Many-Body Basis Set Superposition Effect.
Ouyang, John F; Bettens, Ryan P A
2015-11-10
The basis set superposition effect (BSSE) arises in electronic structure calculations of molecular clusters when questions relating to interactions between monomers within the larger cluster are asked. The binding energy, or total energy, of the cluster may be broken down into many smaller subcluster calculations and the energies of these subsystems linearly combined to, hopefully, produce the desired quantity of interest. Unfortunately, BSSE can plague these smaller fragment calculations. In this work, we carefully examine the major sources of error associated with reproducing the binding energy and total energy of a molecular cluster. In order to do so, we decompose these energies in terms of a many-body expansion (MBE), where a "body" here refers to the monomers that make up the cluster. In our analysis, we found it necessary to introduce something we designate here as a many-ghost many-body expansion (MGMBE). The work presented here produces some surprising results, but perhaps the most significant of all is that BSSE effects up to the order of truncation in a MBE of the total energy cancel exactly. In the case of the binding energy, the only BSSE correction terms remaining arise from the removal of the one-body monomer total energies. Nevertheless, our earlier work indicated that BSSE effects continued to remain in the total energy of the cluster up to very high truncation order in the MBE. We show in this work that the vast majority of these high-order many-body effects arise from BSSE associated with the one-body monomer total energies. Also, we found that, remarkably, the complete basis set limit values for the three-body and four-body interactions differed very little from that at the MP2/aug-cc-pVDZ level for the respective subclusters embedded within a larger cluster. PMID:26574311
Avery, John Scales; Rettrup, Sten; Avery, James Emil
In theoretical physics, theoretical chemistry and engineering, one often wishes to solve partial differential equations subject to a set of boundary conditions. This gives rise to eigenvalue problems of which some solutions may be very difficult to find. For example, the problem of finding...... such problems can be much reduced by making use of symmetry-adapted basis functions. The conventional method for generating symmetry-adapted basis sets is through the application of group theory, but this can be difficult. This book describes an easier method for generating symmetry-adapted basis sets...
An effective scheme for selecting basis sets for ab initio calculations
张瑞勤; 黄建华; 步宇翔; 韩克利; 李述汤; 何国钟
2000-01-01
An effective scheme for selecting economical basis sets for ab initio calculations has been proposed for wide-range systems based on the analysis of different functions in the currently used basis sets. Accordingly, the selection of the basis sets should be made according to the different properties and real chemical surrounding of the atoms in the systems. For normal systems, the size and level of the basis sets used for the descriptions of the constituent atoms should be increased from left to right according to the position of the atom in the periodic table. Moreover, the more the atom is negatively charged, the more the basis functions and suitable polarization functions and diffuse functions should be utilized. whereas, for the positively charged atoms, the size of basis set may be reduced. it is not necessary to use the polarization and diffuse functions for the covalently saturated atoms with normal valence states. However, for the system involving hy-drogen-bonding, weak interactions, functional
An effective scheme for selecting basis sets for ab initio calculations
无
2000-01-01
An effective scheme for selecting economical basis sets for ab initio calculations has been proposed for wide-range systems based on the analysis of different functions in the currently used basis sets. Accordingly, the selection of the basis sets should be made according to the different properties and real chemical surrounding of the atoms in the systems. For normal systems, the size and level of the basis sets used for the descriptions of the constituent atoms should be increased from left to right according to the position of the atom in the periodic table. Moreover, the more the atom is negatively charged, the more the basis functions and suitable polarization functions and diffuse functions should be utilized. Whereas, for the positively charged atoms, the size of basis set may be reduced. It is not necessary to use the polarization and diffuse functions for the covalently saturated atoms with normal valence states. However, for the system involving hydrogen-bonding, weak interactions, functional groups, metallic bonding with zero valence or low positive valence, and other sensitive interactions, the polarization and diffuse functions must be used. With this scheme, reliable calculation results may be obtained with suitable basis sets and smaller computational capability. By detailed analysis of a series of systems, it has been demonstrated that this scheme is very practical and effective. This scheme may be used in Hartree-Fock, M?ller-Plesset and density functional theoretical calculations. It is expected that the scheme would find important applications in the extensive calculations of large systems in chemistry, materials science, and life and biological sciences.
Basis set effects on the Hartree-Fock description of confined many-electron atoms
In this work, the basis sets designed by Clementi, Bunge and Thakkar, for atomic systems, have been used to obtain the electronic structure of confined many-electron atoms by using Roothaan's approach in the Hartree-Fock context with a new code written in C, which uses the message-passing interface library. The confinement was imposed as Ludeña suggested to simulate walls with infinity potential. For closed-shell atoms, the Thakkar basis set functions give the best total energies (TE) as a function of the confinement radius, obtaining the following ordering: TE(Thakkar) < TE(Bunge) < TE(Clementi). However, for few open-shell atoms this ordering is not preserved and a trend, for the basis sets, is not observed. Although there are differences between the TE predicted by these basis set functions, the corresponding pressures are similar to each other; it means that changes in the total energy are described almost in the same way by using any of these basis sets. By analysing the total energy as a function of the inverse of the volume we propose an equation of state; for regions of small volumes, this equation predicts that the pressure is inversely proportional to the square of the volume.
Buimaga-Iarinca, Luiza; Morari, Cristian
2014-01-01
We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the go...
Buimaga-Iarinca, Luiza
2014-01-01
We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.
Silva-Junior, Mario R.; Sauer, Stephan P. A.; Schreiber, Marko; Thiel, Walter
Vertical electronic excitation energies and one-electron properties of 28 medium-sized molecules from a previously proposed benchmark set are revisited using the augmented correlation-consistent triple-zeta aug-cc-pVTZ basis set in CC2, CCSDR(3), and CC3 calculations. The results are compared to...... those obtained previously with the smaller TZVP basis set. For each of the three coupled cluster methods, a correlation coefficient greater than 0.994 is found between the vertical excitation energies computed with the two basis sets. The deviations of the CC2 and CCSDR(3) results from the CC3 reference...
Spackman, Peter R.; Karton, Amir, E-mail: amir.karton@uwa.edu.au [School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009 (Australia)
2015-05-15
Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.
Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/Lα two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol–1. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol–1
Conductance calculations with a wavelet basis set
Thygesen, Kristian Sommer; Bollinger, Mikkel; Jacobsen, Karsten Wedel
2003-01-01
. The linear-response conductance is calculated from the Green's function which is represented in terms of a system-independent basis set containing wavelets with compact support. This allows us to rigorously separate the central region from the contacts and to test for convergence in a systematic way...
Accurate basis set truncation for wavefunction embedding
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
Multiple Spawning with Optimal Basis Set Expansion
Yang, Sandy; Kaduk, Benjamin; Martinez, Todd J
2008-01-01
The Full Multiple Spawning (FMS) method is designed to simulate quantum dynamics in the multi-state electronic problem. The FMS nuclear wavefunction is represented in a basis of coupled, frozen Gaussians, and the spawning procedure prescribes a means of adaptively increasing the size of the basis in order to capture population transfer between electronic states. Parent trajectories create children when passing through regions of significant nonadiabatic coupling. In order to converge branching ratios without allowing the basis to reach an impractical size, population transfer at individual spawning events should be made as effective as possible. Herein we detail a new algorithm for specifying the initial conditions of freshly spawned basis functions, one that minimizes the number of spawns needed for convergence by maximizing the efficiency of individual spawning events. Optimization is achieved by maximizing the coupling between parent and child trajectories, as a function of child position and momentum, at ...
Roghieh Tarlani Bashiz
2015-12-01
Full Text Available Density functional theory calculations (DFT, as well as hybrid methods (B3LYP and HF method for CNT-Calixarene complexes have been carried out to study structural stability. The geometry of the Calixarene has been optimized at DFT methods such as M062x B3LYP and HF methods with 6-31G, 6-31G*and 6-31G** basis sets. According to GIAO method, NMR parameters have been evaluated. The Gaussian quantum chemical package is used for all calculations. The gauge including atomic orbital (GIAO approach was applied for chemical shielding calculations for an isolated calix aren and a complex of Calix-SWCNTs.
Entanglement patterns in mutually unbiased basis sets
A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=pN), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (pN-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (pN-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.
Property-optimized Gaussian basis sets for molecular response calculations
Rappoport, Dmitrij; Furche, Filipp
2010-10-01
With recent advances in electronic structure methods, first-principles calculations of electronic response properties, such as linear and nonlinear polarizabilities, have become possible for molecules with more than 100 atoms. Basis set incompleteness is typically the main source of error in such calculations since traditional diffuse augmented basis sets are too costly to use or suffer from near linear dependence. To address this problem, we construct the first comprehensive set of property-optimized augmented basis sets for elements H-Rn except lanthanides. The new basis sets build on the Karlsruhe segmented contracted basis sets of split-valence to quadruple-zeta valence quality and add a small number of moderately diffuse basis functions. The exponents are determined variationally by maximization of atomic Hartree-Fock polarizabilities using analytical derivative methods. The performance of the resulting basis sets is assessed using a set of 313 molecular static Hartree-Fock polarizabilities. The mean absolute basis set errors are 3.6%, 1.1%, and 0.3% for property-optimized basis sets of split-valence, triple-zeta, and quadruple-zeta valence quality, respectively. Density functional and second-order Møller-Plesset polarizabilities show similar basis set convergence. We demonstrate the efficiency of our basis sets by computing static polarizabilities of icosahedral fullerenes up to C720 using hybrid density functional theory.
Anacker, Tony; Hill, J Grant; Friedrich, Joachim
2016-04-21
Minimal basis sets, denoted DSBSenv, based on the segmented basis sets of Ahlrichs and co-workers have been developed for use as environmental basis sets for the domain-specific basis set (DSBS) incremental scheme with the aim of decreasing the CPU requirements of the incremental scheme. The use of these minimal basis sets within explicitly correlated (F12) methods has been enabled by the optimization of matching auxiliary basis sets for use in density fitting of two-electron integrals and resolution of the identity. The accuracy of these auxiliary sets has been validated by calculations on a test set containing small- to medium-sized molecules. The errors due to density fitting are about 2-4 orders of magnitude smaller than the basis set incompleteness error of the DSBSenv orbital basis sets. Additional reductions in computational cost have been tested with the reduced DSBSenv basis sets, in which the highest angular momentum functions of the DSBSenv auxiliary basis sets have been removed. The optimized and reduced basis sets are used in the framework of the domain-specific basis set of the incremental scheme to decrease the computation time without significant loss of accuracy. The computation times and accuracy of the previously used environmental basis and that optimized in this work have been validated with a test set of medium- to large-sized systems. The optimized and reduced DSBSenv basis sets decrease the CPU time by about 15.4% and 19.4% compared with the old environmental basis and retain the accuracy in the absolute energy with standard deviations of 0.99 and 1.06 kJ/mol, respectively. PMID:27002338
Application of discrete basis set methods to the Dirac equation
The basis sets described provide a convenient method for the direct relativistic calculation of a wide variety of atomic properties. Results have been obtained for the ground state polarizability, and the 2s/sub 1/2/-1s/sub 1/2/ two-photon transition rate of hydrogenic ions. The latter calculation includes all retardation effects and contributions from higher photon multipoles
Relativistic LCAO with Minimax Principle and New Balanced Basis Sets
Zhang, Hui
2008-01-01
Relativistic density functional theory is widely applied in molecular calculations with heavy atoms, where relativistic and correlation effects are on the same footing. Variational stability of the Dirac Hamiltonian is a very important field of research from the beginning of relativistic molecular calculations on, among efforts for accuracy, efficiency, and density functional formulation, etc. Approximations of one- or two-component methods and searching for suitable basis sets are two major ...
Martin, J M L; Martin, Jan M.L.; Sundermann, Andreas
2001-01-01
We propose large-core correlation-consistent 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 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 h...
Point Set Denoising Using Bootstrap-Based Radial Basis Function
Ramli, Ahmad; Abd. Majid, Ahmad
2016-01-01
This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study. PMID:27315105
Localized atomic basis set in the projector augmented wave method
Larsen, Ask Hjorth; Vanin, Marco; Mortensen, Jens Jørgen;
2009-01-01
is tested by calculating atomization energies and equilibrium bulk properties of a variety of molecules and solids, comparing to the grid results. Finally, it is demonstrated how a grid-quality structure optimization can be performed with significantly reduced computational effort by switching......We present an implementation of localized atomic-orbital basis sets in the projector augmented wave (PAW) formalism within the density-functional theory. The implementation in the real-space GPAW code provides a complementary basis set to the accurate but computationally more demanding grid...
Completeness-optimized basis sets: application to ground-state electron momentum densities.
Lehtola, Jussi; Manninen, Pekka; Hakala, Mikko; Hämäläinen, Keijo
2012-09-14
In the current work we apply the completeness-optimization paradigm [P. Manninen and J. Vaara, J. Comput. Chem. 27, 434 (2006)] to investigate the basis set convergence of the moments of the ground-state electron momentum density at the self-consistent field level of theory. We present a black-box completeness-optimization algorithm that can be used to generate computationally efficient basis sets for computing any property at any level of theory. We show that the complete basis set (CBS) limit of the moments of the electron momentum density can be reached more cost effectively using completeness-optimized basis sets than using conventional, energy-optimized Gaussian basis sets. By using the established CBS limits, we generate a series of smaller basis sets which can be used to systematically approach the CBS and to perform calculations on larger, experimentally interesting systems. PMID:22979848
Maroulis, George
1998-04-01
The electric multipole moments, dipole and quadrupole polarizability and hyperpolarizability of hydrogen chloride have been determined from an extensive and systematic study based on finite-field fourth-order many-body perturbation theory and coupled-cluster calculations. Our best values for the dipole, quadrupole, octopole and hexadecapole moment at the experimental internuclear separation of Re=2.408645a0 are μ=0.4238ea0, Θ=2.67ea02, Ω=3.94ea03, and Φ=13.37ea04, respectively. For the mean and the anisotropy of the dipole polarizability ααβ we recommend ᾱ=17.41±0.02 and Δα=1.60±0.03e2a02Eh-1. For the mean value of the first dipole hyperpolarizability βαβγ we advance β¯=-6.8±0.3e3a03Eh-2. Extensive calculations with a [8s6p6d3f/5s4p2d1f] basis set at the CCSD(T) level of theory yield the R-dependence of the Cartesian components and the mean of the second dipole hyperpolarizability γαβγδ(R)/e4a04Eh-3 around Re as γzzzz(R)=1907+1326(R-Re)+570(R-Re)2+10(R-Re)3-40(R-Re)4, γxxxx(R)=3900+747(R-Re)-65(R-Re)2-38(R-Re)3-7(R-Re)4, γxxzz(R)=962+222(R-Re)+88(R-Re)2+49(R-Re)3+5(R-Re)4, γ¯(R)=3230+841(R-Re)+151(R-Re)2+21(R-Re)3-9(R-Re)4, with z as the molecular axis. The present investigation suggests an estimate of (26.7±0.3)×102e4a04Eh-3 for the Hartree-Fock limit of the mean value γ¯ at Re. CCSD(T) calculations with basis sets of [8s6p6d3f/5s4p2d1f] and [9s7p5d4f/6s5p4d1f] size and MP4 calculations with the even larger [15s12p7d3f/12s7p2d1f] give (7.0±0.3)×102e4a04Eh-3 for the electron correlation effects for this property, thus leading to a recommended value of γ¯=(33.7±0.6)×102e4a04Eh-3. For the quadrupole polarizability Cαβ,γδ/e2a04Eh-1 at Re our best values are Czz,zz=41.68, Cxz,xz=26.11, and Cxx,xx=35.38, calculated with the [9s7p5d4f/6s5p4d1f] basis set at the CCSD(T) level of theory. The following CCSD(T) values were obtained with [8s6p6d3f/5s4p2d1f] at Re: dipole-quadrupole polarizability Aα,βγ/e2a03Eh-1, Az,zz=14.0, and
New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of the spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons
Coupled-cluster based basis sets for valence correlation calculations
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.
Basis Set Dependence of Vibrational Raman and Raman Optical Activity Intensities.
Cheeseman, James R; Frisch, Michael J
2011-10-11
* basis set for the geometry optimization and force field calculation is a reliable and cost-effective method for obtaining Raman intensities and ROA intensity differences. PMID:26598166
Lehtola, Susi; Manninen, Pekka; Hakala, Mikko; Hämäläinen, Keijo
2013-01-28
Completeness-optimization is a novel method for the formation of one-electron basis sets. Contrary to conventional methods of basis set generation that optimize the basis set with respect to ground-state energy, completeness-optimization is a completely general, black-box method that can be used to form cost-effective basis sets for any wanted property at any level of theory. In our recent work [J. Lehtola, P. Manninen, M. Hakala, and K. Hämäläinen, J. Chem. Phys. 137, 104105 (2012)] we applied the completeness-optimization approach to forming primitive basis sets tuned for calculations of the electron momentum density at the Hartree-Fock (HF) level of theory. The current work extends the discussion to contracted basis sets and to the post-HF level of theory. Contractions are found to yield significant reductions in the amount of functions without compromising the accuracy. We suggest polarization-consistent and correlation-consistent basis sets for the first three rows of the periodic table, which are completeness-optimized for electron momentum density calculations. PMID:23387570
Petruzielo, Frank R.; Toulouse, Julien; Umrigar, C. J.
2010-01-01
A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multi-configurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis...
Basis set approach in the constrained interpolation profile method
We propose a simple polynomial basis-set that is easily extendable to any desired higher-order accuracy. This method is based on the Constrained Interpolation Profile (CIP) method and the profile is chosen so that the subgrid scale solution approaches the real solution by the constraints from the spatial derivative of the original equation. Thus the solution even on the subgrid scale becomes consistent with the master equation. By increasing the order of the polynomial, this solution quickly converges. 3rd and 5th order polynomials are tested on the one-dimensional Schroedinger equation and are proved to give solutions a few orders of magnitude higher in accuracy than conventional methods for lower-lying eigenstates. (author)
An efficient basis set representation for calculating electrons in molecules
Jones, Jeremiah R; Lawler, Keith V; Vecharynski, Eugene; Ibrahim, Khaled Z; Williams, Samuel; Abeln, Brant; Yang, Chao; Haxton, Daniel J; McCurdy, C William; Li, Xiaoye S; Rescigno, Thomas N
2015-01-01
The method of McCurdy, Baertschy, and Rescigno, J. Phys. B, 37, R137 (2004) is generalized to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O(N log(N)) multiplication operations, not O(N^4), where N is the number of basis functions; N = n^3 on cubic grids. The representation not only is numerically expedient, but also produces energies and proper...
Strategies for reducing basis set superposition error (BSSE) in O/AU and O/Ni
Shuttleworth, I. G.
2015-11-01
The effect of basis set superposition error (BSSE) and effective strategies for the minimisation have been investigated using the SIESTA-LCAO DFT package. Variation of the energy shift parameter ΔEPAO has been shown to reduce BSSE for bulk Au and Ni and across their oxygenated surfaces. Alternative strategies based on either the expansion or contraction of the basis set have been shown to be ineffective in reducing BSSE. Comparison of the binding energies for the surface systems obtained using LCAO were compared with BSSE-free plane wave energies.
Strategies for reducing basis set superposition error (BSSE) in O/AU and O/Ni
Shuttleworth, I.G.
2015-11-01
© 2015 Elsevier Ltd. All rights reserved. The effect of basis set superposition error (BSSE) and effective strategies for the minimisation have been investigated using the SIESTA-LCAO DFT package. Variation of the energy shift parameter ΔEPAO has been shown to reduce BSSE for bulk Au and Ni and across their oxygenated surfaces. Alternative strategies based on either the expansion or contraction of the basis set have been shown to be ineffective in reducing BSSE. Comparison of the binding energies for the surface systems obtained using LCAO were compared with BSSE-free plane wave energies.
Radiobiological basis for setting neutron radiation safety standards
Present neutron standards, adopted more than 20 yr ago from a weak radiobiological data base, have been in doubt for a number of years and are currently under challenge. Moreover, recent dosimetric re-evaluations indicate that Hiroshima neutron doses may have been much lower than previously thought, suggesting that direct data for neutron-induced cancer in humans may in fact not be available. These recent developments make it urgent to determine the extent to which neutron cancer risk in man can be estimated from data that are available. Two approaches are proposed here that are anchored in particularly robust epidemiological and experimental data and appear most likely to provide reliable estimates of neutron cancer risk in man. The first approach uses gamma-ray dose-response relationships for human carcinogenesis, available from Nagasaki (Hiroshima data are also considered), together with highly characterized neutron and gamma-ray data for human cytogenetics. When tested against relevant experimental data, this approach either adequately predicts or somewhat overestimates neutron tumorigenesis (and mutagenesis) in animals. The second approach also uses the Nagasaki gamma-ray cancer data, but together with neutron RBEs from animal tumorigenesis studies. Both approaches give similar results and provide a basis for setting neutron radiation safety standards. They appear to be an improvement over previous approaches, including those that rely on highly uncertain maximum neutron RBEs and unnecessary extrapolations of gamma-ray data to very low doses. Results suggest that, at the presently accepted neutron dose limit of 0.5 rad/yr, the cancer mortality risk to radiation workers is not very different from accidental mortality risks to workers in various nonradiation occupations
Nikolaev, A. V.; Lamoen, D.; Partoens, B.
2016-07-01
In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the u ˙ l -component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.
Network Decomposition and Maximum Independent Set Part Ⅰ: Theoretic Basis
朱松年; 朱嫱
2003-01-01
The structure and characteristics of a connected network are analyzed, and a special kind of sub-network, which can optimize the iteration processes, is discovered. Then, the sufficient and necessary conditions for obtaining the maximum independent set are deduced. It is found that the neighborhood of this sub-network possesses the similar characters, but both can never be allowed incorporated together. Particularly, it is identified that the network can be divided into two parts by a certain style, and then both of them can be transformed into a pair sets network, where the special sub-networks and their neighborhoods appear alternately distributed throughout the entire pair sets network. By use of this characteristic, the network decomposed enough without losing any solutions is obtained. All of these above will be able to make well ready for developing a much better algorithm with polynomial time bound for an odd network in the the application research part of this subject.
Correlation consistent basis sets for actinides. I. The Th and U atoms
Peterson, Kirk A., E-mail: kipeters@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 (United States)
2015-02-21
New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than the DKH2
Petruzielo, F. R.; Toulouse, Julien; Umrigar, C. J.
2011-02-01
A simple yet general method for constructing basis sets for molecular electronic structure calculations is presented. These basis sets consist of atomic natural orbitals from a multiconfigurational self-consistent field calculation supplemented with primitive functions, chosen such that the asymptotics are appropriate for the potential of the system. Primitives are optimized for the homonuclear diatomic molecule to produce a balanced basis set. Two general features that facilitate this basis construction are demonstrated. First, weak coupling exists between the optimal exponents of primitives with different angular momenta. Second, the optimal primitive exponents for a chosen system depend weakly on the particular level of theory employed for optimization. The explicit case considered here is a basis set appropriate for the Burkatzki-Filippi-Dolg pseudopotentials. Since these pseudopotentials are finite at nuclei and have a Coulomb tail, the recently proposed Gauss-Slater functions are the appropriate primitives. Double- and triple-zeta bases are developed for elements hydrogen through argon. These new bases offer significant gains over the corresponding Burkatzki-Filippi-Dolg bases at various levels of theory. Using a Gaussian expansion of the basis functions, these bases can be employed in any electronic structure method. Quantum Monte Carlo provides an added benefit: expansions are unnecessary since the integrals are evaluated numerically.
Kjaer, Hanna; Nielsen, Monia R; Pagola, Gabriel I; Ferraro, Marta B; Lazzeretti, Paolo; Sauer, Stephan P A
2012-09-01
In this article, we present the so far most extended investigation of the calculation of the coupling constant polarizability of a molecule. The components of the coupling constant polarizability are derivatives of the nuclear magnetic resonance (NMR) indirect nuclear spin-spin coupling constant with respect to an external electric field and play an important role for both chiral discrimination and solvation effects on NMR coupling constants. In this study, we illustrate the effects of one-electron basis sets and electron correlation both at the level of density functional theory as well as second-order polarization propagator approximation for the small molecule hydrogen peroxide, which allowed us to perform calculations with the largest available basis sets optimized for the calculation of NMR coupling constants. We find a systematic but rather slow convergence with the one-electron basis set and that augmentation functions are required. We observe also large and nonsystematic correlation effects with significant differences between the density functional and wave function theory methods. PMID:22618604
The cc-pV5Z-F12 basis set: reaching the basis set limit in explicitly correlated calculations
Peterson, Kirk A; Martin, Jan M L
2014-01-01
We have developed and benchmarked a new extended basis set for explicitly correlated calculations, namely cc-pV5Z-F12. It is offered in two variants, cc-pV5Z-F12 and cc- pV5Z-F12(rev2), the latter of which has additional basis functions on hydrogen not present in the cc-pVnZ-F12 (n=D,T,Q) sequence.A large uncontracted 'reference' basis set is used for benchmarking. cc-pVnZ-F12 (n=D, T, Q, 5) is shown to be a convergent hierarchy. Especially the cc- pV5Z-F12(rev2) basis set can yield the valence CCSD component of total atomization energies (TAEs), without any extrapolation, to an accuracy normally associated with aug-cc-pV{5,6}Z extrapolations. SCF components are functionally at the basis set limit, while the MP2 limit can be approached to as little as 0.01 kcal/mol without extrapolation. The determination of (T) appears to be the most difficult of the three components and cannot presently be accomplished without extrapolation or scaling. (T) extrapolation from cc-pV{T,Q}Z-F12 basis sets, combined with CCSD-F1...
Correct quantum chemistry in a minimal basis from effective Hamiltonians
Watson, Thomas J
2015-01-01
We describe how to create ab-initio effective Hamiltonians that qualitatively describe correct chemistry even when used with a minimal basis. The Hamiltonians are obtained by folding correlation down from a large parent basis into a small, or minimal, target basis, using the machinery of canonical transformations. We demonstrate the quality of these effective Hamiltonians to correctly capture a wide range of excited states in water, nitrogen, and ethylene, and to describe ground and excited state bond-breaking in nitrogen and the chromium dimer, all in small or minimal basis sets.
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.
Quantum criticality analysis by finite-size scaling and exponential basis sets
Alharbi, Fahhad H.; Kais, Sabre
2013-04-01
We combine the finite-size scaling method with the mesh-free spectral method to calculate quantum critical parameters for a given Hamiltonian. The basic idea is to expand the exact wave function in a finite exponential basis set and extrapolate the information about system criticality from a finite basis to the infinite basis set limit. The used exponential basis set, though chosen intuitively, allows handling a very wide range of exponential decay rates and calculating multiple eigenvalues simultaneously. As a benchmark system to illustrate the combined approach, we choose the Hulthen potential. The results show that the method is very accurate and converges faster when compared with other basis functions. The approach is general and can be extended to examine near-threshold phenomena for atomic and molecular systems based on even-tempered exponential and Gaussian basis functions.
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
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.
Zaleśny, Robert; Baranowska-Łączkowska, Angelika; Medveď, Miroslav; Luis, Josep M
2015-09-01
In the present work, we perform an assessment of several property-oriented atomic basis sets in computing (hyper)polarizabilities with a focus on the vibrational contributions. Our analysis encompasses the Pol and LPol-ds basis sets of Sadlej and co-workers, the def2-SVPD and def2-TZVPD basis sets of Rappoport and Furche, and the ORP basis set of Baranowska-Łączkowska and Łączkowski. Additionally, we use the d-aug-cc-pVQZ and aug-cc-pVTZ basis sets of Dunning and co-workers to determine the reference estimates of the investigated electric properties for small- and medium-sized molecules, respectively. We combine these basis sets with ab initio post-Hartree-Fock quantum-chemistry approaches (including the coupled cluster method) to calculate electronic and nuclear relaxation (hyper)polarizabilities of carbon dioxide, formaldehyde, cis-diazene, and a medium-sized Schiff base. The primary finding of our study is that, among all studied property-oriented basis sets, only the def2-TZVPD and ORP basis sets yield nuclear relaxation (hyper)polarizabilities of small molecules with average absolute errors less than 5.5%. A similar accuracy for the nuclear relaxation (hyper)polarizabilites of the studied systems can also be reached using the aug-cc-pVDZ basis set (5.3%), although for more accurate calculations of vibrational contributions, i.e., average absolute errors less than 1%, the aug-cc-pVTZ basis set is recommended. It was also demonstrated that anharmonic contributions to first and second hyperpolarizabilities of a medium-sized Schiff base are particularly difficult to accurately predict at the correlated level using property-oriented basis sets. For instance, the value of the nuclear relaxation first hyperpolarizability computed at the MP2/def2-TZVPD level of theory is roughly 3 times larger than that determined using the aug-cc-pVTZ basis set. We link the failure of the def2-TZVPD basis set with the difficulties in predicting the first-order field
Atomic self-consistent-field program by the basis set expansion method: Columbus version
Pitzer, Russell M.
2005-08-01
A revised and extended (Columbus) version of the Chicago atomic self-consistent-field (Hartree-Fock) program of 1963 is described. Its principal present use is in developing Gaussian basis sets for molecular calculations. Complete memory allocation (using Fortran 90) has been added as well as improved integral formulas and efficient and simple programming features. Energy-expression coefficients have been added sufficient to treat the ground states of all atoms to the extent that Russell-Saunders (LS) coupling applies. Excited states with large angular-momentum orbitals can be treated. Relativistic effects can be included to the extent possible with relativistic effective core potentials. A review of earlier work is included. Program summaryProgram title: atmscf Catalogue identifier: ADVR Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVR Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Programming language: Fortran 90 Computer: Sun, SGI, PC Operating system: Solaris, Irix, Linux RAM: 10 Mbytes No. of lines in distributed program, including test data, etc.: 2113 No. of bytes in distributed program, including test data, etc.: 15 379 Distribution format: tar.gz Nature of problem: Energies and wave functions, at the Hartree-Fock level Solution method: Expansions in Gaussian or Slater functions. Iterative minimization of the total energy. Optimization of exponential parameters. Used frequently for developing Gaussian basis sets for molecular use Running time: Typical 30 s per calculation
Gidofalvi, Gergely
2014-01-01
Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{\\"o}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACS...
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT
Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)
2015-08-07
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-01
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods
Hedegård, Erik D.; Jensen, Frank; Kongsted, Jacob
2012-01-01
Even for pure substances, the deduction of the absolute configuration is not always straightforward since there is no direct link between the magnitude and sign of the optical rotation and the absolute configuration. It would be very useful to use computations of the optical rotation to link...... experimentally measured optical rotations to an absolute configuration. Such electronic structure calculations of the optical rotation typically employ regular energy optimized basis sets from wave function theory, and especially the aug-cc-pVDZ basis set has been popular. Here, we have carried out extrapolation...... of the optical rotation to the basis set limits for nine small or medium sized molecules, using basis sets developed specifically for DFT and magnetic properties (aug-pcS-n series). We suggest that assignment of absolute configuration by comparisons between theoretical and experimental optical...
Gaussian Basis Set Optimization for Excited Helium and Helium-like Ions
Šmydke, Jan; Kaprálová-Žďánská, Petra Ruth
Mariapfarr : Univerzity of Graz, 2012. [Central European Symposium on Theoretical Chemistry /11./. 25.09.2011-28.09.2011, Mariapfarr] Institutional support: RVO:61388955 Keywords : helium * Gaussian basis set oprimization Subject RIV: CF - Physical ; Theoretical Chemistry
Boese, A D; Martin, J M L; Klopper, Wim; Martin, Jan M. L.
2005-01-01
In a previous contribution (Mol. Phys. {\\bf 103}, xxxx, 2005), we established the suitability of density functional theory (DFT) for the calculation of molecular anharmonic force fields. In the present work, we have assessed a wide variety of basis sets and exchange-correlation functionals for harmonic and fundamental frequencies, equilibrium and ground-state rotational constants, and thermodynamic functions beyond the RRHO (rigid rotor-harmonic oscillator) approximation. The fairly good performance of double-zeta plus polarization basis sets for frequencies results from an error compensation between basis set incompleteness and the intrinsic error of exchange-correlation functionals. Triple-zeta plus polarization basis sets are recommended, with an additional high-exponent $d$ function on second-row atoms. All conventional hybrid GGA functionals perform about equally well: high-exchange hybrid GGA and meta-GGA functionals designed for kinetics yield poor results, with the exception of of the very recently de...
The Bethe Sum Rule and Basis Set Selection in the Calculation of Generalized Oscillator Strengths
Cabrera-Trujillo, Remigio; Sabin, John R.; Oddershede, Jens; Sauer, Stephan P. A.
1999-01-01
Fulfillment of the Bethe sum rule may be construed as a measure of basis set quality for atomic and molecular properties involving the generalized oscillator strength distribution. It is first shown that, in the case of a complete basis, the Bethe sum rule is fulfilled exactly in the random phase...
Informatics-Based Energy Fitting Scheme for Correlation Energy at Complete Basis Set Limit.
Seino, Junji; Nakai, Hiromi
2016-09-30
Energy fitting schemes based on informatics techniques using hierarchical basis sets with small cardinal numbers were numerically investigated to estimate correlation energies at the complete basis set limits. Numerical validations confirmed that the conventional two-point extrapolation models can be unified into a simple formula with optimal parameters obtained by the same test sets. The extrapolation model was extended to two-point fitting models by a relaxation of the relationship between the extrapolation coefficients or a change of the fitting formula. Furthermore, n-scheme fitting models were developed by the combinations of results calculated at several theory levels and basis sets to compensate for the deficiencies in the fitting model at one level of theory. Systematic assessments on the Gaussian-3X and Gaussian-2 sets revealed that the fitting models drastically reduced errors with equal or smaller computational effort. © 2016 Wiley Periodicals, Inc. PMID:27454327
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex
Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H2, O2, and N2, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species
Representability of Bloch states on Projector-augmented-wave (PAW) basis sets
Agapito, Luis; Ferretti, Andrea; Curtarolo, Stefano; Buongiorno Nardelli, Marco
2015-03-01
Design of small, yet `complete', localized basis sets is necessary for an efficient dual representation of Bloch states on both plane-wave and localized basis. Such simultaneous dual representation permits the development of faster more accurate (beyond DFT) electronic-structure methods for atomistic materials (e.g. the ACBN0 method.) by benefiting from algorithms (real and reciprocal space) and hardware acceleration (e.g. GPUs) used in the quantum-chemistry and solid-state communities. Finding a `complete' atomic-orbital basis (partial waves) is also a requirement in the generation of robust and transferable PAW pseudopotentials. We have employed the atomic-orbital basis from available PAW data sets, which extends through most of the periodic table, and tested the representability of Bloch states on such basis. Our results show that PAW data sets allow systematic and accurate representability of the PAW Bloch states, better than with traditional quantum-chemistry double-zeta- and double-zeta-polarized-quality basis sets.
Full text: Faucher and co-workers have carried out several studies of the effect of electron correlation on the crystal-field splitting of 4fN configurations of lanthanide ions in solids. In their approach the 4fN configuration is supplemented by the 4fN-1 6p configuration. On the other hand, Reid, Burdick, and coworkers have carried out many parameter fits using pure 4fN model spaces, with the one-electron crystal field operators supplemented with two-electron correlation crystal field operators. Both approaches lead to better fits to the experimental data, but since the basis sets are different, it is difficult to compare the resulting parameters. In this work we use the matrices generated by Faucher's calculations to calculate the equivalent two-electron correlation crystal field parametrization in the 4fN model space
A two-dimensional volatility basis set – Part 3: Prognostic modeling and NOx dependence
W. K. Chuang
2015-06-01
Full Text Available When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2-D-VBS to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in AMS measurements. We also discuss the mathematical methods underlying the implementation of the 2-D-VBS and provide the complete code in the Supplemental material. A developer version is available on Bitbucket, an online community repository.
Basis set convergence on static electric dipole polarizability calculations of alkali-metal clusters
Souza, Fabio A. L. de; Jorge, Francisco E., E-mail: jorge@cce.ufes.br [Departamento de Fisica, Universidade Federal do Espirito Santo, 29060-900 Vitoria-ES (Brazil)
2013-07-15
A hierarchical sequence of all-electron segmented contracted basis sets of double, triple and quadruple zeta valence qualities plus polarization functions augmented with diffuse functions for the atoms from H to Ar was constructed. A systematic study of basis sets required to obtain reliable and accurate values of static dipole polarizabilities of lithium and sodium clusters (n = 2, 4, 6 and 8) at their optimized equilibrium geometries is reported. Three methods are examined: Hartree-Fock (HF), second-order Moeller-Plesset perturbation theory (MP2), and density functional theory (DFT). By direct calculations or by fitting the directly calculated values through one extrapolation scheme, estimates of the HF, MP2 and DFT complete basis set limits were obtained. Comparison with experimental and theoretical data reported previously in the literature is done (author)
Real ${\\mathcal L}^2$ basis-set-size scaling of energies and widths of resonance states
Pont, Federico M; Osenda, Omar
2011-01-01
The resonance states of one-particle Hamiltonians are studied using variational expansions with real basis-set functions. The resonance energies, $E_r$, and widths, $\\Gamma$, are calculated using the density of states and an ${\\mathcal L}^2$ golden rule-like formula, respectively. We present a recipe to select adequately some solutions of the variational problem. The set of approximate energies obtained show a very regular behaviour with the basis-set size, $N$. Indeed, these particular variational eigenvalues show a quite simple scaling behaviour and convergence when $N\\rightarrow \\infty$. Following the same prescription to choose particular solutions of the variational problem we obtain a set of approximate widths. Using the scaling function that characterizes the behaviour of the approximate energies as a guide, it is possible to find a very good approximation to the actual value of the resonance width.
Roper, Ian P E; Besley, Nicholas A
2016-03-21
The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals. PMID:27004859
Borges, A; Solomon, G C
2016-05-21
Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and -π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems. PMID:27208940
On the use of locally dense basis sets in the calculation of EPR hyperfine couplings
Milhøj, Birgitte Olai; Hedegård, Erik D.; Sauer, Stephan P. A.
2013-01-01
The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c...
On the use of Locally Dense Basis Sets in the Calculation of EPR Hyperfine Couplings
Hedegård, Erik D.; Sauer, Stephan P. A.; Milhøj, Birgitte O.
2013-01-01
The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c...
Ca+ centers for hydrogen storage: An accurate many-body study with large basis sets
Purwanto, Wirawan; Virgus, Yudistira; Zhang, Shiwei
2011-01-01
Weak H2 physisorption energies present a significant challenge to even the best correlated theoretical many-body methods. We use the phaseless auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca+ - 4H2. Attention has recently focused on this model chemistry to test the reliability of electronic structure methods for H2 binding on dispersed alkaline earth metal centers. A modified Cholesky decomposition is implemented to realize the Hubbard-Stratonovich transformation efficiently with large Gaussian basis sets. We employ the largest correlation-consistent Gaussian type basis sets available, up to cc-pCV5Z for Ca, to accurately extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure.
An editor for the maintenance and use of a bank of contracted Gaussian basis set functions
A bank of basis sets to be used in ab-initio calculations has been created. The bases are sets of contracted Gaussian type orbitals to be used as input to any molecular integral package. In this communication we shall describe the organization of the bank and a portable editor program which was designed for its maintenance and use. This program is operated by commands and it may be used to obtain any kind of information about the bases in the bank as well as to produce output to be directly used as input for different integral programs. The editor may also be used to format basis sets in the conventional way utilized in publications, as well as to generate a complete, or partial, manual of the contents of the bank if so desired. (orig.)
Truncated spherical-wave basis set for first-principles pseudopotential calculations
Monserrat, B.; Haynes, P. D.
2010-11-01
Analytic results for two- and three-centre integrals are derived for the truncated spherical-wave basis set designed for first-principles pseudopotential calculations within density-functional theory. These allow the overlap, kinetic energy and non-local pseudopotential matrix elements to be calculated efficiently and accurately. In particular, the scaling of the computational effort with maximum angular momentum component is dramatically improved and the projection method takes full account of the discontinuities in the basis functions arising from their localization within spherical regions.
Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin
2016-05-21
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems. PMID:27208948
European air quality modelled by CAMx including the volatility basis set scheme
G. Ciarelli
2015-12-01
Full Text Available Four periods of EMEP (European Monitoring and Evaluation Programme intensive measurement campaigns (June 2006, January 2007, September–October 2008 and February–March 2009 were modelled using the regional air quality model CAMx with VBS (Volatility Basis Set approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February–March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosols (OA. Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database Airbase. Sulfur dioxide (SO2 and ozone (O3 were found to be overestimated for all the four periods with O3 having the largest mean bias during June 2006 and January–February 2007 periods (8.93 and 12.30 ppb mean biases, respectively. In contrast, nitrogen dioxide (NO2 and carbon monoxide (CO were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 very well for all the four periods with average biases ranging from −2.13 to 1.04 μg m-3. Comparisons with AMS (Aerosol Mass Spectrometer measurements at different sites in Europe during February–March 2009, showed that in general the model over-predicts the inorganic aerosol fraction and under-predicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of volatility basis set scheme (VBS on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February–March 2009 the chamber-case reduced the total OA concentrations by about 43 % on average. On the other hand, a test based on ambient measurement data increased OA concentrations by about 47 % for the same
European air quality modelled by CAMx including the volatility basis set scheme
Ciarelli, G.; Aksoyoglu, S.; Crippa, M.; Jimenez, J. L.; Nemitz, E.; Sellegri, K.; Äijälä, M.; Carbone, S.; Mohr, C.; O'Dowd, C.; Poulain, L.; Baltensperger, U.; Prévôt, A. S. H.
2015-12-01
Four periods of EMEP (European Monitoring and Evaluation Programme) intensive measurement campaigns (June 2006, January 2007, September-October 2008 and February-March 2009) were modelled using the regional air quality model CAMx with VBS (Volatility Basis Set) approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February-March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosols (OA). Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database Airbase. Sulfur dioxide (SO2) and ozone (O3) were found to be overestimated for all the four periods with O3 having the largest mean bias during June 2006 and January-February 2007 periods (8.93 and 12.30 ppb mean biases, respectively). In contrast, nitrogen dioxide (NO2) and carbon monoxide (CO) were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 very well for all the four periods with average biases ranging from -2.13 to 1.04 μg m-3. Comparisons with AMS (Aerosol Mass Spectrometer) measurements at different sites in Europe during February-March 2009, showed that in general the model over-predicts the inorganic aerosol fraction and under-predicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of volatility basis set scheme (VBS) on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February-March 2009 the chamber-case reduced the total OA concentrations by about 43 % on average. On the other hand, a test based on ambient measurement data increased OA concentrations by about 47 % for the same period bringing model
Structural Identification of Nonlinear Static System on Basis of Analysis Sector Sets
Nikolay Karabutov
2013-12-01
Full Text Available Methods of structural identification of static systems with a vector input and several nonlinearities in the conditions of uncertainty are considered. We consider inputs irregular. The concept of structural space is introduced. In this space special structures (virtual portraits are analyzed. The Holder condition is applied to construction of sector set, to which belongs a virtual portrait of system of identification. Criteria of decision-making on a class of nonlinear functions on the basis of the analysis of proximity of sector sets are described. Procedures of an estimation of structural parameters of two classes of nonlinearities are stated: power and a hysteresis.
Boese, A. Daniel; Klopper, Wim; Martin, Jan M. L.
2005-01-01
In a previous contribution (Mol. Phys. {\\bf 103}, xxxx, 2005), we established the suitability of density functional theory (DFT) for the calculation of molecular anharmonic force fields. In the present work, we have assessed a wide variety of basis sets and exchange-correlation functionals for harmonic and fundamental frequencies, equilibrium and ground-state rotational constants, and thermodynamic functions beyond the RRHO (rigid rotor-harmonic oscillator) approximation. The fairly good perf...
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations.
Sorella, S; Devaux, N; Dagrada, M; Mazzola, G; Casula, M
2015-12-28
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen. PMID:26723656
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
Sorella, S., E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), Via Beirut 2-4, 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste (Italy); Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr [Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France); Mazzola, G., E-mail: gmazzola@phys.ethz.ch [Theoretische Physik, ETH Zurich, 8093 Zurich (Switzerland); Casula, M., E-mail: michele.casula@impmc.upmc.fr [CNRS and Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France)
2015-12-28
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan
2013-09-26
We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface. PMID:23947824
On fast computation of finite-time coherent sets using radial basis functions.
Froyland, Gary; Junge, Oliver
2015-08-01
Finite-time coherent sets inhibit mixing over finite times. The most expensive part of the transfer operator approach to detecting coherent sets is the construction of the operator itself. We present a numerical method based on radial basis function collocation and apply it to a recent transfer operator construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] that has been designed specifically for purely advective dynamics. The construction [G. Froyland, "Dynamic isoperimetry and the geometry of Lagrangian coherent structures," Nonlinearity (unpublished); preprint arXiv:1411.7186] is based on a "dynamic" Laplace operator and minimises the boundary size of the coherent sets relative to their volume. The main advantage of our new approach is a substantial reduction in the number of Lagrangian trajectories that need to be computed, leading to large speedups in the transfer operator analysis when this computation is costly. PMID:26328580
Symmetry-adapted basis sets automatic generation for problems in chemistry and physics
Avery, John Scales; Avery, James Emil
2012-01-01
In theoretical physics, theoretical chemistry and engineering, one often wishes to solve partial differential equations subject to a set of boundary conditions. This gives rise to eigenvalue problems of which some solutions may be very difficult to find. For example, the problem of finding eigenfunctions and eigenvalues for the Hamiltonian of a many-particle system is usually so difficult that it requires approximate methods, the most common of which is expansion of the eigenfunctions in terms of basis functions that obey the boundary conditions of the problem. The computational effort needed
de Silva, Piotr; Wesolowski, Tomasz A.
2012-03-01
Within the linear combination of atomic orbitals (LCAO) approximation, one can distinguish two different Kohn-Sham potentials. One is the potential available numerically in calculations, and the other is the exact potential corresponding to the LCAO density. The latter is usually not available, but can be obtained from the total density by a numerical inversion procedure or, as is done here, analytically using only one LCAO Kohn-Sham orbital. In the complete basis-set limit, the lowest-lying Kohn-Sham orbital suffices to perform the analytical inversion, and the two potentials differ by no more than a constant. The relation between these two potentials is investigated here for diatomic molecules and several atomic basis sets of increasing size and quality. The differences between the two potentials are usually qualitative (wrong behavior at nuclear cusps and far from the molecule even if Slater-type orbitals are used) and δ-like features at nodal planes of the lowest-lying LCAO Kohn-Sham orbital. Such nodes occur frequently in LCAO calculations and are not physical. Whereas the behavior of the potential can be systematically improved locally by the increase of the basis sets, the occurrence of nodes is not correlated with the size of the basis set. The presence of nodes in the lowest-lying LCAO orbital can be used to monitor whether the effective potential in LCAO Kohn-Sham equations can be interpreted as the potential needed for pure-state noninteracting v-representability of the LCAO density. Squares of such node-containing lowest-lying LCAO Kohn-Sham orbitals are nontrivial examples of two-electron densities which are not pure-state noninteracting v-representable.
Corsetti, Fabiano
2014-01-01
The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn-Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better ...
The universal basis set of de Castro and Jorge has been investigated in matrix Hartree - Fock calculations, without truncation for specific atomic species, in electron correlation studies, and in systematic schemes for basis set extension. copyright 1999 American Institute of Physics
Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism
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.
Model for the fast estimation of basis set superposition error in biomolecular systems
Faver, John C.; Zheng, Zheng; Merz, Kenneth M.
2011-01-01
Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds. PMID:22010701
Teodoro, Tiago Quevedo; da Silva, Albérico Borges Ferreira; Haiduke, Roberto Luiz Andrade
2014-09-01
This study reports a new relativistic prolapse-free Gaussian basis set series of quadruple-ζ quality, RPF-4Z, and an augmented version that includes extra diffuse functions, aug-RPF-4Z, for all the s- and p-block elements. The relativistic adapted Gaussian basis sets (RAGBSs), which are free of variational prolapse, were used as the starting primitive sets. Exponents of correlating/polarization functions were taken from a polynomial version of the generator coordinate Dirac-Fock (p-GCDF) method, in which the previously optimized RAGBS parameters are applied. By using such procedure we aimed to reduce the computational demand of these sets in comparison with fully optimized ones. The effect of these basis set increments on the correlation energy was evaluated by atomic multireference configuration interaction calculations with single and double excitations out of the valence shell. Finally, atomic and molecular calculations of fundamental properties (bond lengths, vibrational frequencies, dipole moments and electron affinities) corroborate the quadruple-ζ quality of these new sets that are also about half-time-consuming than the correspondent Dyall's v4z sets. The read-to use format of these (aug-)RPF-4Fz sets are available as Supporting Information files and can also be found at http://basis-sets.iqsc.usp.br/ . PMID:26588525
Assessment of quantum chemical methods and basis sets for excitation energy transfer
The validity of several standard quantum chemical approaches and other models for the prediction of exciton energy transfer is investigated using the HOMO-LUMO excited states of benzene dimer as an example. The configuration interaction singles (CIS), time-dependent Hartree-Fock (TD-HF), time dependent density functional theroy (TD-DFT), and complete-active-space self-consistent-field (CASSCF) methods are applied with a supermolecule approach and compared to the previously established monomer transition density method and the ideal dipole approximation. Strong and physically incorrect admixture of charge-transfer states makes TD-DFT inappropriate for investigations of potential energy surfaces in such dimer systems. CIS, TD-HF and CASSCF perform qualitatively correct. TD-HF seems to be a particularly appropriate method due to its general applicability and overall good performance for the excited state and for transition properties. Double-zeta basis sets with polarisation functions are found to be sufficient to predict transfer rates of dipole allowed excitations. Efficient excitation energy transfer is predicted between degenerate excited states while avoided curve crossings of nearly spaced π-aggregates are identified as a possible trapping mechanism
Holden, Zachary C.; Richard, Ryan M.; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States)
2013-12-28
An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.
Holden, Zachary C.; Richard, Ryan M.; Herbert, John M.
2013-12-01
An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using "ChElPG" atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.
Fully nonadiabatic variational computations of energies of the H2+, HD+, and D2+ ions are carried out, making detailed allowance for the motions of all particles. Computations are performed using the basis set of exponential-trigonometric functions dependent on all the interparticle distances. The method of determining the nonlinear adjustable parameters that are responsible for the vibration-modulated exponential decrease of the basis functions with increasing the interparticle distances is developed in detail. Also examined is how an accuracy of the variational energy computations rises with an increase in the number N of the basis functions. For the maximal basis-set size (N = 300), the calculated ground-state energies of the HD+ and D2+ ions deviate from their exact values by 2 x 10-10 and 1 x 10-10 a.u., respectively; whereas the energy of the 2+ ion coincides with 2 its exact value to ten significant digits. The results obtained with the exponential-trigonometric basis set are eight orders of magnitude more precise than the computations with an even larger-sized (N = 350) basis set of monotonically decreasing purely exponential functions of the interatomic distances. This indicates that the exponential-trigonometric basis functions have considerable promise for accurate fully nonadiabatic variational computations of various three-body Coulomb systems with arbitrary masses of their particles. 18 refs., 4 tabs
Sarvesh Kumar Pandey; Prasanta Das; Puspendu K Das; Elangannan Arunan; Sadasivam Manogaran
2015-06-01
It has been shown earlier1 that the relaxed force constants (RFCs) could be used as a measure of bond strength only when the bonds form a part of the complete valence internal coordinates (VIC) basis. However, if the bond is not a part of the complete VIC basis, its RFC is not necessarily a measure of bond strength. Sometimes, it is possible to have a complete VIC basis that does not contain the intramolecular hydrogen bond (IMHB) as part of the basis. This means the RFC of IMHB is not necessarily a measure of bond strength. However, we know that IMHB is a weak bond and hence its RFC has to be a measure of bond strength. We resolve this problem of IMHB not being part of the complete basis by postulating `equivalent’ basis sets where IMHB is part of the basis at least in one of the equivalent sets of VIC. As long as a given IMHB appears in one of the equivalent complete VIC basis sets, its RFC could be used as a measure of bond strength parameter.
Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.
Bielecki, Jakub; Lipiec, Ewelina
2016-02-01
Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method. PMID:26508426
The authors consider the problem of computing tunneling matrix elements for bridge-mediated electron transfer reactions using the Loewdin [J. Math. Phys. 3, 969 (1962); J. Mol. Spectrosc. 13, 326 (1964)] projection-iteration technique with a nonorthogonal basis set. They compare the convergence properties of two different Loewdin projections, one containing the overlap matrix S and the other containing the inverse S-1 in the projected Hamiltonian. It was suggested in the literature that the projected Hamiltonian with S-1 has better convergence properties compared to the projected Hamiltonian with S. The authors test this proposal using a simple analytical model, and ab initio Hartree-Fock calculations on different molecules with several types of basis sets. Their calculations show that, for Gaussian-type basis sets, the projected Hamiltonian containing S has the best convergence properties, especially for diffuse basis sets and in the strong coupling limit. The limit of diffuse basis sets is relevant to tunneling matrix element calculations involving excited states and anionic electron transfer
Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine
2016-01-01
Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4–6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data. PMID:27471441
Friese, Daniel H; Ringholm, Magnus; Gao, Bin; Ruud, Kenneth
2015-10-13
We present theory, implementation, and applications of a recursive scheme for the calculation of single residues of response functions that can treat perturbations that affect the basis set. This scheme enables the calculation of nonlinear light absorption properties to arbitrary order for other perturbations than an electric field. We apply this scheme for the first treatment of two-photon circular dichroism (TPCD) using London orbitals at the Hartree-Fock level of theory. In general, TPCD calculations suffer from the problem of origin dependence, which has so far been solved by using the velocity gauge for the electric dipole operator. This work now enables comparison of results from London orbital and velocity gauge based TPCD calculations. We find that the results from the two approaches both exhibit strong basis set dependence but that they are very similar with respect to their basis set convergence. PMID:26574270
Turovtsev, V. V.; Orlov, Yu. D.; Tsirulev, A. N.
2015-08-01
The advantages of the orthonormal basis set of 2π-periodic Mathieu functions compared to the trigonometric basis set in calculations of torsional states of molecules are substantiated. Explicit expressions are derived for calculating the Hamiltonian matrix elements of a one-dimensional torsional Schrödinger equation with a periodic potential of the general form in the basis set of Mathieu functions. It is shown that variation of a parameter of Mathieu functions allows the rotation potential and the structural function to be approximated with a good accuracy by a small number of series terms. The conditions for the best choice of this parameter are specified, and approximations are obtained for torsional potentials of n-butane upon rotation about the central C-C bond and of its univalent radical n-butyl C2H5C·H2 upon rotation of the C·H2 group. All algorithms are implemented in the Maple package.
Design basis reconstitution for an effective design control program
Configuration management is a new buzz word in the nuclear power industry. Whatever its definition, everyone agrees that the configuration of a nuclear power plant must be managed effectively. In layman's terms, configuration management means that a plant must be built, operated, and maintained in a manner consistent with its design basis. Thus, control of the design basis is the most important element in any configuration management program. Until recently, the US Nuclear Regulatory Commission's (NRC's) review of design basis focused on the plants that were about to get operating licenses. However, incidents at a few operating nuclear plants and NRC inspections (Safety System Functional Inspection and Safety System Outage Modification Inspection) have indicated weaknesses in older operating plant design basis documentation and design change control programs. Thus, reconstitution of plant design basis has become an important issue. This paper presents the major element of a design basis reconstitution program, which can be an immense undertaking for some of the older operating plants
Heaps, Charles W
2016-01-01
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schr\\"{o}dinger equation with $N$ Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from $\\mathcal{O}(N^2)$ to $\\mathcal{O}(N)$. By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems; the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-d...
Yang, Yanchao; Jiang, Hong; Liu, Congbin; Lan, Zhongli
2013-03-01
Cognitive radio (CR) is an intelligent wireless communication system which can dynamically adjust the parameters to improve system performance depending on the environmental change and quality of service. The core technology for CR is the design of cognitive engine, which introduces reasoning and learning methods in the field of artificial intelligence, to achieve the perception, adaptation and learning capability. Considering the dynamical wireless environment and demands, this paper proposes a design of cognitive engine based on the rough sets (RS) and radial basis function neural network (RBF_NN). The method uses experienced knowledge and environment information processed by RS module to train the RBF_NN, and then the learning model is used to reconfigure communication parameters to allocate resources rationally and improve system performance. After training learning model, the performance is evaluated according to two benchmark functions. The simulation results demonstrate the effectiveness of the model and the proposed cognitive engine can effectively achieve the goal of learning and reconfiguration in cognitive radio.
A large-aperture set-up designed for nuclear physics experiments on beams of radioactive nuclei is described. The set-up includes Multiwire Proportional Chamber (MWPC) for measuring the beam profile, MWPC for measuring reaction product angular distributions, a CsI (Tl)-crystal detector and a longitudinal drift ionization chamber for identifying scattered particles and measuring their energy. The results of tests of coordinate MWPCs, particle identification on photon and ion beams, and preliminary measurements of the elastic scattering and the charge exchange reaction of 170 MeV 6He on a CH2 target are presented
Heaps, Charles W.; Mazziotti, David A.
2016-08-01
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schrödinger equation with N Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from O ( N 2 ) to O ( N ) . By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing the nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems: the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-dimensional model for collinear triatomic vibrational dynamics. In all cases, the pseudospectral Gaussian method is in quantitative agreement with numerically exact calculations. The results are promising for nonadiabatic molecular dynamics in molecular systems where strongly correlated ground or excited states require expensive electronic structure calculations.
Investigation of confined hydrogen atom in spherical cavity, using B-splines basis set
M Barezi
2011-03-01
Full Text Available Studying confined quantum systems (CQS is very important in nano technology. One of the basic CQS is a hydrogen atom confined in spherical cavity. In this article, eigenenergies and eigenfunctions of hydrogen atom in spherical cavity are calculated, using linear variational method. B-splines are used as basis functions, which can easily construct the trial wave functions with appropriate boundary conditions. The main characteristics of B-spline are its high localization and its flexibility. Besides, these functions have numerical stability and are able to spend high volume of calculation with good accuracy. The energy levels as function of cavity radius are analyzed. To check the validity and efficiency of the proposed method, extensive convergence test of eigenenergies in different cavity sizes has been carried out.
Prolapse-free basis sets suitable for four-component relativistic quantum chemical calculations are presented for the superheavy elements up to 118Uuo (104Rf, 105Db, 106Sg, 107Bh, 108Hs, 109Mt, 110Ds, 111Rg, 112Uub, 113Uut, 114Uuq, 115Uup, 116Uuh, 117Uus, 118Uuo) and 103Lr. These basis sets were optimized by minimizing the absolute values of the energy difference between the Dirac-Fock-Roothaan total energy and the corresponding numerical value at a milli-Hartree order of magnitude, resulting in a good balance between cost and accuracy. Parameters for generating exponents and new numerical data for some superheavy elements are also presented
Salvador Sedano, Pedro; Mayer, István
2004-01-01
The basis set superposition error-free second-order MØller-Plesset perturbation theory of intermolecular interactions was studied. The difficulties of the counterpoise (CP) correction in open-shell systems were also discussed. The calculations were performed by a program which was used for testing the new variants of the theory. It was shown that the CP correction for the diabatic surfaces should be preferred to the adiabatic ones
Ran, Jiong; Hobza, Pavel
2009-01-01
Roč. 5, č. 4 (2009), s. 1180-1185. ISSN 1549-9618 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550510 Institutional research plan: CEZ:AV0Z40550506 Keywords : lone pair...pi-electron complexes * nature of bonding * CCSD(T)/ complete basis set limit calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.804, year: 2009
De Silva, Piotr; Wesolowski, Tomasz Adam
2012-01-01
Within the linear combination of atomic orbitals (LCAO) approximation, one can distinguish two different Kohn-Sham potentials. One is the potential available numerically in calculations, and the other is the exact potential corresponding to the LCAO density. The latter is usually not available, but can be obtained from the total density by a numerical inversion procedure or, as is done here, analytically using only one LCAO Kohn-Sham orbital. In the complete basis-set limit, the lowest-lying ...
Systematic sequences of basis sets are used to calculate the spin-orbit splittings of the halogen atoms F, Cl, and Br in the framework of first-order perturbation theory with the Breit-Pauli operator and internally contracted configuration interaction wave functions. The effects of both higher angular momentum functions and the presence of tight functions are studied. By systematically converging the one-particle basis set, an unambiguous evaluation of the effects of correlating different numbers of electrons in the Cl treatment is carried out. Correlation of the 2p-electrons in chlorine increases the spin-orbit splitting by ∼80 cm-1, while in bromine we observe incremental increases of 130, 145, and 93 cm-1, when adding the 3d, 3p, and 2p electrons to the set of explicitly correlated electrons, respectively. For fluorine and chlorine the final basis set limit, all-electrons correlated results match the experimentally observed spin-orbit splittings to within ∼5 cm-1, while for bromine the Breit-Pauli operator underestimates the splitting by about 100 cm-1. More extensive treatment of electron correlation results in only a slight lowering of the spin-orbit matrix elements. Thus, the discrepancy for bromine is proposed to arise from the nonrelativistic character of the underlying wave function. (c) 2000 American Institute of Physics
Kolmann, Stephen J.; Jordan, Meredith J. T.
2010-02-01
One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.
Self-consistent simulations of nanowire transistors using atomistic basis sets
NEOPHYTOU, Neophytos; Paul, Abhijeet; Lundstrom, Mark S.; Klimeck, Gerhard
2007-01-01
As device sizes shrink towards the nanoscale, CMOS development investigates alternative structures and devices. Existing CMOS devices will evolve from planar to 3D non-planar devices at nanometer sizes. These devices will operate under strong confinement and strain, regimes where atomistic effects are important. This work investigates atomistic effects in the transport properties of nanowire devices by using a nearest-neighbor tight binding model (sp3s*d5-SO) for electronic structure calculat...
B. N. Murphy
2012-04-01
Full Text Available Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1 heterogeneous oxidation via OH uptake to the particle-phase and (2 aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and
B. N. Murphy
2012-11-01
Full Text Available Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1 heterogeneous oxidation via OH uptake to the particle-phase and (2 aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and
Selection effects in producer-price setting
Carlsson, Mikael
2014-01-01
We use micro data on product prices linked to information on the firms that set them to test for selection effects (state dependence) in micro-level producer pricing. In contrast to using synthetic data from a canonical menu-cost model, we fi…nd very weak, if any, micro-level selection effects when running price change probability regressions on actual data. Moreover, when fi…tting a model that nests both time- and state-dependent elements (the CalvoPlus model of Nakamura and Steinsson,2010) ...
Selection effects in producer-price setting
Carlsson, Mikael
2014-01-01
We use micro data on product prices linked to information on the firms that set them to test for selection effects (state dependence) in micro-level producer pricing. In contrast to using synthetic data from a canonical Menu-Cost model, we find very weak, if any, micro-level selection effects when running price change probability regressions on actual data. Also, fitting a model that nests both time- and state-dependent elements (the CalvoPlus model of Nakamura and Steinsson, 2010), the param...
Zhang, Gaigong; Hu, Wei; Yang, Chao; Pask, John E
2015-01-01
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 accuracy required in practice. Since the adaptive local basis set has implicit dependence on a...
The utility of many-body decompositions for the accurate basis set extrapolation of ab initio data
We present a powerful new technique for the extrapolation of ab initio data based on many-body decompositions. Using the new methodology and subtle modifications of the standard correlation consistent basis sets, the H+H2 barrier height is estimated at 9.603 kcal/mol with a precision of about 0.003 kcal/mol; this extremely accurate result is all the more striking as it can be obtained using basis sets no larger than aug-cc-pVQZ. The method is also used to yield highly accurate energies for the H+H2 system on a grid of points previously calculated by quantum Monte Carlo. The three-body energy, summed with exact one- and two-body energies, is observed to yield a useful approximate lower bound for the total energy. The highly accurate energies afforded by this method can also be used to assess the accuracy of previously calculated data that has been used to construct potential energy surfaces. As an example, we make a detailed comparison between the new results and the quantum Monte Carlo results for H+H2. copyright 1999 American Institute of Physics
Effective field theory in the harmonic-oscillator basis
Binder, S; Hagen, G; Papenbrock, T; Wendt, K A
2015-01-01
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. We derive useful analytical expressions for an exact and efficient calculation of matrix elements. By fitting to realistic phase shifts and deuteron data we construct an effective interaction from chiral EFT at next-to-leading order. Many-body coupled-cluster calculations of nuclei up to 132Sn exhibit a fast convergence of ground-state energies and radii in feasible model spaces.
I. Riipinen
2014-11-01
Full Text Available We present a theoretical study investigating the cloud condensation nucleus (CCN activation of multicomponent organic mixtures. We modeled these complex mixtures using the solubility basis set (SBS, analogous to the volatility basis set VBS, describing the mixture as a set of surrogate compounds with varying water-solubilities in a given range. We conducted Köhler theory calculations for 144 different mixtures with varying solubility range, number of components, assumption about the organic mixture thermodynamics and the shape of the solubility distribution, yielding approximately 6000 unique CCN-activation points. The results from these comprehensive calculations were compared to three simplifying assumptions about organic aerosol solubility: (1 complete dissolution at the point of activation, (2 combining the aerosol solubility with the molar mass and density into a single hygroscopicity parameter κ, (3 assuming a fixed water-soluble fraction ϵeff. While the complete dissolution was able to reproduce the activation points with a reasonable accuracy only when the majority (70–80% of the material was dissolved at the point of activation, the single parameter representations of complex mixture solubility were confirmed to be powerful semi-empirical tools for representing the CCN activation of organic aerosol. Depending on the condensed-phase interactions between the organic molecules, material with solubilities larger than about 1–10 g L−1 could be treated as completely soluble in the CCN activation process over particle dry diameters between 20 and 500 nm and supersaturations between 0.03 and 8%. Our results indicate that understanding the details of the solubility distribution in the range of 0.1 to 100 g L−1 is critical for capturing the CCN activation, while resolution outside this solubility range will probably not add much information except in some special cases. The connection of these results to the previous
Andrade, Xavier; Aspuru-Guzik, Alán
2013-10-01
We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs. PMID:26589153
Andrade, Xavier
2013-01-01
We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code OCTOPUS, can reach a sustained performance of up to 90 GFlops for a single GPU, representing an important speed-up when compared to the CPU version of the code. Moreover, for some systems our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs.
The issue of basis set size in e- + H(1s → 2s, 2p) collisions
The results of the multichannel eikonal theory and three recent close-coupling calculations are compared for the σ1s→2s and σ1s→2p integral cross sections at intermediate energies. Also, the predictions of the three-state close-coupling theory and the present multichannel eikonal theory results for the moduli and phase angles of the complex scattering amplitudes for the 2p0 and 2p+1 substates of H at 54.40 eV are compared. Good agreement is obtained between previous results and the present results for the phase angles of the scattering amplitudes of both substates at small scattering angles. However, differences are noted in the modulus of the scattering amplitude of the 2p+1 substate at small scattering angles between the two theories. The implications this difference has on the composition and size of the basis sets used are addressed. (author)
Investigation of the physiological basis of the BOLD effect
Pears, J A
2001-01-01
The work described in this thesis is that undertaken by the carried out in the Magnetic Resonance Centre, School of Physics and Astronomy at the University of Nottingham, between October 1997 and September 2001. This thesis describes work performed with the aim of yielding further understanding of the physiological basis behind the BOLD effect. Chapter 1 introduces techniques for monitoring brain function and describes the physiology behind the BOLD effect. Chapter 2 then describes NMR, imaging and the hardware used in the experiments performed in this thesis. A method of measuring cerebral blood volume changes during a visual activation paradigm with high temporal resolution is described in Chapter 3, and the timecourse compared to that of the BOLD response. The slow return to baseline of CBV is discussed. Chapter 4 shows a method of simultaneously measuring blood oxygenation measurements and blood volume changes. The results are shown to be in agreement with published data. The controversial phenomenon know...
Effective field theory in the harmonic oscillator basis
Binder, S.; Ekström, A.; Hagen, G.; Papenbrock, T.; Wendt, K. A.
2016-04-01
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-leading order. Many-body coupled-cluster calculations of nuclei up to 132Sn converge fast for the ground-state energies and radii in feasible model spaces.
SCHEMA CONGRUITY – A BASIS FOR EVALUATING AMBIENT ADVERTISING EFFECTIVENESS
Jurca Maria Alina
2013-07-01
Full Text Available The purpose of this paper is to develop a theoretical basis for evaluating ambient advertising in relation to the schema. Ambient advertising, a creative form of out-of-home advertising that conveys direct and contextual messages by using and often altering existing elements of the environment in a way that surprises the target audience, appears to be a solution to the increasing clutter from the media. This study draws on the schema congruity theory to offer a better understanding of how consumers are processing information received from advertisements. Schemas are organized structures of knowledge and expectations that consumers develop in order to categorize the incoming information, and that they access every time they are experiencing a new situation. The schema-based approach is important in understanding consumer behavior because consumers are facing an environment filled with similar brands and products promoted by ads that sound and look alike. According to schema congruity theory information perceived as schema congruent offers a confortable feeling of familiarity and generates limited cognitive processing, whereas schema incongruent information generates surprise and triggers extensive cognitive processing in order to help individual make sense of the unusual situation. Taking into consideration the combination of the different levels of expectancy and relevancy there have been identified three congruency situations: extreme congruity, moderate incongruity and extreme incongruity. Existing research shows that moderate incongruent information offers the best results in recall and recognition and also the highest affect levels compared to extreme congruity and extreme incongruity. Based on evidence from literature this study attempts to position ambient advertising in the moderate incongruity category, thus theoretically proving the assumed effectiveness of this promotional tool. Therefore, this paper is a starting point in bringing the
Rybczyński, Józef
2011-02-01
This paper presents the results of computer simulation of bearing misalignment defects in a power turbogenerator. This malfunction is typical for great multi-rotor and multi-bearing rotating machines and very common in power turbo-sets. Necessary calculations were carried out by the computer code system MESWIR, developed and used at the IFFM in Gdansk for calculating dynamics of rotors supported on oil bearings. The results are presented in the form of a set of journal and bush trajectories of all turbo-set bearings. Our analysis focuses on the vibrational effects of displacing the two most vulnerable machine bearings in horizontal and vertical directions by the maximum acceptable range calculated with regard to bearing vibration criterion. This assumption required preliminary assessment of the maximum values for the permissible bearing dislocations. We show the relations between the attributes of the particular bearing trajectories and the bearing displacements in relation to their base design position. The shape and dimensions of bearing trajectories are interpreted based on the theory of hydrodynamic lubrication of oil bearings. It was shown that the relative journal trajectories and absolute bush trajectories carry much important information about the dynamic state of the machine, indicating also the way in which bearings are loaded. Therefore, trajectories can be a source of information about the position and direction of bearing misalignments. This article indicates the potential of using trajectory patterns for diagnosing misalignment defects in rotating machines and suggests including sets of trajectory patterns to the knowledge base of a machine diagnostic system.
Claudio Amovilli
2016-02-01
Full Text Available In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy.
Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel
The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.
Hanford Technical Basis for Multiple Dosimetry Effective Dose Methodology
Hill, Robin L.; Rathbone, Bruce A.
2010-08-01
The current method at Hanford for dealing with the results from multiple dosimeters worn during non-uniform irradiation is to use a compartmentalization method to calculate the effective dose (E). The method, as documented in the current version of Section 6.9.3 in the 'Hanford External Dosimetry Technical Basis Manual, PNL-MA-842,' is based on the compartmentalization method presented in the 1997 ANSI/HPS N13.41 standard, 'Criteria for Performing Multiple Dosimetry.' With the adoption of the ICRP 60 methodology in the 2007 revision to 10 CFR 835 came changes that have a direct affect on the compartmentalization method described in the 1997 ANSI/HPS N13.41 standard, and, thus, to the method used at Hanford. The ANSI/HPS N13.41 standard committee is in the process of updating the standard, but the changes to the standard have not yet been approved. And, the drafts of the revision of the standard tend to align more with ICRP 60 than with the changes specified in the 2007 revision to 10 CFR 835. Therefore, a revised method for calculating effective dose from non-uniform external irradiation using a compartmental method was developed using the tissue weighting factors and remainder organs specified in 10 CFR 835 (2007).
The results of LCAO DFT calculations of lattice parameters, cohesive energy and bulk modulus of the crystalline uranium nitrides UN, U2N3 and UN2 are presented and discussed. The LCAO computer codes Gaussian03 and Crystal06 are applied. The calculations are made with the uranium atom relativistic effective small core potential by Stuttgart-Cologne group (60 electrons in the core). The calculations include the U atom basis set optimization. Powell, Hooke-Jeeves, conjugated gradient and Box methods are implemented in the author's optimization package, being external to the codes for molecular and periodic calculations. The basis set optimization in LCAO calculations improves the agreement of the lattice parameter and bulk modulus of UN crystal with the experimental data, the change of the cohesive energy due to the optimization is small. The mixed metallic-covalent chemical bonding is found both in LCAO calculations of UN and U2N3 crystals; UN2 crystal has the semiconducting nature
Effective Mentoring in the Clinical Setting.
Shellenbarger, Teresa; Robb, Meigan
2016-04-01
This article is one in a series on the roles of adjunct clinical faculty and preceptors, who teach nursing students and new graduates to apply knowledge in clinical settings. This article describes mentoring strategies clinical instructors and preceptors can use to help ease novice nurses' transition to practice. PMID:27011145
Molecular Basis for Certain Neuroprotective Effects of Thyroid Hormone
Paul Davis
2011-10-01
Full Text Available The pathophysiology of brain damage that is common to ischemia-reperfusion inury and brain trauma includes disordered neuronal and glial cell energetics, intracellular acidosis, calcium toxicity, extracellular excitotoxic glutamate accumulation and dysfunction of the cytoskeleton and endoplasmic reticulum. Thyroid hormone isoforms, 3, 5, 3'-triiodo-L-thyronine (T3 and L-thyroxine (T4, have nongenomic and genomic actions that are relevant to repair of certain features of the pathophysiology of brain damage. Thyroid hormone can nongenomically repair intracullar H+ accumulation by stimulation of the Na+/H+ exchanger and can support desirably low [Ca2+]i.c. by activation of plasma membrane Ca2+-ATPase. Thyroid hormone nongenomically stimulates astrocyte glutamate uptake, an action that protects both glial cells and neurons. The hormone supports the integrity of the cytoskeleton by its effect on actin. Several proteins linked to thyroid hormone action are also neuroprotective. For example, the hormone stimulates expression of the seladin-1 gene whose gene product is anti-apoptotic and is potentially protection in the setting of neurodegeneration. Transthyretin (TTR is a serum transport protein for T4 that is important to blood-brain barrier transfer of the hormone and TTR has also been found to be neuroprotective in the setting of ischemia. Finally, the interesting thyronamine derivatives of T4 have been shown to protect against ischemic brain damage through their ability to induce hypothermia in the intact organism. Thus, thyroid hromone or hormone derivatives have experimental promise as neuroprotective agents.
Kupka, Teobald; Stachów, Michal; Kaminsky, Jakub; Sauer, Stephan P. A.
2013-01-01
A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2O, H2O, HF, F2, HCN, SiH4 and H2S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T) ), with affordable pcS-2 basis set and corresponding complete basis set results......, estimated from calculations with the family of polarizationconsistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and obtained with significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected...... set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS-2, MP2/pcS-2 and DFT/CBS calculations with pcS-n basis sets. The proposed method...
2010-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule...
Faber, Rasmus; Buczek, Aneta; Kupka, Teobald;
2016-01-01
The method and basis set dependence of zero-point vibrational corrections (ZPVC) to NMR shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree-Fock (HF), second-order Møller-Plesset perturbation theory (MP2......), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn-Sham density functional theory (DFT) with the B3LYP exchange-correlation functional methods in combination with the second order vibrational perturbation theory (VPT2......) approach for the vibrational corrections. As basis sets the correlation consistent basis sets cc-pVXZ, aug-ccpVXZ, cc-pCVXZ and aug-cc-pCVXZ with X = D, T, Q, 5, 6 and the polarization consistent basis sets aug-pc-n and aug-pcS-n with n = 1, 2, 3, 4 were employed. Our results show, that basis set...
Baranowska-Łączkowska, Angelika; Fernández, Berta
2014-01-30
In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto. PMID:24375320
Effects of Goal Setting on Performance and Job Satisfaction
Ivancevich, John M.
1976-01-01
Studied the effect of goal-setting training on the performance and job satisfaction of sales personnel. One group was trained in participative goal setting; one group was trained in assigned goal setting; and one group received no training. Both trained groups showed temporary improvements in performance and job satisfaction. For availability see…
The Griffin-Hill-Wheeler-Hartree-Fock equations are applied to generate universal gaussian and Slater-type basis sets for the title atoms. The results for the energies compare competitively with atom-optimized calculations at a very low computational cost. (author)
Accurate Gaussian basis sets (18s for Li and Be and 20s11p for the atoms from B to Ne) for the first-row atoms, generated with an improved generator coordinate Hartree-Fock method, were contracted and enriched with polarization functions. These basis sets were tested for B2, C2, BeO, Cn-, LiF, N2, CO, BF, NO+, O2, and F2. At the Hartree-Fock (HP), second-order Moeller-Plesset (MP2), fourth-order Moeller-Plesset (MP4), and density functional theory (DFT) levels, the dipole moments, bond lengths, and harmonic vibrational frequencies were studied, and at the MP2, MP4, and DFT levels, the dissociation energies were evaluated and compared with the corresponding experimental values and with values obtained using other contracted Gaussian basis sets and numerical HF calculations. For all diatomic molecules studied, the differences between the total energies, obtained with the largest contracted basis set [6s5p3d1f], and those calculated with the numerical HF methods were always less than 3.2 mhartree
A. Brouwer; M. Hoogendoorn; E. Naarding
2015-01-01
In this paper we evaluate the International Accounting Standards Board’s (IASB) efforts, in a discussion paper (DP) of 2013, to develop a new conceptual framework (CF) in the light of its stated ambition to establish a robust and consistent basis for future standard setting, thereby guiding standard
Brandbyge, Mads
2014-01-01
In a recent paper Reuter and Harrison [J. Chem. Phys.139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current...
The Effects of Goal Setting on Rugby Performance
Mellalieu, Stephen D.; Hanton, Sheldon; O'Brien, Michael
2006-01-01
Goal-setting effects on selected performance behaviors of 5 collegiate rugby players were assessed over an entire competitive season using self-generated targets and goal-attainment scaling. Results suggest that goal setting was effective for enhancing task-specific on-field behavior in rugby union.
The Effects of Goal Setting on Rugby Performance
Mellalieu, Stephen D.; Hanton, Sheldon; O'Brien, Michael
2006-01-01
Goal-setting effects on selected performance behaviors of 5 collegiate rugby players were assessed over an entire competitive season using self-generated targets and goal-attainment scaling. Results suggest that goal setting was effective for enhancing task-specific on-field behavior in rugby union. (Contains 1 figure.)
Transformations on Data Sets and Their Effects on Descriptive Statistics
Fox, Thomas B.
2005-01-01
The activity asks students to examine the effects on the descriptive statistics of a data set that has undergone either a translation or a scale change. They make conjectures relative to the effects on the statistics of a transformation on a data set and then they defend their conjectures and deductively verify several of them.
Oono, Shuhei; Hatsugai, Yasuhiro
2016-01-01
We have characterized robust propagation modes of electromagnetic waves in helical structures by the section Chern number that is defined for two-dimensional (2D) section of the three-dimensional (3D) Brillouin zone. The Weyl point in the photonic bands is associated with a discontinuous jump of the section Chern number. A spatially localized gaussian basis set is used to calculate the section Chern numbers where we have implemented the divergence-free condition on the each basis function in 3D. Validity of the bulk-edge correspondence in a 3D photonic crystal is discussed in relation to the broken inversion symmetry.
Theoretical basis of the community effect in development
Kuttler Celine
2011-04-01
Full Text Available Abstract Background Genetically identical cells often show significant variation in gene expression profile and behaviour even in the same physiological condition. Notably, embryonic cells destined to the same tissue maintain a uniform transcriptional regulatory state and form a homogeneous cell group. One mechanism to keep the homogeneity within embryonic tissues is the so-called community effect in animal development. The community effect is an interaction among a group of many nearby precursor cells, and is necessary for them to maintain tissue-specific gene expression and differentiate in a coordinated manner. Although it has been shown that the cell-cell communication by a diffusible factor plays a crucial role, it is not immediately obvious why a community effect needs many cells. Results In this work, we propose a model of the community effect in development, which consists in a linear gene cascade and cell-cell communication. We examined the properties of the model theoretically using a combination of stochastic and deterministic modelling methods. We have derived the analytical formula for the threshold size of a cell population that is necessary for a community effect, which is in good agreement with stochastic simulation results. Conclusions Our theoretical analysis indicates that a simple model with a linear gene cascade and cell-cell communication is sufficient to reproduce the community effect in development. The model explains why a community needs many cells. It suggests that the community's long-term behaviour is independent of the initial induction level, although the initiation of a community effect requires a sufficient amount of inducing signal. The mechanism of the community effect revealed by our theoretical analysis is analogous to that of quorum sensing in bacteria. The community effect may underlie the size control in animal development and also the genesis of autosomal dominant diseases including tumorigenesis.
Development of neural basis for chinese orthographic neighborhood size effect.
Zhao, Jing; Li, Qing-Lin; Ding, Guo-Sheng; Bi, Hong-Yan
2016-02-01
The brain activity of orthographic neighborhood size (N size) effect in Chinese character naming has been studied in adults, meanwhile behavioral studies have revealed a developmental trend of Chinese N-size effect in developing readers. However, it is unclear whether and how the neural mechanism of N-size effect changes in Chinese children along with development. Here we address this issue using functional magnetic resonance imaging. Forty-four students from the 3(rd) , 5(th) , and 7(th) grades were scanned during silent naming of Chinese characters. After scanning, all participants took part in an overt naming test outside the scanner, and results of the naming task showed that the 3(rd) graders named characters from large neighborhoods faster than those from small neighborhoods, revealing a facilitatory N-size effect; the 5(th) graders showed null N-size effect while the 7(th) graders showed an inhibitory N-size effect. Neuroimaging results revealed that only the 3(rd) graders exhibited a significant N-size effect in the left middle occipital activity, with greater activation for large N-size characters. Results of 5(th) and 7(th) graders showed significant N-size effects in the left middle frontal gyrus, in which 5(th) graders induced greater activation in large N-size condition than in small N-size condition, while 7(th) graders exhibited an opposite effect which was similar to the adult pattern reported in a previous study. The current findings suggested the transition from broadly tuned to finely tuned orthographic representation with reading development, and the inhibition from neighbors' phonology for higher graders. Hum Brain Mapp 37:632-647, 2016. © 2015 Wiley Periodicals, Inc. PMID:26777875
Migration and the Wage-Settings Curve:Reassessing the Labor Market Effects of Migration
Brücker, Herbert; Jahn, Elke
2008-01-01
Germany on basis of a wage-setting curve. The wage-setting curve relies on the assumption that wages respond to a hange in the unemployment rate, albeit imperfectly. This allows one to derive the wage and employment effects of migration simultaneously in a general equilibrium framework. Using administrative micro data we find that the elasticity of the wage-setting curve is particularly high for young workers and workers with an university degree, while it is low for older workers and workers...
A new technique that can efficiently approximate the attracting set of a nonlinear dynamical system is proposed under the framework of point mapping with the cell reference method. With the aid of the approximated attracting set, the difficulties encountered by the PIM-triple method and bisection procedure in finding trajectories on the stable manifolds of chaotic saddles in basins of attraction and on basin boundaries can be overcome well. On the basis of this development, an effective method to determine saddle-type invariant limit sets of nonlinear dynamical systems can be devised. Examples are presented for the purposes of illustration and to demonstrate the capabilities of the proposed method. (general)
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge
2015-07-21
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms. PMID:26203010
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.; Vargas, Rubicelia; Garza, Jorge
2015-07-01
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.
Policies for Effective Risk Management Performance through Goal Setting
L.S. Chien; B.B. Schweig; Yu, P L
1989-01-01
The organizational behavior and management science literature dealing with multiple criteria decision making, suggests that making policies for effective risk management performance through goal setting can in theory be treated as setting-up a complex multiple criteria optimal control system in which the control variables are (1) selecting a set of measurable goals (2) determining goal achievement levels and (3) constructing supportive systems; and the objectives are (i) to maximize time allo...
Sure, Rebecca; Brandenburg, Jan Gerit
2015-01-01
Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221
Insulin glargine: pharmacokinetic and pharmacodynamic basis of clinical effect
Vadim Valeryevich Klimontov
2014-10-01
Full Text Available Glargine became the first long-acting insulin analogue. Glargine was designed to meet basal insulin requirements throughout the day with a single injection. Pharmacokinetics of insulin glargine is characterized by biotransformation into metabolites M1 and M2 that transforms the B chain of glargine so it is similar to the B chain of human insulin. Plasma concentrations of active M1 and M2 metabolites have no pronounced peaks during the day, resulting in lower glucose variability and hypoglycaemia risk when compared with NPH insulin. The metabolic activities of M1 and M2 metabolites are similar to the effect of glargine, whereas the mitogenic effects of these metabolites do not exceed the effect of human insulin. Insulin glargine shows a higher affinity for the insulin-like growth factor-1 (IGF-1 receptor when compared with human insulin. Glargine has no proliferative effect in vivo owing to its rapid conversion into metabolites. Pharmacokinetic and pharmacodynamic variability of glargine is comparable to other insulins. These characteristics are important for the clinical efficacy and safety of glargine.
Petersson, George A; Malick, David K; Frisch, Michael J; Braunstein, Matthew
2006-07-28
Examination of the convergence of full valence complete active space self-consistent-field configuration interaction including all single and double excitation (CASSCF-CISD) energies with expansion of the one-electron basis set reveals a pattern very similar to the convergence of single determinant energies. Calculations on the lowest four singlet states and the lowest four triplet states of N(2) with the sequence of n-tuple-zeta augmented polarized (nZaP) basis sets (n=2, 3, 4, 5, and 6) are used to establish the complete basis set limits. Full configuration-interaction (CI) and core electron contributions must be included for very accurate potential energy surfaces. However, a simple extrapolation scheme that has no adjustable parameters and requires nothing more demanding than CAS(10e(-),8orb)-CISD/3ZaP calculations gives the R(e), omega(e), omega(e)X(e), T(e), and D(e) for these eight states with rms errors of 0.0006 Angstrom, 4.43 cm(-1), 0.35 cm(-1), 0.063 eV, and 0.018 eV, respectively. PMID:16942134
Self-Reinforcement Effects: An Artifact of Social Standard Setting?
Hayes, Steven C.
1985-01-01
Two studies involving college students examined mechanisms responsible for observed self-reinforcement effects. Results seemed to support the view that self-reinforcement procedures work by setting a socially available standard against which performance can be evaluated. (CL)
Knote, C. J.; Hodzic, A.; Aumont, B.; Madronich, S.
2014-12-01
Traditional understanding views secondary organic aerosol (SOA) formation in the atmosphere as continuous gas-phase oxidation of precursors such as isoprene, aromatics or alkanes. Recent research found that these oxidation products are also highly water soluble. It is further understood that the liquid-phase of cloud droplets as well as deliquesced particles could mediate SOA formation through chemistry in the aqueous-phase. While the effect of multi-phase processing has been studied in detailed for specific compounds like glyoxal or methylglyoxal, an integrated approach that considers the large number of individual compounds has been missing due to the complexity involved. In our work we explore the effects of multi-phase processing on secondary organic aerosol from an explicit modeling perspective.Volatility and solubility determine in which phase a given molecule will be found under given atmospheric conditions. Volatility has already been used to simplify the description of SOA formation in the gas-phase in what became known as the Volatility Basis Set approach (VBS). Compounds contributing to SOA formation are grouped by volatility and then treated as a whole. A number of studies extended the VBS by adding a second dimension like oxygen to carbon ratio or the mean oxidation state. In our work we use functional groups as second dimension.Using explicit oxidation chemistry modeling (GECKO-A) we derive SOA yields as well as their composition in terms of functional groups for commonly used precursors. We then investigate the effect of simply partitioning functional-group specific organic mass into cloud droplets and deliquesced aerosol based on their estimated solubility. Finally we apply simple chemistry in the aqueous-phase and relate changes in functional groups to changes in volatility and subsequent changes in partitioning between gas- and aerosol-phase.In our presentation we will explore the sensitivites of the multi-phase system in a box model setting with
Cholinergic basis of memory improving effect of Ocimum tenuiflorum linn
Joshi H
2006-01-01
Full Text Available Dementia is one of the age-related mental problems and a characteristic symptom of Alzheimer′s disease. Nootropic agents are used in situations where there is organic disorder in learning abilities. The present work was undertaken to assess the potential of Ocimum tenuiflorum Linn. as a nootropic and anticholinesterase agent in mice. Ethanol extract of dried whole plant of O. tenuiflorum Linn. ameliorated the amnesic effect of scopolamine (0.4 mg/kg and aging-induced memory deficits in mice. Passive avoidance paradigm served as the exteroceptive behavioural model. O. tenuiflorum extract increased step-down latency and acetyl cholinesterase inhibition significantly. Hence, O. tenuiflorum can be employed in the treatment of cognitive disorders such as dementia and Alzheimer′s disease.
Evarestov, R A; Losev, M V
2009-12-01
For the first time the convergence of the phonon frequencies and dispersion curves in terms of the supercell size is studied in ab initio frozen phonon calculations on LiF crystal. Helmann-Feynman forces over atomic displacements are found in all-electron calculations with the localized atomic functions (LCAO) basis using CRYSTAL06 program. The Parlinski-Li-Kawazoe method and FROPHO program are used to calculate the dynamical matrix and phonon frequencies of the supercells. For fcc lattice, it is demonstrated that use of the full supercell space group (including the supercell inner translations) enables to reduce essentially the number of the displacements under consideration. For Hartree-Fock (HF), PBE and hybrid PBE0, B3LYP, and B3PW exchange-correlation functionals the atomic basis set optimization is performed. The supercells up to 216 atoms (3 x 3 x 3 conventional unit cells) are considered. The phonon frequencies using the supercells of different size and shape are compared. For the commensurate with supercell k-points the best agreement of the theoretical results with the experimental data is found for B3PW exchange-correlation functional calculations with the optimized basis set. The phonon frequencies at the most non-commensurate k-points converged for the supercell consisting of 4 x 4 x 4 primitive cells and ensures the accuracy 1-2% in the thermodynamic properties calculated (the Helmholtz free energy, entropy, and heat capacity at the room temperature). PMID:19382176
Roehle, I.
1999-11-01
A Doppler Global Velocimeter was set up in the frame of a PhD thesis. This velocimeter is optimized to carry out high accuracy, three component, time averaged planar velocity measurements. The anemometer was successfully applied to wind tunnel and test rig flows, and the measurement accuracy was investigated. A volumetric data-set of the flow field inside an industrial combustion chamber was measured. This data field contained about 400.000 vectors. DGV measurements in the intake of a jet engine model were carried out applying a fibre bundle boroskope. The flow structure of the wake of a car model in a wind tunnel was investigated. The measurement accuracy of the DGV-System is {+-}0.5 m/s when operated under ideal conditions. This study can serve as a basis to evaluate the use of DGV for aerodynamic development experiments. (orig.) [German] Im Rahmen der Dissertation wurde ein auf hohe Messgenauigkeit optimiertes DGV-Geraet fuer zeitlich gemittelte Drei-Komponenten-Geschwindigkeitsmessungen entwickelt und gebaut, an Laborstroemungen, an Teststaenden und an Windkanaelen erfolgreich eingesetzt und das Potential der Messtechnik, insbesondere im Hinblick auf Messgenauigkeit, untersucht. Im Fall einer industriellen Brennkammer konnte ein Volumen-Datensatz des Stroemungsfeldes erstellt werden, dessen Umfang bei ca. 400.000 Vektoren lag. Es wurden DGV-Messungen mittels eines flexiblen Endoskops auf Basis eines Faserbuendels durchgefuehrt und damit die Stroemung in einem Flugzeugeinlauf vermessen. Es wurden DGV-Messungen im Nachlauf eines PKW-Modells in einem Windkanal durchgefuehrt. Die Messgenauigkeit des erstellten DGV-Systems betraegt unter Idealbedingungen {+-}0,5 m/s. Durch die Arbeit wurde eine Basis zur Beurteilung des Nutzens der DGV-Technik fuer aerodynamische Entwicklungsarbeiten geschaffen. (orig.)
Unintended effects in settings-based health promotion.
Mittelmark, Maurice B
2014-11-01
The settings-based approach to health promotion (HP) employs a social ecological (SE) framework to integrate HP into the usual activities of the setting and to increase the setting's support for healthy choices. The SE approach calls for systems thinking to account for the inextricable relationship between people, their behaviour and their environment. Knowledge about a setting can be used to mobilise people to participate in HP, to optimise success by taking into account the local context, and to anticipate and avoid barriers to success. In other words, the SE approach aims to help HP reach its goals for better health, established in concert with community needs and wishes. Yet, the focus on HP goals may detract attention from how intervention may have unanticipated, and even untoward effects on the setting. There is much evidence from classical ecological research that well-meaning interventions have unintended effects. Biology is so tuned to the possibility that the study of unintended effects is integral to the field. There is some evidence--but much less--that HP also has unexpected, deleterious effects. The evidence is limited because of neglect; the subject of unintended effects is only of peripheral interest in HP. This is a call for a more robust SE approach, in which frameworks used to guide settings-based HP are augmented so as to be concerned with planned effects, and also unplanned effects. What can be done to more responsibly monitor, document and report the full panoply of our effects, including detecting and preventing untoward effects? PMID:25416569
Effect of cluster sets on plyometric jump power.
Moreno, Steven D; Brown, Lee E; Coburn, Jared W; Judelson, Daniel A
2014-09-01
Cluster sets may lead to enhanced power (PW) production by allowing for partial recovery. The purpose of this study was to determine the effects of cluster sets vs. traditional sets on plyometric jump PW, ground reaction force, take-off velocity (TOV), and jump height (JH). Twenty-six recreationally trained college men completed 3 testing sessions, which involved performing repeated body-weight (BW) plyometric squat jumps across 3 different set configurations: traditional (2 sets of 10 with 90-second rest between sets), cluster 1 (4 sets of 5 with 30-second rest between sets), and cluster 2 (10 sets of 2 with 10-second rest between sets). Ground reaction force results demonstrated no interaction or main effect for condition, but there was a significant (p ≤ 0.05) main effect for repetition, where repetition 1 was significantly less than repetitions 3-5, 7-10, 12-15, and 17-20. For TOV, PW, and JH, there were significant interactions. Take-off velocity resulted in the following: Traditional, repetition 1 was significantly greater than repetitions 7-10 and 17-20, but was significantly less than repetition 13; cluster 1, repetition 1 was significantly less than repetitions 2-5; and cluster 2, there were no significant differences. Power resulted in the following: Traditional, repetition 1 was significantly greater than repetitions 4-10 and 14-20; cluster 1, repetition 1 was significantly greater than repetitions 7-10 and 12-20; and cluster 2, repetition 1 was significantly greater than repetitions 3, 6-18, and 20. Jump height resulted in the following: Traditional, repetition 1 was significantly greater than repetitions 18-20, but was significantly less than repetitions 3 and 13. For cluster 1 and cluster 2, there were no significant differences. These results demonstrate that cluster sets, specifically 10 sets of 2, allow for a greater maintenance of PW, TOV, and JH compared with a traditional 2 sets of 10 when performing repeated BW plyometric squat jumps. A lack
Rangel, Tonatiuh; Genovese, Luigi; Torrent, Marc
2016-01-01
We present a Projector Augmented-Wave~(PAW) method based on a wavelet basis set. We implemented our wavelet-PAW method as a PAW library in the ABINIT package [http://www.abinit.org] and into BigDFT [http://www.bigdft.org]. We test our implementation in prototypical systems to illustrate the potential usage of our code. By using the wavelet-PAW method, we can simulate charged and special boundary condition systems with frozen-core all-electron precision. Furthermore, our work paves the way to large-scale and potentially order-N simulations within a PAW method.
A self-consistent version of the discrete variational method is described based on the use of numerical LCAO basis functions obtained as solutions of the Hartree-Fock equations for free atoms. Sets of single-zeta Slater function are applied to approximate atomic densities further employed in the calculations of the Coulomb potential. The computer programs realizing this approach have been written and utilized to calculated electronic structures of molybdenum, tungsten and uranium hexafluorides. The ionization potentials calculated are in good quantitative agreement with experimental data. The deviations of the calculated valence state IP's from those determined by photoelectron spectroscopy do not exceed 1 eV. (orig.)
M Talebian; E Talebian; A Abdi
2012-05-01
We obtained an approximation of the force ﬁeld of -quartz crystal using a new idea of applying density functional theory [J Purton, R Jones, C R A Catlow and M Leslie, Phys. Chem. Minerals 19, 392 (1993)]. Our calculations were based on B3LYP Hamiltonian [A N Lazarev and A P Mirgorodsky, Phys. Chem. Minerals 18, 231 (1991)] in 6−311+G(2d) basis set for H16Si7O6 cluster and included a unit cell of the lattice. The advantage of our method is the increase in the speed of calculations and the better adaption of simulation results with the experimental data.
Balabanov, Nikolai B.; Peterson, Kirk A.
2006-08-01
Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.
Core excitation effects in halo nuclei using a transformed oscillator basis
A recent generalization of the Transformed Harmonic Oscillator basis, intended to consider core excitations in the structure of one nucleon halo nuclei, is applied to the break up of 11Be. The reaction studied is 11Be+208Pb at 69 MeV/nucleon. The experimental set up is designed to ensure pure dipole Coulomb excitations. Making use of the Equivalent Photon Method and the electromagnetic transition probabilities obtained with the transformed oscillator basis, a relevant contribution of the quadrupole excitations of the core is found. The inclusion of core excitations is, therefore, necessary for the correct extraction of the dipole electromagnetic transition probability of halo nuclei.
Zarycz, Natalia; Provasi, Patricio F; Pagola, Gabriel I; Ferraro, Marta B; Pelloni, Stefano; Lazzeretti, Paolo
2016-06-30
In the presence of a static, nonhomogeneous magnetic field, represented by the axial vector B at the origin of the coordinate system and by the polar vector C=∇×B, assumed to be spatially uniform, the chiral molecules investigated in this paper carry an orbital electronic anapole, described by the polar vector A. The electronic interaction energy of these molecules in nonordered media is a cross term, coupling B and C via a¯, one third of the trace of the anapole magnetizability aαβ tensor, that is, WBC=-a¯B·C. Both A and W(BC) have opposite sign in the two enantiomeric forms, a fact quite remarkable from the conceptual point of view. The magnitude of a¯ predicted in the present computational investigation for five chiral molecules is very small and significantly biased by electron correlation contributions, estimated at the density functional level via three different functionals. © 2016 Wiley Periodicals, Inc. PMID:27010603
Basis set effects on the energy and hardness profiles of the hydrogen fluoride dimer
Miquel Torrent-Sucarrat; Miquel Duran; Josep M Luis; Miquel Solà
2005-09-01
In earlier work, the present authors have shown that hardness profiles are less dependent on the level of calculation than energy profiles for potential energy surfaces (PESs) having pathological behaviors. At variance with energy profiles, hardness profiles always show the correct number of stationary points. This characteristic has been used to indicate the existence of spurious stationary points on the PESs. In the present work, we apply this methodology to the hydrogen fluoride dimer, a classical difficult case for the density functional theory methods.
Effect of transporting saltstone samples prior to set
The Saltstone Sampling and Analyses Plan provides a basis for the quantity (and configuration) of saltstone grout samples required for conducting a study directed towards correlation of the Performance Assessment (PA) related properties of field-emplaced samples and samples processed and cured in the laboratory. The testing described in the saltstone sampling and analyses plan will be addressed in phases. The initial testing (Phase I) includes collecting samples from the process room in the Saltstone Production Facility (SPF) and transporting them to Savannah River National Laboratory (SRNL) where they will cure under a temperature profile that mimics the temperature in the Saltstone Disposal Unit (SDU) and then be analyzed. SRNL has previously recommended that after the samples of fresh (uncured) saltstone are obtained from the SPF process room, they are allowed to set prior to transporting them to SRNL for curing. The concern was that if the samples are transported before they are set, the vibrations during transport may cause artificial delay of structure development which could result in preferential settling or segregation of the saltstone slurry. However, the results of this testing showed there was no clear distinction between the densities of the cylinder sections for any of the transportation scenarios tested (1 day, 1 hour, and 0 minutes set time prefer to transportation). The bottom section of each cylinder was the densest for each transportation scenario, which indicates some settling in all the samples. Triplicate hydraulic conductivity measurements on samples from each set of time and transportation scenarios indicated that those samples transported immediately after pouring had the highest hydraulic conductivity. Conversely, samples that were allowed to sit for an hour before being transported had the lowest hydraulic conductivity. However, the hydraulic conductivities of all three samples fell within an acceptable range. Based on the cured property
Schmitz, G. J.
2016-01-01
The importance of microstructure simulation in integrated computational materials engineering settings in relation to the added value provided for macroscopic process simulation, as well as the contribution this kind of simulation can make in predicting material properties, are discussed. The roles of microstructure simulation in integrating scales ranging from component/process scales down to atomistic scales, and also in integrating experimental and virtual worlds, are highlighted. The hierarchical data format (HDF5) as a basis for enhancing the interoperability of the heterogeneous range of simulation tools and experimental datasets in the area of computational materials engineering is discussed. Several ongoing developments indicate that HDF5 might evolve into a de facto standard for digital microstructure representation of all length scales.
Alam, Aftab; Johnson, D. D.
2009-09-01
Site-centered, electronic-structure methods use an expansion inside nonoverlapping “muffin-tin” (MT) spheres plus an interstitial basis set. As the boundary separating the more spherical from nonspherical density between atoms, the “saddle-point” radii (SPR) in the density provide an optimal spherical region for expanding in spherical harmonics, as used in augmented plane wave, muffin-tin orbital, and multiple-scattering [Korringa, Kohn, and Rostoker (KKR)] methods. These MT-SPR guarantee unique, convex Voronoi polyhedra at each site, in distinction to Bader topological cells. We present a numerically fast, two-center expansion to find SPR a priori from overlapping atomic charge densities, valid also for disordered alloys. We adopt this MT-SPR basis for KKR in the atomic sphere approximation and study (dis)ordered alloys with large differences in atomic size (fcc CoPt and bcc CrW). For this simple and unique improvement, we find formation energies and structural parameters in strikingly better agreement with more exact methods or experiment, and resolve issues with former results.
We present the self-consistent numerical-basis-set linear combination of atomic orbitals (LCAO) discrete variational method for treating the electronic structure of thin films. As in the case of bulk solids, this method provides for thin films accurate solutions of the one-particle local density equations with a non-muffin-tin potential. Hamiltonian and overlap matrix elements are evaluated accurately by means of a three-dimensional numerical Diophantine integration scheme. Application of this method is made to the self-consistent solution of one-, three-, and five-layer Ni(001) unsupported films. The LCAO Bloch basis set consists of valence orbitals (3d, 4s, and 4p states for transition metals) orthogonalized to the frozen-core wave functions. The self-consistent potential is obtained iteratively within the superposition of overlapping spherical atomic charge density model with the atomic configurations treated as adjustable parameters. Thus the crystal Coulomb potential is constructed as a superposition of overlapping spherically symmetric atomic potentials and, correspondingly, the local density Kohn-Sham (α = 2/3) potential is determined from a superposition of atomic charge densities. At each iteration in the self-consistency procedure, the crystal charge density is evaluated using a sampling of 15 independent k points in (1/8)th of the irreducible two-dimensional Brillouin zone. The total density of states (DOS) and projected local DOS (by layer plane) are calculated using an analytic linear energy triangle method (presented as an Appendix) generalized from the tetrahedron scheme for bulk systems. Distinct differences are obtained between the surface and central plane local DOS. The central plane DOS is found to converge rapidly to the DOS of bulk paramagnetic Ni obtained by Wang and Callaway. Only a very small surplus charge (0.03 electron/atom) is found on the surface planes, in agreement with jellium model calculations
Li, Y. Q.; Ma, F. C.; Sun, M. T.
2013-10-01
A full three-dimensional global potential energy surface is reported first time for the title system, which is important for the photodissociation processes. It is obtained using double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. Such a work can be recommended for dynamics studies of the N(2D) + H2 reaction, a reliable theoretical treatment of the photodissociation dynamics and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen containing systems. In turn, a preliminary theoretical study of the reaction N(^2D)+H_2(X^1Σ _g^+)(ν =0,j=0)rArr NH(a^1Δ )+H(^2S) has been carried out with the method of quasi-classical trajectory on the new potential energy surface. Integral cross sections and thermal rate constants have been calculated, providing perhaps the most reliable estimate of the integral cross sections and the rate constants known thus far for such a reaction.
Augmented quasiparticle (QP) mappings, as applied to indistinguishable point sets of (Liouvillian) democratic-recoupled (DR) tensors, provide for a 1:1 invariant labelling of the underlying (disjoint) dual projective map carrier subspaces, where the Liouville pattern basis set is defined via superboson unit-tensor actions on a null space, | )). The co-operative-action Liouville algebras described here imply parallel limitations to Jucys graph recoupling and its related Racah-Wigner (R-W) algebras once DR indistinguishable point tensorial sets are involved, as in non-SR Sn,n>=4 dominant (NMR) spin symmetry. The importance of Sn G-invariants, as labels for disjoint carrier subspaces in such automorphic spin symmetries, arises from their essential role in defining the quantal-completeness of indistinguishable point sets. From the established properties of augmented-QPs as super-bosons (Temme 2002 Int. J. Quantum Chem. 89 429) (i.e., beyond the earlier Hilbert-space-based Louck and Biedenharn boson pattern views), insight into Atiyah and Sutcliffe's (A-S) assertions (Atiyah and Sutcliffe 2002 Proc. R. Soc. A 458 1089) on the limitations of graph recoupling theory to distinct point sets is obtained. This clarifies the wider analytic intractible of automorphic DR spin systems-beyond the Levi-Civita cyclic-commutation (R-W) approach (Levy-Leblond and Levy-Nahas 1965 J. Math. Phys. 6 1372) which holds for a mono-invariant problem. For (rotating-frame) density matrix approaches to [A]n, [A]n(X) and [AX]n(SU(2) x Sn) (dual) NMR systems, the focus is necessarily on the specialized nature of indistinguishable point sets within multiple invariant-theoretic-based, dynamical spin physics. Here, the GI(s) (GI-cardinality) constitute an important part of the dual irrep set, {Dk(U-tilde) x Γ-tilde[λ](v-tilde)(P)}, with combinatorics, as a central facet of invariant theory, playing a crucial role in the concept of 'quantal completeness' and the impact of A-S's assertion on the
Rakhimyanov, Kh M.; Rakhimyanov, K. Kh; Rakhimyanov, A. Kh; Kutyshkin, A. V.
2016-04-01
This paper considers the issues of setting the modes of thermal and deformation effects in the basic schemes at combined hardening and finishing operations. On the basis of solving the thermal physical problem of material high rate heating, the parameters of a thermohardened layer were determined within the range of the investigated modes. An algorithm for setting the mode parameters of high rate heating responsible for the hardening effect at the combined processing was proposed. The analysis of the mathematical model for forming a surface microrelief at ultrasonic deformation showed that the sizes, the form of fragments and the density of a microrelief were determined by the processing kinematic parameters. An algorithm for setting the rotation speed and feeding at ultrasonic deformation according to microrelief characteristics was developed. The conditions to form a completely regular microrelief on the processed surface that represent the ratio between a single imprint diameter at the ultrasonic deformation and the processing kinematic parameters were determined. The complex of the algorithms suggested for setting the mode parameters of high rate heating and ultrasonic deformation constitutes the techniques for setting the modes of combined hardening and finishing operations.
Molecular basis of the mutagenic and lethal effects of ultraviolet irradiation
Using bacteria as a model, the molecular basis of the mutagenic and lethal effects of uv radiation is being studied. Attention is focused on the mechanism of action of uv-1 specific endonucleases in the repair of damaged DNA. The isolation and identification of similar enzymes in human cells are being conducted concurrently
Genetic basis and detection of unintended effects in genetically modified crop plants
Ladics, Gregory S.; Bartholomaeus, Andrew; Bregitzer, Phil; Doerrer, Nancy G.; Gray, Alan; Holzhauser, Thomas; Jordan, Mark; Keese, Paul; Kok, Esther; Macdonald, Phil; Parrott, Wayne; Privalle, Laura; Raybould, Alan; Rhee, Seung Yon; Rice, Elena
2015-01-01
In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled “Genetic Basis of Unintended Effects in Modified Plants” was held in Ottawa, Canada, bringing together over 75 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects ...
Richard, Ryan M; Marshall, Michael S; Dolgounitcheva, O; Ortiz, J V; Brédas, Jean-Luc; Marom, Noa; Sherrill, C David
2016-02-01
In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates. PMID:26731487
Lee, Hee-Seung; Tuckerman, Mark E
2008-12-14
An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer. PMID:19071908
A. P. Tsimpidi
2010-01-01
Full Text Available New primary and secondary organic aerosol modules have been added to PMCAMx, a three dimensional chemical transport model (CTM, for use with the SAPRC99 chemistry mechanism based on recent smog chamber studies. The new modelling framework is based on the volatility basis-set approach: both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. This new framework with the use of the new volatility basis parameters for low-NO_{x} and high-NO_{x} conditions tends to predict 4–6 times higher anthropogenic SOA concentrations than those predicted with the older generation of models. The resulting PMCAMx-2008 was applied in Mexico City Metropolitan Area (MCMA for approximately a week during April 2003 during a period of very low regional biomass burning impact. The emission inventory, which uses as a starting point the MCMA 2004 official inventory, is modified and the primary organic aerosol (POA emissions are distributed by volatility based on dilution experiments. The predicted organic aerosol (OA concentrations peak in the center of Mexico City, reaching values above 40 μg m^{−3}. The model predictions are compared with the results of the Positive Matrix Factorization (PMF analysis of the Aerosol Mass Spectrometry (AMS observations. The model reproduces both Hydrocarbon-like Organic Aerosol (HOA and Oxygenated Organic Aerosol (OOA concentrations and diurnal profiles. The small OA underprediction during the rush-hour periods and overprediction in the afternoon suggest potential improvements to the description of fresh primary organic emissions and the formation of the oxygenated organic aerosols, respectively, although they may also be due to errors in the simulation of dispersion and vertical mixing. However, the AMS OOA data are not specific enough to prove that the model reproduces the organic aerosol
Manion, Jo
2004-01-01
One of the most significant challenges facing any health care leader today is that of building commitment among followers. The last decade, with its tumultuous changes in our organizations, left many employees emotionally detached from their workplace. Mistrust, increasing cynicism, escalating financial pressures, and continuing challenges adversely impact our workforce's organizational commitment. The author explores the concept of commitment, which can serve as a basis for developing practical effective retention strategies. PMID:15192998
Tsimpidi, A. P.; Karydis, V. A.; Pandis, S. N.; Zavala, M.; Lei, W.; Molina, L. T.
2007-12-01
Anthropogenic air pollution is an increasingly serious problem for public health, agriculture, and global climate. Organic material (OM) contributes ~ 20-50% to the total fine aerosol mass at continental mid-latitudes. Although OM accounts for a large fraction of PM2.5 concentration worldwide, the contributions of primary and secondary organic aerosol have been difficult to quantify. In this study, new primary and secondary organic aerosol modules were added to PMCAMx, a three dimensional chemical transport model (Gaydos et al., 2007), for use with the SAPRC99 chemistry mechanism (Carter, 2000; ENVIRON, 2006) based on recent smog chamber studies (Robinson et al., 2007). The new modeling framework is based on the volatility basis-set approach (Lane et al., 2007): both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The emission inventory, which uses as starting point the MCMA 2004 official inventory (CAM, 2006), is modified and the primary organic aerosol (POA) emissions are distributed by volatility based on dilution experiments (Robinson et al., 2007). Sensitivity tests where POA is considered as nonvolatile and POA and SOA as chemically reactive are also described. In all cases PMCAMx is applied in the Mexico City Metropolitan Area during March 2006. The modeling domain covers a 180x180x6 km region in the MCMA with 3x3 km grid resolution. The model predictions are compared with Aerodyne's Aerosol Mass Spectrometry (AMS) observations from the MILAGRO Campaign. References Robinson, A. L.; Donahue, N. M.; Shrivastava, M. K.; Weitkamp, E. A.; Sage, A. M.; Grieshop, A. P.; Lane, T. E.; Pandis, S. N.; Pierce, J. R., 2007. Rethinking organic aerosols: semivolatile emissions and photochemical aging. Science 315, 1259-1262. Gaydos, T. M.; Pinder, R. W.; Koo, B.; Fahey, K. M.; Pandis, S. N., 2007. Development and application of a three- dimensional aerosol
Q. J. Zhang
2012-11-01
Full Text Available Results of the chemistry transport model CHIMERE are compared with the measurements performed during the MEGAPOLI summer campaign in the Greater Paris Region in July, 2009. The Volatility-Basis-Set approach (VBS is implemented into this model, taking into account the volatility of primary organic aerosol (POA and the chemical aging of semi-volatile organic species. Organic aerosol is the main focus and is simulated with three different configurations related to the volatility of POA and the scheme of secondary organic aerosol (SOA formation. In addition, two types of emission inventories are used as model input in order to test the uncertainty related to the emissions. Predictions of basic meteorological parameters and primary and secondary pollutant concentrations are evaluated and four pollution regimes according to the air mass origin are defined. Primary pollutants are generally overestimated, while ozone is consistent with observations. Sulfate is generally overestimated, while ammonium and nitrate levels are well simulated with the refined emission data set. As expected, the simulation with non-volatile POA and a single-step SOA formation mechanism largely overestimates POA and underestimates SOA. Simulation of organic aerosol with the VBS approach taking into account the aging of semi-volatile organic compounds (SVOC shows the best correlation with measurements. All observed high concentration events are reproduced by the model mostly after long range transport, indicating that long range transport of SOA to Paris is well reproduced. Depending on the emission inventory used, simulated POA levels are either reasonable or underestimated, while SOA levels tend to be overestimated. Several uncertainties related to the VBS scheme (POA volatility, SOA yields, the aging parameterization, to emission input data, and to simulated OH levels can be responsible for this behavior. Despite these uncertainties, the implementation of the VBS scheme into
Bán, Zoltán; Győri, Erzsébet; János Katona, Tamás; Tóth, László
2015-04-01
Preparedness of nuclear power plants to beyond design base external effects became high importance after 11th of March 2011 Great Tohoku Earthquakes. In case of some nuclear power plants constructed at the soft soil sites, liquefaction should be considered as a beyond design basis hazard. The consequences of liquefaction have to be analysed with the aim of definition of post-event plant condition, identification of plant vulnerabilities and planning the necessary measures for accident management. In the paper, the methodology of the analysis of liquefaction effects for nuclear power plants is outlined. The case of Nuclear Power Plant at Paks, Hungary is used as an example for demonstration of practical importance of the presented results and considerations. Contrary to the design, conservatism of the methodology for the evaluation of beyond design basis liquefaction effects for an operating plant has to be limited to a reasonable level. Consequently, applicability of all existing methods has to be considered for the best estimation. The adequacy and conclusiveness of the results is mainly limited by the epistemic uncertainty of the methods used for liquefaction hazard definition and definition of engineering parameters characterizing the consequences of liquefaction. The methods have to comply with controversial requirements. They have to be consistent and widely accepted and used in the practice. They have to be based on the comprehensive database. They have to provide basis for the evaluation of dominating engineering parameters that control the post-liquefaction response of the plant structures. Experience of Kashiwazaki-Kariwa plant hit by Niigata-ken Chuetsu-oki earthquake of 16 July 2007 and analysis of site conditions and plant layout at Paks plant have shown that the differential settlement is found to be the dominating effect in case considered. They have to be based on the probabilistic seismic hazard assessment and allow the integration into logic
Genetic basis and detection of unintended effects in genetically modified crop plants.
Ladics, Gregory S; Bartholomaeus, Andrew; Bregitzer, Phil; Doerrer, Nancy G; Gray, Alan; Holzhauser, Thomas; Jordan, Mark; Keese, Paul; Kok, Esther; Macdonald, Phil; Parrott, Wayne; Privalle, Laura; Raybould, Alan; Rhee, Seung Yon; Rice, Elena; Romeis, Jörg; Vaughn, Justin; Wal, Jean-Michel; Glenn, Kevin
2015-08-01
In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled "Genetic Basis of Unintended Effects in Modified Plants" was held in Ottawa, Canada, bringing together over 75 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects in plants and to discuss how this information can inform and improve genetically modified (GM) crop risk assessments. The meeting featured presentations on the molecular basis of plant genome variability in general, unintended changes at the molecular and phenotypic levels, and the development and use of hypothesis-driven evaluations of unintended effects in assessing conventional and GM crops. The development and role of emerging "omics" technologies in the assessment of unintended effects was also discussed. Several themes recurred in a number of talks; for example, a common observation was that no system for genetic modification, including conventional methods of plant breeding, is without unintended effects. Another common observation was that "unintended" does not necessarily mean "harmful". This paper summarizes key points from the information presented at the meeting to provide readers with current viewpoints on these topics. PMID:25716164
An Effective Feature Set for ECG Pattern Classification
Ghongade, Rajesh; Ghatol, Ashok
In this paper, QRS morphological features and the artificial neural network method was used for Electrocardiogram (ECG) pattern classification. Four types of ECG patterns were chosen from the MIT-BIH database to be recognized, including normal sinus rhythm, premature ventricular contraction, atrial premature beat and left bundle branch block beat. Authors propose a set of six ECG morphological features to reduce the feature vector size considerably and make the training process fast in addition to a simple but effective ECG heartbeat extraction scheme. Three types of artificial neural network models, MLP, RBF neural networks and SOFM were separately trained and tested for ECG pattern recognition and the experimental results of the different models have been compared. The MLP network exhibited the best performance and reached an overall test accuracy of 99.65%, and RBF and SOFM network both reached 99.1%. The performance of these classifiers was also evaluated in presence of additive Gaussian noise. MLP network was found to be more robust in this respect.
Effectiveness of MAP Goal Setting on Reading for Middle School
Empirical Education Inc., 2010
2010-01-01
Student goal setting and academic planning has been a major focus for PUSD, with the aim of increasing the level of student engagement and student ownership over their learning. Goal setting has been implemented in conjunction with the Northwest Evaluation Association's Measure of Academic Progress (MAP) tests, which provide educators with a tool…
Effects of "Status Sets" on Rotter's Locus of Control Scale
Bailey, Kent G.; Davidson, Kay M.
1978-01-01
Subjects were given sets based on varying levels of social class to determine susceptibility of Internal-External Locus of Control Scale (I-E) scores to situationally induced frames of reference. College students (N=90) took the I-E scale twice. Present results are that the I-E scale may be subject to faking. (Author)
Effects of Social Class and Interactive Setting on Maternal Speech.
Hoff-Ginsberg, Erika
The speech that upper-middle class mothers used with their young children was compared to that used by working class mothers. Mother-child interaction was recorded in four settings: mealtime, dressing, reading, and playing with toys. Also investigated were mothers' child rearing beliefs and goals. Participants included 33 upper-middle class and 30…
Bor, G.; Kettle, Sidney F. A.
1999-12-01
The unifying power of the use of trigonometric basis functions in group character tables is demonstrated. Additionally, these functions provide a simple way of generating pictures of symmetry coordinates. This is illustrated for the in-plane stretch and out-of-plane deformation motions of the C-H bonds in benzene. Their application to orbital symmetry applications is also indicated.
Quiney, HM; Glushkov, VN; Wilson, S
2002-01-01
Using basis sets of distributed s-type Gaussian functions with positions and exponents optimized so as to support Hartree-Fock total energies with an accuracy approaching the sub-muHartree level, Dirac-Hartree-Fock-Coulomb calculations are reported for the ground states of the H-2, LiH, and BH molec
Li, F.; Wang, L.; Zhao, J.; Xie, J. R. H.; Riley, Kevin Eugene; Chen, Z.
2011-01-01
Roč. 130, 2/3 (2011), s. 341-352. ISSN 1432-881X Institutional research plan: CEZ:AV0Z40550506 Keywords : water cluster * density functional theory * MP2 . CCSD(T) * basis set * relative energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011
Mind-set Matters: Exercise and the Placebo Effect
Langer, Ellen; Crum, Alia J.
2007-01-01
In a study testing whether the relationship between exercise and health is moderated by one's mind-set, 84 female room attendants working in seven different hotels were measured on physiological health variables affected by exercise. Those in the informed condition were told that the work they do (cleaning hotel rooms) is good exercise and satisfies the Surgeon General's recommendations for an active lifestyle. Examples of how their work was exercise were provided. Subjects in the control gro...
The ICRP protection quantities, equivalent and effective dose: their basis and application
Harrison, J.D. [Health Protection Agency, Radiation Protection Division, Chilton, Didcot, Oxon OX11 0RQ (United Kingdom); Streffer, C. [Institute for Science and Ethics, University Duisburg-Essen, 45117 Essen (Germany)
2007-07-01
Equivalent and effective dose are protection quantities defined by the The International Commission on Radiological Protection (ICRP). They are frequently referred to simply as dose and may be misused. They provide a method for the summation of doses received from external sources and from intakes of radionuclides for comparison with dose limits and constraints, set to limit the risk of cancer and hereditary effects. For the assessment of internal doses, ICRP provides dose coefficients (Sv Bq{sup -1}) for the ingestion or inhalation of radionuclides by workers and members of the public, including children. Dose coefficients have also been calculated for in utero exposures following maternal intakes and for the transfer of radionuclides in breast milk. In each case, values are given of committed equivalent doses to organs and tissues and committed effective dose. Their calculation involves the use of defined biokinetic and dosimetric models, including the use of reference phantoms representing the human body. Radiation weighting factors are used as a simple representation of the different effectiveness of different radiations in causing stochastic effects at low doses. A single set of tissue weighting factors is used to take account of the contribution of individual organs and tissues to overall detriment from cancer and hereditary effects, despite age- and gender-related differences in estimates of risk and contributions to risk. The results are quantities that are not individual specific but are reference values for protection purposes, relating to doses to phantoms. The ICRP protection quantities are not intended for detailed assessments of dose and risk to individuals. They should not be used in epidemiological analyses or the assessment of the possibility of occurrence and severity of tissue reactions (deterministic effects) at higher doses. Dose coefficients are published as reference values and as such have no associated uncertainty. Assessments of
The ICRP protection quantities, equivalent and effective dose: their basis and application.
Harrison, J D; Streffer, C
2007-01-01
Equivalent and effective dose are protection quantities defined by the The International Commission on Radiological Protection (ICRP). They are frequently referred to simply as dose and may be misused. They provide a method for the summation of doses received from external sources and from intakes of radionuclides for comparison with dose limits and constraints, set to limit the risk of cancer and hereditary effects. For the assessment of internal doses, ICRP provides dose coefficients (Sv Bq(-1)) for the ingestion or inhalation of radionuclides by workers and members of the public, including children. Dose coefficients have also been calculated for in utero exposures following maternal intakes and for the transfer of radionuclides in breast milk. In each case, values are given of committed equivalent doses to organs and tissues and committed effective dose. Their calculation involves the use of defined biokinetic and dosimetric models, including the use of reference phantoms representing the human body. Radiation weighting factors are used as a simple representation of the different effectiveness of different radiations in causing stochastic effects at low doses. A single set of tissue weighting factors is used to take account of the contribution of individual organs and tissues to overall detriment from cancer and hereditary effects, despite age- and gender-related differences in estimates of risk and contributions to risk. The results are quantities that are not individual specific but are reference values for protection purposes, relating to doses to phantoms. The ICRP protection quantities are not intended for detailed assessments of dose and risk to individuals. They should not be used in epidemiological analyses or the assessment of the possibility of occurrence and severity of tissue reactions (deterministic effects) at higher doses. Dose coefficients are published as reference values and as such have no associated uncertainty. Assessments of uncertainties
The ICRP protection quantities, equivalent and effective dose: their basis and application
Equivalent and effective dose are protection quantities defined by the The International Commission on Radiological Protection (ICRP). They are frequently referred to simply as dose and may be misused. They provide a method for the summation of doses received from external sources and from intakes of radionuclides for comparison with dose limits and constraints, set to limit the risk of cancer and hereditary effects. For the assessment of internal doses, ICRP provides dose coefficients (Sv Bq-1) for the ingestion or inhalation of radionuclides by workers and members of the public, including children. Dose coefficients have also been calculated for in utero exposures following maternal intakes and for the transfer of radionuclides in breast milk. In each case, values are given of committed equivalent doses to organs and tissues and committed effective dose. Their calculation involves the use of defined biokinetic and dosimetric models, including the use of reference phantoms representing the human body. Radiation weighting factors are used as a simple representation of the different effectiveness of different radiations in causing stochastic effects at low doses. A single set of tissue weighting factors is used to take account of the contribution of individual organs and tissues to overall detriment from cancer and hereditary effects, despite age- and gender-related differences in estimates of risk and contributions to risk. The results are quantities that are not individual specific but are reference values for protection purposes, relating to doses to phantoms. The ICRP protection quantities are not intended for detailed assessments of dose and risk to individuals. They should not be used in epidemiological analyses or the assessment of the possibility of occurrence and severity of tissue reactions (deterministic effects) at higher doses. Dose coefficients are published as reference values and as such have no associated uncertainty. Assessments of uncertainties
Evaluation of the separate effects tests (SET) validation matrix
This work is the result of a one year extended mandate which has been given by the CSNI on the request of the PWG 2 and the Task Group on Thermal Hydraulic System Behaviour (TG THSB) in late 1994. The aim was to evaluate the SET validation matrix in order to define the real needs for further experimental work. The statistical evaluation tables of the SET matrix provide an overview of the data base including the parameter ranges covered for each phenomenon and selected parameters, and questions posed to obtain answers concerning the need for additional experimental data with regard to the objective of nuclear power plant safety. A global view of the data base is first presented focussing on areas lacking in data and on hot topics. A new systematic evaluation has been done based on the authors technical judgments and giving evaluation tables. In these tables, global and indicative information are included. Four main parameters have been chosen as the most important and relevant parameters: a state parameter given by the operating pressure of the tests, a flow parameter expressed as mass flux, mass flow rate or volumetric flow rate in the tests, a geometrical parameter provided through a typical dimension expressed by a diameter, an equivalent diameter (hydraulic or heated) or a cross sectional area of the test sections, and an energy or heat transfer parameter given as the fluid temperature, the heat flux or the heat transfer surface temperature of the tests
Clinical evidence and mechanistic basis for vildagliptin's effect in combination with insulin
Schweizer A
2013-02-01
Full Text Available Anja Schweizer,1 James E Foley,2 Wolfgang Kothny,2 Bo Ahrén31Novartis Pharma AG, Basel, Switzerland; 2Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA; 3Department of Clinical Sciences, Lund University, Lund, SwedenAbstract: Due to the progressive nature of type 2 diabetes, many patients need insulin as add-on to oral antidiabetic drugs (OADs in order to maintain adequate glycemic control. Insulin therapy primarily targets elevated fasting glycemia but is less effective to reduce postprandial hyperglycemia. In addition, the risk of hypoglycemia limits its effectiveness and there is a concern of weight gain. These drawbacks may be overcome by combining insulin with incretin-based therapies as these increase glucose sensitivity of both the α- and β-cells, resulting in improved postprandial glycemia without the hypoglycemia and weight gain associated with increasing the dose of insulin. The dipeptidyl peptidase-IV (DPP-4 inhibitor vildagliptin has also been shown to protect from hypoglycemia by enhancing glucagon counterregulation. The effectiveness of combining vildagliptin with insulin was demonstrated in three different studies in which vildagliptin decreased A1C levels when added to insulin therapy without increasing hypoglycemia. This was established with and without concomitant metformin therapy. Furthermore, the effectiveness of vildagliptin appears to be greater when insulin is used as a basal regimen as opposed to being used to reduce postprandial hyperglycemia, since improvement in insulin secretion likely plays a minor role when relatively high doses of insulin are administered before meals. This article reviews the clinical experience with the combination of vildagliptin and insulin and discusses the mechanistic basis for the beneficial effects of the combination. The data support the use of vildagliptin in combination with insulin in general and, in line with emerging clinical practice, suggest that treating patients with
Large basis space effects in electron scattering form factors of light nuclei
Large basis space projected Hartree-Fock wave functions have been used to calculate the longitudinal and transverse (electric) form factors from the excitations of 21+ and 41+ states in 12C, 20Ne and 24Mg. The results obtained by use of such large basis space models of structure are compared with limited basis space (Shell model) predictions to show how diverse momentum transfer dependent corrections can be. 9 refs., 4 figs.,
Davies-Colley, Robert J; Ballantine, Deborah J; Elliott, Sandy H; Swales, Andrew; Hughes, Andrew O; Gall, Mark P
2014-01-01
Fine sediment continues to be a major diffuse pollution concern with its multiple effects on aquatic ecosystems. Mass concentrations (and loads) of fine sediment are usually measured and modelled, apparently with the assumption that environmental effects of sediment are predictable from mass concentrations. However, some severe impacts of fine sediment may not correlate well with mass concentration, notably those related to light attenuation by suspended particles. Light attenuation per unit mass concentration of suspended particulate matter in waters varies widely with particle size, shape and composition. Data for suspended sediment concentration, turbidity and visual clarity (which is inversely proportional to light beam attenuation) from 77 diverse New Zealand rivers provide valuable insights into the mutual relationships of these quantities. Our analysis of these relationships, both across multiple rivers and within individual rivers, supports the proposition that light attenuation by fine sediment is a more generally meaningful basis for environmental management than sediment mass. Furthermore, optical measurements are considerably more practical, being much cheaper (by about four-fold) to measure than mass concentrations, and amenable to continuous measurement. Mass concentration can be estimated with sufficient precision for many purposes from optical surrogates locally calibrated for particular rivers. PMID:24804661
Polarity correspondence effect between loudness and lateralized response set
Chang, Seah; Cho, Yang Seok
2015-01-01
Performance is better when a high pitch tone is associated with an up or right response and a low pitch tone with a down or left response compared to the opposite pairs, which is called the spatial-musical association of response codes effect. The current study examined whether polarity codes are formed in terms of the variation in loudness. In Experiments 1 and 2, in which participants performed a loudness-judgment task and a timbre-judgment task respectively, the correspondence effect was o...
Natural Treatment and Control Settings for Research on the Effects of Television.
Keeter, Scott; Wilson, Harry
1986-01-01
Describes the basic method of using naturally occurring settings for research on media effects. Suggests research questions that could be studied and identifies settings (and media markets) most promising for such research. (PD)
Effectiveness of Relationship Marketing Tactics in a University Setting
Trocchia, Philip J.; Finney, R. Zachary; Finney, Treena Gillespie
2013-01-01
We test the correlation between student perception of three university relationship-building tactics--commercial friendships, preferential treatment, and tangible rewards--with university student satisfaction. We also test whether two student characteristics--enduring involvement with education and sense of entitlement--have a moderating effect on…
Effectiveness of Assertive Discipline in a Rural Setting.
Ferre, Victor; Ferre, Louise
1991-01-01
Assertive discipline can help teachers develop more consistent and effective communication strategies for influencing student behavior. Over a nine-week period, two teachers using assertive discipline reduced the off-task and disruptive behavior of a male kindergarten student by defining behavioral limits and providing positive and negative…
The Effects of Conjoint Behavioral Consultation in Early Childhood Settings
Sheridan, Susan M.; Clarke, Brandy L.; Knoche, Lisa L.; Edwards, Carolyn Pope
2006-01-01
Conjoint behavioral consultation (CBC) is an ecological model of service delivery that brings together parents and educators to collaboratively address shared concerns for a child. This study provides exploratory data investigating the effects of CBC on home and school concerns for 48 children aged 6 and younger. Single-subject methods were used…
School Composition and Peer Effects in Distinctive Organizational Settings
Marks, Helen M.
2002-01-01
This chapter reviews the research on school composition and peer effects from three comparative perspectives--Catholic and public schools, single-sex and coeducational schools, and small and large schools. Most of the research is sociological, focuses on high schools, and draws on national samples. The chapter seeks to discern cumulative trends in…
An effective filter for IBD detection in large data sets.
Huang, Lin
2014-03-25
Identity by descent (IBD) inference is the task of computationally detecting genomic segments that are shared between individuals by means of common familial descent. Accurate IBD detection plays an important role in various genomic studies, ranging from mapping disease genes to exploring ancient population histories. The majority of recent work in the field has focused on improving the accuracy of inference, targeting shorter genomic segments that originate from a more ancient common ancestor. The accuracy of these methods, however, is achieved at the expense of high computational cost, resulting in a prohibitively long running time when applied to large cohorts. To enable the study of large cohorts, we introduce SpeeDB, a method that facilitates fast IBD detection in large unphased genotype data sets. Given a target individual and a database of individuals that potentially share IBD segments with the target, SpeeDB applies an efficient opposite-homozygous filter, which excludes chromosomal segments from the database that are highly unlikely to be IBD with the corresponding segments from the target individual. The remaining segments can then be evaluated by any IBD detection method of choice. When examining simulated individuals sharing 4 cM IBD regions, SpeeDB filtered out 99.5% of genomic regions from consideration while retaining 99% of the true IBD segments. Applying the SpeeDB filter prior to detecting IBD in simulated fourth cousins resulted in an overall running time that was 10,000x faster than inferring IBD without the filter and retained 99% of the true IBD segments in the output.
DIMENSIONS AND EFFECTS OF EMOTIONS IN ORGANIZATIONAL SETTINGS
Andreea ARMEAN
2014-01-01
The emotions and their management in the workplace have become popular topics in the literature as a result of their effects in organizations. With regards to the conceptualization of emotions and their impact within the organizational context, terms such as emotion, affect, and affective state are often used as synonyms by many authors, but there are situations when they have different significance. The meanings associated with these concepts are herein discussed. The affect is present in al...
Xiaojin Luo; Yongcai Fu; Peijiang Zhang; Shuang Wu; Feng Tian; Jiayong Liu; Zuofeng Zhu; Jinshui Yang; Chuanqing Sun
2009-01-01
A set of 148 F9 recombinant inbred lines (RILs) was developed from the cross of an indica cultivar 93-11 and japonica cultivar DTT13,showing strong F1 heterosis.Subsequently,two backcross F1 (BCF1) populations were constructed by backcrossing these 148 RILs to two parents,93-11 and DT713.These three related populations (281BCF1 lines,148 RILs) were phenotyped for six yield-related traits in two locations.Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations.A total of 42 main-effect quantitative trait loci (M-QTLs) and 109 epistatic effect QTL pairs (E-QTLs) were detected in the three related populations using the mixed model approach.By comparing the genetic effects of these QTLs detected in the RILs,BCF1 performance and mid-parental heterosis (HMp),we found that,in both BCF1 populations,the QTLs detected could be classified into two predominant types:additive and over-domlnant loci,which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs.Further,we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations.All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.
Kobus, J [Instytut Fizyki, Uniwersytet Mikolaja Kopernika, ul. Grudziadzka 5/7, 87-100 Torun (Poland); Moncrieff, D [School of Computational Science and Information Technology, Florida State University, Tallahassee, FL 32306 (United States); Wilson, S [Department of Chemical Physics, Faculty of Mathematics and Physics, Comenius University, 842 15 Bratislava (Slovakia)
2007-03-14
We investigate the accuracy with which the electric dipole polarizability, {alpha}{sub zz}, and the hyperpolarizability, {beta}{sub zzz}, can be calculated by using the algebraic approximation, i.e. finite basis set expansions, and by means of the finite difference method in calculations for the ground states of the 14 electron systems N{sub 2}, CO and BF within the Hartree-Fock model at their respective experimental equilibrium geometries. For a well-chosen grid, the finite difference technique can provide Hartree-Fock energy and dipole moment expectation values approaching machine precision which can be used to assess the accuracy of corresponding calculations carried out within the algebraic approximation. The finite field approximation is used to determine polarizabilities and hyperpolarizabilities from finite difference Hartree-Fock dipole moment expectation values. The results are compared with finite basis set calculations of the corresponding quantities which are carried out analytically using coupled perturbed Hartree-Fock theory. For the N{sub 2} molecule, the Hartree-Fock polarizability is found to be 14.9512 au within the finite basis set approximation and 14.945 au within the finite difference approach. For the CO molecule, the corresponding results are 14.4668 au and 14.4668 au, whilst for the BF molecule the values are 16.6450 au and 16.6450 au, respectively. The Hartree-Fock hyperpolarizability of the CO molecule is found to be 31.4081 au and 31.411 au within the finite basis set and finite difference approximations, respectively. The corresponding hyperpolarizability values for the BF molecule are 63.9687 au and 63.969 au, respectively.
Neural basis of music imagery and the effect of musical expertise.
Herholz, Sibylle C; Lappe, Claudia; Knief, Arne; Pantev, Christo
2008-12-01
Although the influence of long-term musical training on the processing of heard music has been the subject of many studies, the neural basis of music imagery and the effect of musical expertise remain insufficiently understood. By means of magnetoencephalography (MEG) we compared musicians and nonmusicians in a musical imagery task with familiar melodies. Subjects listened to the beginnings of the melodies, continued them in their imagination and then heard a tone which was either a correct or an incorrect further continuation of the melody. Only in musicians was the imagery of these melodies strong enough to elicit an early preattentive brain response to unexpected incorrect continuations of the imagined melodies; this response, the imagery mismatch negativity (iMMN), peaked approximately 175 ms after tone onset and was right-lateralized. In contrast to previous studies the iMMN was not based on a heard but on a purely imagined memory trace. Our results suggest that in trained musicians imagery and perception rely on similar neuronal correlates, and that the musicians' intense musical training has modified this network to achieve a superior ability for imagery and preattentive processing of music. PMID:19046375
DIMENSIONS AND EFFECTS OF EMOTIONS IN ORGANIZATIONAL SETTINGS
Andreea ARMEAN
2014-12-01
Full Text Available The emotions and their management in the workplace have become popular topics in the literature as a result of their effects in organizations. With regards to the conceptualization of emotions and their impact within the organizational context, terms such as emotion, affect, and affective state are often used as synonyms by many authors, but there are situations when they have different significance. The meanings associated with these concepts are herein discussed. The affect is present in all the organizational parts, is the root of all its relationships. The emotions influence many organizational dimensions such as decision-making, creativity, teamwork, negotiation, leadership, turnover, and job performance. Another essential construct in this field is emotional labor or the management of emotions. This concept has a special significance in the tertiary sector because it is an important driver of customer satisfaction.
Johanna Egetemeir
2011-09-01
Full Text Available Many everyday life situations require two or more individuals to execute actions together. Assessing brain activation during naturalistic tasks to uncover relevant processes underlying such real-life joint action situations has remained a methodological challenge. In the present study, we introduce a novel joint action paradigm that enables the assessment of brain activation during real-life joint action tasks using functional near-infrared spectroscopy (fNIRS. We monitored brain activation of participants who coordinated complex actions with a partner sitting opposite them. Participants performed table-setting tasks, either alone (solo action or in cooperation with a partner (joint action, or they observed the partner performing the task (action observation. Comparing joint action and solo action revealed stronger activation (higher [oxy-Hb]-concentration during joint action in a number of areas. Among these were areas in the inferior parietal lobule (IPL that additionally showed an overlap of activation during action observation and solo action. Areas with such a close link between action observation and action execution have been associated with action simulation processes. The magnitude of activation in these IPL areas also varied according to joint action type and its respective demand on action simulation. The results validate fNIRS as an imaging technique for exploring the functional correlates of interindividual action coordination in real-life settings and suggest that coordinating actions in real-life situations requires simulating the actions of the partner.
Nirmal Sukul
2012-09-01
Full Text Available Background: Homeopathic potencies 12 cH and above cross the Avogadro number and, for this, do not contain any original drug molecules. Two major problems involved in the scientific study of potencies are (1 understanding the physical basis of potencies and (2 demonstrating the biological effects of potencies. The present study aims to address these questions. Methods and Results: In course of our experimental studies spanned over more than 30 years we have demonstrated significant effects of homeopathic potencies on man, animals and plants. We have also showed that potencies could be differentiated through their electronic spectra, and this difference in spectra can be attributed to the electron transfer interaction. In a molecular complex, electron of one molecule absorbs a quantum of visible radiation and is excited, not to a higher energy level of this molecule, but to one of the vacant high energy levels of the neighboring molecules. This process is known as electron or charge transfer interaction. This has been demonstrated in Iodine Ã“Â© in two different solvents of CCl4 and aqueous ethanol (Sukul N C, Environ Ecol 17,866-872, 1999. We have further demonstrated that the effect of a homeopathic potency can be transmitted from one part of a plant to another, and also from one plant to another through water. I am presenting here a few selected cases of our experimental studies. Potentized Nux vomica significantly reduced ethanol consumption in rats by 73.7%and ethanol-induced sleep time in albino mice by 44.4%. Causticum 30 C and Rhus tox 30 C produced anti-inflamatory and anti-nocicptive effect on adjuvant arthritis in albino rats. Potentized homeopathic drugs reduced microfilaraemia by 28 to 100% and filariasis in two villages of West Bengal endemic for Bancroftian filaiasis. Potentized Cina and Thuja ameliorated trichinellosis in mice reducing larval population in muscles by 84% and 68%, respectively. Potencies of Agaricus and Nux
The Effects of Participative versus Assigned Goal Setting on Intrinsic Motivation.
Chang, Grace Shing-Yung; Lorenzi, Peter
1983-01-01
Investigated the effects of participative versus assigned goal setting on intrinsic motivation for interesting and boring tasks. Participative and assigned goal setting had no significantly different effects on performance if the goal was held consistently difficult, but had different effects on intrinsic motivation at different levels of task…
Conroy, Maureen A.; Fox, James J.
1994-01-01
This article describes a model that deals with classroom behavior problems by incorporating contextual or setting events with traditional learning theory models. The paper discusses examples of setting events that affect children's aggression, ways to assess the effects of setting events on student behavior, and ways in which teachers can…
Effect of Stretching--Setting Treatment on Dyeing Behavior of Wool
林琳
2003-01-01
Changes of dyeing behavior of wool after stretching - setting treatment are studied.Effects of stretching - setting on wool structure are analyzed.It is concluded that stretching - setting treatment not only reduces wool diameter and increases wool length,but also brings about low-temperature dyeing of wool.
Han, Seungil; Zaniewski, Richard P.; Marr, Eric S.; Lacey, Brian M.; Tomaras, Andrew P.; Evdokimov, Artem; Miller, J. Richard; Shanmugasundaram, Veerabahu (Pfizer)
2012-02-08
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes nosocomial infections for which there are limited treatment options. Penicillin-binding protein PBP3, a key therapeutic target, is an essential enzyme responsible for the final steps of peptidoglycan synthesis and is covalently inactivated by {beta}-lactam antibiotics. Here we disclose the first high resolution cocrystal structures of the P. aeruginosa PBP3 with both novel and marketed {beta}-lactams. These structures reveal a conformational rearrangement of Tyr532 and Phe533 and a ligand-induced conformational change of Tyr409 and Arg489. The well-known affinity of the monobactam aztreonam for P. aeruginosa PBP3 is due to a distinct hydrophobic aromatic wall composed of Tyr503, Tyr532, and Phe533 interacting with the gem-dimethyl group. The structure of MC-1, a new siderophore-conjugated monocarbam complexed with PBP3 provides molecular insights for lead optimization. Importantly, we have identified a novel conformation that is distinct to the high-molecular-weight class B PBP subfamily, which is identifiable by common features such as a hydrophobic aromatic wall formed by Tyr503, Tyr532, and Phe533 and the structural flexibility of Tyr409 flanked by two glycine residues. This is also the first example of a siderophore-conjugated triazolone-linked monocarbam complexed with any PBP. Energetic analysis of tightly and loosely held computed hydration sites indicates protein desolvation effects contribute significantly to PBP3 binding, and analysis of hydration site energies allows rank ordering of the second-order acylation rate constants. Taken together, these structural, biochemical, and computational studies provide a molecular basis for recognition of P. aeruginosa PBP3 and open avenues for future design of inhibitors of this class of PBPs.
The drift resonance of a charged particle moving in the toroidal spiral magnetic field with a magnetic excitation and the particle trapping effect on the heterogeneities of the toroidal spiral magnetic field are studied. The composition of two approaches: the solution of the system of the drift equations and the Newton-Lorentz exact equations is carried out. It is shown that by the drift resonance description there is a good quantitative agreement of the two approaches; by the trapped particle motion description there exists a qualitative agreement
Christensen, Niels Johan; Kepp, Kasper Planeta
2014-01-01
and activity for unknown reasons, and are thus useful probes of stability-function trade-offs relevant to protein engineering. We report here the first systematic comparison of ABTS-binding to different proteins, i.e. the four isoforms of Trametes versicolor, using a combination of sequence clustering...... the four T. versicolor isoforms belonging to separate classes. The T1 oxidation state had minor effect on ABTS binding, whereas the protonation state of Asp206 was important, consistent with site-directed mutagenesis studies. The absence of active poses for the δ-isoform agrees with its large Km...
Gao, Wei; Feng, Huajie; Xuan, Xiaopeng; Chen, Liuping
2012-10-01
An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA + DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA + BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA + BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics. PMID:22643965
Plasma experiments with relevance for the actual physical basis of the gun effect
Based on the fact that plasma offered many answers to challenging problems of solid state physics we describe in this paper some of the striking similarities that can be observed between the nonlinear behaviour of a plasma diode and that of a Gunn diode. Our proposal is to present experimental arguments that the dynamical behaviour of the complex space charge configuration formed after selforganization in front of the anode, is the genuine cause of oscillations' stimulation in both diodes. As known the theoretical model used at present to explain the negative differential resistance behaviour of a Gunn diode is based on the intervalley transfer mechanism. In this mechanism fast electrons are converted to a slower species by shifting the population of carriers from a light to a heavier-mass valley with the increasing field. On the other hand, it is known from semiconductors that the occurrence of negative differential resistance can be associated with dynamic current instabilities arising during nonequilibrium phase transitions between different conducting states. Based on recent experimental results performed on a plasma subjected to an external constraint, in the form of a local acting electric field, we have revealed a selforganization physical scenario, the possible presence of which in semiconductors can suggest answers to many problems not yet conclusively solved.The selforganization scenario is essentially based on collective effects related to the spatial separation of the regions where the neutral excitation and ionization cross sections suddenly increase. Such phenomena appear in front of the anode where after local acceleration, a gradient of electron kinetic energy is present. Reaching the kinetic energy for which the excitation cross section suddenly increases, the part of electrons that produce excitations lose their momentum forming, after thermalization, a well localized net negative space charge at a certain distance from the anode. This is the
The U.S. Department of Energy (DOE), Office of Environmental Management (EM) conducted its first Remediation Process Optimization (RPO) review in 2004, following the methodology and guidance issued by the Interstate Technology and Regulatory Council (ITRC). The intent of this paper is to briefly summarize the following: (1) the overall benefits of the review process toward improving remedial effectiveness and efficiency at DOE, (2) the types and objectives of completed reviews, and (3) how RPO facilitates technology transfer and is complementary to performance-based environmental management (PBEM). Contract reform began in 1993, at the U.S. Department of Energy (DOE) as a result of the Government Performance and Results Act, followed by recommendations from oversight groups. The precedence of using management and operating (M and O) contracts at DOE facilities, exempt from open competition by definition, shifted to performance basis. Since 1994, DOE has competed over 70% of its then existing M and O contracts; most now contain specific performance objectives, measures, and targets that focus on results in mission critical areas. In 2001, DOE's Office of Environmental Management (EM) integrated performance-based contracting as a core business process. EM resolved to manage cleanup as a project, encourage innovative contracting strategies, as well as incentives to accelerate risk reduction and cleanup. DOE's efforts to implement performance-based environmental management (PBEM) were further realized by establishing a centralized Office of Acquisitions and the Consolidated Business Center, which support all EM procurements. In 2004, EM began conducting Remediation Process Optimization (RPO) reviews at select field sites, following the methodology published in the 2004 ITRC guidance. To date, EM has completed nine RPO reviews, including: pump and treat system optimization, monitoring program optimization, in situ barrier performance improvement, remedial design review
We present a theoretical framework for calculating the recoil-angle dependence of the photofragment angular momentum polarization taking into account both radial and Coriolis nonadiabatic interactions in the diatomic/linear photodissociating molecules. The parity-adapted representation of the total molecular wave function has been used throughout the paper. The obtained full quantum-mechanical expressions for the photofragment state multipoles have been simplified by using the semiclassical approximation in the high-J limit and then analyzed for the cases of direct photodissociation and slow predissociation in terms of the anisotropy parameters. In both cases, each anisotropy parameter can be presented as a linear combination of the generalized dynamical functions fK(q,q',q-tilde,q-tilde') of the rank K representing contribution from different dissociation mechanisms including possible radial and Coriolis nonadiabatic transitions, coherent effects, and the rotation of the recoil axis. In the absence of the Coriolis interactions, the obtained results are equivalent to the earlier published ones. The angle-recoil dependence of the photofragment state multipoles for an arbitrary photolysis reaction is derived. As shown, the polarization of the photofragments in the photolysis of a diatomic or a polyatomic molecule can be described in terms of the anisotropy parameters irrespective of the photodissociation mechanism
Meta-analysis of choice set generation effects on route choice model estimates and predictions
Prato, Carlo Giacomo
2012-01-01
modeling, but require them to generate choice sets by selecting a path generation technique and its parameters according to personal judgments. This paper proposes a methodology and an experimental setting to provide general indications about objective judgments for an effective route choice set generation....... Initially, path generation techniques are implemented within a synthetic network to generate possible subjective choice sets considered by travelers. Next, ‘true model estimates’ and ‘postulated predicted routes’ are assumed from the simulation of a route choice model. Then, objective choice sets are...... applied for model estimation and results are compared to the ‘true model estimates’. Last, predictions from the simulation of models estimated with objective choice sets are compared to the ‘postulated predicted routes’. A meta-analytical approach allows synthesizing the effect of judgments for the...
The Construal (In)compatibility Effect: The Moderating Role of a Creative Mind-Set
Xiaojing Yang; Torsten Ringberg; Huifang Mao; Laura A. Peracchio
2011-01-01
This research examines how consumers with a creative mind-set are persuaded by advertising claims construed at different levels (i.e., abstract vs. concrete ad claims). Across four experiments, we show that consumers with a creative mind-set are more persuaded by ad claims construed at a level incompatible with their mental construal, while ad claims construed at a level compatible with consumers’ mental construal are more effective for those who possess a less creative mind-set. We document ...
Migration and Wage-Setting: Reassessing the Labor Market Effects of Migration
Brücker, Herbert; Jahn, Elke J.
2009-01-01
This paper employs a wage-setting approach to analyze the labor market effects of immigration into Germany. The wage-setting framework relies on the assumption that wages tend to decline with rising unemployment, albeit imperfectly. This enables us to consider labor market rigidities, which are particularly relevant in Germany and other European countries. We find that the elasticity of the wage-setting curve is particularly high for young and well-educated workers. Moreover, we find evidence...
The Effects of a Goal Setting Intervention on Productivity and Persistence in an Analogue Work Task
Tammemagi, Triona; O'Hora, Denis; Maglieri, Kristen A.
2013-01-01
The authors of this study sought to quantify the beneficial effect of goal setting on work performance, and to characterize the persistence or deterioration of goal-directed behavior over time. Twenty-six participants completed a computer-based data entry task. Performance was measured during an initial baseline, a goal setting intervention that…
Enhancing Willingness to Communicate: Relative Effects of Visualization and Goal Setting
Munezane, Yoko
2015-01-01
This article examines the relative effects of two treatments--goal setting and visualization--on enhancing Willingness to Communicate (WTC) among a group of 373 Japanese university EFL learners. Although longitudinal studies in both EFL and ESL settings have been conducted to examine the developmental aspect of WTC, no solid results of enhancing…
The Effects of a Goal Setting Intervention on Aerobic Fitness in Middle School Students
McDonald, Samantha M.; Trost, Stewart G.
2015-01-01
Purpose: This study evaluated the effects of a goal setting intervention on aerobic fitness (AF) in 6 to 8 grade students. Method: Students at the intervention school received a lesson on SMART goal setting. Students in the comparison school served as a measurement-only group. AF was assessed via the PACER multi-stage shuttle run test pre and post…
The convex hull of a regular set of integer vectors is polyhedral and effectively computable
Finkel, Alain; 10.1016/j.ipl.2005.04.004
2008-01-01
Number Decision Diagrams (NDD) provide a natural finite symbolic representation for regular set of integer vectors encoded as strings of digit vectors (least or most significant digit first). The convex hull of the set of vectors represented by a NDD is proved to be an effectively computable convex polyhedron.
The Effects of Graphic Feedback, Goal-Setting, and Manager Praise on Customer Service Behaviors
Loewy, Shannon; Bailey, Jon
2007-01-01
The current study used a multiple baseline design to investigate the effects of graphic feedback, goal setting, and manager praise on customer service behaviors in a large retail setting. Direct observation of customer greeting, eye contact, and smiling was used to collect data. After baseline data were collected feedback graphs were posted twice…
Acee, Taylor Wayne
2009-01-01
The purpose of this dissertation was to investigate the differential effects of goal setting and value reappraisal on female students' self-efficacy beliefs, value perceptions, exam performance and continued interest in statistics. It was hypothesized that the Enhanced Goal Setting Intervention (GS-E) would positively impact students'…
Schlosser, Ralf W.; Koul, Rajinder; Shane, Howard; Sorce, James; Brock, Kristofer; Harmon, Ashley; Moerlein, Dorothy; Hearn, Emilia
2014-01-01
Purpose: The effects of animation on naming and identification of graphic symbols for verbs and prepositions were studied in 2 graphic symbol sets in preschoolers. Method: Using a 2 × 2 × 2 × 3 completely randomized block design, preschoolers across three age groups were randomly assigned to combinations of symbol set (Autism Language Program…
The Effect of the Number of Sets on Power Output for Different Loads
Morales-Artacho Antonio J.; Padial Paulino; García-Ramos Amador; Feriche Belén
2015-01-01
There is much debate concerning the optimal load (OL) for power training. The purpose of this study was to investigate the effect of the number of sets performed for a given load on mean power output (Pmean). Fourteen physically active men performed 3 sets of 3 bench-press repetitions with 30, 40 and 50 kg. The highest mean power value (Pmax) across all loads and Pmean were compared when data were taken from the first set at each absolute load vs. from the best of three sets performed. Pmean ...
Canning, Tom
2011-01-01
During extensive prosthodontic treatment, the use of an accurately adjusted articulator is recommended to simulate mandibular movements. This clinical study was undertaken to assess any possible effect of the underlying skeletal pattern on programming articulator settings.
Renata Bocciardi
2010-01-01
Full Text Available Thiazolidinediones (TZDs, among which Rosiglitazone, are known agonists of the peroxisome-proliferator-activated receptor γ (PPARγ commonly used for treatment of hyperglycemia. A recently published article describing a case report on a patient affected by Fibrodysplasia Ossificans Progressiva (FOP treated with Rosiglitazone has prompted interest for careful analysis of the rational basis of such treatment. This article reviews the effects of PPARγ agonists in relationship with various pathogenic steps that occur during the course of FOP by reviewing the particularly rich literature on the effects of Rosiglitazone, to underscore their relevance to FOP and to consider possible adverse effects.
Chen, Xing
2016-01-01
Projective measurement can increase the entropy of a state $\\rho$, the increased entropy is not only up to the basis of projective measurement, but also has something to do with the properties of the state itself. In this paper we define this increased entropy as basis entropy. And then we discuss the usefulness of this new concept by showing its application in explaining the success probability of Grover's algorithm and the existence of quantum discord. And as shown in the paper, this new co...
Psychology of Agenda-Setting Effects. Mapping the Paths of Information Processing
Maxwell McCombs
2014-01-01
Full Text Available The concept of Need for Orientation introduced in the early years of agenda-setting research provided a psychological explanation for why agenda-setting effects occur in terms of what individuals bring to the media experience that determines the strength of these effects. Until recently, there had been no significant additions to our knowledge about the psychology of agenda-setting effects. However, the concept of Need for Orientation is only one part of the answer to the question about why agenda setting occurs. Recent research outlines a second way to answer the why question by describing the psychological process through which these effects occur. In this review, we integrate four contemporary studies that explicate dual psychological paths that lead to agenda-setting effects at the first and second levels. We then examine how information preferences and selective exposure can be profitably included in the agenda-setting framework. Complementing these new models of information processing and varying attention to media content and presentation cues, an expanded concept of psychological relevance, motivated reasoning goals (accuracy versus directional goals, and issue publics are discussed.
The Effect of the Number of Sets on Power Output for Different Loads
Morales-Artacho Antonio J.
2015-06-01
Full Text Available There is much debate concerning the optimal load (OL for power training. The purpose of this study was to investigate the effect of the number of sets performed for a given load on mean power output (Pmean. Fourteen physically active men performed 3 sets of 3 bench-press repetitions with 30, 40 and 50 kg. The highest mean power value (Pmax across all loads and Pmean were compared when data were taken from the first set at each absolute load vs. from the best of three sets performed. Pmean increased from the first to the third set (from 5.99 ± 0.81 to 6.16 ± 0.96 W·kg−1, p = 0.017, resulting in a main effect of the set number (p 0.05. Pmax and velocity were significantly affected by the method employed to determine Pmean at each load (p < 0.05. These results show a positive effect of the number of sets per load on Pmean, affecting Pmax, OL and potentially power training prescription.
The Effect of the Number of Sets on Power Output for Different Loads.
Morales-Artacho, Antonio J; Padial, Paulino; García-Ramos, Amador; Feriche, Belén
2015-06-27
There is much debate concerning the optimal load (OL) for power training. The purpose of this study was to investigate the effect of the number of sets performed for a given load on mean power output (Pmean). Fourteen physically active men performed 3 sets of 3 bench-press repetitions with 30, 40 and 50 kg. The highest mean power value (Pmax) across all loads and Pmean were compared when data were taken from the first set at each absolute load vs. from the best of three sets performed. Pmean increased from the first to the third set (from 5.99 ± 0.81 to 6.16 ± 0.96 W·kg(-1), p = 0.017), resulting in a main effect of the set number (p 0.05). Pmax and velocity were significantly affected by the method employed to determine Pmean at each load (p < 0.05). These results show a positive effect of the number of sets per load on Pmean, affecting Pmax, OL and potentially power training prescription. PMID:26240658
Korte, E.M. de; Spiekman, M.; Hoes-van Oeffelen, L.; Zande, B. van der; Vissenberg, G.; Huiskes, G.; Kuijt-Evers, L.F.M.
2015-01-01
The effects of pre-set environmental conditions of temperature and lighting on the preferred personal settings, comfort experience and task performance of office workers were investigated in an individually controlled workstation. Twenty subjects performed standardized tasks at a prototype workstati
Differential GPS effectiveness in measuring area and perimeter in forested settings
This study quantifies area and perimeter measurement errors, traverse times, recording intervals, and overall time and cost effectiveness for using a mapping-grade differential Global Positioning System (GPS) receiver in forested settings. We compared two configurations including one that maximized data collection productivity (position dilution of precision (PDOP) 20, signal to noise ratio (SNR 33), and minimum elevation mask 5°) and a second that involved traditional receiver settings that was designed to improve accuracies (PDOP 6, SNR 39, and minimum elevation mask 15°). We determined that averaging 30 positions and using the settings that maximized productivity was the most time effective combination of recording interval and settings. This combination of recording interval and settings proved slightly more cost effective than other traditional surveying methods such as a laser with digital compass and string box. Average absolute per cent area errors when averaging 30 positions and using maximum settings were 2.6% and average absolute per cent perimeter errors were 2.0%. These results should help forest resource professionals more effectively evaluate GPS techniques and receiver configurations. (paper)
Effects of goal setting on fear of failure in young elite athletes
Wikman, Johan Michael; Stelter, Reinhard; Melzer, Marcus;
2014-01-01
This study reports the effects of a goal-setting intervention on fear of failure in young elite athletes. Using the hierarchical model of approach and avoidance motivation as a theoretical vantage point, a goal-setting intervention using mastery-approach goals and existing goalsetting...... recommendations was used as intervention. The goal-setting group (n = 33) attended 12 weekly, one-hour goal-setting sessions, while the control group (n = 16) did not. A Danish version of the short form of the Achievement Motives Scale-Sport was tested with a confirmatory factor analysis and showed good fit. It...... was used to measure fear of failure at baseline, at the end of intervention and at follow-up, 12 weeks after intervention had ended. Results showed that in the goal-setting group, fear of failure decreased significantly from baseline to end of intervention, but increased again from end of intervention...
Earlier work on the chemical basis of mutagenesis led to certain chemical generalities sufficient to explain how certain mutagens such as uv light and hydroxylamine functioned in information transfer systems (replicative, transcriptive and translational). When such modifications were applied to biologically active DNA in a controlled manner biological expression was non-stoichiometric because much of the damage was removed from the DNA by repair systems. Our efforts were then directed to these systems which led to: (1) the isolation, purification and characterization of endonucleases responsible for the first and controlling step in DNA repair - referred to as incision in both M. luteus and E. coli. The biological role of these enzymes was inferred in appropriate mutants; (2) the isolation, purification and characterization of exonucleases responsible for the removal or excision of damaged nucleotides in M. luteus and human placental trophoblasts; (3) the repair of uv damaged biologically active transforming and transfecting DNAs by purified endonucleases, exonucleases, DNA polymerase I and polynucleotide ligase from M. luteus and E. coli; (4) the characterization of the dual gene control for incision phenomenon in M. luteus and E. coli; and (5) isolation, purification and characterization of repair enzymes from human placenta
Lanzhi Li; Xiaohong He; Hongyan Zhang; Zhiming Wang; Congwei Sun; Tongmin Mou; Xinqi Li; Yuanming Zhang; Zhongli Hu
2015-06-01
North Carolina design III (NCIII) is one of the most powerful and widely used mating designs for understanding the genetic basis of heterosis. However, the quantitative trait mapping (QTL) conducted in previous studies with this design was mainly based on analysis of variance (ANOVA), composite interval or multiple interval mapping methods. These methodologies could not investigate all kinds of genetic effects, especially epistatic effects, simultaneously on the whole genome. In this study, with a statistical method for mapping epistatic QTL associated with heterosis using the recombinant inbred line (RIL)-based NCIII design, we conducted QTL mapping for nine agronomic traits of two elite hybrids to characterize the mode of gene action contributing to heterosis on a whole genomewide scale. In total, 23 main-effect QTL (M-QTL) and 23 digenic interactions in IJ (indica × japonica) hybrids, 11 M-QTL and 82 digenic interactions in II (indica × indica) hybrid QTLs were identified in the present study. The variation explained by individual M-QTL or interactions ranged from 2.3 to 11.0%. The number of digenic interactions and the total variation explained by interactions of each trait were larger than those of M-QTL. The augmented genetic effect ratio of most M-QTL and digenic interactions in (L1–L2) data of two backcross populations (L1 and L2) showed complete dominance or overdominance, and in (L1 + L2) data showed an additive effect. Our results indicated that the dominance, overdominance and epistatic effect were important in conditioning the genetic basis of heterosis of the two elite hybrids. The relative contributions of the genetic components varied with traits and the genetic basis of the two hybrids was different.
Potential future impact of a partially effective HIV vaccine in a southern African setting
Phillips, Andrew N; Cambiano, Valentina; Nakagawa, Fumiyo;
2014-01-01
of a realistic future implementation scenario in resource limited settings. METHODS: An individual level model of HIV transmission, progression and the effect of antiretroviral therapy was used to predict the outcome to 2060 of introduction in 2025 of a partially effective vaccine with various...... public health goal....
Testing the effect of defaults on the thermostat settings of OECD employees
We describe a randomized controlled experiment in which the default settings on office thermostats in an OECD office building were manipulated during the winter heating season, and employees' chosen thermostat setting observed over a 6-week period. Using difference-in-differences, panel, and censored regression models (to control for maximum allowable thermostat settings), we find that a 1 °C decrease in the default caused a reduction in the chosen setting by 0.38 °C, on average. Sixty-five percent of this effect could be attributed to office occupant behavior (p-value = 0.044). The difference-in-differences models show that small decreases in the default (1°) led to a greater reduction in chosen settings than large decreases (2°). We also find that office occupants who were more apt to adjust their thermostats prior to the intervention were less susceptible to the default. We conclude that this kind of intervention can increase building-level energy efficiency, and discuss potential explanations and broader policy implications of our findings. - Highlights: • We conduct a randomized controlled trial to test if thermostat defaults affect agent behavior. • Two treatments (schedules of default settings) were tested against a control for 6 weeks at OECD. • Small changes in defaults had a greater effect on chosen settings than larger changes in defaults. • Occupants who frequently changed their thermostats in baseline were less affected by defaults. • Thermostat defaults in office environments can be manipulated to increase energy efficiency