that builds upon the previously proposed state-specific PNO approach to the excited state eigenvalue problem. We construct the excited state PNOs for each state separately in a truncated orbital specific virtual basis and use a local density-fitting approximation to achieve an at most quadratic scaling of the computational costs for the PNO construction. The earlier reported excited state PNO construction is generalized such that a smooth convergence of the results for charge transfer states is ensured for general coupled cluster methods. We investigate the accuracy of our implementation by applying it to a large and diverse test set comprising 153 singlet excitations in organic molecules. Already moderate PNO thresholds yield mean absolute errors below 0.01 eV. The performance of the implementation is investigated through the calculations on alkene chains and reveals an at most cubic cost-scaling for the CCSD iterations with the system size.

High-level theoretical rovibrational spectroscopy beyond fc-CCSD(T): The C3 molecule.

PubMed

Schröder, Benjamin; Sebald, Peter

2016-01-28

An accurate local (near-equilibrium) potential energy surface (PES) is reported for the C3 molecule in its electronic ground state (X̃(1)Σg (+)). Special care has been taken in the convergence of the potential relative to high-order correlation effects, core-valence correlation, basis set size, and scalar relativity. Based on the aforementioned PES, several rovibrational states of all (12)C and (13)C substituted isotopologues have been investigated, and spectroscopic parameters based on term energies up to J = 30 have been calculated. Available experimental vibrational term energies are reproduced to better than 1 cm(-1) and rotational constants show relative errors of not more than 0.01%. The equilibrium bond length has been determined in a mixed experimental/theoretical approach to be 1.294 07(10) Å in excellent agreement with the ab initio composite value of 1.293 97 Å. Theoretical band intensities based on a newly developed electric dipole moment function also suggest that the infrared active (1, 1(1), 0)←(0, 0(0), 0) combination band might be observable by high-resolution spectroscopy.

Construction of CASCI-type wave functions for very large active spaces.

PubMed

Boguslawski, Katharina; Marti, Konrad H; Reiher, Markus

2011-06-14

We present a procedure to construct a configuration-interaction expansion containing arbitrary excitations from an underlying full-configuration-interaction-type wave function defined for a very large active space. Our procedure is based on the density-matrix renormalization group (DMRG) algorithm that provides the necessary information in terms of the eigenstates of the reduced density matrices to calculate the coefficient of any basis state in the many-particle Hilbert space. Since the dimension of the Hilbert space scales binomially with the size of the active space, a sophisticated Monte Carlo sampling routine is employed. This sampling algorithm can also construct such configuration-interaction-type wave functions from any other type of tensor network states. The configuration-interaction information obtained serves several purposes. It yields a qualitatively correct description of the molecule's electronic structure, it allows us to analyze DMRG wave functions converged for the same molecular system but with different parameter sets (e.g., different numbers of active-system (block) states), and it can be considered a balanced reference for the application of a subsequent standard multi-reference configuration-interaction method.

Musical hallucinations: a brief review of functional neuroimaging findings.

PubMed

Bernardini, Francesco; Attademo, Luigi; Blackmon, Karen; Devinsky, Orrin

2017-10-01

Musical hallucinations are uncommon phenomena characterized by intrusive and frequently distressful auditory musical percepts without an external source, often associated with hypoacusis, psychiatric illness, focal brain lesion, epilepsy, and intoxication/pharmacology. Their physiological basis is thought to involve diverse mechanisms, including "release" from normal sensory or inhibitory inputs as well as stimulation during seizures, or they can be produced by functional or structural disorders in diverse cortical and subcortical areas. The aim of this review is to further explore their pathophysiology, describing the functional neuroimaging findings regarding musical hallucinations. A literature search of the PubMed electronic database was conducted through to 29 December 2015. Search terms included "musical hallucinations" combined with the names of specific functional neuroimaging techniques. A total of 18 articles, all clinical case reports, providing data on 23 patients, comprised the set we reviewed. Diverse pathological processes and patient populations with musical hallucinations were included in the studies. Converging data from multiple studies suggest that the superior temporal sulcus is the most common site and that activation is the most common mechanism. Further neurobiological research is needed to clarify the pathophysiology of musical hallucinations.

State-to-state reactive scattering in six dimensions using reactant-product decoupling: OH + H2 → H2O + H (J = 0).

PubMed

Cvitaš, Marko T; Althorpe, Stuart C

2011-01-14

We extend to full dimensionality a recently developed wave packet method [M. T. Cvitaš and S. C. Althorpe, J. Phys. Chem. A 113, 4557 (2009)] for computing the state-to-state quantum dynamics of AB + CD → ABC + D reactions and also increase the computational efficiency of the method. This is done by introducing a new set of product coordinates, by applying the Crank-Nicholson approximation to the angular kinetic energy part of the split-operator propagator and by using a symmetry-adapted basis-to-grid transformation to evaluate integrals over the potential energy surface. The newly extended method is tested on the benchmark OH + H(2) → H(2)O + H reaction, where it allows us to obtain accurately converged state-to-state reaction probabilities (on the Wu-Schatz-Fang-Lendvay-Harding potential energy surface) with modest computational effort. These methodological advances will make possible efficient calculations of state-to-state differential cross sections on this system in the near future.

A fast and accurate algorithm for QTAIM integration in solids.

PubMed

Otero-de-la-Roza, A; Luaña, Víctor

2011-01-30

A new algorithm is presented for the calculation of atomic properties, in the sense of the quantum theory of atoms in molecules. This new method, named QTREE, applies to solid-state densities and allows the computation of the atomic properties of all the atoms in the crystal in seconds to minutes. The basis of the method is the recursive subdivision of a symmetry-reduced wedge of the Wigner-Seitz cell, which in turn is expressed as a union of tetrahedra, plus the use of β-spheres to improve the performance. A considerable speedup is thus achieved compared with traditional quadrature-based schemes, justified by the poor performance of the latter because of the particular features of atomic basins in solids. QTREE can use both analytical or interpolated densities, calculates all the atomic properties available, and converges to the correct values in the limit of infinite precision. Several gradient path tracing and integration techniques are tested. Basin volumes and charges for a selected set of 11 crystals are determined as a test of the new method. Copyright © 2010 Wiley Periodicals, Inc.

Machine learning for a Toolkit for Image Mining

NASA Technical Reports Server (NTRS)

Delanoy, Richard L.

1995-01-01

A prototype user environment is described that enables a user with very limited computer skills to collaborate with a computer algorithm to develop search tools (agents) that can be used for image analysis, creating metadata for tagging images, searching for images in an image database on the basis of image content, or as a component of computer vision algorithms. Agents are learned in an ongoing, two-way dialogue between the user and the algorithm. The user points to mistakes made in classification. The algorithm, in response, attempts to discover which image attributes are discriminating between objects of interest and clutter. It then builds a candidate agent and applies it to an input image, producing an 'interest' image highlighting features that are consistent with the set of objects and clutter indicated by the user. The dialogue repeats until the user is satisfied. The prototype environment, called the Toolkit for Image Mining (TIM) is currently capable of learning spectral and textural patterns. Learning exhibits rapid convergence to reasonable levels of performance and, when thoroughly trained, Fo appears to be competitive in discrimination accuracy with other classification techniques.

Using immersive media and digital technology to communicate Earth Science

NASA Astrophysics Data System (ADS)

Kapur, Ravi

2016-04-01

A number of technologies in digital media and interactivity have rapidly advanced and are now converging to enable rich, multi-sensoral experiences which create opportunities for both digital art and science communication. Techniques used in full-dome film-making can now be deployed in virtual reality experiences; gaming technologies can be utilised to explore real data sets; and collaborative interactivity enable new forms of public artwork. This session will explore these converging trends through a number of emerging and forthcoming projects dealing with Earth science, climate change and planetary science.

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.

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

ERIC Educational Resources Information Center

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

2007-01-01

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

Increased onset of vergence adaptation reduces excessive accommodation during the orthoptic treatment of convergence insufficiency.

PubMed

Sreenivasan, Vidhyapriya; Bobier, William R

2015-06-01

This research tested the hypothesis that the successful treatment of convergence insufficiency (CI) with vision-training (VT) procedures, leads to an increased capacity of vergence adaptation (VAdapt) allowing a more rapid downward adjustment of the convergence accommodation cross-link. Nine subjects with CI were recruited from a clinical population, based upon reduced fusional vergence amplitudes, receded near point of convergence or symptomology. VAdapt and the resulting changes to convergence accommodation (CA) were measured at specific intervals over 15 min (pre-training). Separate clinical measures of the accommodative convergence cross link, horizontal fusion limits and near point of convergence were taken and a symptomology questionnaire completed. Subjects then participated in a VT program composed of 2.5h at home and 1h in-office weekly for 12-14 weeks. Clinical testing was done weekly. VAdapt and CA measures were retaken once clinical measures normalized for 2 weeks (mid-training) and then again when symptoms had cleared (post-training). VAdapt and CA responses as well as the clinical measures were taken on a control group showing normal clinical findings. Six subjects provided complete data sets. CI clinical findings reached normal levels between 4 and 7 weeks of training but symptoms, VAdapt, and CA output remained significantly different from the controls until 12-14 weeks. The hypothesis was retained. The reduced VAdapt and excessive CA found in CI were normalized through orthoptic treatment. This time course was underestimated by clinical findings but matched symptom amelioration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Clinical test responses to different orthoptic exercise regimes in typical young adults.

PubMed

Horwood, Anna; Toor, Sonia

2014-03-01

The relative efficiency of different eye exercise regimes is unclear, and in particular the influences of practice, placebo and the amount of effort required are rarely considered. This study measured conventional clinical measures following different regimes in typical young adults. A total of 156 asymptomatic young adults were directed to carry out eye exercises three times daily for 2 weeks. Exercises were directed at improving blur responses (accommodation), disparity responses (convergence), both in a naturalistic relationship, convergence in excess of accommodation, accommodation in excess of convergence, and a placebo regime. They were compared to two control groups, neither of which were given exercises, but the second of which were asked to make maximum effort during the second testing. Instruction set and participant effort were more effective than many exercises. Convergence exercises independent of accommodation were the most effective treatment, followed by accommodation exercises, and both regimes resulted in changes in both vergence and accommodation test responses. Exercises targeting convergence and accommodation working together were less effective than those where they were separated. Accommodation measures were prone to large instruction/effort effects and monocular accommodation facility was subject to large practice effects. Separating convergence and accommodation exercises seemed more effective than exercising both systems concurrently and suggests that stimulation of accommodation and convergence may act in an additive fashion to aid responses. Instruction/effort effects are large and should be carefully controlled if claims for the efficacy of any exercise regime are to be made. © 2014 The Authors Ophthalmic & Physiological Optics published by John Wiley & Sons Ltd on behalf of The College of Optometrists.

Oceanic Geoid and Tides Obtained from GEOS-3 Satellite Data in the Northwestern Atlantic Ocean

NASA Technical Reports Server (NTRS)

Won, I. J.; Miller, L. S.

1978-01-01

Two sets of GEO-3 altimeter data which fall within about a 2.5 degree width are analyzed for ocean geoid and tides. One set covers a linear path from Newfoundland to Cuba and the other from Puerto Rico to the North Carolina coast. Forty different analyses using various parameters are performed in order to investigate convergence. Profiles of the geoid and four tides, M sub 2 O sub 1, S sub 2, and K sub 1, are obtained along the two strips. The results demonstrate convergent solutions for all forty cases and show, within expectation, fair agreement with those obtained from the MODE deep-sea tide gauge. It is also shown that the oceanic geoid obtained through this analysis can potentially improve the short wavelength structure over existing geoid models.

Motion of Discrete Interfaces Through Mushy Layers

NASA Astrophysics Data System (ADS)

Braides, Andrea; Solci, Margherita

2016-08-01

We study the geometric motion of sets in the plane derived from the homogenization of discrete ferromagnetic energies with weak inclusions. We show that the discrete sets are composed by a `bulky' part and an external `mushy region' composed only of weak inclusions. The relevant motion is that of the bulky part, which asymptotically obeys to a motion by crystalline mean curvature with a forcing term, due to the energetic contribution of the mushy layers, and pinning effects, due to discreteness. From an analytical standpoint, it is interesting to note that the presence of the mushy layers implies only a weak and not strong convergence of the discrete motions, so that the convergence of the energies does not commute with the evolution. From a mechanical standpoint it is interesting to note the geometrical similarity of some phenomena in the cooling of binary melts.

G-sequentially connectedness for topological groups with operations

NASA Astrophysics Data System (ADS)

Mucuk, Osman; Cakalli, Huseyin

2016-08-01

It is a well-known fact that for a Hausdorff topological group X, the limits of convergent sequences in X define a function denoted by lim from the set of all convergent sequences in X to X. This notion has been modified by Connor and Grosse-Erdmann for real functions by replacing lim with an arbitrary linear functional G defined on a linear subspace of the vector space of all real sequences. Recently some authors have extended the concept to the topological group setting and introduced the concepts of G-sequential continuity, G-sequential compactness and G-sequential connectedness. In this work, we present some results about G-sequentially closures, G-sequentially connectedness and fundamental system of G-sequentially open neighbourhoods for topological group with operations which include topological groups, topological rings without identity, R-modules, Lie algebras, Jordan algebras, and many others.

A recurrent neural network for nonlinear optimization with a continuously differentiable objective function and bound constraints.

PubMed

Liang, X B; Wang, J

2000-01-01

This paper presents a continuous-time recurrent neural-network model for nonlinear optimization with any continuously differentiable objective function and bound constraints. Quadratic optimization with bound constraints is a special problem which can be solved by the recurrent neural network. The proposed recurrent neural network has the following characteristics. 1) It is regular in the sense that any optimum of the objective function with bound constraints is also an equilibrium point of the neural network. If the objective function to be minimized is convex, then the recurrent neural network is complete in the sense that the set of optima of the function with bound constraints coincides with the set of equilibria of the neural network. 2) The recurrent neural network is primal and quasiconvergent in the sense that its trajectory cannot escape from the feasible region and will converge to the set of equilibria of the neural network for any initial point in the feasible bound region. 3) The recurrent neural network has an attractivity property in the sense that its trajectory will eventually converge to the feasible region for any initial states even at outside of the bounded feasible region. 4) For minimizing any strictly convex quadratic objective function subject to bound constraints, the recurrent neural network is globally exponentially stable for almost any positive network parameters. Simulation results are given to demonstrate the convergence and performance of the proposed recurrent neural network for nonlinear optimization with bound constraints.

Dimensional threshold for fracture linkage and hooking

NASA Astrophysics Data System (ADS)

Lamarche, Juliette; Chabani, Arezki; Gauthier, Bertrand D. M.

2018-03-01

Fracture connectivity in rocks depends on spatial properties of the pattern including length, abundance and orientation. When fractures form a single-strike set, they hardly cross-cut each other and the connectivity is limited. Linkage probability increases with increasing fracture abundance and length as small fractures connect to each other to form longer ones. A process for parallel fracture linkage is the "hooking", where two converging fracture tips mutually deviate and then converge to connect due to the interaction of their crack-tip stresses. Quantifying the processes and conditions for fracture linkage in single-strike fracture sets is crucial to better predicting fluid flow in Naturally Fractured Reservoirs. For 1734 fractures in Permian shales of the Lodève Basin, SE France, we measured geometrical parameters in 2D, characterizing three stages of the hooking process: underlapping, overlapping and linkage. We deciphered the threshold values, shape ratios and limiting conditions to switch from one stage to another one. The hook set up depends on the spacing (S) and fracture length (Lh) with the relation S ≈ 0.15 Lh. Once the hooking is initiated, with the fracture deviation length (L) L ≈ 0.4 Lh, the fractures reaches the linkage stage only when the spacing is reduced to S ≈ 0.02 Lh and the convergence (C) is < 0.1 L. These conditions apply to multi-scale fractures with a shape ratio L/S = 10 and for fracture curvature of 10°-20°.

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

The Shock and Vibration Bulletin. Part 2. Fluid-Structure Dynamics and Dynamic Analysis

DTIC Science & Technology

1983-05-01

0.060041-03 1 ~~~COLUMN 13701010 ý41 44 13 3.483001-03 2499 T2 8.377715-02 2491 13 2.323511-02 3701 73 1.700031-03 5702 12 3.36397E-03 572 133.792&31-03...plausible, there is no theoretical basis Finite-Element Method", UCRL -52066, to assure the convergence of either Lawrence Livermore Laboratory, calculations

HARM: A Numerical Scheme for General Relativistic Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Gammie, Charles, F.; McKinney, Jonathan C.; Tóth, Gábor

2012-09-01

HARM uses a conservative, shock-capturing scheme for evolving the equations of general relativistic magnetohydrodynamics. The fluxes are calculated using the Harten, Lax, & van Leer scheme. A variant of constrained transport, proposed earlier by Tóth, is used to maintain a divergence-free magnetic field. Only the covariant form of the metric in a coordinate basis is required to specify the geometry. On smooth flows HARM converges at second order.

Parallel deterioration to language processing in a bilingual speaker.

PubMed

Druks, Judit; Weekes, Brendan Stuart

2013-01-01

The convergence hypothesis [Green, D. W. (2003). The neural basis of the lexicon and the grammar in L2 acquisition: The convergence hypothesis. In R. van Hout, A. Hulk, F. Kuiken, & R. Towell (Eds.), The interface between syntax and the lexicon in second language acquisition (pp. 197-218). Amsterdam: John Benjamins] assumes that the neural substrates of language representations are shared between the languages of a bilingual speaker. One prediction of this hypothesis is that neurodegenerative disease should produce parallel deterioration to lexical and grammatical processing in bilingual aphasia. We tested this prediction with a late bilingual Hungarian (first language, L1)-English (second language, L2) speaker J.B. who had nonfluent progressive aphasia (NFPA). J.B. had acquired L2 in adolescence but was premorbidly proficient and used English as his dominant language throughout adult life. Our investigations showed comparable deterioration to lexical and grammatical knowledge in both languages during a one-year period. Parallel deterioration to language processing in a bilingual speaker with NFPA challenges the assumption that L1 and L2 rely on different brain mechanisms as assumed in some theories of bilingual language processing [Ullman, M. T. (2001). The neural basis of lexicon and grammar in first and second language: The declarative/procedural model. Bilingualism: Language and Cognition, 4(1), 105-122].

The processing of social stimuli in early infancy: from faces to biological motion perception.

PubMed

Simion, Francesca; Di Giorgio, Elisa; Leo, Irene; Bardi, Lara

2011-01-01

There are several lines of evidence which suggests that, since birth, the human system detects social agents on the basis of at least two properties: the presence of a face and the way they move. This chapter reviews the infant research on the origin of brain specialization for social stimuli and on the role of innate mechanisms and perceptual experience in shaping the development of the social brain. Two lines of convergent evidence on face detection and biological motion detection will be presented to demonstrate the innate predispositions of the human system to detect social stimuli at birth. As for face detection, experiments will be presented to demonstrate that, by virtue of nonspecific attentional biases, a very coarse template of faces become active at birth. As for biological motion detection, studies will be presented to demonstrate that, since birth, the human system is able to detect social stimuli on the basis of their properties such as the presence of a semi-rigid motion named biological motion. Overall, the empirical evidence converges in supporting the notion that the human system begins life broadly tuned to detect social stimuli and that the progressive specialization will narrow the system for social stimuli as a function of experience. Copyright © 2011 Elsevier B.V. All rights reserved.

Large-scale exact diagonalizations reveal low-momentum scales of nuclei

NASA Astrophysics Data System (ADS)

Forssén, C.; Carlsson, B. D.; Johansson, H. T.; Sääf, D.; Bansal, A.; Hagen, G.; Papenbrock, T.

2018-03-01

Ab initio methods aim to solve the nuclear many-body problem with controlled approximations. Virtually exact numerical solutions for realistic interactions can only be obtained for certain special cases such as few-nucleon systems. Here we extend the reach of exact diagonalization methods to handle model spaces with dimension exceeding 1010 on a single compute node. This allows us to perform no-core shell model (NCSM) calculations for 6Li in model spaces up to Nmax=22 and to reveal the 4He+d halo structure of this nucleus. Still, the use of a finite harmonic-oscillator basis implies truncations in both infrared (IR) and ultraviolet (UV) length scales. These truncations impose finite-size corrections on observables computed in this basis. We perform IR extrapolations of energies and radii computed in the NCSM and with the coupled-cluster method at several fixed UV cutoffs. It is shown that this strategy enables information gain also from data that is not fully UV converged. IR extrapolations improve the accuracy of relevant bound-state observables for a range of UV cutoffs, thus making them profitable tools. We relate the momentum scale that governs the exponential IR convergence to the threshold energy for the first open decay channel. Using large-scale NCSM calculations we numerically verify this small-momentum scale of finite nuclei.

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

NASA Astrophysics Data System (ADS)

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

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

COMPARISONS OF THE FINITE-ELEMENT-WITH-DISCONTIGUOUS-SUPPORT METHOD TO CONTINUOUS-ENERGY MONTE CARLO FOR PIN-CELL PROBLEMS

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

A. T. Till; M. Hanuš; J. Lou

The standard multigroup (MG) method for energy discretization of the transport equation can be sensitive to approximations in the weighting spectrum chosen for cross-section averaging. As a result, MG often inaccurately treats important phenomena such as self-shielding variations across a material. From a finite-element viewpoint, MG uses a single fixed basis function (the pre-selected spectrum) within each group, with no mechanism to adapt to local solution behavior. In this work, we introduce the Finite-Element-with-Discontiguous-Support (FEDS) method, whose only approximation with respect to energy is that the angular flux is a linear combination of unknowns multiplied by basis functions. A basismore » function is non-zero only in the discontiguous set of energy intervals associated with its energy element. Discontiguous energy elements are generalizations of bands and are determined by minimizing a norm of the difference between snapshot spectra and their averages over the energy elements. We begin by presenting the theory of the FEDS method. We then compare to continuous-energy Monte Carlo for one-dimensional slab and two-dimensional pin-cell problem. We find FEDS to be accurate and efficient at producing quantities of interest such as reaction rates and eigenvalues. Results show that FEDS converges at a rate that is approximately first-order in the number of energy elements and that FEDS is less sensitive to weighting spectrum than standard MG.« less

Habitability at the frontlines of sea level rise: a spatiotemporal analysis of settlements and coastal inundation in eight global sea level rise hotspots between 1990 and 2015

NASA Astrophysics Data System (ADS)

Rose, S. A.; Wrathall, D.

2017-12-01

Over the coming centuries and millennia, sea level rise will greatly redistribute global human population through displacement and migration. Sudden, large-scale displacement is extremely disruptive to society both for migrants and host communities, and there is a great scientific and policy need to anticipate where, when and how this could happen around sea level rise. We can meet these needs by examining how long-term coastal inundation of settlements has already occurred. Using two global geospatial data sets, the Global Human Settlement Layer and the Global Surface Water Layer, we examine the global spatial concentration of settlement inundation that occurred between 1990 and 2015. We focus on the eight sea level rise hotspots identified in Clark et al (2016), which include Bangladesh, Mekong Delta, Indonesia, Japan, Nile Delta, Philippines, and the US Mid-Atlantic and Gulf of Mexico, and examine areas of convergence between settlement loss density and negative population change. This analysis reveals specific areas of concern within vulnerable countries, and forms the basis for focused investigations of the long-term impact of coastal inundation on various migration systems. This analysis shows us how long-term sets of satellite derived data on human population can help anticipate how sea level rise will alter future patterns of human settlement and migration into the 21st century and beyond.