A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

PubMed

Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach. This spatial model constitutes an elegant alternative to voxel-based approaches in neuroimaging studies; not only are their atoms biologically informed, they are also adaptive to high resolutions, represent high dimensions efficiently, and capture long-range spatial dependencies, which are important and challenging objectives for neuroimaging data. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Form and Function in Early Clause-Combining

ERIC Educational Resources Information Center

Lustigman, Lyle; Berman, Ruth A.

2016-01-01

The study characterizes developmental trends in early Hebrew clause-combining (CC) by analyzing the interplay between linguistic form and communicative function in different interactional settings. Analysis applied to all utterances produced by three children aged 2;0-3;0 who combined two or more clauses, either self-initiated or on the basis of…

A comparative study of DFT calculated and experimental UV/Visible spectra for thirty carboline and carbazole based compounds

NASA Astrophysics Data System (ADS)

Zara, Zeenat; Iqbal, Javed; Ayub, Khurshid; Irfan, Muhammad; Mahmood, Athar; Khera, Rasheed Ahmad; Eliasson, Bertil

2017-12-01

A comparative study of UV/Visible spectra of carboline and carbazole derivatives was conducted by employing the Density Functional Theory (DFT) approach. In this study, the geometries of ground and excited states, excitation energy and absorption spectra were estimated by using seven different DFT functional; CAM-B3LYP, B3LYP, MPW1PW91, PBE, B3PW91, WB97XD and HSE06 with 6-31G basis set. Moreover, five different basis sets 3-21G, 6-31G, DGDZVP, DGTZVP and SDD were also investigated with the CAM-B3LYP and WB97XD functional to take out the best combination of functional and basis set. CAM-B3LYP/6-31G and WB97XD/DGDZVP combination were found to have closest agreement with the experimental values of β-carboline derivatives and carbazole derivatives, respectively. This study provided an insight about the electronic characteristics of the selected compounds and provided an effective tool for developing and designing the better UV absorber compounds.

Direct recovery of regional tracer kinetics from temporally inconsistent dynamic ECT projections using dimension-reduced time-activity basis

NASA Astrophysics Data System (ADS)

Maltz, Jonathan S.

2000-11-01

We present an algorithm of reduced computational cost which is able to estimate kinetic model parameters directly from dynamic ECT sinograms made up of temporally inconsistent projections. The algorithm exploits the extreme degree of parameter redundancy inherent in linear combinations of the exponential functions which represent the modes of first-order compartmental systems. The singular value decomposition is employed to find a small set of orthogonal functions, the linear combinations of which are able to accurately represent all modes within the physiologically anticipated range in a given study. The reduced-dimension basis is formed as the convolution of this orthogonal set with a measured input function. The Moore-Penrose pseudoinverse is used to find coefficients of this basis. Algorithm performance is evaluated at realistic count rates using MCAT phantom and clinical 99mTc-teboroxime myocardial study data. Phantom data are modelled as originating from a Poisson process. For estimates recovered from a single slice projection set containing 2.5×105 total counts, recovered tissue responses compare favourably with those obtained using more computationally intensive methods. The corresponding kinetic parameter estimates (coefficients of the new basis) exhibit negligible bias, while parameter variances are low, falling within 30% of the Cramér-Rao lower bound.

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

PubMed

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

2008-06-21

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

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

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

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

General contraction of Gaussian basis sets. II - Atomic natural orbitals and the calculation of atomic and molecular properties

NASA Technical Reports Server (NTRS)

Almlof, Jan; Taylor, Peter R.

1990-01-01

A recently proposed scheme for using natural orbitals from atomic configuration interaction wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outermost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital sets.

Economic communication model set

NASA Astrophysics Data System (ADS)

Zvereva, Olga M.; Berg, Dmitry B.

2017-06-01

This paper details findings from the research work targeted at economic communications investigation with agent-based models usage. The agent-based model set was engineered to simulate economic communications. Money in the form of internal and external currencies was introduced into the models to support exchanges in communications. Every model, being based on the general concept, has its own peculiarities in algorithm and input data set since it was engineered to solve the specific problem. Several and different origin data sets were used in experiments: theoretic sets were estimated on the basis of static Leontief's equilibrium equation and the real set was constructed on the basis of statistical data. While simulation experiments, communication process was observed in dynamics, and system macroparameters were estimated. This research approved that combination of an agent-based and mathematical model can cause a synergetic effect.

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

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

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

2016-08-07

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

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

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

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

General contraction of Gaussian basis sets. Part 2: Atomic natural orbitals and the calculation of atomic and molecular properties

NASA Technical Reports Server (NTRS)

Almloef, Jan; Taylor, Peter R.

1989-01-01

A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.

Quantum-chemical investigation of the structures and electronic spectra of the nucleic acid bases at the coupled cluster CC2 level.

PubMed

Fleig, Timo; Knecht, Stefan; Hättig, Christof

2007-06-28

We study the ground-state structures and singlet- and triplet-excited states of the nucleic acid bases by applying the coupled cluster model CC2 in combination with a resolution-of-the-identity approximation for electron interaction integrals. Both basis set effects and the influence of dynamic electron correlation on the molecular structures are elucidated; the latter by comparing CC2 with Hartree-Fock and Møller-Plesset perturbation theory to second order. Furthermore, we investigate basis set and electron correlation effects on the vertical excitation energies and compare our highest-level results with experiment and other theoretical approaches. It is shown that small basis sets are insufficient for obtaining accurate results for excited states of these molecules and that the CC2 approach to dynamic electron correlation is a reliable and efficient tool for electronic structure calculations on medium-sized molecules.

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

PubMed

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

2017-12-12

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

Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

NASA Astrophysics Data System (ADS)

Langhoff, P. W.; Winstead, C. L.

Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

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

PubMed

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

2005-09-01

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

Science basis for changing forest structure to modify wildfire behavior and severity

Treesearch

Russell T. Graham; Sarah McCaffrey; Theresa B. Jain

2004-01-01

Fire, other disturbances, physical setting, weather, and climate shape the structure and function of forests throughout the Western United States. More than 80 years of fire research have shown that physical setting, fuels, and weather combine to determine wildfire intensity (the rate at which it consumes fuel) and severity (the effect fire has on vegetation, soils,...

Benchmark quality total atomization energies of small polyatomic molecules

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Taylor, Peter R.

1997-05-01

Successive coupled-cluster [CCSD(T)] calculations in basis sets of spdf, spdfg, and spdfgh quality, combined with separate Schwartz-type extrapolations A+B/(l+1/2)α of the self-consistent field (SCF) and correlation energies, permit the calculations of molecular total atomization energies (TAEs) with a mean absolute error of as low as 0.12 kcal/mol. For the largest molecule treated, C2H4, we find ∑D0=532.0 kcal/mol, in perfect agreement with experiment. The aug-cc-pV5Z basis set recovers on average about 99% of the valence correlation contribution to the TAE, and essentially the entire SCF contribution.

Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths.

PubMed

El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas

2013-12-23

A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.

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

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

An unbiased Hessian representation for Monte Carlo PDFs.

PubMed

Carrazza, Stefano; Forte, Stefano; Kassabov, Zahari; Latorre, José Ignacio; Rojo, Juan

We develop a methodology for the construction of a Hessian representation of Monte Carlo sets of parton distributions, based on the use of a subset of the Monte Carlo PDF replicas as an unbiased linear basis, and of a genetic algorithm for the determination of the optimal basis. We validate the methodology by first showing that it faithfully reproduces a native Monte Carlo PDF set (NNPDF3.0), and then, that if applied to Hessian PDF set (MMHT14) which was transformed into a Monte Carlo set, it gives back the starting PDFs with minimal information loss. We then show that, when applied to a large Monte Carlo PDF set obtained as combination of several underlying sets, the methodology leads to a Hessian representation in terms of a rather smaller set of parameters (MC-H PDFs), thereby providing an alternative implementation of the recently suggested Meta-PDF idea and a Hessian version of the recently suggested PDF compression algorithm (CMC-PDFs). The mc2hessian conversion code is made publicly available together with (through LHAPDF6) a Hessian representations of the NNPDF3.0 set, and the MC-H PDF set.

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

NASA Astrophysics Data System (ADS)

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

2004-07-01

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

Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

PubMed Central

Sure, Rebecca; Brandenburg, Jan Gerit

2015-01-01

Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221

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

PubMed Central

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

2016-01-01

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

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

PubMed

Grimme, Stefan; Steinmetz, Marc; Korth, Martin

2007-03-16

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

Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

PubMed

Zhang, Jun; Dolg, Michael

2013-07-09

An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

An auxiliary-field quantum Monte Carlo study of the chromium dimer

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

Purwanto, Wirawan, E-mail: wirawan0@gmail.com; Zhang, Shiwei; Krakauer, Henry

2015-02-14

The chromium dimer (Cr{sub 2}) presents an outstanding challenge for many-body electronic structure methods. Its complicated nature of binding, with a formal sextuple bond and an unusual potential energy curve (PEC), is emblematic of the competing tendencies and delicate balance found in many strongly correlated materials. We present an accurate calculation of the PEC and ground state properties of Cr{sub 2}, using the auxiliary-field quantum Monte Carlo (AFQMC) method. Unconstrained, exact AFQMC calculations are first carried out for a medium-sized but realistic basis set. Elimination of the remaining finite-basis errors and extrapolation to the complete basis set limit are thenmore » achieved with a combination of phaseless and exact AFQMC calculations. Final results for the PEC and spectroscopic constants are in excellent agreement with experiment.« less

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

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

NASA Technical Reports Server (NTRS)

Friedli, C.; Ashcroft, N. W.

1975-01-01

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

Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

PubMed

Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

2014-02-11

An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

Groebner Basis Solutions to Satellite Trajectory Control by Pole Placement

NASA Astrophysics Data System (ADS)

Kukelova, Z.; Krsek, P.; Smutny, V.; Pajdla, T.

2013-09-01

Satellites play an important role, e.g., in telecommunication, navigation and weather monitoring. Controlling their trajectories is an important problem. In [1], an approach to the pole placement for the synthesis of a linear controller has been presented. It leads to solving five polynomial equations in nine unknown elements of the state space matrices of a compensator. This is an underconstrained system and therefore four of the unknown elements need to be considered as free parameters and set to some prior values to obtain a system of five equations in five unknowns. In [1], this system was solved for one chosen set of free parameters with the help of Dixon resultants. In this work, we study and present Groebner basis solutions to this problem of computation of a dynamic compensator for the satellite for different combinations of input free parameters. We show that the Groebner basis method for solving systems of polynomial equations leads to very simple solutions for all combinations of free parameters. These solutions require to perform only the Gauss-Jordan elimination of a small matrix and computation of roots of a single variable polynomial. The maximum degree of this polynomial is not greater than six in general but for most combinations of the input free parameters its degree is even lower. [1] B. Palancz. Application of Dixon resultant to satellite trajectory control by pole placement. Journal of Symbolic Computation, Volume 50, March 2013, Pages 79-99, Elsevier.

Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.

PubMed

Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J

2013-09-01

The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set. Copyright © 2013 Elsevier B.V. All rights reserved.

Adsorption of Emerging Munitions Contaminants on Cellulose Surface: A Combined Theoretical and Experimental Investigation.

PubMed

Shukla, Manoj K; Poda, Aimee

2016-06-01

This manuscript reports results of an integrated theoretical and experimental investigation of adsorption of two emerging contaminants (DNAN and FOX-7) and legacy compound TNT on cellulose surface. Cellulose was modeled as trimeric form of the linear chain of 1 → 4 linked of β-D-glucopyranos in (4)C1 chair conformation. Geometries of modeled cellulose, munitions compounds and their complexes were optimized at the M06-2X functional level of Density Functional Theory using the 6-31G(d,p) basis set in gas phase and in water solution. The effect of water solution was modeled using the CPCM approach. Nature of potential energy surfaces was ascertained through harmonic vibrational frequency analysis. Interaction energies were corrected for basis set superposition error and the 6-311G(d,p) basis set was used. Molecular electrostatic potential mapping was performed to understand the reactivity of the investigated systems. It was predicted that adsorbates will be weakly adsorbed on the cellulose surface in water solution than in the gas phase.

Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

NASA Astrophysics Data System (ADS)

Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.; Sato, S. A.; Rehr, J. J.; Yabana, K.; Prendergast, David

2018-05-01

The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. Potential applications of the LCAO based scheme in the context of extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.

Using Readers' Theatre in the Classroom.

ERIC Educational Resources Information Center

Annarella, Lorie A.

Reader's Theatre can be used to combine basic literature and writing instruction with creative arts. Improvisational playmaking by students, using literature in the form of plays, prose, and poetry, forms the basis of Reader's Theatre. Use of Reader's Theatre in the classroom can: (1) foster deeper understanding of character, setting, and plot…

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

Papajak, Ewa; Truhlar, Donald G.

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

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

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

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

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

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

NASA Astrophysics Data System (ADS)

Spackman, Peter R.; Karton, Amir

2015-05-01

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

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

PubMed

Kolmann, Stephen J; Jordan, Meredith J T

2010-02-07

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

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

NASA Astrophysics Data System (ADS)

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

2010-02-01

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

Validity in Teachers' Summative Assessments

ERIC Educational Resources Information Center

Black, Paul; Harrison, Christine; Hodgen, Jeremy; Marshall, Bethan; Serret, Natasha

2010-01-01

This paper describes some of the findings of a project which set out to explore and develop teachers' understanding and practices in their summative assessments. The focus was on those summative assessments that are used on a regular basis within schools for guiding the progress of pupils and for internal accountability. The project combined both…

Evaluation of a Theory of Instructional Sequences for Physics Instruction

ERIC Educational Resources Information Center

Wackermann, Rainer; Trendel, Georg; Fischer, Hans E.

2010-01-01

The background of the study is the theory of "basis models of teaching and learning", a comprehensive set of models of learning processes which includes, for example, learning through experience and problem-solving. The combined use of different models of learning processes has not been fully investigated and it is frequently not clear…

Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

DOE PAGES

Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.; ...

2018-02-07

The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. As a result, potential applications of the LCAO based scheme in the context ofmore » extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.« less

Velocity-gauge real-time TDDFT within a numerical atomic orbital basis set

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

Pemmaraju, C. D.; Vila, F. D.; Kas, J. J.

The interaction of laser fields with solid-state systems can be modeled efficiently within the velocity-gauge formalism of real-time time dependent density functional theory (RT-TDDFT). In this article, we discuss the implementation of the velocity-gauge RT-TDDFT equations for electron dynamics within a linear combination of atomic orbitals (LCAO) basis set framework. Numerical results obtained from our LCAO implementation, for the electronic response of periodic systems to both weak and intense laser fields, are compared to those obtained from established real-space grid and Full-Potential Linearized Augmented Planewave approaches. As a result, potential applications of the LCAO based scheme in the context ofmore » extreme ultra-violet and soft X-ray spectroscopies involving core-electronic excitations are discussed.« less

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

NASA Astrophysics Data System (ADS)

Kruse, Holger; Grimme, Stefan

2012-04-01

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

Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements

PubMed Central

2015-01-01

We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly developed code is used to calculate the one-, two-, three- and four-photon absorption cross sections of para-nitroaniline and para-nitroaminostilbene, making this the first treatment of four-photon absorption in the framework of response theory. We find that the calculated multiphoton absorption cross sections are not very sensitive to the size of the basis set as long as a reasonably large basis set with diffuse functions is used. The choice of exchange–correlation functional, however, significantly affects the calculated cross sections of both charge-transfer transitions and other transitions, in particular, for the larger para-nitroaminostilbene molecule. We therefore recommend the use of a range-separated exchange–correlation functional in combination with the augmented correlation-consistent double-ζ basis set aug-cc-pVDZ for the calculation of multiphoton absorption properties. PMID:25821415

Functional Parallel Factor Analysis for Functions of One- and Two-dimensional Arguments.

PubMed

Choi, Ji Yeh; Hwang, Heungsun; Timmerman, Marieke E

2018-03-01

Parallel factor analysis (PARAFAC) is a useful multivariate method for decomposing three-way data that consist of three different types of entities simultaneously. This method estimates trilinear components, each of which is a low-dimensional representation of a set of entities, often called a mode, to explain the maximum variance of the data. Functional PARAFAC permits the entities in different modes to be smooth functions or curves, varying over a continuum, rather than a collection of unconnected responses. The existing functional PARAFAC methods handle functions of a one-dimensional argument (e.g., time) only. In this paper, we propose a new extension of functional PARAFAC for handling three-way data whose responses are sequenced along both a two-dimensional domain (e.g., a plane with x- and y-axis coordinates) and a one-dimensional argument. Technically, the proposed method combines PARAFAC with basis function expansion approximations, using a set of piecewise quadratic finite element basis functions for estimating two-dimensional smooth functions and a set of one-dimensional basis functions for estimating one-dimensional smooth functions. In a simulation study, the proposed method appeared to outperform the conventional PARAFAC. We apply the method to EEG data to demonstrate its empirical usefulness.

Heavier alkali-metal monosulfides (KS, RbS, CsS, and FrS) and their cations.

PubMed

Lee, Edmond P F; Wright, Timothy G

2005-10-08

The heavier alkali-metal monosulfides (KS, RbS, CsS, and FrS) have been studied by high-level ab initio calculations. The RCCSD(T) method has been employed, combined with large flexible valence basis sets. All-electron basis sets are used for potassium and sulfur, with effective core potentials being used for the other metals, describing the core electrons. Potential-energy curves are calculated for the lowest two neutral and cationic states: all neutral monosulfide species have a (2)Pi ground state, in contrast with the alkali-metal monoxide species, which undergo a change in the electronic ground state from (2)Pi to (2)Sigma(+) as the group is descended. In the cases of KS, RbS, and CsS, spin-orbit curves are also calculated. We also calculate potential-energy curves for the lowest (3)Sigma(-) and (3)Pi states of the cations. From the potential-energy curves, spectroscopic constants are derived, and for KS the spectroscopic results are compared to experimental spectroscopic values. Ionization energies, dissociation energies, and heats of formation are also calculated; for KS, we explore the effects of relativity and basis set extrapolation on these values.

Algebraic Approaches for Scalable End-to-End Monitoring and Diagnosis

NASA Astrophysics Data System (ADS)

Zhao, Yao; Chen, Yan

The rigidity of the Internet architecture led to flourish in the research of end-to-end based systems. In this chapter, we describe a linear algebra-based end-to-end monitoring and diagnosis system. We first propose a tomography-based overlay monitoring system (TOM). Given n end hosts, TOM selectively monitors a basis set of O(nlogn) paths out of all n(n - 1) end-to-end paths. Any end-to-end path can be written as a unique linear combination of paths in the basis set. Consequently, by monitoring loss rates for the paths in the basis set, TOM infers loss rates for all end-to-end paths. Furthermore, leveraging on the scalable measurements from the TOM system, we propose the Least-biased End-to-End Network Diagnosis (in short, LEND) system. We define a minimal identifiable link sequence (MILS) as a link sequence of minimal length whose properties can be uniquely identified from end-to-end measurements. LEND applies an algebraic approach to find out the MILSes and infers the properties of the MILSes efficiently. This also means LEND system achieves the finest diagnosis granularity under the least biased statistical assumptions.

Correlation consistent basis sets for the atoms In–Xe

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

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

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

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

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

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

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

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

A systematic way for the cost reduction of density fitting methods

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

Kállay, Mihály, E-mail: kallay@mail.bme.hu

2014-12-28

We present a simple approach for the reduction of the size of auxiliary basis sets used in methods exploiting the density fitting (resolution of identity) approximation for electron repulsion integrals. Starting out of the singular value decomposition of three-center two-electron integrals, new auxiliary functions are constructed as linear combinations of the original fitting functions. The new functions, which we term natural auxiliary functions (NAFs), are analogous to the natural orbitals widely used for the cost reduction of correlation methods. The use of the NAF basis enables the systematic truncation of the fitting basis, and thereby potentially the reduction of themore » computational expenses of the methods, though the scaling with the system size is not altered. The performance of the new approach has been tested for several quantum chemical methods. It is demonstrated that the most pronounced gain in computational efficiency can be expected for iterative models which scale quadratically with the size of the fitting basis set, such as the direct random phase approximation. The approach also has the promise of accelerating local correlation methods, for which the processing of three-center Coulomb integrals is a bottleneck.« less

Monitoring the size and protagonists of the drug market: combining supply and demand data sources and estimates.

PubMed

Rossi, Carla

2013-06-01

The size of the illicit drug market is an important indicator to assess the impact on society of an important part of the illegal economy and to evaluate drug policy and law enforcement interventions. The extent of illicit drug use and of the drug market can essentially only be estimated by indirect methods based on indirect measures and on data from various sources, as administrative data sets and surveys. The combined use of several methodologies and data sets allows to reduce biases and inaccuracies of estimates obtained on the basis of each of them separately. This approach has been applied to Italian data. The estimation methods applied are capture-recapture methods with latent heterogeneity and multiplier methods. Several data sets have been used, both administrative and survey data sets. First, the retail dealer prevalence has been estimated on the basis of administrative data, then the user prevalence by multiplier methods. Using information about behaviour of dealers and consumers from survey data, the average amount of a substance used or sold and the average unit cost have been estimated and allow estimating the size of the drug market. The estimates have been obtained using a supply-side approach and a demand-side approach and have been compared. These results are in turn used for estimating the interception rate for the different substances in term of the value of the substance seized with respect to the total value of the substance to be sold at retail prices.

Yielding physically-interpretable emulators - A Sparse PCA approach

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics.

PubMed

Darkhovskii, M B; Pletnev, I V; Tchougréeff, A L

2003-11-15

A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie-Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d-shell. The quantum mechanical EHCF part is limited to the metal ion d-shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. Copyright 2003 Wiley Periodicals, Inc.

Climatology of ozone at altitudes from 19,000 at 59,000 feet based on combined GASP and ozonesonde data

NASA Technical Reports Server (NTRS)

Jasperson, W. H.; Nastrom, G. D.; Holdeman, J. D.

1984-01-01

A climatology of ozone for altitudes from FL190 to FL590 (19,000 to 59,000 ft) is presented. Climatological tables are given in two appendixes: one with d deg latitude resolution on a monthly basis, and one with 10 deg latitude resolution on a seasonal basis. Data were taken from 11,472 balloon-borne ozonesondes launched at 60 stations from 1963 to 1980 and from over 160,000 observations made by the Global Atmospheric Sampling Program on 4417 commercial airliner flights from 1975 to 1979. Case study and statistical comparisons of results from these two data sets showed that they are compatible and can be combined. Several examples of analyses that can be made by using the tabulated data are given and discussed.

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

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

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

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

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

Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

2015-03-07

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

[Study on the detection of active ingredient contents of Paecilomyces hepiali mycelium via near infrared spectroscopy].

PubMed

Teng, Wei-Zhuo; Song, Jia; Meng, Fan-Xin; Meng, Qing-Fan; Lu, Jia-Hui; Hu, Shuang; Teng, Li-Rong; Wang, Di; Xie, Jing

2014-10-01

Partial least squares (PLS) and radial basis function neural network (RBFNN) combined with near infrared spectros- copy (NIR) were applied to develop models for cordycepic acid, polysaccharide and adenosine analysis in Paecilomyces hepialid fermentation mycelium. The developed models possess well generalization and predictive ability which can be applied for crude drugs and related productions determination. During the experiment, 214 Paecilomyces hepialid mycelium samples were obtained via chemical mutagenesis combined with submerged fermentation. The contents of cordycepic acid, polysaccharide and adenosine were determined via traditional methods and the near infrared spectroscopy data were collected. The outliers were removed and the numbers of calibration set were confirmed via Monte Carlo partial least square (MCPLS) method. Based on the values of degree of approach (Da), both moving window partial least squares (MWPLS) and moving window radial basis function neural network (MWRBFNN) were applied to optimize characteristic wavelength variables, optimum preprocessing methods and other important variables in the models. After comparison, the RBFNN, RBFNN and PLS models were developed successfully for cordycepic acid, polysaccharide and adenosine detection, and the correlation between reference values and predictive values in both calibration set (R2c) and validation set (R2p) of optimum models was 0.9417 and 0.9663, 0.9803 and 0.9850, and 0.9761 and 0.9728, respectively. All the data suggest that these models possess well fitness and predictive ability.

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

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

Biomass equations for major tree species of the Northeast

Treesearch

Louise M. Tritton; James W. Hornbeck

1982-01-01

Regression equations are used in both forestry and ecosystem studies to estimate tree biomass from field measurements of dbh (diameter at breast height) or a combination of dbh and height. Literature on biomass is reviewed, and 178 sets of publish equation for 25 species common to the Northeastern Unites States are listed. On the basis of these equations, estimates of...

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

PubMed

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

2011-06-07

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

Novel transform for image description and compression with implementation by neural architectures

NASA Astrophysics Data System (ADS)

Ben-Arie, Jezekiel; Rao, Raghunath K.

1991-10-01

A general method for signal representation using nonorthogonal basis functions that are composed of Gaussians are described. The Gaussians can be combined into groups with predetermined configuration that can approximate any desired basis function. The same configuration at different scales forms a set of self-similar wavelets. The general scheme is demonstrated by representing a natural signal employing an arbitrary basis function. The basic methodology is demonstrated by two novel schemes for efficient representation of 1-D and 2- D signals using Gaussian basis functions (BFs). Special methods are required here since the Gaussian functions are nonorthogonal. The first method employs a paradigm of maximum energy reduction interlaced with the A* heuristic search. The second method uses an adaptive lattice system to find the minimum-squared error of the BFs onto the signal, and a lateral-vertical suppression network to select the most efficient representation in terms of data compression.

Cholesky-decomposed density MP2 with density fitting: Accurate MP2 and double-hybrid DFT energies for large systems

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

Maurer, Simon A.; Clin, Lucien; Ochsenfeld, Christian, E-mail: christian.ochsenfeld@uni-muenchen.de

2014-06-14

Our recently developed QQR-type integral screening is introduced in our Cholesky-decomposed pseudo-densities Møller-Plesset perturbation theory of second order (CDD-MP2) method. We use the resolution-of-the-identity (RI) approximation in combination with efficient integral transformations employing sparse matrix multiplications. The RI-CDD-MP2 method shows an asymptotic cubic scaling behavior with system size and a small prefactor that results in an early crossover to conventional methods for both small and large basis sets. We also explore the use of local fitting approximations which allow to further reduce the scaling behavior for very large systems. The reliability of our method is demonstrated on test sets formore » interaction and reaction energies of medium sized systems and on a diverse selection from our own benchmark set for total energies of larger systems. Timings on DNA systems show that fast calculations for systems with more than 500 atoms are feasible using a single processor core. Parallelization extends the range of accessible system sizes on one computing node with multiple cores to more than 1000 atoms in a double-zeta basis and more than 500 atoms in a triple-zeta basis.« less

Guided ion beam and theoretical studies of the bond energy of SmS+

NASA Astrophysics Data System (ADS)

Armentrout, P. B.; Demireva, Maria; Peterson, Kirk A.

2017-12-01

Previous work has shown that atomic samarium cations react with carbonyl sulfide to form SmS+ + CO in an exothermic and barrierless process. To characterize this reaction further, the bond energy of SmS+ is determined in the present study using guided ion beam tandem mass spectrometry. Reactions of SmS+ with Xe, CO, and O2 are examined. Results for collision-induced dissociation processes with all three molecules along with the endothermicity of the SmS+ + CO → Sm+ + COS exchange reaction are combined to yield D0(Sm+-S) = 3.37 ± 0.20 eV. The CO and O2 reactions also yield a SmSO+ product, with measured endothermicities that indicate D0(SSm+-O) = 3.73 ± 0.16 eV and D0(OSm+-S) = 1.38 ± 0.27 eV. The SmS+ bond energy is compared with theoretical values characterized at several levels of theory, including CCSD(T) complete basis set extrapolations using all-electron basis sets. Multireference configuration interaction calculations with explicit spin-orbit calculations along with composite thermochemistry using the Feller-Peterson-Dixon method and all-electron basis sets were also explored for SmS+, and for comparison, SmO, SmO+, and EuO.

Guided ion beam and theoretical studies of the bond energy of SmS.

PubMed

Armentrout, P B; Demireva, Maria; Peterson, Kirk A

2017-12-07

Previous work has shown that atomic samarium cations react with carbonyl sulfide to form SmS + + CO in an exothermic and barrierless process. To characterize this reaction further, the bond energy of SmS + is determined in the present study using guided ion beam tandem mass spectrometry. Reactions of SmS + with Xe, CO, and O 2 are examined. Results for collision-induced dissociation processes with all three molecules along with the endothermicity of the SmS + + CO → Sm + + COS exchange reaction are combined to yield D 0 (Sm + -S) = 3.37 ± 0.20 eV. The CO and O 2 reactions also yield a SmSO + product, with measured endothermicities that indicate D 0 (SSm + -O) = 3.73 ± 0.16 eV and D 0 (OSm + -S) = 1.38 ± 0.27 eV. The SmS + bond energy is compared with theoretical values characterized at several levels of theory, including CCSD(T) complete basis set extrapolations using all-electron basis sets. Multireference configuration interaction calculations with explicit spin-orbit calculations along with composite thermochemistry using the Feller-Peterson-Dixon method and all-electron basis sets were also explored for SmS + , and for comparison, SmO, SmO + , and EuO.

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

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

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

Security of quantum key distribution with iterative sifting

NASA Astrophysics Data System (ADS)

Tamaki, Kiyoshi; Lo, Hoi-Kwong; Mizutani, Akihiro; Kato, Go; Lim, Charles Ci Wen; Azuma, Koji; Curty, Marcos

2018-01-01

Several quantum key distribution (QKD) protocols employ iterative sifting. After each quantum transmission round, Alice and Bob disclose part of their setting information (including their basis choices) for the detected signals. This quantum phase then ends when the basis dependent termination conditions are met, i.e., the numbers of detected signals per basis exceed certain pre-agreed threshold values. Recently, however, Pfister et al (2016 New J. Phys. 18 053001) showed that the basis dependent termination condition makes QKD insecure, especially in the finite key regime, and they suggested to disclose all the setting information after finishing the quantum phase. However, this protocol has two main drawbacks: it requires that Alice possesses a large memory, and she also needs to have some a priori knowledge about the transmission rate of the quantum channel. Here we solve these two problems by introducing a basis-independent termination condition to the iterative sifting in the finite key regime. The use of this condition, in combination with Azuma’s inequality, provides a precise estimation on the amount of privacy amplification that needs to be applied, thus leading to the security of QKD protocols, including the loss-tolerant protocol (Tamaki et al 2014 Phys. Rev. A 90 052314), with iterative sifting. Our analysis indicates that to announce the basis information after each quantum transmission round does not compromise the key generation rate of the loss-tolerant protocol. Our result allows the implementation of wider classes of classical post-processing techniques in QKD with quantified security.

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

NASA Astrophysics Data System (ADS)

Chmela, Jiří; Harding, Michael E.

2018-06-01

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

Fast and accurate 3D tensor calculation of the Fock operator in a general basis

NASA Astrophysics Data System (ADS)

Khoromskaia, V.; Andrae, D.; Khoromskij, B. N.

2012-11-01

The present paper contributes to the construction of a “black-box” 3D solver for the Hartree-Fock equation by the grid-based tensor-structured methods. It focuses on the calculation of the Galerkin matrices for the Laplace and the nuclear potential operators by tensor operations using the generic set of basis functions with low separation rank, discretized on a fine N×N×N Cartesian grid. We prove the Ch2 error estimate in terms of mesh parameter, h=O(1/N), that allows to gain a guaranteed accuracy of the core Hamiltonian part in the Fock operator as h→0. However, the commonly used problem adapted basis functions have low regularity yielding a considerable increase of the constant C, hence, demanding a rather large grid-size N of about several tens of thousands to ensure the high resolution. Modern tensor-formatted arithmetics of complexity O(N), or even O(logN), practically relaxes the limitations on the grid-size. Our tensor-based approach allows to improve significantly the standard basis sets in quantum chemistry by including simple combinations of Slater-type, local finite element and other basis functions. Numerical experiments for moderate size organic molecules show efficiency and accuracy of grid-based calculations to the core Hamiltonian in the range of grid parameter N3˜1015.

Renormalization, conformal ward identities and the origin of a conformal anomaly pole

NASA Astrophysics Data System (ADS)

Corianò, Claudio; Maglio, Matteo Maria

2018-06-01

We investigate the emergence of a conformal anomaly pole in conformal field theories in the case of the TJJ correlator. We show how it comes to be generated in dimensional renormalization, using a basis of 13 form factors (the F-basis), where only one of them requires renormalization (F13), extending previous studies. We then combine recent results on the structure of the non-perturbative solutions of the conformal Ward identities (CWI's) for the TJJ in momentum space, expressed in terms of a minimal set of 4 form factors (A-basis), with the properties of the F-basis, and show how the singular behaviour of the corresponding form factors in both basis can be related. The result proves the centrality of such massless effective interactions induced by the anomaly, which have recently found realization in solid state, in the theory of topological insulators and of Weyl semimetals. This pattern is confirmed in massless abelian and nonabelian theories (QED and QCD) investigated at one-loop.

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

PubMed

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

2009-06-09

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

Actively addressed single pixel full-colour plasmonic display

NASA Astrophysics Data System (ADS)

Franklin, Daniel; Frank, Russell; Wu, Shin-Tson; Chanda, Debashis

2017-05-01

Dynamic, colour-changing surfaces have many applications including displays, wearables and active camouflage. Plasmonic nanostructures can fill this role by having the advantages of ultra-small pixels, high reflectivity and post-fabrication tuning through control of the surrounding media. However, previous reports of post-fabrication tuning have yet to cover a full red-green-blue (RGB) colour basis set with a single nanostructure of singular dimensions. Here, we report a method which greatly advances this tuning and demonstrates a liquid crystal-plasmonic system that covers the full RGB colour basis set, only as a function of voltage. This is accomplished through a surface morphology-induced, polarization-dependent plasmonic resonance and a combination of bulk and surface liquid crystal effects that manifest at different voltages. We further demonstrate the system's compatibility with existing LCD technology by integrating it with a commercially available thin-film-transistor array. The imprinted surface interfaces readily with computers to display images as well as video.

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

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

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

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

PubMed

Lemke, Kono H

2017-06-21

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

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

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

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

Generalization of multifractal theory within quantum calculus

NASA Astrophysics Data System (ADS)

Olemskoi, A.; Shuda, I.; Borisyuk, V.

2010-03-01

On the basis of the deformed series in quantum calculus, we generalize the partition function and the mass exponent of a multifractal, as well as the average of a random variable distributed over a self-similar set. For the partition function, such expansion is shown to be determined by binomial-type combinations of the Tsallis entropies related to manifold deformations, while the mass exponent expansion generalizes the known relation τq=Dq(q-1). We find the equation for the set of averages related to ordinary, escort, and generalized probabilities in terms of the deformed expansion as well. Multifractals related to the Cantor binomial set, exchange currency series, and porous-surface condensates are considered as examples.

[Ionization energies and infrared spectra studies of histidine using density functional theory].

PubMed

Hu, Qiong; Wang, Guo-Ying; Liu, Gang; Ou, Jia-Ming; Wang, Rui-Li

2010-05-01

Histidines provide axial ligands to the primary electron donors in photosynthetic reaction centers (RCs) and play an important role in the protein environments of these donors. In this paper the authors present a systematic study of ionization energies and vibrational properties of histidine using hybrid density functional theory (DFT). All calculations were undertaken by using B3LYP method in combination with four basis sets: 6-31G(d), 6-31G(df, p), 6-31+G(d) and 6-311+G(2d, 2p) with the aim to investigate how the basis sets influence the calculation results. To investigate solvent effects and gain a detailed understanding of marker bands of histidine, the ionization energies of histidine and the vibrational frequencies of histidine which are unlabeled and 13C, 15N, and 2H labeled in the gas phase, CCl4, protein environment, THF and water solution, which span a wide range of dielectric constant, were also calculated. Our results showed that: (1) The main geometry parameters of histidine were impacted by basis sets and mediums, and C2-N3 and N3-C4 bond of imidazole ring of histidine side chain display the maximum bond lengths in the gas phase; (2) single point energies and frequencies calculated were decreased while ionization energies increased with the increasing level of basis sets and diffuse function applied in the same solvent; (3) with the same computational method, the higher the dielectric constant of the solvent used, the lower the ionization energy and vibrational frequency and the higher the intensity obtained. In addition, calculated ionization energy in the gas phase and marker bands of histidine as well as frequency shift upon 13C and 15N labeling at the computationally more expensive 6-311+G(2d, 2p) level are in good agreement with experimental observations available in literatures. All calculations indicated that the results calculated by using higher level basis set with diffuse function were more accurate and closer to the experimental value. In conclusion, the results provide useful information for the further studies of the functional and vibrational properties of chlorophyll-a ligated to histidine residue in photosynthetic reaction center.

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

PubMed

Gaspari, Roberto; Rapallo, Arnaldo

2008-06-28

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

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets.

PubMed

Tillmar, Andreas O; Phillips, Chris

2017-01-01

Advances in massively parallel sequencing technology have enabled the combination of a much-expanded number of DNA markers (notably STRs and SNPs in one or combined multiplexes), with the aim of increasing the weight of evidence in forensic casework. However, when data from multiple loci on the same chromosome are used, genetic linkage can affect the final likelihood calculation. In order to study the effect of linkage for different sets of markers we developed the biostatistical tool ILIR, (Impact of Linkage on forensic markers for Identity and Relationship tests). The ILIR tool can be used to study the overall impact of genetic linkage for an arbitrary set of markers used in forensic testing. Application of ILIR can be useful during marker selection and design of new marker panels, as well as being highly relevant for existing marker sets as a way to properly evaluate the effects of linkage on a case-by-case basis. ILIR, implemented via the open source platform R, includes variation and genomic position reference data for over 40 STRs and 140 SNPs, combined with the ability to include additional forensic markers of interest. The use of the software is demonstrated with examples from several different established marker sets (such as the expanded CODIS core loci) including a review of the interpretation of linked genetic data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Ensemble Methods for Classification of Physical Activities from Wrist Accelerometry.

PubMed

Chowdhury, Alok Kumar; Tjondronegoro, Dian; Chandran, Vinod; Trost, Stewart G

2017-09-01

To investigate whether the use of ensemble learning algorithms improve physical activity recognition accuracy compared to the single classifier algorithms, and to compare the classification accuracy achieved by three conventional ensemble machine learning methods (bagging, boosting, random forest) and a custom ensemble model comprising four algorithms commonly used for activity recognition (binary decision tree, k nearest neighbor, support vector machine, and neural network). The study used three independent data sets that included wrist-worn accelerometer data. For each data set, a four-step classification framework consisting of data preprocessing, feature extraction, normalization and feature selection, and classifier training and testing was implemented. For the custom ensemble, decisions from the single classifiers were aggregated using three decision fusion methods: weighted majority vote, naïve Bayes combination, and behavior knowledge space combination. Classifiers were cross-validated using leave-one subject out cross-validation and compared on the basis of average F1 scores. In all three data sets, ensemble learning methods consistently outperformed the individual classifiers. Among the conventional ensemble methods, random forest models provided consistently high activity recognition; however, the custom ensemble model using weighted majority voting demonstrated the highest classification accuracy in two of the three data sets. Combining multiple individual classifiers using conventional or custom ensemble learning methods can improve activity recognition accuracy from wrist-worn accelerometer data.

Tight-binding model for borophene and borophane

NASA Astrophysics Data System (ADS)

Nakhaee, M.; Ketabi, S. A.; Peeters, F. M.

2018-03-01

Starting from the simplified linear combination of atomic orbitals method in combination with first-principles calculations, we construct a tight-binding (TB) model in the two-centre approximation for borophene and hydrogenated borophene (borophane). The Slater and Koster approach is applied to calculate the TB Hamiltonian of these systems. We obtain expressions for the Hamiltonian and overlap matrix elements between different orbitals for the different atoms and present the SK coefficients in a nonorthogonal basis set. An anisotropic Dirac cone is found in the band structure of borophane. We derive a Dirac low-energy Hamiltonian and compare the Fermi velocities with that of graphene.

On-line diagnosis of sequential systems, 3

NASA Technical Reports Server (NTRS)

Sundstrom, R. J.

1975-01-01

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

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

PubMed

Saller, Maximilian A C; Habershon, Scott

2017-07-11

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

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

PubMed

Mitin, Alexander V

2013-09-05

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

How Many Environmental Impact Indicators Are Needed in the Evaluation of Product Life Cycles?

PubMed

Steinmann, Zoran J N; Schipper, Aafke M; Hauck, Mara; Huijbregts, Mark A J

2016-04-05

Numerous indicators are currently available for environmental impact assessments, especially in the field of Life Cycle Impact Assessment (LCIA). Because decision-making on the basis of hundreds of indicators simultaneously is unfeasible, a nonredundant key set of indicators representative of the overall environmental impact is needed. We aimed to find such a nonredundant set of indicators based on their mutual correlations. We have used Principal Component Analysis (PCA) in combination with an optimization algorithm to find an optimal set of indicators out of 135 impact indicators calculated for 976 products from the ecoinvent database. The first four principal components covered 92% of the variance in product rankings, showing the potential for indicator reduction. The same amount of variance (92%) could be covered by a minimal set of six indicators, related to climate change, ozone depletion, the combined effects of acidification and eutrophication, terrestrial ecotoxicity, marine ecotoxicity, and land use. In comparison, four commonly used resource footprints (energy, water, land, materials) together accounted for 84% of the variance in product rankings. We conclude that the plethora of environmental indicators can be reduced to a small key set, representing the major part of the variation in environmental impacts between product life cycles.

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

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

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

2016-07-28

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

An integrated theoretical and experimental investigation of insensitive munition compounds adsorption on cellulose, cellulose triacetate, chitin and chitosan surfaces.

PubMed

Gurtowski, Luke A; Griggs, Chris S; Gude, Veera G; Shukla, Manoj K

2018-02-01

This manuscript reports results of combined computational chemistry and batch adsorption investigation of insensitive munition compounds, 2,4-dinitroanisole (DNAN), triaminotrinitrobenzene (TATB), 1,1-diamino-2,2-dinitroethene (FOX-7) and nitroguanidine (NQ), and traditional munition compound 2,4,6-trinitrotoluene (TNT) on the surfaces of cellulose, cellulose triacetate, chitin and chitosan biopolymers. Cellulose, cellulose triacetate, chitin and chitosan were modeled as trimeric form of the linear chain of 4 C 1 chair conformation of β-d-glucopyranos, its triacetate form, β-N-acetylglucosamine and D-glucosamine, respectively, in the 1➔4 linkage. Geometries were optimized at the M062X functional level of the density functional theory (DFT) using the 6-31G(d,p) basis set in the gas phase and in the bulk water solution using the conductor-like polarizable continuum model (CPCM) approach. The nature of potential energy surfaces of the optimized geometries were ascertained through the harmonic vibrational frequency analysis. The basis set superposition error (BSSE) corrected interaction energies were obtained using the 6-311G(d,p) basis set at the same theoretical level. The computed BSSE in the gas phase was used to correct interaction energy in the bulk water solution. Computed and experimental results regarding the ability of considered surfaces in adsorbing the insensitive munitions compounds are discussed. Copyright © 2017. Published by Elsevier B.V.

Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT-GIAO calculations

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona

2009-09-01

Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.

SIEST-A-RT: a study of vacancy diffusion in crystalline silicon using a local-basis first-principle (SIESTA) activation technique (ART).

NASA Astrophysics Data System (ADS)

El Mellouhi, Fedwa; Mousseau, Normand; Ordejón, Pablo

2003-03-01

We report on a first-principle study of vacancy-induced self-diffusion in crystalline silicon. Our simulations are performed on supercells containing 63 and 215 atoms. We generate the diffusion paths using the activation-relaxation technique (ART) [1], which can sample efficiently the energy landscape of complex systems. The forces and energy are evaluated using SIESTA [2], a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible numerical linear combination of atomic orbitals basis set. Combining these two methods allows us to identify diffusion paths that would not be reachable with this degree of accuracy, using other methods. After a full relaxation of the neutral vacancy, we proceed to search for local diffusion paths. We identify various mechanisms like the formation of the four fold coordinated defect, and the recombination of dangling bonds by WWW process. The diffusion of the vacancy proceeds by hops to first nearest neighbor with an energy barrier of 0.69 eV. This work is funded in part by NSERC and NATEQ. NM is a Cottrell Scholar of the Research Corporation. [1] G. T. Barkema and N. Mousseau, Event-based relaxation of continuous disordered systems, Phys. Rev. Lett. 77, 4358 (1996); N. Mousseau and G. T. Barkema, Traveling through potential energy landscapes of disordered materials: ART, Phys. Rev. E 57, 2419 (1998). [2] Density functional method for very large systems with LCAO basis sets D. Sánchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quant. Chem. 65, 453 (1997).

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

NASA Astrophysics Data System (ADS)

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

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

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

PubMed Central

Yim, Yung-Chang; Eyring, Henry

1981-01-01

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

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

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

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

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

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

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

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

Combining Gene Signatures Improves Prediction of Breast Cancer Survival

PubMed Central

Zhao, Xi; Naume, Bjørn; Langerød, Anita; Frigessi, Arnoldo; Kristensen, Vessela N.; Børresen-Dale, Anne-Lise; Lingjærde, Ole Christian

2011-01-01

Background Several gene sets for prediction of breast cancer survival have been derived from whole-genome mRNA expression profiles. Here, we develop a statistical framework to explore whether combination of the information from such sets may improve prediction of recurrence and breast cancer specific death in early-stage breast cancers. Microarray data from two clinically similar cohorts of breast cancer patients are used as training (n = 123) and test set (n = 81), respectively. Gene sets from eleven previously published gene signatures are included in the study. Principal Findings To investigate the relationship between breast cancer survival and gene expression on a particular gene set, a Cox proportional hazards model is applied using partial likelihood regression with an L2 penalty to avoid overfitting and using cross-validation to determine the penalty weight. The fitted models are applied to an independent test set to obtain a predicted risk for each individual and each gene set. Hierarchical clustering of the test individuals on the basis of the vector of predicted risks results in two clusters with distinct clinical characteristics in terms of the distribution of molecular subtypes, ER, PR status, TP53 mutation status and histological grade category, and associated with significantly different survival probabilities (recurrence: p = 0.005; breast cancer death: p = 0.014). Finally, principal components analysis of the gene signatures is used to derive combined predictors used to fit a new Cox model. This model classifies test individuals into two risk groups with distinct survival characteristics (recurrence: p = 0.003; breast cancer death: p = 0.001). The latter classifier outperforms all the individual gene signatures, as well as Cox models based on traditional clinical parameters and the Adjuvant! Online for survival prediction. Conclusion Combining the predictive strength of multiple gene signatures improves prediction of breast cancer survival. The presented methodology is broadly applicable to breast cancer risk assessment using any new identified gene set. PMID:21423775

Goce and Its Role in Combined Global High Resolution Gravity Field Determination

NASA Astrophysics Data System (ADS)

Fecher, T.; Pail, R.; Gruber, T.

2013-12-01

Combined high-resolution gravity field models serve as a mandatory basis to describe static and dynamic processes in system Earth. Ocean dynamics can be modeled referring to a high-accurate geoid as reference surface, solid earth processes are initiated by the gravity field. Also geodetic disciplines such as height system determination depend on high-precise gravity field information. To fulfill the various requirements concerning resolution and accuracy, any kind of gravity field information, that means satellite as well as terrestrial and altimetric gravity field observations have to be included in one combination process. A key role is here reserved for GOCE observations, which contribute with its optimal signal content in the long to medium wavelength part and enable a more accurate gravity field determination than ever before especially in areas, where no high-accurate terrestrial gravity field observations are available, such as South America, Asia or Africa. For our contribution we prepare a combined high-resolution gravity field model up to d/o 720 based on full normal equation including recent GOCE, GRACE and terrestrial / altimetric data. For all data sets, normal equations are set up separately, relative weighted to each other in the combination step and solved. This procedure is computationally challenging and can only be performed using super computers. We put special emphasis on the combination process, for which we modified especially our procedure to include GOCE data optimally in the combination. Furthermore we modified our terrestrial/altimetric data sets, what should result in an improved outcome. With our model, in which we included the newest GOCE TIM4 gradiometry results, we can show how GOCE contributes to a combined gravity field solution especially in areas of poor terrestrial data coverage. The model is validated by independent GPS leveling data in selected regions as well as computation of the mean dynamic topography over the oceans. Further, we analyze the statistical error estimates derived from full covariance propagation and compare them with the absolute validation with independent data sets.

Combinations of SNP genotypes from the Wellcome Trust Case Control Study of bipolar patients.

PubMed

Mellerup, Erling; Jørgensen, Martin Balslev; Dam, Henrik; Møller, Gert Lykke

2018-04-01

Combinations of genetic variants are the basis for polygenic disorders. We examined combinations of SNP genotypes taken from the 446 729 SNPs in The Wellcome Trust Case Control Study of bipolar patients. Parallel computing by graphics processing units, cloud computing, and data mining tools were used to scan The Wellcome Trust data set for combinations. Two clusters of combinations were significantly associated with bipolar disorder. One cluster contained 68 combinations, each of which included five SNP genotypes. Of the 1998 patients, 305 had combinations from this cluster in their genome, but none of the 1500 controls had any of these combinations in their genome. The other cluster contained six combinations, each of which included five SNP genotypes. Of the 1998 patients, 515 had combinations from the cluster in their genome, but none of the 1500 controls had any of these combinations in their genome. Clusters of combinations of genetic variants can be considered general risk factors for polygenic disorders, whereas accumulation of combinations from the clusters in the genome of a patient can be considered a personal risk factor.

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

PubMed

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

2017-06-07

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

Actively addressed single pixel full-colour plasmonic display

PubMed Central

Franklin, Daniel; Frank, Russell; Wu, Shin-Tson; Chanda, Debashis

2017-01-01

Dynamic, colour-changing surfaces have many applications including displays, wearables and active camouflage. Plasmonic nanostructures can fill this role by having the advantages of ultra-small pixels, high reflectivity and post-fabrication tuning through control of the surrounding media. However, previous reports of post-fabrication tuning have yet to cover a full red-green-blue (RGB) colour basis set with a single nanostructure of singular dimensions. Here, we report a method which greatly advances this tuning and demonstrates a liquid crystal-plasmonic system that covers the full RGB colour basis set, only as a function of voltage. This is accomplished through a surface morphology-induced, polarization-dependent plasmonic resonance and a combination of bulk and surface liquid crystal effects that manifest at different voltages. We further demonstrate the system's compatibility with existing LCD technology by integrating it with a commercially available thin-film-transistor array. The imprinted surface interfaces readily with computers to display images as well as video. PMID:28488671

A combined experimental and DFT investigation of disazo dye having pyrazole skeleton

NASA Astrophysics Data System (ADS)

Şener, Nesrin; Bayrakdar, Alpaslan; Kart, Hasan Hüseyin; Şener, İzzet

2017-02-01

Disazo dye containing pyrazole skeleton has been synthesized. The structure of the dye has been confirmed by using FT-IR, 1H NMR, 13C NMR, HRMS spectral technique and elemental analysis. The molecular geometry and infrared spectrum are also calculated by the Density Functional Theory (DFT) employing B3LYP level with 6-311G (d,p) basis set. The chemical shifts calculation for 1H NMR of the title molecule is done by using by Gauge-Invariant Atomic Orbital (GIAO) method by utilizing the same basis sets. The total density of state, the partial density of state and the overlap population density of state diagram analysis are done via Gauss Sum 3.0 program. Frontier molecular orbitals such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential surface on the title molecule are predicted for various intramolecular interactions that are responsible for the stabilization of the molecule. The experimental results and theoretical values have been compared.

The resolution of identity and chain of spheres approximations for the LPNO-CCSD singles Fock term

NASA Astrophysics Data System (ADS)

Izsák, Róbert; Hansen, Andreas; Neese, Frank

2012-10-01

In the present work, the RIJCOSX approximation, developed earlier for accelerating the SCF procedure, is applied to one of the limiting factors of LPNO-CCSD calculations: the evaluation of the singles Fock term. It turns out that the introduction of RIJCOSX in the evaluation of the closed shell LPNO-CCSD singles Fock term causes errors below the microhartree limit. If the proposed procedure is also combined with RIJCOSX in SCF, then a somewhat larger error occurs, but reaction energy errors will still remain negligible. The speedup for the singles Fock term only is about 9-10 fold for the largest basis set applied. For the case of Penicillin using the def2-QZVPP basis set, a single point energy evaluation takes 2 day 16 h on a single processor leading to a total speedup of 2.6 as compared to a fully analytic calculation. Using eight processors, the same calculation takes only 14 h.

Application of satellite remote sensing to North Carolina. Development of a monitoring methodology for trophic states of lakes in North Carolina

NASA Technical Reports Server (NTRS)

Welby, C. W.; Holman, R. E.

1977-01-01

Conjunctive study of four shallow coastal plain lakes in northeastern North Carolina and their LANDSAT-2 images demonstrates that it is possible to differentiate between the lakes and their respective trophic states on the basis of the multispectral scanner imagery. The year-long investigation established that monitoring of the trophic states of the lakes on a seasonal basis through application of color additive imagery enchancement techniques is possible. Utilizing a standard setting of the color additive viewer, an investigator can normalize the imagery to an internal standard of constant reflectance characteristics. By comparison of the false color renditions with a standard interference color chart combined with brightness measurements made on the viewer screen, one can relate the lake reflectances to their trophic states. Two or more bands of the imagery are required, and the present study established that for the lakes studied, Band 5 and Band 6 form a good combination.

Improving Critical Skills Using Wikis and CGPS in a Physics Classroom

NASA Astrophysics Data System (ADS)

Mohottala, H. E.

2016-10-01

We report the combined use of Wikispaces (wikis) and collaborative group problem solving (CGPS) sessions conducted in introductory-level calculus-based physics classes. As a part of this new teaching tool, some essay-type problems were posted on the wiki page on a weekly basis and students were encouraged to participate in problem solving without providing numerical final answers but only the steps. Each week students were further evaluated on problem solving skills, opening up more opportunity for peer interaction through CGPS. Students developed a set of skills in decision making, problem solving, communication, negotiation, critical and independent thinking, and teamwork through the combination of wikis and CGPS.

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

NASA Technical Reports Server (NTRS)

Kim, Hakil; Swain, Philip H.

1990-01-01

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

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

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

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

Estimating the intrinsic limit of the Feller-Peterson-Dixon composite approach when applied to adiabatic ionization potentials in atoms and small molecules

NASA Astrophysics Data System (ADS)

Feller, David

2017-07-01

Benchmark adiabatic ionization potentials were obtained with the Feller-Peterson-Dixon (FPD) theoretical method for a collection of 48 atoms and small molecules. In previous studies, the FPD method demonstrated an ability to predict atomization energies (heats of formation) and electron affinities well within a 95% confidence level of ±1 kcal/mol. Large 1-particle expansions involving correlation consistent basis sets (up to aug-cc-pV8Z in many cases and aug-cc-pV9Z for some atoms) were chosen for the valence CCSD(T) starting point calculations. Despite their cost, these large basis sets were chosen in order to help minimize the residual basis set truncation error and reduce dependence on approximate basis set limit extrapolation formulas. The complementary n-particle expansion included higher order CCSDT, CCSDTQ, or CCSDTQ5 (coupled cluster theory with iterative triple, quadruple, and quintuple excitations) corrections. For all of the chemical systems examined here, it was also possible to either perform explicit full configuration interaction (CI) calculations or to otherwise estimate the full CI limit. Additionally, corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, non-adiabatic effects, and other minor factors were considered. The root mean square deviation with respect to experiment for the ionization potentials was 0.21 kcal/mol (0.009 eV). The corresponding level of agreement for molecular enthalpies of formation was 0.37 kcal/mol and for electron affinities 0.20 kcal/mol. Similar good agreement with experiment was found in the case of molecular structures and harmonic frequencies. Overall, the combination of energetic, structural, and vibrational data (655 comparisons) reflects the consistent ability of the FPD method to achieve close agreement with experiment for small molecules using the level of theory applied in this study.

Combined spectroscopic and quantum chemical studies of ezetimibe

NASA Astrophysics Data System (ADS)

Prajapati, Preeti; Pandey, Jaya; Shimpi, Manishkumar R.; Srivastava, Anubha; Tandon, Poonam; Velaga, Sitaram P.; Sinha, Kirti

2016-12-01

Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.

Localized basis sets for unbound electrons in nanoelectronics.

PubMed

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

2008-02-21

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

Materials prediction via classification learning

DOE PAGES

Balachandran, Prasanna V.; Theiler, James; Rondinelli, James M.; ...

2015-08-25

In the paradigm of materials informatics for accelerated materials discovery, the choice of feature set (i.e. attributes that capture aspects of structure, chemistry and/or bonding) is critical. Ideally, the feature sets should provide a simple physical basis for extracting major structural and chemical trends and furthermore, enable rapid predictions of new material chemistries. Orbital radii calculated from model pseudopotential fits to spectroscopic data are potential candidates to satisfy these conditions. Although these radii (and their linear combinations) have been utilized in the past, their functional forms are largely justified with heuristic arguments. Here we show that machine learning methods naturallymore » uncover the functional forms that mimic most frequently used features in the literature, thereby providing a mathematical basis for feature set construction without a priori assumptions. We apply these principles to study two broad materials classes: (i) wide band gap AB compounds and (ii) rare earth-main group RM intermetallics. The AB compounds serve as a prototypical example to demonstrate our approach, whereas the RM intermetallics show how these concepts can be used to rapidly design new ductile materials. In conclusion, our predictive models indicate that ScCo, ScIr, and YCd should be ductile, whereas each was previously proposed to be brittle.« less

Materials Prediction via Classification Learning

PubMed Central

Balachandran, Prasanna V.; Theiler, James; Rondinelli, James M.; Lookman, Turab

2015-01-01

In the paradigm of materials informatics for accelerated materials discovery, the choice of feature set (i.e. attributes that capture aspects of structure, chemistry and/or bonding) is critical. Ideally, the feature sets should provide a simple physical basis for extracting major structural and chemical trends and furthermore, enable rapid predictions of new material chemistries. Orbital radii calculated from model pseudopotential fits to spectroscopic data are potential candidates to satisfy these conditions. Although these radii (and their linear combinations) have been utilized in the past, their functional forms are largely justified with heuristic arguments. Here we show that machine learning methods naturally uncover the functional forms that mimic most frequently used features in the literature, thereby providing a mathematical basis for feature set construction without a priori assumptions. We apply these principles to study two broad materials classes: (i) wide band gap AB compounds and (ii) rare earth-main group RM intermetallics. The AB compounds serve as a prototypical example to demonstrate our approach, whereas the RM intermetallics show how these concepts can be used to rapidly design new ductile materials. Our predictive models indicate that ScCo, ScIr, and YCd should be ductile, whereas each was previously proposed to be brittle. PMID:26304800

Mapping Dependence Between Extreme Rainfall and Storm Surge

NASA Astrophysics Data System (ADS)

Wu, Wenyan; McInnes, Kathleen; O'Grady, Julian; Hoeke, Ron; Leonard, Michael; Westra, Seth

2018-04-01

Dependence between extreme storm surge and rainfall can have significant implications for flood risk in coastal and estuarine regions. To supplement limited observational records, we use reanalysis surge data from a hydrodynamic model as the basis for dependence mapping, providing information at a resolution of approximately 30 km along the Australian coastline. We evaluated this approach by comparing the dependence estimates from modeled surge to that calculated using historical surge records from 79 tide gauges around Australia. The results show reasonable agreement between the two sets of dependence values, with the exception of lower seasonal variation in the modeled dependence values compared to the observed data, especially at locations where there are multiple processes driving extreme storm surge. This is due to the combined impact of local bathymetry as well as the resolution of the hydrodynamic model and its meteorological inputs. Meteorological drivers were also investigated for different combinations of extreme rainfall and surge—namely rain-only, surge-only, and coincident extremes—finding that different synoptic patterns are responsible for each combination. The ability to supplement observational records with high-resolution modeled surge data enables a much more precise quantification of dependence along the coastline, strengthening the physical basis for assessments of flood risk in coastal regions.

Prospective gas turbine and combined-cycle units for power engineering (a Review)

NASA Astrophysics Data System (ADS)

Ol'khovskii, G. G.

2013-02-01

The modern state of technology for making gas turbines around the world and heat-recovery combined-cycle units constructed on their basis are considered. The progress achieved in this field by Siemens, Mitsubishi, General Electric, and Alstom is analyzed, and the objectives these companies set forth for themselves for the near and more distant future are discussed. The 375-MW gas turbine unit with an efficiency of 40% produced by Siemens, which is presently the largest one, is subjected to a detailed analysis. The main specific features of this turbine are that the gas turbine unit's hot-path components have purely air cooling, due to which the installation has enhanced maneuverability. The single-shaft combined-cycle plant constructed on the basis of this turbine has a capacity of 570 MW and efficiency higher than 60%. Programs adopted by different companies for development of new-generation gas turbine units firing synthesis gas and fitted with low-emission combustion chambers and new cooling systems are considered. Concepts of rotor blades for new gas turbine units with improved thermal barrier coatings and composite blades different parts of which are made of materials selected in accordance with the conditions of their operation are discussed.

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

NASA Technical Reports Server (NTRS)

Partridge, Harry

1987-01-01

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

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

PubMed

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

2017-03-14

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

Systematic theoretical study of non-nuclear electron density maxima in some diatomic molecules.

PubMed

Terrabuio, Luiz A; Teodoro, Tiago Q; Rachid, Marina G; Haiduke, Roberto L A

2013-10-10

First, exploratory calculations were performed to investigate the presence of non-nuclear maxima (NNMs) in ground-state electron densities of homonuclear diatomic molecules from hydrogen up to calcium at their equilibrium geometries. In a second stage, only for the cases in which these features were previously detected, a rigorous analysis was carried out by several combinations of theoretical methods and basis sets in order to ensure that they are not only calculation artifacts. Our best results support that Li2, B2, C2, and P2 are molecules that possess true NNMs. A NNM was found in values obtained from the largest basis sets for Na2, but it disappeared at the experimental geometry because optimized bond lengths are significantly inaccurate for this case (deviations of 0.10 Å). Two of these maxima are also observed in Si2 with CCSD and large basis sets, but they are no longer detected as core-valence correlation or multiconfigurational wave functions are taken into account. Therefore, the NNMs in Si2 can be considered unphysical features due to an incomplete treatment of electron correlation. Finally, we show that a NNM is encountered in LiNa, representing the first discovery of such electron density maxima in a heteronuclear diatomic system at its equilibrium geometry, to our knowledge. Some results for LiNa, found in variations in internuclear distances, suggest that molecular electric moments, such as dipole and quadrupole, are sensitive to the presence of NNMs.

Staging of colorectal liver metastases after preoperative chemotherapy. Diffusion-weighted imaging in combination with Gd-EOB-DTPA MRI sequences increases sensitivity and diagnostic accuracy.

PubMed

Macera, Annalisa; Lario, Chiara; Petracchini, Massimo; Gallo, Teresa; Regge, Daniele; Floriani, Irene; Ribero, Dario; Capussotti, Lorenzo; Cirillo, Stefano

2013-03-01

To compare the diagnostic accuracy and sensitivity of Gd-EOB-DTPA MRI and diffusion-weighted (DWI) imaging alone and in combination for detecting colorectal liver metastases in patients who had undergone preoperative chemotherapy. Thirty-two consecutive patients with a total of 166 liver lesions were retrospectively enrolled. Of the lesions, 144 (86.8 %) were metastatic at pathology. Three image sets (1, Gd-EOB-DTPA; 2, DWI; 3, combined Gd-EOB-DTPA and DWI) were independently reviewed by two observers. Statistical analysis was performed on a per-lesion basis. Evaluation of image set 1 correctly identified 127/166 lesions (accuracy 76.5 %; 95 % CI 69.3-82.7) and 106/144 metastases (sensitivity 73.6 %, 95 % CI 65.6-80.6). Evaluation of image set 2 correctly identified 108/166 (accuracy 65.1 %, 95 % CI 57.3-72.3) and 87/144 metastases (sensitivity of 60.4 %, 95 % CI 51.9-68.5). Evaluation of image set 3 correctly identified 148/166 (accuracy 89.2 %, 95 % CI 83.4-93.4) and 131/144 metastases (sensitivity 91 %, 95 % CI 85.1-95.1). Differences were statistically significant (P < 0.001). Notably, similar results were obtained analysing only small lesions (<1 cm). The combination of DWI with Gd-EOB-DTPA-enhanced MRI imaging significantly increases the diagnostic accuracy and sensitivity in patients with colorectal liver metastases treated with preoperative chemotherapy, and it is particularly effective in the detection of small lesions.

Quantum phase space with a basis of Wannier functions

NASA Astrophysics Data System (ADS)

Fang, Yuan; Wu, Fan; Wu, Biao

2018-02-01

A quantum phase space with Wannier basis is constructed: (i) classical phase space is divided into Planck cells; (ii) a complete set of Wannier functions are constructed with the combination of Kohn’s method and Löwdin method such that each Wannier function is localized at a Planck cell. With these Wannier functions one can map a wave function unitarily onto phase space. Various examples are used to illustrate our method and compare it to Wigner function. The advantage of our method is that it can smooth out the oscillations in wave functions without losing any information and is potentially a better tool in studying quantum-classical correspondence. In addition, we point out that our method can be used for time-frequency analysis of signals.

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

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

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

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

Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

PubMed

Benassi, Enrico

2017-01-15

A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

High quality Gaussian basis sets for fourth-row atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Faegri, Knut, Jr.

1992-01-01

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

Relativistic well-tempered Gaussian basis sets for helium through mercury

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

Okada, S.; Matsuoka, O.

1989-10-01

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

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

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

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

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

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

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

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

PubMed

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

2009-12-07

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

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

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

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

Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

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

ERIC Educational Resources Information Center

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

2007-01-01

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

Modeling of hydrogen/deuterium dynamics and heat generation on palladium nanoparticles for hydrogen storage and solid-state nuclear fusion.

PubMed

Tanabe, Katsuaki

2016-01-01

We modeled the dynamics of hydrogen and deuterium adsorbed on palladium nanoparticles including the heat generation induced by the chemical adsorption and desorption, as well as palladium-catalyzed reactions. Our calculations based on the proposed model reproduce the experimental time-evolution of pressure and temperature with a single set of fitting parameters for hydrogen and deuterium injection. The model we generated with a highly generalized set of formulations can be applied for any combination of a gas species and a catalytic adsorbent/absorbent. Our model can be used as a basis for future research into hydrogen storage and solid-state nuclear fusion technologies.

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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

NASA Astrophysics Data System (ADS)

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

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

The underlying pathway structure of biochemical reaction networks

PubMed Central

Schilling, Christophe H.; Palsson, Bernhard O.

1998-01-01

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function. PMID:9539712

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

PubMed

Derosa, Pedro A

2009-06-01

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

On the optimization of Gaussian basis sets

NASA Astrophysics Data System (ADS)

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

2003-01-01

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

Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields.

PubMed

Zhu, Wuming; Trickey, S B

2017-12-28

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li + , Be + , and B + , in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.

Accurate and balanced anisotropic Gaussian type orbital basis sets for atoms in strong magnetic fields

NASA Astrophysics Data System (ADS)

Zhu, Wuming; Trickey, S. B.

2017-12-01

In high magnetic field calculations, anisotropic Gaussian type orbital (AGTO) basis functions are capable of reconciling the competing demands of the spherically symmetric Coulombic interaction and cylindrical magnetic (B field) confinement. However, the best available a priori procedure for composing highly accurate AGTO sets for atoms in a strong B field [W. Zhu et al., Phys. Rev. A 90, 022504 (2014)] yields very large basis sets. Their size is problematical for use in any calculation with unfavorable computational cost scaling. Here we provide an alternative constructive procedure. It is based upon analysis of the underlying physics of atoms in B fields that allow identification of several principles for the construction of AGTO basis sets. Aided by numerical optimization and parameter fitting, followed by fine tuning of fitting parameters, we devise formulae for generating accurate AGTO basis sets in an arbitrary B field. For the hydrogen iso-electronic sequence, a set depends on B field strength, nuclear charge, and orbital quantum numbers. For multi-electron systems, the basis set formulae also include adjustment to account for orbital occupations. Tests of the new basis sets for atoms H through C (1 ≤ Z ≤ 6) and ions Li+, Be+, and B+, in a wide B field range (0 ≤ B ≤ 2000 a.u.), show an accuracy better than a few μhartree for single-electron systems and a few hundredths to a few mHs for multi-electron atoms. The relative errors are similar for different atoms and ions in a large B field range, from a few to a couple of tens of millionths, thereby confirming rather uniform accuracy across the nuclear charge Z and B field strength values. Residual basis set errors are two to three orders of magnitude smaller than the electronic correlation energies in multi-electron atoms, a signal of the usefulness of the new AGTO basis sets in correlated wavefunction or density functional calculations for atomic and molecular systems in an external strong B field.

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

NASA Astrophysics Data System (ADS)

Choi, Chu Hwan

2002-09-01

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

New 1,3,4-thiadiazole compounds including pyrazine moiety: Synthesis, structural properties and antimicrobial features

NASA Astrophysics Data System (ADS)

Gür, Mahmut; Şener, Nesrin; Muğlu, Halit; Çavuş, M. Serdar; Özkan, Osman Emre; Kandemirli, Fatma; Şener, İzzet

2017-07-01

In the study, some new 1,3,4-thiadiazole compounds were synthesized and we have reported identification of the structures by using UV-Vis, FT-IR, 1H NMR, 13C NMR and Mass spectroscopic methods. Antimicrobial activities of the compounds against three microorganisms, namely, Candida albicans ATCC 26555, Staphylococcus aureus ATCC 9144, and Escherichia coli ATCC 25922 were investigated by using disk diffusion method. These thiadiazoles exhibited an antimicrobial activity against Staphylococcus aureus and Candida albicans. The experimental data was supported by the quantum chemical calculations. Density functional theory (DFT) calculations were carried out to obtain the ground state optimized geometries of the molecules using the B3LYP, M06 and PBE1PBE methods with 3-21 g, 4-31 g, 6-311++g(2d,2p), cc-pvtz and cc-pvqz basis sets in the different combinations. Frontier molecular orbitals (FMOs) energies, band gap energies and some chemical reactivity parameters were calculated by using the aforementioned methods and basis sets, and the results were also compared with the experimental UV-Vis data.

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

NASA Astrophysics Data System (ADS)

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

2006-03-01

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

Raman spectra of thiolated arsenicals with biological importance.

PubMed

Yang, Mingwei; Sun, Yuzhen; Zhang, Xiaobin; McCord, Bruce; McGoron, Anthony J; Mebel, Alexander; Cai, Yong

2018-03-01

Surface enhanced Raman scattering (SERS) has great potential as an alternative tool for arsenic speciation in biological matrices. SERS measurements have advantages over other techniques due to its ability to maintain the integrity of arsenic species and its minimal requirements for sample preparation. Up to now, very few Raman spectra of arsenic compounds have been reported. This is particularly true for thiolated arsenicals, which have recently been found to be widely present in humans. The lack of data for Raman spectra in arsenic speciation hampers the development of new tools using SERS. Herein, we report the results of a study combining the analysis of experimental Raman spectra with that obtained from density functional calculations for some important arsenic metabolites. The results were obtained with a hybrid functional B3LYP approach using different basis sets to calculate Raman spectra of the selected arsenicals. By comparing experimental and calculated spectra of dimethylarsinic acid (DMA V ), the basis set 6-311++G** was found to provide computational efficiency and precision in vibrational frequency prediction. The Raman frequencies for the rest of organoarsenicals were studied using this basis set, including monomethylarsonous acid (MMA III ), dimethylarsinous acid (DMA III ), dimethylmonothioarinic acid (DMMTA V ), dimethyldithioarsinic acid (DMDTA V ), S-(Dimethylarsenic) cysteine (DMA III (Cys)) and dimethylarsinous glutathione (DMA III GS). The results were compared with fingerprint Raman frequencies from As─O, As─C, and As─S obtained under different chemical environments. These fingerprint vibrational frequencies should prove useful in future measurements of different species of arsenic using SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Recovery of sparse translation-invariant signals with continuous basis pursuit

PubMed Central

Ekanadham, Chaitanya; Tranchina, Daniel; Simoncelli, Eero

2013-01-01

We consider the problem of decomposing a signal into a linear combination of features, each a continuously translated version of one of a small set of elementary features. Although these constituents are drawn from a continuous family, most current signal decomposition methods rely on a finite dictionary of discrete examples selected from this family (e.g., shifted copies of a set of basic waveforms), and apply sparse optimization methods to select and solve for the relevant coefficients. Here, we generate a dictionary that includes auxiliary interpolation functions that approximate translates of features via adjustment of their coefficients. We formulate a constrained convex optimization problem, in which the full set of dictionary coefficients represents a linear approximation of the signal, the auxiliary coefficients are constrained so as to only represent translated features, and sparsity is imposed on the primary coefficients using an L1 penalty. The basis pursuit denoising (BP) method may be seen as a special case, in which the auxiliary interpolation functions are omitted, and we thus refer to our methodology as continuous basis pursuit (CBP). We develop two implementations of CBP for a one-dimensional translation-invariant source, one using a first-order Taylor approximation, and another using a form of trigonometric spline. We examine the tradeoff between sparsity and signal reconstruction accuracy in these methods, demonstrating empirically that trigonometric CBP substantially outperforms Taylor CBP, which in turn offers substantial gains over ordinary BP. In addition, the CBP bases can generally achieve equally good or better approximations with much coarser sampling than BP, leading to a reduction in dictionary dimensionality. PMID:24352562

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

PubMed

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

2011-02-14

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

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

PubMed

Hill, J Grant

2013-09-30

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

Structural Basis for Modulation of Quality Control Fate in a Marginally Stable Protein.

PubMed

Brock, Kelly P; Abraham, Ayelet-chen; Amen, Triana; Kaganovich, Daniel; England, Jeremy L

2015-07-07

The human von Hippel-Lindau (VHL) tumor suppressor is a marginally stable protein previously used as a model substrate of eukaryotic refolding and degradation pathways. When expressed in the absence of its cofactors, VHL cannot fold and is quickly degraded by the quality control machinery of the cell. We combined computational methods with in vivo experiments to examine the basis of the misfolding propensity of VHL. By expressing a set of randomly mutated VHL sequences in yeast, we discovered a more stable mutant form. Subsequent modeling suggested the mutation had caused a conformational change affecting cofactor and chaperone interaction, and this hypothesis was then confirmed by additional knockout and overexpression experiments targeting a yeast cofactor homolog. These findings offer a detailed structural basis for the modulation of quality control fate in a model misfolded protein and highlight burial mode modeling as a rapid means to detect functionally important conformational changes in marginally stable globular domains. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

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

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

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

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

DOE PAGES

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

2017-01-27

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

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

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Integrating Genetic, Neuropsychological and Neuroimaging Data to Model Early-Onset Obsessive Compulsive Disorder Severity

PubMed Central

Mas, Sergi; Gassó, Patricia; Morer, Astrid; Calvo, Anna; Bargalló, Nuria; Lafuente, Amalia; Lázaro, Luisa

2016-01-01

We propose an integrative approach that combines structural magnetic resonance imaging data (MRI), diffusion tensor imaging data (DTI), neuropsychological data, and genetic data to predict early-onset obsessive compulsive disorder (OCD) severity. From a cohort of 87 patients, 56 with complete information were used in the present analysis. First, we performed a multivariate genetic association analysis of OCD severity with 266 genetic polymorphisms. This association analysis was used to select and prioritize the SNPs that would be included in the model. Second, we split the sample into a training set (N = 38) and a validation set (N = 18). Third, entropy-based measures of information gain were used for feature selection with the training subset. Fourth, the selected features were fed into two supervised methods of class prediction based on machine learning, using the leave-one-out procedure with the training set. Finally, the resulting model was validated with the validation set. Nine variables were used for the creation of the OCD severity predictor, including six genetic polymorphisms and three variables from the neuropsychological data. The developed model classified child and adolescent patients with OCD by disease severity with an accuracy of 0.90 in the testing set and 0.70 in the validation sample. Above its clinical applicability, the combination of particular neuropsychological, neuroimaging, and genetic characteristics could enhance our understanding of the neurobiological basis of the disorder. PMID:27093171

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

NASA Astrophysics Data System (ADS)

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

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

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

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

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

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

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

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

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

Validation and Improvement of SRTM Performance over Rugged Terrain

NASA Technical Reports Server (NTRS)

Zebker, Howard A.

2004-01-01

We have previously reported work related to basic technique development in phase unwrapping and generation of digital elevation models (DEM). In the final year of this work we have applied our technique work to the improvement of DEM's produced by SRTM. In particular, we have developed a rigorous mathematical algorithm and means to fill in missing data over rough terrain from other data sets. We illustrate this method by using a higher resolution, but globally less accurate, DEM produced by the TOPSAR airborne instrument over the Galapagos Islands to augment the SRTM data set in this area, We combine this data set with SRTM to use each set to fill in holes left over by the other imaging system. The infilling is done by first interpolating each data set using a prediction error filter that reproduces the same statistical characterization as exhibited by the entire data set within the interpolated region. After this procedure is implemented on each data set, the two are combined on a point by point basis with weights that reflect the accuracy of each data point in its original image. In areas that are better covered by SRTM, TOPSAR data are weighted down but still retain TOPSAR statistics. The reverse is true for regions better covered by TOPSAR. The resulting DEM passes statistical tests and appears quite feasible to the eye, but as this DEM is the best available for the region we cannot fully veri@ its accuracy. Spot checks with GPS points show that locally the technique results in a more comprehensive and accurate map than either data set alone.

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

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

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

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Hunt, Ron; Fulcher, Clay; Towner, Robert; McDonald, Emmett

2012-01-01

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

On the Contribution of Curl-Free Current Patterns to the Ultimate Intrinsic Signal-to-Noise Ratio at Ultra-High Field Strength.

PubMed

Pfrommer, Andreas; Henning, Anke

2017-05-01

The ultimate intrinsic signal-to-noise ratio (SNR) is a coil independent performance measure to compare different receive coil designs. To evaluate this benchmark in a sample, a complete electromagnetic basis set is required. The basis set can be obtained by curl-free and divergence-free surface current distributions, which excite linearly independent solutions to Maxwell's equations. In this work, we quantitatively investigate the contribution of curl-free current patterns to the ultimate intrinsic SNR in a spherical head-sized model at 9.4 T. Therefore, we compare the ultimate intrinsic SNR obtained with having only curl-free or divergence-free current patterns, with the ultimate intrinsic SNR obtained from a combination of curl-free and divergence-free current patterns. The influence of parallel imaging is studied for various acceleration factors. Moreover results for different field strengths (1.5 T up to 11.7 T) are presented at specific voxel positions and acceleration factors. The full-wave electromagnetic problem is analytically solved using dyadic Green's functions. We show, that at ultra-high field strength (B 0 ⩾7T) a combination of curl-free and divergence-free current patterns is required to achieve the best possible SNR at any position in a spherical head-sized model. On 1.5- and 3T platforms, divergence-free current patterns are sufficient to cover more than 90% of the ultimate intrinsic SNR. Copyright © 2017 John Wiley & Sons, Ltd.

A combined MOIP-MCDA approach to building and screening atmospheric pollution control strategies in urban regions.

PubMed

Mavrotas, George; Ziomas, Ioannis C; Diakouaki, Danae

2006-07-01

This article presents a methodological approach for the formulation of control strategies capable of reducing atmospheric pollution at the standards set by European legislation. The approach was implemented in the greater area of Thessaloniki and was part of a project aiming at the compliance with air quality standards in five major cities in Greece. The methodological approach comprises two stages: in the first stage, the availability of several measures contributing to a certain extent to reducing atmospheric pollution indicates a combinatorial problem and favors the use of Integer Programming. More specifically, Multiple Objective Integer Programming is used in order to generate alternative efficient combinations of the available policy measures on the basis of two conflicting objectives: public expenditure minimization and social acceptance maximization. In the second stage, these combinations of control measures (i.e., the control strategies) are then comparatively evaluated with respect to a wider set of criteria, using tools from Multiple Criteria Decision Analysis, namely, the well-known PROMETHEE method. The whole procedure is based on the active involvement of local and central authorities in order to incorporate their concerns and preferences, as well as to secure the adoption and implementation of the resulting solution.

A Combined MOIP-MCDA Approach to Building and Screening Atmospheric Pollution Control Strategies in Urban Regions

NASA Astrophysics Data System (ADS)

Mavrotas, George; Ziomas, Ioannis C.; Diakouaki, Danae

2006-07-01

This article presents a methodological approach for the formulation of control strategies capable of reducing atmospheric pollution at the standards set by European legislation. The approach was implemented in the greater area of Thessaloniki and was part of a project aiming at the compliance with air quality standards in five major cities in Greece. The methodological approach comprises two stages: in the first stage, the availability of several measures contributing to a certain extent to reducing atmospheric pollution indicates a combinatorial problem and favors the use of Integer Programming. More specifically, Multiple Objective Integer Programming is used in order to generate alternative efficient combinations of the available policy measures on the basis of two conflicting objectives: public expenditure minimization and social acceptance maximization. In the second stage, these combinations of control measures (i.e., the control strategies) are then comparatively evaluated with respect to a wider set of criteria, using tools from Multiple Criteria Decision Analysis, namely, the well-known PROMETHEE method. The whole procedure is based on the active involvement of local and central authorities in order to incorporate their concerns and preferences, as well as to secure the adoption and implementation of the resulting solution.

Improvement of the GPS/A system for extensive observation along subduction zones around Japan

NASA Astrophysics Data System (ADS)

Fujimoto, H.; Kido, M.; Tadokoro, K.; Sato, M.; Ishikawa, T.; Asada, A.; Mochizuki, M.

2011-12-01

Combined high-resolution gravity field models serve as a mandatory basis to describe static and dynamic processes in system Earth. Ocean dynamics can be modeled referring to a high-accurate geoid as reference surface, solid earth processes are initiated by the gravity field. Also geodetic disciplines such as height system determination depend on high-precise gravity field information. To fulfill the various requirements concerning resolution and accuracy, any kind of gravity field information, that means satellite as well as terrestrial and altimetric gravity field observations have to be included in one combination process. A key role is here reserved for GOCE observations, which contribute with its optimal signal content in the long to medium wavelength part and enable a more accurate gravity field determination than ever before especially in areas, where no high-accurate terrestrial gravity field observations are available, such as South America, Asia or Africa. For our contribution we prepare a combined high-resolution gravity field model up to d/o 720 based on full normal equation including recent GOCE, GRACE and terrestrial / altimetric data. For all data sets, normal equations are set up separately, relative weighted to each other in the combination step and solved. This procedure is computationally challenging and can only be performed using super computers. We put special emphasis on the combination process, for which we modified especially our procedure to include GOCE data optimally in the combination. Furthermore we modified our terrestrial/altimetric data sets, what should result in an improved outcome. With our model, in which we included the newest GOCE TIM4 gradiometry results, we can show how GOCE contributes to a combined gravity field solution especially in areas of poor terrestrial data coverage. The model is validated by independent GPS leveling data in selected regions as well as computation of the mean dynamic topography over the oceans. Further, we analyze the statistical error estimates derived from full covariance propagation and compare them with the absolute validation with independent data sets.

Ab Initio Theoretical Studies on the Kinetics of Hydrogen Abstraction Type Reactions of Hydroxyl Radicals with CH3CCl2F and CH3CClF2

NASA Astrophysics Data System (ADS)

Saheb, Vahid; Maleki, Samira

2018-03-01

The hydrogen abstraction reactions from CH3Cl2F (R-141b) and CH3CClF2 (R-142b) by OH radicals are studied theoretically by semi-classical transition state theory. The stationary points for the reactions are located by using KMLYP density functional method along with 6-311++G(2 d,2 p) basis set and MP2 method along with 6-311+G( d, p) basis set. Single-point energy calculations are performed by the CBS-Q and G4 combination methods on the geometries optimized at the KMLYP/6-311++G(2 d,2 p) level of theory. Vibrational anharmonicity coefficients, x ij , which are needed for semi-classical transition state theory calculations, are computed at the KMLYP/6-311++G(2 d,2 p) and MP2/6-311+G( d, p) levels of theory. The computed barrier heights are slightly sensitive to the quantum-chemical method. Thermal rate coefficients are computed over the temperature range from 200 to 2000 K and they are shown to be in accordance with available experimental data. On the basis of the computed rate coefficients, the tropospheric lifetime of the CH3CCl2F and CH3CClF2 are estimated to be about 6.5 and 12.0 years, respectively.

Vibrational spectroscopic studies, NLO, HOMO-LUMO and electronic structure calculations of α,α,α-trichlorotoluene using HF and DFT.

PubMed

Govindarajan, M; Karabacak, M; Periandy, S; Xavier, S

2012-08-01

FT-IR and FT-Raman spectra of α,α,α-trichlorotoluene have been recorded and analyzed. The geometry, fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) B3LYP/6-311++G(d,p) method and a comparative study between HF level and various basis sets combination. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. The complete vibrational assignments of wavenumbers are made on the basis of potential energy distribution (PED). The effects due to the substitutions of methyl group and halogen were investigated. The absorption energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT). The electric dipole moment, polarizability and the first hyperpolarizability values of the α,α,α-trichlorotoluene have been calculated. (1)H NMR chemical shifts were calculated by using the gauge independent atomic orbital (GIAO) method with HF and B3LYP methods with 6-311++G(d,p) basis set. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken and natural charges of the title molecule were also calculated and interpreted. Copyright © 2012 Elsevier B.V. All rights reserved.

Common spatial pattern combined with kernel linear discriminate and generalized radial basis function for motor imagery-based brain computer interface applications

NASA Astrophysics Data System (ADS)

Hekmatmanesh, Amin; Jamaloo, Fatemeh; Wu, Huapeng; Handroos, Heikki; Kilpeläinen, Asko

2018-04-01

Brain Computer Interface (BCI) can be a challenge for developing of robotic, prosthesis and human-controlled systems. This work focuses on the implementation of a common spatial pattern (CSP) base algorithm to detect event related desynchronization patterns. Utilizing famous previous work in this area, features are extracted by filter bank with common spatial pattern (FBCSP) method, and then weighted by a sensitive learning vector quantization (SLVQ) algorithm. In the current work, application of the radial basis function (RBF) as a mapping kernel of linear discriminant analysis (KLDA) method on the weighted features, allows the transfer of data into a higher dimension for more discriminated data scattering by RBF kernel. Afterwards, support vector machine (SVM) with generalized radial basis function (GRBF) kernel is employed to improve the efficiency and robustness of the classification. Averagely, 89.60% accuracy and 74.19% robustness are achieved. BCI Competition III, Iva data set is used to evaluate the algorithm for detecting right hand and foot imagery movement patterns. Results show that combination of KLDA with SVM-GRBF classifier makes 8.9% and 14.19% improvements in accuracy and robustness, respectively. For all the subjects, it is concluded that mapping the CSP features into a higher dimension by RBF and utilization GRBF as a kernel of SVM, improve the accuracy and reliability of the proposed method.

A new proton fluence model for E greater than 10 MeV

NASA Technical Reports Server (NTRS)

Feynman, Joan; Armstrong, T. P.; Dao-Gibner, L.; Silverman, S.

1988-01-01

Researchers describe a new engineering model for the fluence of protons with energies greater than 10 MeV. The data set used is a combination of observations made primarily from the Earth's surface between 1956 and 1963 and observations made from spacecraft in the vicinity of Earth between 1963 and 1985. With this data set we find that the distinction between ordinary proton events and anomalously large proton events made in earlier work disappears. The greater than 10 MeV fluences at 1 AU calculated with the new model are about twice those expected on the basis of models now in use. In contrast to earlier models, results do not depend critically on the fluence from any one event.

The SEASAT altimeter wet tropospheric range correction revisited

NASA Technical Reports Server (NTRS)

Tapley, D. B.; Lundberg, J. B.; Born, G. H.

1984-01-01

An expanded set of radiosonde observations was used to calculate the wet tropospheric range correction for the brightness temperature measurements of the SEASAT scanning multichannel microwave radiometer (SMMR). The accuracy of the conventional algorithm for wet tropospheric range correction was evaluated. On the basis of the expanded observational data set, the algorithm was found to have a bias of about 1.0 cm, and a standard deviation 2.8 cm. In order to improve the algorithm, the exact linear, quadratic and logarithmic relationships between brightness temperatures and range corrections were determined. Various combinations of measurement parameters were used to reduce the standard deviation between SEASAT SMMR and radiosonde observations to about 2.1 cm. The performance of various range correction formulas is compared in a table.

Visual feature extraction from voxel-weighted averaging of stimulus images in 2 fMRI studies.

PubMed

Hart, Corey B; Rose, William J

2013-11-01

Multiple studies have provided evidence for distributed object representation in the brain, with several recent experiments leveraging basis function estimates for partial image reconstruction from fMRI data. Using a novel combination of statistical decomposition, generalized linear models, and stimulus averaging on previously examined image sets and Bayesian regression of recorded fMRI activity during presentation of these data sets, we identify a subset of relevant voxels that appear to code for covarying object features. Using a technique we term "voxel-weighted averaging," we isolate image filters that these voxels appear to implement. The results, though very cursory, appear to have significant implications for hierarchical and deep-learning-type approaches toward the understanding of neural coding and representation.

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

PubMed

Xu, ZongRong; Matsika, Spiridoula

2006-11-02

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

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

Code of Federal Regulations, 2010 CFR

2010-10-01

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

Parametric Grid Information in the DOE Knowledge Base: Data Preparation, Storage, and Access

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

HIPP,JAMES R.; MOORE,SUSAN G.; MYERS,STEPHEN C.

The parametric grid capability of the Knowledge Base provides an efficient, robust way to store and access interpolatable information which is needed to monitor the Comprehensive Nuclear Test Ban Treaty. To meet both the accuracy and performance requirements of operational monitoring systems, we use a new approach which combines the error estimation of kriging with the speed and robustness of Natural Neighbor Interpolation (NNI). The method involves three basic steps: data preparation (DP), data storage (DS), and data access (DA). The goal of data preparation is to process a set of raw data points to produce a sufficient basis formore » accurate NNI of value and error estimates in the Data Access step. This basis includes a set of nodes and their connectedness, collectively known as a tessellation, and the corresponding values and errors that map to each node, which we call surfaces. In many cases, the raw data point distribution is not sufficiently dense to guarantee accurate error estimates from the NNI, so the original data set must be densified using a newly developed interpolation technique known as Modified Bayesian Kriging. Once appropriate kriging parameters have been determined by variogram analysis, the optimum basis for NNI is determined in a process they call mesh refinement, which involves iterative kriging, new node insertion, and Delauny triangle smoothing. The process terminates when an NNI basis has been calculated which will fir the kriged values within a specified tolerance. In the data storage step, the tessellations and surfaces are stored in the Knowledge Base, currently in a binary flatfile format but perhaps in the future in a spatially-indexed database. Finally, in the data access step, a client application makes a request for an interpolated value, which triggers a data fetch from the Knowledge Base through the libKBI interface, a walking triangle search for the containing triangle, and finally the NNI interpolation.« less

Projected Hybrid Orbitals: A General QM/MM Method

PubMed Central

2015-01-01

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

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

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

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-07-11

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

A relational approach to durable poverty, inequality and power.

PubMed

Mosse, David

2010-01-01

The article argues for what can be called a 'relational' approach to poverty: one that first views persistent poverty as the consequence of historically developed economic and political relations, and second, that emphasises poverty and inequality as an effect of social categorisation and identity, drawing in particular on the experience of adivasis ("tribals") and dalits ("untouchables") subordinated in Indian society. The approach follows Charles Tilly's Durable Inequality in combining Marxian ideas of exploitation and dispossession with Weberian notions of social closure. The article then draws on the work of Steven Lukes, Pierre Bourdieu and Arjun Appadurai to argue for the need to incorporate a multidimensional conception of power; including not only power as the direct assertion of will but also 'agenda-setting power' that sets the terms in which poverty becomes (or fails to become) politicised, and closely related to power as political representation. This sets the basis for discussion of the politics of poverty and exclusion.

Feature construction can improve diagnostic criteria for high-dimensional metabolic data in newborn screening for medium-chain acyl-CoA dehydrogenase deficiency.

PubMed

Ho, Sirikit; Lukacs, Zoltan; Hoffmann, Georg F; Lindner, Martin; Wetter, Thomas

2007-07-01

In newborn screening with tandem mass spectrometry, multiple intermediary metabolites are quantified in a single analytical run for the diagnosis of fatty-acid oxidation disorders, organic acidurias, and aminoacidurias. Published diagnostic criteria for these disorders normally incorporate a primary metabolic marker combined with secondary markers, often analyte ratios, for which the markers have been chosen to reflect metabolic pathway deviations. We applied a procedure to extract new markers and diagnostic criteria for newborn screening to the data of newborns with confirmed medium-chain acyl-CoA dehydrogenase deficiency (MCADD) and a control group from the newborn screening program, Heidelberg, Germany. We validated the results with external data of the screening center in Hamburg, Germany. We extracted new markers by performing a systematic search for analyte combinations (features) with high discriminatory performance for MCADD. To select feature thresholds, we applied automated procedures to separate controls and cases on the basis of the feature values. Finally, we built classifiers from these new markers to serve as diagnostic criteria in screening for MCADD. On the basis of chi(2) scores, we identified approximately 800 of >628,000 new analyte combinations with superior discriminatory performance compared with the best published combinations. Classifiers built with the new features achieved diagnostic sensitivities and specificities approaching 100%. Feature construction methods provide ways to disclose information hidden in the set of measured analytes. Other diagnostic tasks based on high-dimensional metabolic data might also profit from this approach.

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

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

Application of Hyperspectral Imaging to Detect Sclerotinia sclerotiorum on Oilseed Rape Stems

PubMed Central

Kong, Wenwen; Zhang, Chu; Huang, Weihao

2018-01-01

Hyperspectral imaging covering the spectral range of 384–1034 nm combined with chemometric methods was used to detect Sclerotinia sclerotiorum (SS) on oilseed rape stems by two sample sets (60 healthy and 60 infected stems for each set). Second derivative spectra and PCA loadings were used to select the optimal wavelengths. Discriminant models were built and compared to detect SS on oilseed rape stems, including partial least squares-discriminant analysis, radial basis function neural network, support vector machine and extreme learning machine. The discriminant models using full spectra and optimal wavelengths showed good performance with classification accuracies of over 80% for the calibration and prediction set. Comparing all developed models, the optimal classification accuracies of the calibration and prediction set were over 90%. The similarity of selected optimal wavelengths also indicated the feasibility of using hyperspectral imaging to detect SS on oilseed rape stems. The results indicated that hyperspectral imaging could be used as a fast, non-destructive and reliable technique to detect plant diseases on stems. PMID:29300315

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

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

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

Circumcision-incision orchidopexy: A novel technique for palpable, low inguinal undescended testis.

PubMed

Chua, Michael E; Silangcruz, Jan Michael A; Gomez, Odina; Dy, Jun S; Morales, Marcelino L

2017-11-01

Given that both orchidopexy and circumcision are commonly done in a single operative setting, we adopted a technique of combined orchidopexy and circumcision using a single circumcision incision. We applied this new technique to boys with palpable, low inguinal cryptorchidism. Here we describe a case series of 7 boys who underwent concurrent orchidopexy via the circumcision site. We present this novel technique and discuss our preliminary outcomes, including the anatomic basis and feasibility. The technique appears to be an alternative for concurrent circumcision and cryptorchid cases with palpable, low inguinal testes.

Handbook of satellite pointing errors and their statistical treatment

NASA Astrophysics Data System (ADS)

Weinberger, M. C.

1980-03-01

This handbook aims to provide both satellite payload and attitude control system designers with a consistent, unambiguous approach to the formulation, definition and interpretation of attitude pointing and measurement specifications. It reviews and assesses the current terminology and practices, and from them establishes a set of unified terminology, giving the user a sound basis to understand the meaning and implications of various specifications and requirements. Guidelines are presented for defining the characteristics of the error sources influencing satellite pointing and attitude measurement, and their combination in performance verification.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

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

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

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

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

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

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

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

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

NASA Astrophysics Data System (ADS)

Rohmer, Jeremy

2016-04-01

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

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

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

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

1997-12-01

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

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

PubMed

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

2017-02-15

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

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

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

2016-01-01

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

Sparse Gaussian elimination with controlled fill-in on a shared memory multiprocessor

NASA Technical Reports Server (NTRS)

Alaghband, Gita; Jordan, Harry F.

1989-01-01

It is shown that in sparse matrices arising from electronic circuits, it is possible to do computations on many diagonal elements simultaneously. A technique for obtaining an ordered compatible set directly from the ordered incompatible table is given. The ordering is based on the Markowitz number of the pivot candidates. This technique generates a set of compatible pivots with the property of generating few fills. A novel heuristic algorithm is presented that combines the idea of an order-compatible set with a limited binary tree search to generate several sets of compatible pivots in linear time. An elimination set for reducing the matrix is generated and selected on the basis of a minimum Markowitz sum number. The parallel pivoting technique presented is a stepwise algorithm and can be applied to any submatrix of the original matrix. Thus, it is not a preordering of the sparse matrix and is applied dynamically as the decomposition proceeds. Parameters are suggested to obtain a balance between parallelism and fill-ins. Results of applying the proposed algorithms on several large application matrices using the HEP multiprocessor (Kowalik, 1985) are presented and analyzed.

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

NASA Astrophysics Data System (ADS)

van Hoeve, Miriam D.; Klobukowski, Mariusz

2018-03-01

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

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

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

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

PubMed

Varandas, A J C

2009-02-01

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

Exact exchange-correlation potentials of singlet two-electron systems

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Effect of Small Numbers of Test Results on Accuracy of Hoek-Brown Strength Parameter Estimations: A Statistical Simulation Study

NASA Astrophysics Data System (ADS)

Bozorgzadeh, Nezam; Yanagimura, Yoko; Harrison, John P.

2017-12-01

The Hoek-Brown empirical strength criterion for intact rock is widely used as the basis for estimating the strength of rock masses. Estimations of the intact rock H-B parameters, namely the empirical constant m and the uniaxial compressive strength σc, are commonly obtained by fitting the criterion to triaxial strength data sets of small sample size. This paper investigates how such small sample sizes affect the uncertainty associated with the H-B parameter estimations. We use Monte Carlo (MC) simulation to generate data sets of different sizes and different combinations of H-B parameters, and then investigate the uncertainty in H-B parameters estimated from these limited data sets. We show that the uncertainties depend not only on the level of variability but also on the particular combination of parameters being investigated. As particular combinations of H-B parameters can informally be considered to represent specific rock types, we discuss that as the minimum number of required samples depends on rock type it should correspond to some acceptable level of uncertainty in the estimations. Also, a comparison of the results from our analysis with actual rock strength data shows that the probability of obtaining reliable strength parameter estimations using small samples may be very low. We further discuss the impact of this on ongoing implementation of reliability-based design protocols and conclude with suggestions for improvements in this respect.

Molecular conformational analysis, vibrational spectra and normal coordinate analysis of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene based on density functional theory calculations.

PubMed

Joseph, Lynnette; Sajan, D; Chaitanya, K; Isac, Jayakumary

2014-03-25

The conformational behavior and structural stability of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene (TDBE) were investigated by using density functional theory (DFT) method with the B3LYP/6-311++G(d,p) basis set combination. The vibrational wavenumbers of TDBE were computed at DFT level and complete vibrational assignments were made on the basis of normal coordinate analysis calculations (NCA). The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The infrared and Raman spectra were also predicted from the calculated intensities. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Copyright © 2013 Elsevier B.V. All rights reserved.

Rotational and fine structure of open-shell molecules in nearly degenerate electronic states

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2018-03-01

An effective Hamiltonian without symmetry restriction has been developed to model the rotational and fine structure of two nearly degenerate electronic states of an open-shell molecule. In addition to the rotational Hamiltonian for an asymmetric top, this spectroscopic model includes the energy separation between the two states due to difference potential and zero-point energy difference, as well as the spin-orbit (SO), Coriolis, and electron spin-molecular rotation (SR) interactions. Hamiltonian matrices are computed using orbitally and fully symmetrized case (a) and case (b) basis sets. Intensity formulae and selection rules for rotational transitions between a pair of nearly degenerate states and a nondegenerate state have also been derived using all four basis sets. It is demonstrated using real examples of free radicals that the fine structure of a single electronic state can be simulated with either a SR tensor or a combination of SO and Coriolis constants. The related molecular constants can be determined precisely only when all interacting levels are simulated simultaneously. The present study suggests that analysis of rotational and fine structure can provide quantitative insights into vibronic interactions and related effects.

Quantum chemical modeling of perovskite: An investigation of piezoelectricity in ferrite of yttrium.

PubMed

de Lira, Fábio Augusto M; Farias, Márcio de Souza; de Figueiredo, Antonio Florêncio; Gil, Fábio dos Santos; dos Santos, Marcos Antonio B; Malheiros, Bruno Veiga; Ferreira, João Elias V; Pinheiro, José Ciríaco; Treu-Filho, Oswaldo; Kondo, Rogério Toshiaki

2011-07-01

In a previous article, we used Hartree-Fock (HF) theory to study the piezoelectricity in BaTiO₃. In this paper, we applied the Douglas-Kroll-Hess second order scalar relativistic method to investigate the possible piezoelectric properties in the perovskite YFeO₃ structure, which has not yet been studied experimentally. The 30s20p13d and 31s21p17d Gaussian basis sets for the Fe (⁵D) and Y (²D) atoms, respectively, were built with the Generator Coordinate HF method. After contraction to [13s7p5d] and [13s8p7d], in combination with the 20s14p/6s4p basis set for the O (³P) atom from literature, they had their quality evaluated using calculations of the total and the orbital energies for the ²FeO⁺¹ and ¹YO⁺¹ fragments. The dipole moment, the total energy, and the total atomic charges in YFeO₃ in C(s) space group were calculated. The results and the analysis lead us to believe that the perovskite YFeO₃ does not present piezoelectric properties.

Proper Orthogonal Decomposition in Optimal Control of Fluids

NASA Technical Reports Server (NTRS)

Ravindran, S. S.

1999-01-01

In this article, we present a reduced order modeling approach suitable for active control of fluid dynamical systems based on proper orthogonal decomposition (POD). The rationale behind the reduced order modeling is that numerical simulation of Navier-Stokes equations is still too costly for the purpose of optimization and control of unsteady flows. We examine the possibility of obtaining reduced order models that reduce computational complexity associated with the Navier-Stokes equations while capturing the essential dynamics by using the POD. The POD allows extraction of certain optimal set of basis functions, perhaps few, from a computational or experimental data-base through an eigenvalue analysis. The solution is then obtained as a linear combination of these optimal set of basis functions by means of Galerkin projection. This makes it attractive for optimal control and estimation of systems governed by partial differential equations. We here use it in active control of fluid flows governed by the Navier-Stokes equations. We show that the resulting reduced order model can be very efficient for the computations of optimization and control problems in unsteady flows. Finally, implementational issues and numerical experiments are presented for simulations and optimal control of fluid flow through channels.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Refined energetic ordering for sulphate-water (n = 3-6) clusters using high-level electronic structure calculations

NASA Astrophysics Data System (ADS)

Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Epifanovsky, Evgeny; Head-Gordon, Martin

2012-10-01

This work reports refinements of the energetic ordering of the known low-energy structures of sulphate-water clusters ? (n = 3-6) using high-level electronic structure methods. Coupled cluster singles and doubles with perturbative triples (CCSD(T)) is used in combination with an estimate of basis set effects up to the complete basis set limit using second-order Møller-Plesset theory. Harmonic zero-point energy (ZPE), included at the B3LYP/6-311 + + G(3df,3pd) level, was found to have a significant effect on the energetic ordering. In fact, we show that the energetic ordering is a result of a delicate balance between the electronic and vibrational energies. Limitations of the ZPE calculations, both due to electronic structure errors, and use of the harmonic approximation, probably constitute the largest remaining errors. Due to the often small energy differences between cluster isomers, and the significant role of ZPE, deuteration can alter the relative energies of low-lying structures, and, when it is applied in conjunction with calculated harmonic ZPEs, even alters the global minimum for n = 5. Experiments on deuterated clusters, as well as more sophisticated vibrational calculations, may therefore be quite interesting.

The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient

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

Bykov, Dmytro; Kristensen, Kasper; Kjærgaard, Thomas

We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems. A test set of supramolecular complexes containing up to 158 atoms and 1960 contracted basis functions has been employed to demonstrate the general applicability of the DEC-RI-MP2 methodmore » and to analyze the errors of the DEC approximation. Moreover, the test set contains molecules of complicated electronic structures and is thus deliberately chosen to stress test the DEC-RI-MP2 gradient implementation. Additionally, as a showcase example the full molecular gradient for insulin (787 atoms and 7604 contracted basis functions) has been evaluated.« less

Some comparisons of complexity in dictionary-based and linear computational models.

PubMed

Gnecco, Giorgio; Kůrková, Věra; Sanguineti, Marcello

2011-03-01

Neural networks provide a more flexible approximation of functions than traditional linear regression. In the latter, one can only adjust the coefficients in linear combinations of fixed sets of functions, such as orthogonal polynomials or Hermite functions, while for neural networks, one may also adjust the parameters of the functions which are being combined. However, some useful properties of linear approximators (such as uniqueness, homogeneity, and continuity of best approximation operators) are not satisfied by neural networks. Moreover, optimization of parameters in neural networks becomes more difficult than in linear regression. Experimental results suggest that these drawbacks of neural networks are offset by substantially lower model complexity, allowing accuracy of approximation even in high-dimensional cases. We give some theoretical results comparing requirements on model complexity for two types of approximators, the traditional linear ones and so called variable-basis types, which include neural networks, radial, and kernel models. We compare upper bounds on worst-case errors in variable-basis approximation with lower bounds on such errors for any linear approximator. Using methods from nonlinear approximation and integral representations tailored to computational units, we describe some cases where neural networks outperform any linear approximator. Copyright © 2010 Elsevier Ltd. All rights reserved.

New model for distributed multimedia databases and its application to networking of museums

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1998-02-01

This paper proposes a new distributed multimedia data base system where the databases storing MPEG-2 videos and/or super high definition images are connected together through the B-ISDN's, and also refers to an example of the networking of museums on the basis of the proposed database system. The proposed database system introduces a new concept of the 'retrieval manager' which functions an intelligent controller so that the user can recognize a set of image databases as one logical database. A user terminal issues a request to retrieve contents to the retrieval manager which is located in the nearest place to the user terminal on the network. Then, the retrieved contents are directly sent through the B-ISDN's to the user terminal from the server which stores the designated contents. In this case, the designated logical data base dynamically generates the best combination of such a retrieving parameter as a data transfer path referring to directly or data on the basis of the environment of the system. The generated retrieving parameter is then executed to select the most suitable data transfer path on the network. Therefore, the best combination of these parameters fits to the distributed multimedia database system.

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

PubMed

Peterson, Kirk A

2015-02-21

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

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

PubMed Central

Hofer, Thomas S.

2013-01-01

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

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

PubMed

Hofer, Thomas S

2013-01-01

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

Characterization of B-H agostic compounds involved in the dehydrogenation of amine-boranes by group 4 metallocenes.

PubMed

Zhu, Jingwen; Zins, Emilie-Laure; Alikhani, Mohammad Esmaïl

2016-12-01

For over a decade, amine-borane has been considered as a potential chemical hydrogen vector in the context of a search for cleaner energy sources. When catalyzed by organometallic complexes, the reaction mechanisms currently considered involve the formation of β-BH agostic intermediates. A thorough understanding of these intermediates may constitute a crucial step toward the identification of ideal catalysts. Topological approaches such as QTAIM and ELF revealed to be particularly suitable for the description of β-agostic interactions. When studying model catalysts, accurate theoretical calculations may be carried out. However, for a comparison with experimental data, calculations should also be carried out on large organo-metallic species, often including transition metals belonging to the second or the third row. In such a case, DFT methods are particularly attractive. Unfortunately, triple-ζ all electrons basis sets are not easily available for heavy transition metal elements. Thus, a subtle balance should be reached between the affordable level of calculations and the required accuracy of the electronic description of the systems. Herein we propose the use of B3LYP functional in combination with the LanL2DZ pseudopotential for the metal atom and 6-311++G(2d,2p) basis set for the other atoms, followed by a single point using the DKH2 relativistic Hamiltonian in combination with the B3LYP/DZP-DKH level, as a "minimum level of theory" leading to a consistent topological description of the interaction within the ELF and QTAIM framework, in the context of isolated (gas-phase) group 4 metallocene catalysts.

Performance of the Effective Core Potentials of Ca, Hg and Pb in Complexes with Ligands Containing N and O Donor Atoms.

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

Ramirez, Jose Z.; Vargas, Rubicelia; Garza, Jorge

This paper presents a systematic study of the performance of the relativistic effective core potentials (RECPs) proposed by Stoll-Preuss, Christiansen-Ermler and Hay-Wadt for Ca2+, Hg2+ and Pb2+. The RECPs performance is studied when these cations are combined with ethylene glycol, 2-aminoethanol and ethylenediamine to form bidentate complexes. First, the description of the bidentate ligands is analyzed with the Kohn-Sham method by using SVWN, BLYP and B3LYP exchange-correlation functionals and they are compared with the Moeller-Plesset perturbation theory (MP2), for all these methods the TZVP basis set was used. We found that the BLYP exchange-correlation functional gives similar results that thosemore » obtained by the B3LYP and MP2 methods. Thus, the bidentate metal complexes were studied with the BLYP method combined with the RECPs. In order to compare RECPs performance, all the systems considered in this work were studied with the relativistic all-electron Douglas-Kroll (DK3) method. We observed that the Christiansen-Ermler RECPs give the best energetic and geometrical description for Ca and Hg complexes when compared with the all-electron method. For Pb complexes the spin-orbit interaction and Basis Set Superposition error must be taken into account in the RECP. In general, the trend showed in the complexation energies with the all-electron method is followed by the complexation energies computed with all the pseudopotential tested in this work. Battelle operates PNNL for the USDOE.« less

Orbital-Dependent Density Functionals for Chemical Catalysis

DTIC Science & Technology

2014-10-17

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

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

NASA Technical Reports Server (NTRS)

Green, S.

1972-01-01

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

High-order nonlinear susceptibilities of He

NASA Astrophysics Data System (ADS)

Liu, W.-C.; Clark, Charles W.

1996-05-01

High-order nonlinear optical response of noble gases to intense laser radiation is of considerable experimental interest, but is difficult to measure or calculate accurately. We have begun a set of calculations of frequency-dependent nonlinear susceptibilities of He 1s^2, within the framework of Rayleigh-Schrödinger perturbation theory at lowest applicable order, with the goal of providing critically evaluated atomic data for modelling high harmonic generation processes. The atomic Hamiltonian is decomposed in term of Hylleraas coordinates and spherical harmonics using the formalism of Pont and Shakeshaft (M. Pont and R. Shakeshaft, Phy. Rev. A 51), 257 (1995), and the hierarchy of inhomogeneous equations of perturbation theory is solved iteratively. A combination of Hylleraas and Frankowski basis functions is used(J. D. Baker, Master thesis, U. Delaware (1988); J. D. Baker, R. N. Hill, and J. D. Morgan, AIP Conference Proceedings 189) 123(1989); the compact Hylleraas basis provides a highly accurate representation of the ground state wavefunction, whereas the diffuse Frankowski basis functions efficiently reproduce the correct asymptotic structure of the perturbed orbitals.

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

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Land cover/use classification of Cairns, Queensland, Australia: A remote sensing study involving the conjunctive use of the airborne imaging spectrometer, the large format camera and the thematic mapper simulator

NASA Technical Reports Server (NTRS)

Heric, Matthew; Cox, William; Gordon, Daniel K.

1987-01-01

In an attempt to improve the land cover/use classification accuracy obtainable from remotely sensed multispectral imagery, Airborne Imaging Spectrometer-1 (AIS-1) images were analyzed in conjunction with Thematic Mapper Simulator (NS001) Large Format Camera color infrared photography and black and white aerial photography. Specific portions of the combined data set were registered and used for classification. Following this procedure, the resulting derived data was tested using an overall accuracy assessment method. Precise photogrammetric 2D-3D-2D geometric modeling techniques is not the basis for this study. Instead, the discussion exposes resultant spectral findings from the image-to-image registrations. Problems associated with the AIS-1 TMS integration are considered, and useful applications of the imagery combination are presented. More advanced methodologies for imagery integration are needed if multisystem data sets are to be utilized fully. Nevertheless, research, described herein, provides a formulation for future Earth Observation Station related multisensor studies.

On the preventive management of sediment-related sewer blockages: a combined maintenance and routing optimization approach.

PubMed

Fontecha, John E; Akhavan-Tabatabaei, Raha; Duque, Daniel; Medaglia, Andrés L; Torres, María N; Rodríguez, Juan Pablo

In this work we tackle the problem of planning and scheduling preventive maintenance (PM) of sediment-related sewer blockages in a set of geographically distributed sites that are subject to non-deterministic failures. To solve the problem, we extend a combined maintenance and routing (CMR) optimization approach which is a procedure based on two components: (a) first a maintenance model is used to determine the optimal time to perform PM operations for each site and second (b) a mixed integer program-based split procedure is proposed to route a set of crews (e.g., sewer cleaners, vehicles equipped with winches or rods and dump trucks) in order to perform PM operations at a near-optimal minimum expected cost. We applied the proposed CMR optimization approach to two (out of five) operative zones in the city of Bogotá (Colombia), where more than 100 maintenance operations per zone must be scheduled on a weekly basis. Comparing the CMR against the current maintenance plan, we obtained more than 50% of cost savings in 90% of the sites.

Temporal Lobe and “Default” Hemodynamic Brain Modes Discriminate Between Schizophrenia and Bipolar Disorder

PubMed Central

Calhoun, Vince D.; Maciejewski, Paul K.; Pearlson, Godfrey D.; Kiehl, Kent A.

2009-01-01

Schizophrenia and bipolar disorder are currently diagnosed on the basis of psychiatric symptoms and longitudinal course. The determination of a reliable, biologically-based diagnostic indicator of these diseases (a biomarker) could provide the groundwork for developing more rigorous tools for differential diagnosis and treatment assignment. Recently, methods have been used to identify distinct sets of brain regions or “spatial modes” exhibiting temporally coherent brain activity. Using functional magnetic resonance imaging (fMRI) data and a multivariate analysis method, independent component analysis, we combined the temporal lobe and the default modes to discriminate subjects with bipolar disorder, chronic schizophrenia, and healthy controls. Temporal lobe and default mode networks were reliably identified in all participants. Classification results on an independent set of individuals revealed an average sensitivity and specificity of 90 and 95%, respectively. The use of coherent brain networks such as the temporal lobe and default mode networks may provide a more reliable measure of disease state than task-correlated fMRI activity. A combination of two such hemodynamic brain networks shows promise as a biomarker for schizophrenia and bipolar disorder. PMID:17894392

Temporal lobe and "default" hemodynamic brain modes discriminate between schizophrenia and bipolar disorder.

PubMed

Calhoun, Vince D; Maciejewski, Paul K; Pearlson, Godfrey D; Kiehl, Kent A

2008-11-01

Schizophrenia and bipolar disorder are currently diagnosed on the basis of psychiatric symptoms and longitudinal course. The determination of a reliable, biologically-based diagnostic indicator of these diseases (a biomarker) could provide the groundwork for developing more rigorous tools for differential diagnosis and treatment assignment. Recently, methods have been used to identify distinct sets of brain regions or "spatial modes" exhibiting temporally coherent brain activity. Using functional magnetic resonance imaging (fMRI) data and a multivariate analysis method, independent component analysis, we combined the temporal lobe and the default modes to discriminate subjects with bipolar disorder, chronic schizophrenia, and healthy controls. Temporal lobe and default mode networks were reliably identified in all participants. Classification results on an independent set of individuals revealed an average sensitivity and specificity of 90 and 95%, respectively. The use of coherent brain networks such as the temporal lobe and default mode networks may provide a more reliable measure of disease state than task-correlated fMRI activity. A combination of two such hemodynamic brain networks shows promise as a biomarker for schizophrenia and bipolar disorder.

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

PubMed

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

2009-04-21

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

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES.

PubMed

Rand, Alexander; Gillette, Andrew; Bajaj, Chandrajit

2014-01-01

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

Analysis of STM images with pure and CO-functionalized tips: A first-principles and experimental study

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Okabayashi, Norio; Peronio, Angelo; Giessibl, Franz J.; Paulsson, Magnus

2017-08-01

We describe a first-principles method to calculate scanning tunneling microscopy (STM) images, and compare the results to well-characterized experiments combining STM with atomic force microscopy (AFM). The theory is based on density functional theory with a localized basis set, where the wave functions in the vacuum gap are computed by propagating the localized-basis wave functions into the gap using a real-space grid. Constant-height STM images are computed using Bardeen's approximation method, including averaging over the reciprocal space. We consider copper adatoms and single CO molecules adsorbed on Cu(111), scanned with a single-atom copper tip with and without CO functionalization. The calculated images agree with state-of-the-art experiments, where the atomic structure of the tip apex is determined by AFM. The comparison further allows for detailed interpretation of the STM images.

Basis for selecting optimum antibiotic regimens for secondary peritonitis.

PubMed

Maseda, Emilio; Gimenez, Maria-Jose; Gilsanz, Fernando; Aguilar, Lorenzo

2016-01-01

Adequate management of severely ill patients with secondary peritonitis requires supportive therapy of organ dysfunction, source control of infection and antimicrobial therapy. Since secondary peritonitis is polymicrobial, appropriate empiric therapy requires combination therapy in order to achieve the needed coverage for both common and more unusual organisms. This article reviews etiological agents, resistance mechanisms and their prevalence, how and when to cover them and guidelines for treatment in the literature. Local surveillances are the basis for the selection of compounds in antibiotic regimens, which should be further adapted to the increasing number of patients with risk factors for resistance (clinical setting, comorbidities, previous antibiotic treatments, previous colonization, severity…). Inadequate antimicrobial regimens are strongly associated with unfavorable outcomes. Awareness of resistance epidemiology and of clinical consequences of inadequate therapy against resistant bacteria is crucial for clinicians treating secondary peritonitis, with delicate balance between optimization of empirical therapy (improving outcomes) and antimicrobial overuse (increasing resistance emergence).

Using an optimal CC-PLSR-RBFNN model and NIR spectroscopy for the starch content determination in corn

NASA Astrophysics Data System (ADS)

Jiang, Hao; Lu, Jiangang

2018-05-01

Corn starch is an important material which has been traditionally used in the fields of food and chemical industry. In order to enhance the rapidness and reliability of the determination for starch content in corn, a methodology is proposed in this work, using an optimal CC-PLSR-RBFNN calibration model and near-infrared (NIR) spectroscopy. The proposed model was developed based on the optimal selection of crucial parameters and the combination of correlation coefficient method (CC), partial least squares regression (PLSR) and radial basis function neural network (RBFNN). To test the performance of the model, a standard NIR spectroscopy data set was introduced, containing spectral information and chemical reference measurements of 80 corn samples. For comparison, several other models based on the identical data set were also briefly discussed. In this process, the root mean square error of prediction (RMSEP) and coefficient of determination (Rp2) in the prediction set were used to make evaluations. As a result, the proposed model presented the best predictive performance with the smallest RMSEP (0.0497%) and the highest Rp2 (0.9968). Therefore, the proposed method combining NIR spectroscopy with the optimal CC-PLSR-RBFNN model can be helpful to determine starch content in corn.

Effect of Aggregation Operators on Network-Based Disease Gene Prioritization: A Case Study on Blood Disorders.

PubMed

Grewal, Nivit; Singh, Shailendra; Chand, Trilok

2017-01-01

Owing to the innate noise in the biological data sources, a single source or a single measure do not suffice for an effective disease gene prioritization. So, the integration of multiple data sources or aggregation of multiple measures is the need of the hour. The aggregation operators combine multiple related data values to a single value such that the combined value has the effect of all the individual values. In this paper, an attempt has been made for applying the fuzzy aggregation on the network-based disease gene prioritization and investigate its effect under noise conditions. This study has been conducted for a set of 15 blood disorders by fusing four different network measures, computed from the protein interaction network, using a selected set of aggregation operators and ranking the genes on the basis of the aggregated value. The aggregation operator-based rankings have been compared with the "Random walk with restart" gene prioritization method. The impact of noise has also been investigated by adding varying proportions of noise to the seed set. The results reveal that for all the selected blood disorders, the Mean of Maximal operator has relatively outperformed the other aggregation operators for noisy as well as non-noisy data.

Aggregate Measures of Watershed Health from Reconstructed ...

EPA Pesticide Factsheets

Risk-based indices such as reliability, resilience, and vulnerability (R-R-V), have the potential to serve as watershed health assessment tools. Recent research has demonstrated the applicability of such indices for water quality (WQ) constituents such as total suspended solids and nutrients on an individual basis. However, the calculations can become tedious when time-series data for several WQ constituents have to be evaluated individually. Also, comparisons between locations with different sets of constituent data can prove difficult. In this study, data reconstruction using relevance vector machine algorithm was combined with dimensionality reduction via variational Bayesian noisy principal component analysis to reconstruct and condense sparse multidimensional WQ data sets into a single time series. The methodology allows incorporation of uncertainty in both the reconstruction and dimensionality-reduction steps. The R-R-V values were calculated using the aggregate time series at multiple locations within two Indiana watersheds. Results showed that uncertainty present in the reconstructed WQ data set propagates to the aggregate time series and subsequently to the aggregate R-R-V values as well. serving as motivating examples. Locations with different WQ constituents and different standards for impairment were successfully combined to provide aggregate measures of R-R-V values. Comparisons with individual constituent R-R-V values showed that v

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

NASA Astrophysics Data System (ADS)

Balabanov, Nikolai B.; Peterson, Kirk A.

2005-08-01

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

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

NASA Astrophysics Data System (ADS)

Hill, J. Grant; Peterson, Kirk A.

2017-12-01

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

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

The promises and challenges of pre-exposure prophylaxis as part of the emerging paradigm of combination HIV prevention.

PubMed

Cáceres, Carlos F; Koechlin, Florence; Goicochea, Pedro; Sow, Papa-Salif; O'Reilly, Kevin R; Mayer, Kenneth H; Godfrey-Faussett, Peter

2015-01-01

Towards the end of the twentieth century, significant success was achieved in reducing incidence in several global HIV epidemics through ongoing prevention strategies. However, further progress in risk reduction was uncertain. For one thing, it was clear that social vulnerability had to be addressed, through research on interventions addressing health systems and other structural barriers. As soon as antiretroviral treatment became available, researchers started to conceive that antiretrovirals might play a role in decreasing either susceptibility in uninfected people or infectiousness among people living with HIV. In this paper we focus on the origin, present status, and potential contribution of pre-exposure prophylaxis (PrEP) within the combination HIV prevention framework. After a phase of controversy, PrEP efficacy trials took off. By 2015, daily oral PrEP, using tenofovir alone or in combination with emtricitabine, has been proven efficacious, though efficacy seems heavily contingent upon adherence to pill uptake. Initial demonstration projects after release of efficacy results have shown that PrEP can be implemented in real settings and adherence can be high, leading to high effectiveness. Despite its substantial potential, beliefs persist about unfeasibility in real-life settings due to stigma, cost, adherence, and potential risk compensation barriers. The strategic synergy of behavioural change communication, biomedical strategies (including PrEP), and structural programmes is providing the basis for the combination HIV prevention framework. If PrEP is to ever become a key component of that framework, several negative beliefs must be confronted based on emerging evidence; moreover, research gaps regarding PrEP implementation must be filled, and appropriate prioritization strategies must be set up. Those challenges are significant, proportional to the impact that PrEP implementation may have in the global response to HIV.

The promises and challenges of pre-exposure prophylaxis as part of the emerging paradigm of combination HIV prevention

PubMed Central

Cáceres, Carlos F; Koechlin, Florence; Goicochea, Pedro; Sow, Papa-Salif; O'Reilly, Kevin R; Mayer, Kenneth H; Godfrey-Faussett, Peter

2015-01-01

Introduction Towards the end of the twentieth century, significant success was achieved in reducing incidence in several global HIV epidemics through ongoing prevention strategies. However, further progress in risk reduction was uncertain. For one thing, it was clear that social vulnerability had to be addressed, through research on interventions addressing health systems and other structural barriers. As soon as antiretroviral treatment became available, researchers started to conceive that antiretrovirals might play a role in decreasing either susceptibility in uninfected people or infectiousness among people living with HIV. In this paper we focus on the origin, present status, and potential contribution of pre-exposure prophylaxis (PrEP) within the combination HIV prevention framework. Discussion After a phase of controversy, PrEP efficacy trials took off. By 2015, daily oral PrEP, using tenofovir alone or in combination with emtricitabine, has been proven efficacious, though efficacy seems heavily contingent upon adherence to pill uptake. Initial demonstration projects after release of efficacy results have shown that PrEP can be implemented in real settings and adherence can be high, leading to high effectiveness. Despite its substantial potential, beliefs persist about unfeasibility in real-life settings due to stigma, cost, adherence, and potential risk compensation barriers. Conclusions The strategic synergy of behavioural change communication, biomedical strategies (including PrEP), and structural programmes is providing the basis for the combination HIV prevention framework. If PrEP is to ever become a key component of that framework, several negative beliefs must be confronted based on emerging evidence; moreover, research gaps regarding PrEP implementation must be filled, and appropriate prioritization strategies must be set up. Those challenges are significant, proportional to the impact that PrEP implementation may have in the global response to HIV. PMID:26198341

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

NASA Astrophysics Data System (ADS)

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

1984-08-01

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

Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

NASA Astrophysics Data System (ADS)

Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

2008-12-01

This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

Global Gravity Field Determination by Combination of terrestrial and Satellite Gravity Data

NASA Astrophysics Data System (ADS)

Fecher, T.; Pail, R.; Gruber, T.

2011-12-01

A multitude of impressive results document the success of the satellite gravity field mission GOCE with a wide field of applications in geodesy, geophysics and oceanography. The high performance of GOCE gravity field models can be further improved by combination with GRACE data, which is contributing the long wavelength signal content of the gravity field with very high accuracy. An example for such a consistent combination of satellite gravity data are the satellite-only models GOCO01S and GOCO02S. However, only the further combination with terrestrial and altimetric gravity data enables to expand gravity field models up to very high spherical harmonic degrees and thus to achieve a spatial resolution down to 20-30 km. First numerical studies for high-resolution global gravity field models combining GOCE, GRACE and terrestrial/altimetric data on basis of the DTU10 model have already been presented. Computations up to degree/order 600 based on full normal equations systems to preserve the full variance-covariance information, which results mainly from different weights of individual terrestrial/altimetric data sets, have been successfully performed. We could show that such large normal equations systems (degree/order 600 corresponds to a memory demand of almost 1TByte), representing an immense computational challenge as computation time and memory requirements put high demand on computational resources, can be handled. The DTU10 model includes gravity anomalies computed from the global model EGM08 in continental areas. Therefore, the main focus of this presentation lies on the computation of high-resolution combined gravity field models based on real terrestrial gravity anomaly data sets. This is a challenge due to the inconsistency of these data sets, including also systematic error components, but a further step to a real independent gravity field model. This contribution will present our recent developments and progress by using independent data sets at certain land areas, which are combined with DTU10 in the ocean areas, as well as satellite gravity data. Investigations have been made concerning the preparation and optimum weighting of the different data sources. The results, which should be a major step towards a GOCO-C model, will be validated using external gravity field data and by applying different validation methods.

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

NASA Astrophysics Data System (ADS)

Varandas, António J. C.

2018-04-01

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

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

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

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

Quantum Mechanical Calculations of Monoxides of Silicon Carbide Molecules

DTIC Science & Technology

2003-03-01

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

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

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

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

1990-10-01

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

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

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

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

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

First principle investigation of structural and optical properties of cubic titanium dioxide

NASA Astrophysics Data System (ADS)

Dash, Debashish; Chaudhury, Saurabh; Tripathy, Susanta K.

2018-05-01

This paper presents an analysis of structural and optical properties of cubic titanium dioxide (TiO2) using Orthogonalzed Linear Combinations of Atomic Orbitals (OLCAO) basis set under the framework of Density Functional Theory (DFT). The structural property, specially the lattice constant `a' and the optical properties such as refractive index, extinction coefficient, and reflectivity are investigated and discussed in the energy range of 0-16 eV. Further, the results have compared with previous theoretical as well as with experimental results. It was found that DFT based simulation results are approximation to experimental results.

Non-Line of Sight-Combined Arms (NLOS-CA) Manpower, Personnel and Logistics Impact Analysis (LIA)

DTIC Science & Technology

1993-11-15

total weight and volume to explosive weight have been used. These measure the size of the round relative to the killing power in the round. On this basis...the weapon system is powered up. (3) Alert Time is that time during which radios are operating, but the system is not powered up. For this analysis...TELEPHONE MANUA: SB-22/PT 1S U99185 UTILITY RECEPTACLE I V31211 TELEPHONE SET TA312 26 V•1788 POWER SUPPLY YE8 HYP-571TSEC 2I N32593 SHOP EQUIP AUTO

Circumcision-incision orchidopexy: A novel technique for palpable, low inguinal undescended testis

PubMed Central

Silangcruz, Jan Michael A.; Gomez, Odina; Dy, Jun S.; Morales, Marcelino L.

2017-01-01

Given that both orchidopexy and circumcision are commonly done in a single operative setting, we adopted a technique of combined orchidopexy and circumcision using a single circumcision incision. We applied this new technique to boys with palpable, low inguinal cryptorchidism. Here we describe a case series of 7 boys who underwent concurrent orchidopexy via the circumcision site. We present this novel technique and discuss our preliminary outcomes, including the anatomic basis and feasibility. The technique appears to be an alternative for concurrent circumcision and cryptorchid cases with palpable, low inguinal testes. PMID:29124248

Magnetic anisotropy in nickel complexes as determined by combined magnetic susceptibility/magnetization/theoretical studies

NASA Astrophysics Data System (ADS)

Mašlejová, Anna; Boča, Roman; Dlháň, L.'ubor; Herchel, Radovan

2004-05-01

The zero-field splitting in nickel(II) complexes was modeled by considering all relevant operators (electron repulsion, crystal-field, spin-orbit coupling, orbital-Zeeman, and spin-Zeeman) in the complete basis set spanned by d n-atomic terms. D-values between weak and strong crystal field limits were evaluated from the crystal-field multiplets as well as using the spin Hamiltonian formalism. Importance of the anisotropic orbital reduction factors is discussed and exemplified by D/hc=-22 cm-1 as subtracted from magnetic data for [Ni(imidazole) 4(acetate) 2] complex.

General analysis of group velocity effects in collinear optical parametric amplifiers and generators.

PubMed

Arisholm, Gunnar

2007-05-14

Group velocity mismatch (GVM) is a major concern in the design of optical parametric amplifiers (OPAs) and generators (OPGs) for pulses shorter than a few picoseconds. By simplifying the coupled propagation equations and exploiting their scaling properties, the number of free parameters for a collinear OPA is reduced to a level where the parameter space can be studied systematically by simulations. The resulting set of figures show the combinations of material parameters and pulse lengths for which high performance can be achieved, and they can serve as a basis for a design.

Specific methodology for capacitance imaging by atomic force microscopy: A breakthrough towards an elimination of parasitic effects

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

Estevez, Ivan; Concept Scientific Instruments, ZA de Courtaboeuf, 2 rue de la Terre de Feu, 91940 Les Ulis; Chrétien, Pascal

2014-02-24

On the basis of a home-made nanoscale impedance measurement device associated with a commercial atomic force microscope, a specific operating process is proposed in order to improve absolute (in sense of “nonrelative”) capacitance imaging by drastically reducing the parasitic effects due to stray capacitance, surface topography, and sample tilt. The method, combining a two-pass image acquisition with the exploitation of approach curves, has been validated on sets of calibration samples consisting in square parallel plate capacitors for which theoretical capacitance values were numerically calculated.

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

NASA Astrophysics Data System (ADS)

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

Locally dense basis sets (

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

NASA Technical Reports Server (NTRS)

Partridge, Harry

1989-01-01

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

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

PubMed

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

2014-05-15

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

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

PubMed

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

2016-08-03

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

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

PubMed

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

2015-10-13

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

Core-core and core-valence correlation

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

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

PubMed

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

2011-04-01

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

[Study thought of material basis of secondary development of major traditional Chinese medicine varieties on basis of combination of in vivo and in vitro experiments].

PubMed

Cheng, Xu-Dong; Jia, Xiao-Bin; Feng, Liang; Jiang, Jun

2013-12-01

The secondary development of major traditional Chinese medicine varieties is one of important links during the modernization, scientification and standardization of traditional Chinese medicines. How to accurately and effectively identify the pharmacodynamic material basis of original formulae becomes the primary problem in the secondary development, as well as the bottleneck in the modernization development of traditional Chinese medicines. On the basis of the existing experimental methods, and according to the study thought that the multi-component and complex effects of traditional Chinese medicine components need to combine multi-disciplinary methods and technologies, we propose the study thought of the material basis of secondary development of major traditional Chinese medicine varieties based on the combination of in vivo and in vitro experiments. It is believed that studies on material basis needs three links, namely identification, screening and verification, and in vivo and in vitro study method corresponding to each link is mutually complemented and verified. Finally, the accurate and reliable material basis is selected. This thought provides reference for the secondary development of major traditional Chinese medicine varieties and studies on compound material basis.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

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

NASA Astrophysics Data System (ADS)

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

2005-03-01

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

Decomposability and convex structure of thermal processes

NASA Astrophysics Data System (ADS)

Mazurek, Paweł; Horodecki, Michał

2018-05-01

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

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

PubMed

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

2017-11-14

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

Is performance in task-cuing experiments mediated by task set selection or associative compound retrieval?

PubMed

Forrest, Charlotte L D; Monsell, Stephen; McLaren, Ian P L

2014-07-01

Task-cuing experiments are usually intended to explore control of task set. But when small stimulus sets are used, they plausibly afford learning of the response associated with a combination of cue and stimulus, without reference to tasks. In 3 experiments we presented the typical trials of a task-cuing experiment: a cue (colored shape) followed, after a short or long interval, by a digit to which 1 of 2 responses was required. In a tasks condition, participants were (as usual) directed to interpret the cue as an instruction to perform either an odd/even or a high/low classification task. In a cue + stimulus → response (CSR) condition, to induce learning of mappings between cue-stimulus compound and response, participants were, in Experiment 1, given standard task instructions and additionally encouraged to learn the CSR mappings; in Experiment 2, informed of all the CSR mappings and asked to learn them, without standard task instructions; in Experiment 3, required to learn the mappings by trial and error. The effects of a task switch, response congruence, preparation, and transfer to a new set of stimuli differed substantially between the conditions in ways indicative of classification according to task rules in the tasks condition, and retrieval of responses specific to stimulus-cue combinations in the CSR conditions. Qualitative features of the latter could be captured by an associative learning network. Hence associatively based compound retrieval can serve as the basis for performance with a small stimulus set. But when organization by tasks is apparent, control via task set selection is the natural and efficient strategy. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus

PubMed Central

Cao, Xiaoxiao; Li, Shaohua; Chen, Liucun; Ding, Hongmei; Xu, Hua; Huang, Yanping; Li, Jie; Liu, Nongle; Cao, Weihong; Zhu, Yanjun; Shen, Beifen; Shao, Ningsheng

2009-01-01

In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer. PMID:19498077

Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus.

PubMed

Cao, Xiaoxiao; Li, Shaohua; Chen, Liucun; Ding, Hongmei; Xu, Hua; Huang, Yanping; Li, Jie; Liu, Nongle; Cao, Weihong; Zhu, Yanjun; Shen, Beifen; Shao, Ningsheng

2009-08-01

In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

Spiraling between qualitative and quantitative data on women's health behaviors: a double helix model for mixed methods.

PubMed

Mendlinger, Sheryl; Cwikel, Julie

2008-02-01

A double helix spiral model is presented which demonstrates how to combine qualitative and quantitative methods of inquiry in an interactive fashion over time. Using findings on women's health behaviors (e.g., menstruation, breast-feeding, coping strategies), we show how qualitative and quantitative methods highlight the theory of knowledge acquisition in women's health decisions. A rich data set of 48 semistructured, in-depth ethnographic interviews with mother-daughter dyads from six ethnic groups (Israeli, European, North African, Former Soviet Union [FSU], American/Canadian, and Ethiopian), plus seven focus groups, provided the qualitative sources for analysis. This data set formed the basis of research questions used in a quantitative telephone survey of 302 Israeli women from the ages of 25 to 42 from four ethnic groups. We employed multiple cycles of data analysis from both data sets to produce a more detailed and multidimensional picture of women's health behavior decisions through a spiraling process.

Identification of Autophagosome-associated Proteins and Regulators by Quantitative Proteomic Analysis and Genetic Screens*

PubMed Central

Dengjel, Jörn; Høyer-Hansen, Maria; Nielsen, Maria O.; Eisenberg, Tobias; Harder, Lea M.; Schandorff, Søren; Farkas, Thomas; Kirkegaard, Thomas; Becker, Andrea C.; Schroeder, Sabrina; Vanselow, Katja; Lundberg, Emma; Nielsen, Mogens M.; Kristensen, Anders R.; Akimov, Vyacheslav; Bunkenborg, Jakob; Madeo, Frank; Jäättelä, Marja; Andersen, Jens S.

2012-01-01

Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection. PMID:22311637

The prefabricated building risk decision research of DM technology on the basis of Rough Set

NASA Astrophysics Data System (ADS)

Guo, Z. L.; Zhang, W. B.; Ma, L. H.

2017-08-01

With the resources crises and more serious pollution, the green building has been strongly advocated by most countries and become a new building style in the construction field. Compared with traditional building, the prefabricated building has its own irreplaceable advantages but is influenced by many uncertainties. So far, a majority of scholars have been studying based on qualitative researches from all of the word. This paper profoundly expounds its significance about the prefabricated building. On the premise of the existing research methods, combined with rough set theory, this paper redefines the factors which affect the prefabricated building risk. Moreover, it quantifies risk factors and establish an expert knowledge base through assessing. And then reduced risk factors about the redundant attributes and attribute values, finally form the simplest decision rule. This simplest decision rule, which is based on the DM technology of rough set theory, provides prefabricated building with a controllable new decision-making method.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-09-28

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

Mapping working memory retrieval in space and in time: A combined electroencephalography and electrocorticography approach.

PubMed

Zhang, Qiong; van Vugt, Marieke; Borst, Jelmer P; Anderson, John R

2018-07-01

In this study, we investigated the time course and neural correlates of the retrieval process underlying visual working memory. We made use of a rare dataset in which the same task was recorded using both scalp electroencephalography (EEG) and Electrocorticography (ECoG), respectively. This allowed us to examine with great spatial and temporal detail how the retrieval process works, and in particular how the medial temporal lobe (MTL) is involved. In each trial, participants judged whether a probe face had been among a set of recently studied faces. With a method that combines hidden semi-Markov models and multivariate pattern analysis, the neural signal was decomposed into a sequence of latent cognitive stages with information about their durations on a trial-by-trial basis. Analyzed separately, EEG and ECoG data yielded converging results on discovered stages and their interpretation, which reflected 1) a brief pre-attention stage, 2) encoding the stimulus, 3) retrieving the studied set, and 4) making a decision. Combining these stages with the high spatial resolution of ECoG suggested that activity in the temporal cortex reflected item familiarity in the retrieval stage; and that once retrieval is complete, there is active maintenance of the studied face set in the decision stage in the MTL. During this same period, the frontal cortex guides the decision by means of theta coupling with the MTL. These observations generalize previous findings on the role of MTL theta from long-term memory tasks to short-term memory tasks. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis.

PubMed

Kujala, S T; Knürr, T; Kärkkäinen, K; Neale, D B; Sillanpää, M J; Savolainen, O

2017-05-01

Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin.

Interactions between methylmercury and selenomethionine injected into mallard eggs

USGS Publications Warehouse

Klimstra, J.D.; Yee, J.L.; Heinz, G.H.; Hoffman, D.J.; Stebbins, K.R.

2012-01-01

Methylmercury chloride and seleno-L-methionine were injected separately or in combinations into mallard eggs (Anas platyrhynchos), and embryo mortality and teratogenic effects (deformities) were modeled using a logistic regression model. Methylmercury was injected at doses that resulted in concentrations of 0, 0.2, 0.4, 0.8, and 1.6 µg/g Hg in the egg on a wet weight basis and selenomethionine at doses that resulted in concentrations of 0, 0.1, 0.2, 0.4, and 0.6 µg/g Se in the egg, also on a wet weight basis. When selenomethionine and methylmercury were injected separately, hatching probability decreased in both cases. However, when methylmercury was injected at 1.6 µg/g in combination with selenomethionine at 0.2 µg/g, the presence of the methylmercury resulted in less embryo mortality than had been seen with 0.2 µg/g Se by itself, but it increased the number of deformed embryos and hatchlings. Selenomethionine appeared to be more embryotoxic than equivalent doses of methylmercury when injected into eggs, and both injected methylmercury and selenomethionine were more toxic to mallard embryos than when deposited naturally in the egg by the mother. The underlying mechanisms behind the interactions between methylmercury and selenomethionine and why methylmercury appeared to improve hatching probability of Se-dosed eggs yet increased deformities when the two compounds were combined are unclear. These findings warrant further studies to understand these mechanisms in both laboratory and field settings.

Convergence of third order correlation energy in atoms and molecules.

PubMed

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

2007-01-30

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

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

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

Ozkanlar, Abdullah; Clark, Aurora E.

2012-05-23

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

Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-09-01

The dual-kinetic-balance (DKB) finite basis set method for solving the Dirac equation for hydrogen-like ions [V.M. Shabaev et al., Phys. Rev. Lett. 93 (2004) 130405] is extended to problems with a non-local spherically-symmetric Dirac-Hartree-Fock potential. We implement the DKB method using B-spline basis sets and compare its performance with the widely-employed approach of Notre Dame (ND) group [W.R. Johnson, S.A. Blundell, J. Sapirstein, Phys. Rev. A 37 (1988) 307-315]. We compare the performance of the ND and DKB methods by computing various properties of Cs atom: energies, hyperfine integrals, the parity-non-conserving amplitude of the 6s-7s transition, and the second-order many-body correction to the removal energy of the valence electrons. We find that for a comparable size of the basis set the accuracy of both methods is similar for matrix elements accumulated far from the nuclear region. However, for atomic properties determined by small distances, the DKB method outperforms the ND approach. In addition, we present a strategy for optimizing the size of the basis sets by choosing progressively smaller number of basis functions for increasingly higher partial waves. This strategy exploits suppression of contributions of high partial waves to typical many-body correlation corrections.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories

NASA Astrophysics Data System (ADS)

Zhang, Chuan-Biao; Ming, Li; Xin, Zhou

2015-12-01

Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics (RED) is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions, are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation (RMSD) among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space. Project supported by the National Natural Science Foundation of China (Grant No. 11175250).

Antigenic Competition Between and Endotoxic Adjuvant and a Protein Antigen

PubMed Central

Leong, Daniel L. Y.; Rudbach, Jon A.

1971-01-01

Antigenic competition between bovine gamma globulin (BGG) and endotoxin from a smooth strain (S-ET) and a rough (R-ET) heptoseless mutant strain of Salmonella minnesota was studied in mice. Both endotoxins acted as adjuvants for enhancing the antibody response to BGG. However, other work showed that the R-ET had minimal antigenicity, and it was used as a control for the competition studies. Antigenic competition between BGG and endotoxin as expressed by a suppression of the antibody response to BGG could not be demonstrated when varying adjuvant doses of S-ET or R-ET were injected simultaneously with a small constant dose of BGG into normal mice. However, mice presensitized with S-ET several weeks before immunization with the S-ET and BGG combination produced anti-BGG levels which were four to eightfold lower than in normal mice. Nearly complete suppression of the anti-BGG response could be obtained in presensitized mice by reducing the BGG dose 10-fold or by increasing the adjuvant dose of endotoxin. Mice pretreated with R-ET and challenged with BGG plus S-ET or R-ET showed no depression of the anti-BGG response. These and other experiments confirmed the immunological basis of the competitive effect. PMID:16557970

Compressive Detection of Highly Overlapped Spectra Using Walsh-Hadamard-Based Filter Functions.

PubMed

Corcoran, Timothy C

2018-03-01

In the chemometric context in which spectral loadings of the analytes are already known, spectral filter functions may be constructed which allow the scores of mixtures of analytes to be determined in on-the-fly fashion directly, by applying a compressive detection strategy. Rather than collecting the entire spectrum over the relevant region for the mixture, a filter function may be applied within the spectrometer itself so that only the scores are recorded. Consequently, compressive detection shrinks data sets tremendously. The Walsh functions, the binary basis used in Walsh-Hadamard transform spectroscopy, form a complete orthonormal set well suited to compressive detection. A method for constructing filter functions using binary fourfold linear combinations of Walsh functions is detailed using mathematics borrowed from genetic algorithm work, as a means of optimizing said functions for a specific set of analytes. These filter functions can be constructed to automatically strip the baseline from analysis. Monte Carlo simulations were performed with a mixture of four highly overlapped Raman loadings and with ten excitation-emission matrix loadings; both sets showed a very high degree of spectral overlap. Reasonable estimates of the true scores were obtained in both simulations using noisy data sets, proving the linearity of the method.

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

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

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

2016-06-07

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

A Combined Kinetic and Volatility Basis Set Approach to Model Secondary Organic Aerosol from Toluene and Diesel Exhaust/Meat Cooking Mixtures

NASA Astrophysics Data System (ADS)

Parikh, H. M.; Carlton, A. G.; Zhang, H.; Kamens, R.; Vizuete, W.

2011-12-01

Secondary organic aerosol (SOA) is simulated for 6 outdoor smog chamber experiments using a SOA model based on a kinetic chemical mechanism in conjunction with a volatility basis set (VBS) approach. The experiments include toluene, a non-SOA-forming hydrocarbon mixture, diesel exhaust or meat cooking emissions and NOx, and are performed under varying conditions of relative humidity. SOA formation from toluene is modeled using a condensed kinetic aromatic mechanism that includes partitioning of lumped semi-volatile products in particle organic-phase and incorporates particle aqueous-phase chemistry to describe uptake of glyoxal and methylglyoxal. Modeling using the kinetic mechanism alone, along with primary organic aerosol (POA) from diesel exhaust (DE) /meat cooking (MC) fails to simulate the rapid SOA formation at the beginning hours of the experiments. Inclusion of a VBS approach with the kinetic mechanism to characterize the emissions and chemistry of complex mixture of intermediate volatility organic compounds (IVOCs) from DE/MC, substantially improves SOA predictions when compared with observed data. The VBS model includes photochemical aging of IVOCs and evaporation of POA after dilution. The relative contribution of SOA mass from DE/MC is as high as 95% in the morning, but substantially decreases after mid-afternoon. For high humidity experiments, aqueous-phase SOA fraction dominates the total SOA mass at the end of the day (approximately 50%). In summary, the combined kinetic and VBS approach provides a new and improved framework to semi-explicitly model SOA from VOC precursors in conjunction with a VBS approach that can be used on complex emission mixtures comprised with hundreds of individual chemical species.

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

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

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less

Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

NASA Astrophysics Data System (ADS)

Sippl, Wolfgang

2000-08-01

One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient ( r 2 = 0.617, q 2 LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained ( r 2 = 0.991, q 2 LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

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

NASA Astrophysics Data System (ADS)

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

2001-08-01

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

Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: theory and analysis of the water dimer.

PubMed

Azar, R Julian; Horn, Paul Richard; Sundstrom, Eric Jon; Head-Gordon, Martin

2013-02-28

The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative. The polMO basis is minimal in the sense that one polarization function is provided for each unpolarized orbital that is occupied; such an approach is exact in second-order perturbation theory. Based on formal grounds and practical calculations, the polMO approach is shown to underestimate the strength of polarization effects. In contrast to the ALMO method, however, the polMO approach yields results that are very stable to improvements in the underlying AO basis expansion. Combining the ALMO and polMO approaches allows an estimate of the range of energy-lowering due to polarization. Extensive numerical calculations on the water dimer using a large range of basis sets with Hartree-Fock theory and a variety of different density functionals illustrate the key considerations. Results are also presented for the polarization-dominated Na(+)CH4 complex. Implications for energy decomposition analysis of intermolecular interactions are discussed.

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

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

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

Structure elucidation and absolute stereochemistry of isomeric monoterpene chromane esters.

PubMed

Batista, João M; Batista, Andrea N L; Mota, Jonas S; Cass, Quezia B; Kato, Massuo J; Bolzani, Vanderlan S; Freedman, Teresa B; López, Silvia N; Furlan, Maysa; Nafie, Laurence A

2011-04-15

Six novel monoterpene chromane esters were isolated from the aerial parts of Peperomia obtusifolia (Piperaceae) using chiral chromatography. This is the first time that chiral chromane esters of this kind, ones with a tethered chiral terpene, have been isolated in nature. Due to their structural features, it is not currently possible to assess directly their absolute stereochemistry using any of the standard classical approaches, such as X-ray crystallography, NMR, optical rotation, or electronic circular dichroism (ECD). Herein we report the absolute configuration of these molecules, involving four chiral centers, using vibrational circular dichroism (VCD) and density functional theory (DFT) (B3LYP/6-31G*) calculations. This work further reinforces the capability of VCD to determine unambiguously the absolute configuration of structurally complex molecules in solution, without crystallization or derivatization, and demonstrates the sensitivity of VCD to specify the absolute configuration for just one among a number of chiral centers. We also demonstrate the sufficiency of using the so-called inexpensive basis set 6-31G* compared to the triple-ζ basis set TZVP for absolute configuration analysis of larger molecules using VCD. Overall, this work extends our knowledge of secondary metabolites in plants and provides a straightforward way to determine the absolute configuration of complex natural products involving a chiral parent moiety combined with a chiral terpene adduct.

Conversations between anthropology and psychiatry: drawing out the best from interdisciplinarity in global mental health.

PubMed

Rosso Buckton, Amanda

2015-12-01

Conversations between anthropologists and psychiatrists have led to new theoretical trajectories, research agendas and clinical practices as social scientists and medical practitioners forged new understandings about the interaction of culture, personhood and illness. However, the demands of global mental health, coupled with health service provision requirements, mean that mental health interventions set up with the best intentions can fail to take into account the knowledge and expertise that social sciences can contribute to a programme's success. In this paper, I reflect on conversations between an anthropologist and mental health professionals in direct reference to data analysis of an AusAID mental health capacity-building programme undertaken in the Pacific region. Social and cultural perspectives embedded within programmes can provide richer, more contextualised interventions. In drawing on the combined expertise of anthropology and psychiatry, new taken-for-granted reference points embedding cultural approaches form the basis for delivery of global mental health programmes. These perspectives include: Locating mental health programmes within development critiques. Situating the subjects of development within contextualised settings, acknowledging and respecting local knowledge, understandings and practices. A focus on interdisciplinarity as the basis for future practice in global mental health projects. © The Royal Australian and New Zealand College of Psychiatrists 2015.

Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

2015-01-01

In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm-1 and 4000-50 cm-1, respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion-1 and anion-2 conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1sbnd C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed.

Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: a combined experimental and theoretical study.

PubMed

Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

2015-01-25

In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1), respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion(-1) and anion(-2) conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. (1)H and (13)C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed. Copyright © 2014 Elsevier B.V. All rights reserved.

[Epigenetic inheritance and its possible role in the evolution of plant species].

PubMed

Lavrov, S A; Mavrodiev, E V

2003-01-01

As it is clear now, the level of gene expression in eukariotes is determined mainly by chromatin composition. Chromatin structure of a particular gene (it is a complex item, which includes nucleosome positioning, histone modifications and non-histone chromatin proteins) can be modified externally and is able to be inherited mitotically and meiotically. Changes in chromatine structure are the basis of so called epigenetic inheritance that occurs without modification of DNA sequence. One of the most striking examples of epigenetic inheritance in plants is epimutations--stable for many generation's alleles of some genes that do not differ in primary DNA structure. Molecular basis of epimutations seems to be DNA metylation. Epimutations may be widely distributed in nature and affect some basis morphological features that have a systematic significance. Possibility of inheritance of acquired epigenetic modifications lead us to reconsider an idea of multipLe independent origins of some plant forms (or ecotypes) under action of similar external conditions. Different populations of the same species may in this case be unrelated and has no common ancestor. Species should be considered as invariant of multiple ways of origin. Wide distribution of polyploids amongst higher plants suggests effective mechanism of repression of multicopy genes. Each allopolyploidisation event is followed by repression of random set of parent genes via changes in its chromatin structure. As a result, in the limits of the same hybrid formula may arise different stable combinations of epigenetically controlled features of parent species. These combinations may be classified as different species of other taxa.

Using the framework of corporate culture in "mergers" to support the development of a cultural basis for integrative medicine - guidance for building an integrative medicine department or service.

PubMed

Witt, Claudia M; Pérard, Marion; Berman, Brian; Berman, Susan; Birdsall, Timothy C; Defren, Horst; Kümmel, Sherko; Deng, Gary; Dobos, Gustav; Drexler, Atje; Holmberg, Christine; Horneber, Markus; Jütte, Robert; Knutson, Lori; Kummer, Christopher; Volpers, Susanne; Schweiger, David

2015-01-01

An increasing number of clinics offer complementary or integrative medicine services; however, clear guidance about how complementary medicine could be successfully and efficiently integrated into conventional health care settings is still lacking. Combining conventional and complementary medicine into integrative medicine can be regarded as a kind of merger. In a merger, two or more organizations - usually companies - are combined into one in order to strengthen the companies financially and strategically. The corporate culture of both merger partners has an important influence on the integration. The aim of this project was to transfer the concept of corporate culture in mergers to the merging of two medical systems. A two-step approach (literature analyses and expert consensus procedure) was used to develop practical guidance for the development of a cultural basis for integrative medicine, based on the framework of corporate culture in "mergers," which could be used to build an integrative medicine department or integrative medicine service. Results include recommendations for general strategic dimensions (definition of the medical model, motivation for integration, clarification of the available resources, development of the integration team, and development of a communication strategy), and recommendations to overcome cultural differences (the clinic environment, the professional language, the professional image, and the implementation of evidence-based medicine). The framework of mergers in corporate culture provides an understanding of the difficulties involved in integrative medicine projects. The specific recommendations provide a good basis for more efficient implementation.

Using the framework of corporate culture in “mergers” to support the development of a cultural basis for integrative medicine – guidance for building an integrative medicine department or service

PubMed Central

Witt, Claudia M; Pérard, Marion; Berman, Brian; Berman, Susan; Birdsall, Timothy C; Defren, Horst; Kümmel, Sherko; Deng, Gary; Dobos, Gustav; Drexler, Atje; Holmberg, Christine; Horneber, Markus; Jütte, Robert; Knutson, Lori; Kummer, Christopher; Volpers, Susanne; Schweiger, David

2015-01-01

Background An increasing number of clinics offer complementary or integrative medicine services; however, clear guidance about how complementary medicine could be successfully and efficiently integrated into conventional health care settings is still lacking. Combining conventional and complementary medicine into integrative medicine can be regarded as a kind of merger. In a merger, two or more organizations − usually companies − are combined into one in order to strengthen the companies financially and strategically. The corporate culture of both merger partners has an important influence on the integration. Purpose The aim of this project was to transfer the concept of corporate culture in mergers to the merging of two medical systems. Methods A two-step approach (literature analyses and expert consensus procedure) was used to develop practical guidance for the development of a cultural basis for integrative medicine, based on the framework of corporate culture in “mergers,” which could be used to build an integrative medicine department or integrative medicine service. Results Results include recommendations for general strategic dimensions (definition of the medical model, motivation for integration, clarification of the available resources, development of the integration team, and development of a communication strategy), and recommendations to overcome cultural differences (the clinic environment, the professional language, the professional image, and the implementation of evidence-based medicine). Conclusion The framework of mergers in corporate culture provides an understanding of the difficulties involved in integrative medicine projects. The specific recommendations provide a good basis for more efficient implementation. PMID:25632226

Molecular structure, spectral investigation (1H NMR, 13C NMR, UV-Visible, FT-IR, FT-Raman), NBO, intramolecular hydrogen bonding, chemical reactivity and first hyperpolarizability analysis of formononetin [7-hydroxy-3(4-methoxyphenyl)chromone]: A quantum chemical study

NASA Astrophysics Data System (ADS)

Srivastava, Anubha; Mishra, Rashmi; Kumar, Sudhir; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

2015-03-01

Formononetin [7-hydroxy-3(4-methoxyphenyl)chromone or 4‧-methoxy daidzein] is a soy isoflavonoid that is found abundantly in traditional Chinese medicine Astragalus mongholicus (Bunge) and Trifolium pretense L. (red clover), and in an Indian medicinal plant, Butea (B.) monosperma. Crude extract of B.monosperma is used for rapid healing of fracture in Indian traditional medicine. In this study, a combined theoretical and experimental approach is used to study the properties of formononetin. The optimized geometry was calculated by B3LYP method using 6-311++G(d,p) as a large basis set. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution (PED) analysis. Density functional theory (DFT) is applied to explore the nonlinear optical properties of the molecule. Good consistency is found between the calculated results and observed data for the electronic absorption, IR and Raman spectra. The solvent effects have been calculated using time-dependent density functional theory in combination with the integral equation formalism polarized continuum model, and the results are in good agreement with observed measurements. The double well potential energy curve of the molecule about the respective bonds, have been plotted, as obtained from DFT/6-31G basis set. The computational results diagnose the most stable conformer of formononetin. The HOMO-LUMO energy gap of possible conformers has been calculated for comparing their chemical activity. Chemical reactivity has been measured by reactivity descriptors and molecular electrostatic potential surface (MEP). The 1H and 13C NMR chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. Furthermore, the role of CHsbnd O intramolecular hydrogen bond in the stability of molecule is investigated on the basis of the results of topological properties of AIM theory and NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics.

Machine learning approach to automatic exudate detection in retinal images from diabetic patients

NASA Astrophysics Data System (ADS)

Sopharak, Akara; Dailey, Matthew N.; Uyyanonvara, Bunyarit; Barman, Sarah; Williamson, Tom; Thet Nwe, Khine; Aye Moe, Yin

2010-01-01

Exudates are among the preliminary signs of diabetic retinopathy, a major cause of vision loss in diabetic patients. Early detection of exudates could improve patients' chances to avoid blindness. In this paper, we present a series of experiments on feature selection and exudates classification using naive Bayes and support vector machine (SVM) classifiers. We first fit the naive Bayes model to a training set consisting of 15 features extracted from each of 115,867 positive examples of exudate pixels and an equal number of negative examples. We then perform feature selection on the naive Bayes model, repeatedly removing features from the classifier, one by one, until classification performance stops improving. To find the best SVM, we begin with the best feature set from the naive Bayes classifier, and repeatedly add the previously-removed features to the classifier. For each combination of features, we perform a grid search to determine the best combination of hyperparameters ν (tolerance for training errors) and γ (radial basis function width). We compare the best naive Bayes and SVM classifiers to a baseline nearest neighbour (NN) classifier using the best feature sets from both classifiers. We find that the naive Bayes and SVM classifiers perform better than the NN classifier. The overall best sensitivity, specificity, precision, and accuracy are 92.28%, 98.52%, 53.05%, and 98.41%, respectively.

A new digitized reverse correction method for hypoid gears based on a one-dimensional probe

NASA Astrophysics Data System (ADS)

Li, Tianxing; Li, Jubo; Deng, Xiaozhong; Yang, Jianjun; Li, Genggeng; Ma, Wensuo

2017-12-01

In order to improve the tooth surface geometric accuracy and transmission quality of hypoid gears, a new digitized reverse correction method is proposed based on the measurement data from a one-dimensional probe. The minimization of tooth surface geometrical deviations is realized from the perspective of mathematical analysis and reverse engineering. Combining the analysis of complex tooth surface generation principles and the measurement mechanism of one-dimensional probes, the mathematical relationship between the theoretical designed tooth surface, the actual machined tooth surface and the deviation tooth surface is established, the mapping relation between machine-tool settings and tooth surface deviations is derived, and the essential connection between the accurate calculation of tooth surface deviations and the reverse correction method of machine-tool settings is revealed. Furthermore, a reverse correction model of machine-tool settings is built, a reverse correction strategy is planned, and the minimization of tooth surface deviations is achieved by means of the method of numerical iterative reverse solution. On this basis, a digitized reverse correction system for hypoid gears is developed by the organic combination of numerical control generation, accurate measurement, computer numerical processing, and digitized correction. Finally, the correctness and practicability of the digitized reverse correction method are proved through a reverse correction experiment. The experimental results show that the tooth surface geometric deviations meet the engineering requirements after two trial cuts and one correction.

Unitary Transformations in the Quantum Model for Conceptual Conjunctions and Its Application to Data Representation

PubMed Central

Veloz, Tomas; Desjardins, Sylvie

2015-01-01

Quantum models of concept combinations have been successful in representing various experimental situations that cannot be accommodated by traditional models based on classical probability or fuzzy set theory. In many cases, the focus has been on producing a representation that fits experimental results to validate quantum models. However, these representations are not always consistent with the cognitive modeling principles. Moreover, some important issues related to the representation of concepts such as the dimensionality of the realization space, the uniqueness of solutions, and the compatibility of measurements, have been overlooked. In this paper, we provide a dimensional analysis of the realization space for the two-sector Fock space model for conjunction of concepts focusing on the first and second sectors separately. We then introduce various representation of concepts that arise from the use of unitary operators in the realization space. In these concrete representations, a pair of concepts and their combination are modeled by a single conceptual state, and by a collection of exemplar-dependent operators. Therefore, they are consistent with cognitive modeling principles. This framework not only provides a uniform approach to model an entire data set, but, because all measurement operators are expressed in the same basis, allows us to address the question of compatibility of measurements. In particular, we present evidence that it may be possible to predict non-commutative effects from partial measurements of conceptual combinations. PMID:26617556

Unitary Transformations in the Quantum Model for Conceptual Conjunctions and Its Application to Data Representation.

PubMed

Veloz, Tomas; Desjardins, Sylvie

2015-01-01

Quantum models of concept combinations have been successful in representing various experimental situations that cannot be accommodated by traditional models based on classical probability or fuzzy set theory. In many cases, the focus has been on producing a representation that fits experimental results to validate quantum models. However, these representations are not always consistent with the cognitive modeling principles. Moreover, some important issues related to the representation of concepts such as the dimensionality of the realization space, the uniqueness of solutions, and the compatibility of measurements, have been overlooked. In this paper, we provide a dimensional analysis of the realization space for the two-sector Fock space model for conjunction of concepts focusing on the first and second sectors separately. We then introduce various representation of concepts that arise from the use of unitary operators in the realization space. In these concrete representations, a pair of concepts and their combination are modeled by a single conceptual state, and by a collection of exemplar-dependent operators. Therefore, they are consistent with cognitive modeling principles. This framework not only provides a uniform approach to model an entire data set, but, because all measurement operators are expressed in the same basis, allows us to address the question of compatibility of measurements. In particular, we present evidence that it may be possible to predict non-commutative effects from partial measurements of conceptual combinations.

Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Cantrell, Sean A.

2010-01-01

The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

Dynamic least-squares kernel density modeling of Fokker-Planck equations with application to neural population.

PubMed

Shotorban, Babak

2010-04-01

The dynamic least-squares kernel density (LSQKD) model [C. Pantano and B. Shotorban, Phys. Rev. E 76, 066705 (2007)] is used to solve the Fokker-Planck equations. In this model the probability density function (PDF) is approximated by a linear combination of basis functions with unknown parameters whose governing equations are determined by a global least-squares approximation of the PDF in the phase space. In this work basis functions are set to be Gaussian for which the mean, variance, and covariances are governed by a set of partial differential equations (PDEs) or ordinary differential equations (ODEs) depending on what phase-space variables are approximated by Gaussian functions. Three sample problems of univariate double-well potential, bivariate bistable neurodynamical system [G. Deco and D. Martí, Phys. Rev. E 75, 031913 (2007)], and bivariate Brownian particles in a nonuniform gas are studied. The LSQKD is verified for these problems as its results are compared against the results of the method of characteristics in nondiffusive cases and the stochastic particle method in diffusive cases. For the double-well potential problem it is observed that for low to moderate diffusivity the dynamic LSQKD well predicts the stationary PDF for which there is an exact solution. A similar observation is made for the bistable neurodynamical system. In both these problems least-squares approximation is made on all phase-space variables resulting in a set of ODEs with time as the independent variable for the Gaussian function parameters. In the problem of Brownian particles in a nonuniform gas, this approximation is made only for the particle velocity variable leading to a set of PDEs with time and particle position as independent variables. Solving these PDEs, a very good performance by LSQKD is observed for a wide range of diffusivities.

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

NASA Astrophysics Data System (ADS)

Reinscheid, F.; Reinscheid, U. M.

2016-02-01

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

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

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

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

2014-07-28

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

Covariance Based Pre-Filters and Screening Criteria for Conjunction Analysis

NASA Astrophysics Data System (ADS)

George, E., Chan, K.

2012-09-01

Several relationships are developed relating object size, initial covariance and range at closest approach to probability of collision. These relationships address the following questions: - Given the objects' initial covariance and combined hard body size, what is the maximum possible value of the probability of collision (Pc)? - Given the objects' initial covariance, what is the maximum combined hard body radius for which the probability of collision does not exceed the tolerance limit? - Given the objects' initial covariance and the combined hard body radius, what is the minimum miss distance for which the probability of collision does not exceed the tolerance limit? - Given the objects' initial covariance and the miss distance, what is the maximum combined hard body radius for which the probability of collision does not exceed the tolerance limit? The first relationship above allows the elimination of object pairs from conjunction analysis (CA) on the basis of the initial covariance and hard-body sizes of the objects. The application of this pre-filter to present day catalogs with estimated covariance results in the elimination of approximately 35% of object pairs as unable to ever conjunct with a probability of collision exceeding 1x10-6. Because Pc is directly proportional to object size and inversely proportional to covariance size, this pre-filter will have a significantly larger impact on future catalogs, which are expected to contain a much larger fraction of small debris tracked only by a limited subset of available sensors. This relationship also provides a mathematically rigorous basis for eliminating objects from analysis entirely based on element set age or quality - a practice commonly done by rough rules of thumb today. Further, these relations can be used to determine the required geometric screening radius for all objects. This analysis reveals the screening volumes for small objects are much larger than needed, while the screening volumes for pairs of large objects may be inadequate. These relationships may also form the basis of an important metric for catalog maintenance by defining the maximum allowable covariance size for effective conjunction analysis. The application of these techniques promises to greatly improve the efficiency and completeness of conjunction analysis.

Assessment of health risks due to arsenic from iron ore lumps in a beach setting.

PubMed

Swartjes, Frank A; Janssen, Paul J C M

2016-09-01

In 2011, an artificial hook-shaped peninsula of 128ha beach area was created along the Dutch coast, containing thousands of iron ore lumps, which include arsenic from natural origin. Elemental arsenic and inorganic arsenic induce a range of toxicological effects and has been classified as proven human carcinogens. The combination of easy access to the beach and the presence of arsenic raised concern about possible human health effects by the local authorities. The objective of this study is therefore to investigate human health risks from the presence of arsenic-containing iron ore lumps in a beach setting. The exposure scenarios underlying the human health-based risk limits for contaminated land in The Netherlands, based on soil material ingestion and a residential setting, are not appropriate. Two specific exposure scenarios related to the playing with iron ore lumps on the beach ('sandcastle building') are developed on the basis of expert judgement, relating to children in the age of 2 to 12years, i.e., a worst case exposure scenario and a precautionary scenario. Subsequently, exposure is calculated by the quantification of the following factors: hand loading, soil-mouth transfer effectivity, hand-mouth contact frequency, contact surface, body weight and the relative oral bioavailability factor. By lack of consensus on a universal reference dose for arsenic for use in the stage of risk characterization, three different types of assessments have been evaluated: on the basis of the current Provisional Tolerable Daily Intake (PTWI), on the basis of the Benchmark Dose Lower limit (BMDL), and by a comparison of exposure from the iron ore lumps with background exposure. It is concluded, certainly from the perspective of the conservative exposure assessment, that unacceptable human health risks due to exposure to arsenic from the iron ore lumps are unlikely and there is no need for risk management actions. Copyright © 2016 Elsevier B.V. All rights reserved.

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

Fu, Zheng; Li, Xue; Merz, Kenneth M.

2012-01-01

The conformational profiles of unbound all-trans and 9-cis retinoic acid (RA) have been determined using classical and quantum mechanical calculations. Sixty-six all-trans-RA (ATRA) and forty-eight 9-cis-RA energy minimum conformers were identified via HF/6-31G* geometry optimizations in vacuo. Their relative conformational energies were estimated utilizing the M06, M06-2x and MP2 methods combined with the 6-311+G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets, as well as complete basis set MP2 extrapolations using the latter two basis sets. Single-point energy calculations performed with the M06-2x density functional were found to yield similar results to MP2/CBS for the low-energy retinoic acid conformations. Not unexpectedly, the conformational propensities of retinoic acid were governed by the orientation and arrangement of the torsion angles associated with the polyene tail. We also used previously reported QM/MM X-ray refinement results on four ATRA-protein crystal structures plus one newly refined 9-cis-RA complex (PDB ID 1XDK) in order to investigate the conformational preferences of bound retinoic acid. In the re-refined RA conformers the conjugated double bonds are nearly coplanar, which is consistent with the global minimum identified by the Omega/QM method rather than the corresponding crystallographically determined conformations given in the PDB. Consequently, a 91.3% average reduction of the local strain energy in the gas phase, as well as 92.1% in PCM solvent, was observed using the QM/MM refined structures versus the PDB deposited RA conformations. These results thus demonstrate that our QM/MM X-ray refinement approach can significantly enhance the quality of X-ray crystal structures refined by conventional refinement protocols, thereby providing reliable drug-target structural information for use in structure-based drug discovery applications. PMID:22844234

Basis set study of classical rotor lattice dynamics.

PubMed

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

2004-03-22

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

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

NASA Astrophysics Data System (ADS)

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

2012-05-01

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

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

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

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

2014-05-07

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

Real-time flight conflict detection and release based on Multi-Agent system

NASA Astrophysics Data System (ADS)

Zhang, Yifan; Zhang, Ming; Yu, Jue

2018-01-01

This paper defines two-aircrafts, multi-aircrafts and fleet conflict mode, sets up space-time conflict reservation on the basis of safety interval and conflict warning time in three-dimension. Detect real-time flight conflicts combined with predicted flight trajectory of other aircrafts in the same airspace, and put forward rescue resolutions for the three modes respectively. When accorded with the flight conflict conditions, determine the conflict situation, and enter the corresponding conflict resolution procedures, so as to avoid the conflict independently, as well as ensure the flight safety of aimed aircraft. Lastly, the correctness of model is verified with numerical simulation comparison.

Vibrational spectroscopic analysis of 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione

NASA Astrophysics Data System (ADS)

Soliman, H. S.; Eid, Kh. M.; Ali, H. A. M.; Atef, S. M.; El-Mansy, M. A. M.

2012-11-01

In the present work, a combined experimental and computational study for the optimized molecular structural parameters, FT-IR spectra, thermo-chemical parameters, total dipole moment and HOMO-LUMO energy gap for 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione have been investigated using B3LYP/6-311G basis set. Our calculated results have showed that the investigated compound possesses a dipole moment of 4.9 Debye and HOMO-LUMO energy gap of 3 eV which indicate high recommendations for photovoltaic devices fabrication.

FT-IR spectroscopic analyses of 2-(2-furanylmethylene) propanedinitrile

NASA Astrophysics Data System (ADS)

Soliman, H. S.; Eid, Kh. M.; Ali, H. A. M.; El-Mansy, M. A. M.; Atef, S. M.

2013-03-01

In the present work, a computational study for the optimized molecular structural parameters, thermo-chemical parameters, total dipole moment, HOMO-LUMO energy gap and a combined experimental and computational study for FT-IR spectra for 2-(2-furanylmethylene) propanedinitrile have been investigated using B3LYP utilizing 6-31G and 6-311G basis set. Our calculated results showed that the investigated compound possesses a dipole moment of 7.5 D and HOMO-LUMO energy gap of 3.92 eV using B3LYP/6-311G which indicates that our investigated compound is highly applicable for photovoltaic solar cell applications.

Water detection at the moon, Mars and comets with a combined neutron gamma ray instrument

NASA Technical Reports Server (NTRS)

Metzger, Albert E.; Haines, Eldon L.

1991-01-01

Measuring the fluxes of thermal and epithermal neutrons at a planetary object in conjunction with gamma-ray spectroscopic observations will provide information about the chemical composition of the surface which is less model dependent than the gamma ray measurements by themselves. Researchers devised a passive neutron detector for this purpose. An experimental model was designed and built. Three variables provided the basis for a set of experiments: thickness of the Sm and B layers, the presence or absence of the ACS, and the position of the source relative to the PND's cylindrical axis. Experimental results are given.

Ab initio approaches for the determination of heavy element energetics: Ionization energies of trivalent lanthanides (Ln = La-Eu)

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

Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K., E-mail: wilson@chemistry.msu.edu

2015-11-21

An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.

Spectroscopic notes of Methyl Red (MR) dye.

PubMed

El-Mansy, M A M; Yahia, I S

2014-09-15

In the present work, a combined experimental and theoretical study on molecular structure and vibrational frequencies of MR were reported. The FT-IR spectrum of MR is recorded in the solid phase. The equilibrium geometries, harmonic vibrational frequencies, thermo-chemical parameters, total dipole moment and HOMO-LUMO energies are calculated by DFT/B3LYP utilizing 6-311G(d,p) basis set. Results showed that MR is highly recommended to be a promising structure for many applications in optoelectronic devices due to its high calculated dipole moment value (7.2 Debye) and lower HOMO-LUMO energy gap of 3.5 eV. Copyright © 2014 Elsevier B.V. All rights reserved.

An evidential reasoning extension to quantitative model-based failure diagnosis

NASA Technical Reports Server (NTRS)

Gertler, Janos J.; Anderson, Kenneth C.

1992-01-01

The detection and diagnosis of failures in physical systems characterized by continuous-time operation are studied. A quantitative diagnostic methodology has been developed that utilizes the mathematical model of the physical system. On the basis of the latter, diagnostic models are derived each of which comprises a set of orthogonal parity equations. To improve the robustness of the algorithm, several models may be used in parallel, providing potentially incomplete and/or conflicting inferences. Dempster's rule of combination is used to integrate evidence from the different models. The basic probability measures are assigned utilizing quantitative information extracted from the mathematical model and from online computation performed therewith.

Influence of water on the surface of graphene

NASA Astrophysics Data System (ADS)

Kaya, Yunus; Kalkan, Yalçin; Veenhof, Rob

2018-02-01

We have studied how water modifies the surface of graphene and in particular how the surface conductivity of graphene is affected. According to the literature, two types of interactions should be distinguished: physical, where a water molecule remains intact and is located at some distance from the mesh, and chemical, where a water molecule is imbricated in the graphene bond structure. We have developed theoretical models for both types of interactions using the density functional theory (DFT) with the B3LYP hybrid functional combined with the 6-31G(d) basis set. Our calculations show that the surface conductivity of graphene is reduced in the presence of water.

Clutter and target discrimination in forward-looking ground penetrating radar using sparse structured basis pursuits

NASA Astrophysics Data System (ADS)

Camilo, Joseph A.; Malof, Jordan M.; Torrione, Peter A.; Collins, Leslie M.; Morton, Kenneth D.

2015-05-01

Forward-looking ground penetrating radar (FLGPR) is a remote sensing modality that has recently been investigated for buried threat detection. FLGPR offers greater standoff than other downward-looking modalities such as electromagnetic induction and downward-looking GPR, but it suffers from high false alarm rates due to surface and ground clutter. A stepped frequency FLGPR system consists of multiple radars with varying polarizations and bands, each of which interacts differently with subsurface materials and therefore might potentially be able to discriminate clutter from true buried targets. However, it is unclear which combinations of bands and polarizations would be most useful for discrimination or how to fuse them. This work applies sparse structured basis pursuit, a supervised statistical model which searches for sets of bands that are collectively effective for discriminating clutter from targets. The algorithm works by trying to minimize the number of selected items in a dictionary of signals; in this case the separate bands and polarizations make up the dictionary elements. A structured basis pursuit algorithm is employed to gather groups of modes together in collections to eliminate whole polarizations or sensors. The approach is applied to a large collection of FLGPR data for data around emplaced target and non-target clutter. The results show that a sparse structure basis pursuits outperforms a conventional CFAR anomaly detector while also pruning out unnecessary bands of the FLGPR sensor.

Some considerations about Gaussian basis sets for electric property calculations

NASA Astrophysics Data System (ADS)

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

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

Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

PubMed

Plessow, Philipp N

2018-02-13

This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.

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

ERIC Educational Resources Information Center

Lee, Liangshiu

2010-01-01

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

Training a cell-level classifier for detecting basal-cell carcinoma by combining human visual attention maps with low-level handcrafted features

PubMed Central

Corredor, Germán; Whitney, Jon; Arias, Viviana; Madabhushi, Anant; Romero, Eduardo

2017-01-01

Abstract. Computational histomorphometric approaches typically use low-level image features for building machine learning classifiers. However, these approaches usually ignore high-level expert knowledge. A computational model (M_im) combines low-, mid-, and high-level image information to predict the likelihood of cancer in whole slide images. Handcrafted low- and mid-level features are computed from area, color, and spatial nuclei distributions. High-level information is implicitly captured from the recorded navigations of pathologists while exploring whole slide images during diagnostic tasks. This model was validated by predicting the presence of cancer in a set of unseen fields of view. The available database was composed of 24 cases of basal-cell carcinoma, from which 17 served to estimate the model parameters and the remaining 7 comprised the evaluation set. A total of 274 fields of view of size 1024×1024  pixels were extracted from the evaluation set. Then 176 patches from this set were used to train a support vector machine classifier to predict the presence of cancer on a patch-by-patch basis while the remaining 98 image patches were used for independent testing, ensuring that the training and test sets do not comprise patches from the same patient. A baseline model (M_ex) estimated the cancer likelihood for each of the image patches. M_ex uses the same visual features as M_im, but its weights are estimated from nuclei manually labeled as cancerous or noncancerous by a pathologist. M_im achieved an accuracy of 74.49% and an F-measure of 80.31%, while M_ex yielded corresponding accuracy and F-measures of 73.47% and 77.97%, respectively. PMID:28382314

Operational wave now- and forecast in the German Bight as a basis for the assessment of wave-induced hydrodynamic loads on coastal dikes

NASA Astrophysics Data System (ADS)

Dreier, Norman; Fröhle, Peter

2017-12-01

The knowledge of the wave-induced hydrodynamic loads on coastal dikes including their temporal and spatial resolution on the dike in combination with actual water levels is of crucial importance of any risk-based early warning system. As a basis for the assessment of the wave-induced hydrodynamic loads, an operational wave now- and forecast system is set up that consists of i) available field measurements from the federal and local authorities and ii) data from numerical simulation of waves in the German Bight using the SWAN wave model. In this study, results of the hindcast of deep water wave conditions during the winter storm on 5-6 December, 2013 (German name `Xaver') are shown and compared with available measurements. Moreover field measurements of wave run-up from the local authorities at a sea dike on the German North Sea Island of Pellworm are presented and compared against calculated wave run-up using the EurOtop (2016) approach.

Influence of Silicon-Containing Additives on Concrete Waterproofness Property

NASA Astrophysics Data System (ADS)

Butakova, M. D.; Saribekyan, S. S.; Mikhaylov, A. V.

2017-11-01

The article studies the influence of silicon-containing additives on the property of the water resistance of concrete samples. It provides a review of the literature on common approaches and technologies improving concrete waterproofness and reinforced concrete structures. Normal hardening samples were obtained on the basis of concretes containing microsilica, aerosil or ash, or the combinations thereof. This research is aimed at the study of the complex modifier effect r on the basis of metakaolin, superplasticizer and silicon containing additives on the property of concrete water resistance. The need to use a superplasticizer to reduce the water-cement ratio and metakaolin as a hardening accelerator along with the set of strength is substantiated. This article describes a part of the results of the experiment conducted to find alternative options for colmatizing expensive additives used in the concreting foundations of private house-building. The implementation of the scientific work will not only clarify this area but will also broaden the knowledge of such additive as aerosol.

QUADRATIC SERENDIPITY FINITE ELEMENTS ON POLYGONS USING GENERALIZED BARYCENTRIC COORDINATES

PubMed Central

RAND, ALEXANDER; GILLETTE, ANDREW; BAJAJ, CHANDRAJIT

2013-01-01

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

Multiple stressors threatening the future of the Baltic Sea-Kattegat marine ecosystem: implications for policy and management actions.

PubMed

Jutterström, S; Andersson, H C; Omstedt, A; Malmaeus, J M

2014-09-15

The paper discusses the combined effects of ocean acidification, eutrophication and climate change on the Baltic Sea and the implications for current management strategies. The scientific basis is built on results gathered in the BONUS+ projects Baltic-C and ECOSUPPORT. Model results indicate that the Baltic Sea is likely to be warmer, more hypoxic and more acidic in the future. At present management strategies are not taking into account temporal trends and potential ecosystem change due to warming and/or acidification, and therefore fulfilling the obligations specified within the Marine Strategy Framework Directive, OSPAR and HELCOM conventions and national environmental objectives may become significantly more difficult. The paper aims to provide a basis for a discussion on the effectiveness of current policy instruments and possible strategies for setting practical environmental objectives in a changing climate and with multiple stressors. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Gaussian functional regression for output prediction: Model assimilation and experimental design

NASA Astrophysics Data System (ADS)

Nguyen, N. C.; Peraire, J.

2016-03-01

In this paper, we introduce a Gaussian functional regression (GFR) technique that integrates multi-fidelity models with model reduction to efficiently predict the input-output relationship of a high-fidelity model. The GFR method combines the high-fidelity model with a low-fidelity model to provide an estimate of the output of the high-fidelity model in the form of a posterior distribution that can characterize uncertainty in the prediction. A reduced basis approximation is constructed upon the low-fidelity model and incorporated into the GFR method to yield an inexpensive posterior distribution of the output estimate. As this posterior distribution depends crucially on a set of training inputs at which the high-fidelity models are simulated, we develop a greedy sampling algorithm to select the training inputs. Our approach results in an output prediction model that inherits the fidelity of the high-fidelity model and has the computational complexity of the reduced basis approximation. Numerical results are presented to demonstrate the proposed approach.

Computerized system for recognition of autism on the basis of gene expression microarray data.

PubMed

Latkowski, Tomasz; Osowski, Stanislaw

2015-01-01

The aim of this paper is to provide a means to recognize a case of autism using gene expression microarrays. The crucial task is to discover the most important genes which are strictly associated with autism. The paper presents an application of different methods of gene selection, to select the most representative input attributes for an ensemble of classifiers. The set of classifiers is responsible for distinguishing autism data from the reference class. Simultaneous application of a few gene selection methods enables analysis of the ill-conditioned gene expression matrix from different points of view. The results of selection combined with a genetic algorithm and SVM classifier have shown increased accuracy of autism recognition. Early recognition of autism is extremely important for treatment of children and increases the probability of their recovery and return to normal social communication. The results of this research can find practical application in early recognition of autism on the basis of gene expression microarray analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

12 CFR 630.20 - Contents of the annual report to investors.

Code of Federal Regulations, 2012 CFR

2012-01-01

... data. At a minimum, furnish the following combined financial data of the System in comparative columnar... results of operations of System institutions, on a combined basis, for the comparative years required by...) Describe, on a comparative basis, changes in the major components of net interest income. Include a...

12 CFR 630.20 - Contents of the annual report to investors.

Code of Federal Regulations, 2014 CFR

2014-01-01

... data. At a minimum, furnish the following combined financial data of the System in comparative columnar... results of operations of System institutions, on a combined basis, for the comparative years required by...) Describe, on a comparative basis, changes in the major components of net interest income. Include a...

12 CFR 630.20 - Contents of the annual report to investors.

Code of Federal Regulations, 2010 CFR

2010-01-01

... data. At a minimum, furnish the following combined financial data of the System in comparative columnar... results of operations of System institutions, on a combined basis, for the comparative years required by...) Describe, on a comparative basis, changes in the major components of net interest income. Include a...

12 CFR 630.20 - Contents of the annual report to investors.

Code of Federal Regulations, 2011 CFR

2011-01-01

... data. At a minimum, furnish the following combined financial data of the System in comparative columnar... results of operations of System institutions, on a combined basis, for the comparative years required by...) Describe, on a comparative basis, changes in the major components of net interest income. Include a...

12 CFR 630.20 - Contents of the annual report to investors.

Code of Federal Regulations, 2013 CFR

2013-01-01

... data. At a minimum, furnish the following combined financial data of the System in comparative columnar... results of operations of System institutions, on a combined basis, for the comparative years required by...) Describe, on a comparative basis, changes in the major components of net interest income. Include a...

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

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

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

2015-06-15

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

Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Groff, Loren; Newman, Richard L.; Foster, John V.; Crider, Dennis H.; Klyde, David H.; Huston, A. McCall

2014-01-01

Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

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

PubMed

Petrenko, Taras; Kossmann, Simone; Neese, Frank

2011-02-07

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed

Buryak, Ilya; Lokshtanov, Sergei; Vigasin, Andrey

2012-09-21

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

Rapid insights from remote sensing in the geosciences

NASA Astrophysics Data System (ADS)

Plaza, Antonio

2015-03-01

The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Dept. of Energy's National Nuclear Security Admin. under Contract DE-AC04-94AL85000.

Vibrational spectra of halide-water dimers: Insights on ion hydration from full-dimensional quantum calculations on many-body potential energy surfaces

NASA Astrophysics Data System (ADS)

Bajaj, Pushp; Wang, Xiao-Gang; Carrington, Tucker; Paesani, Francesco

2018-03-01

Full-dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers (X = F, Cl, Br, I) at the quantum-mechanical level. The calculations are carried out on two sets of recently developed potential energy functions (PEFs), namely, Thole-type model energy (TTM-nrg) and many-body energy (MB-nrg), using the symmetry-adapted Lanczos algorithm with a product basis set including all six vibrational coordinates. Although both TTM-nrg and MB-nrg PEFs are derived from coupled-cluster single double triple-F12 data obtained in the complete basis set limit, they differ in how many-body effects are represented at short range. Specifically, while both models describe long-range interactions through the combination of two-body dispersion and many-body classical electrostatics, the relatively simple Born-Mayer functions employed in the TTM-nrg PEFs to represent short-range interactions are replaced in the MB-nrg PEFs by permutationally invariant polynomials to achieve chemical accuracy. For all dimers, the MB-nrg vibrational spectra are in close agreement with the available experimental data, correctly reproducing anharmonic and nuclear quantum effects. In contrast, the vibrational frequencies calculated with the TTM-nrg PEFs exhibit significant deviations from the experimental values. The comparison between the TTM-nrg and MB-nrg results thus reinforces the notion that an accurate representation of both short-range interactions associated with electron density overlap and long-range many-body electrostatic interactions is necessary for a correct description of hydration phenomena at the molecular level.

Pilot climate data system: A state-of-the-art capability in scientific data management

NASA Technical Reports Server (NTRS)

Smith, P. H.; Treinish, L. A.; Novak, L. V.

1983-01-01

The Pilot Climate Data System (PCDS) was developed by the Information Management Branch of NASA's Goddard Space Flight Center to manage a large collection of climate-related data of interest to the research community. The PCDS now provides uniform data catalogs, inventories, access methods, graphical displays and statistical calculations for selected NASA and non-NASA data sets. Data manipulation capabilities were developed to permit researchers to easily combine or compare data. The current capabilities of the PCDS include many tools for the statistical survey of climate data. A climate researcher can examine any data set of interest via flexible utilities to create a variety of two- and three-dimensional displays, including vector plots, scatter diagrams, histograms, contour plots, surface diagrams and pseudo-color images. The graphics and statistics subsystems employ an intermediate data storage format which is data-set independent. Outside of the graphics system there exist other utilities to select, filter, list, compress, and calculate time-averages and variances for any data of interest. The PCDS now fully supports approximately twenty different data sets and is being used on a trial basis by several different in-house research grounds.

Integrated performance and reliability specification for digital avionics systems

NASA Technical Reports Server (NTRS)

Brehm, Eric W.; Goettge, Robert T.

1995-01-01

This paper describes an automated tool for performance and reliability assessment of digital avionics systems, called the Automated Design Tool Set (ADTS). ADTS is based on an integrated approach to design assessment that unifies traditional performance and reliability views of system designs, and that addresses interdependencies between performance and reliability behavior via exchange of parameters and result between mathematical models of each type. A multi-layer tool set architecture has been developed for ADTS that separates the concerns of system specification, model generation, and model solution. Performance and reliability models are generated automatically as a function of candidate system designs, and model results are expressed within the system specification. The layered approach helps deal with the inherent complexity of the design assessment process, and preserves long-term flexibility to accommodate a wide range of models and solution techniques within the tool set structure. ADTS research and development to date has focused on development of a language for specification of system designs as a basis for performance and reliability evaluation. A model generation and solution framework has also been developed for ADTS, that will ultimately encompass an integrated set of analytic and simulated based techniques for performance, reliability, and combined design assessment.

Development of a deep convolutional neural network to predict grading of canine meningiomas from magnetic resonance images.

PubMed

Banzato, T; Cherubini, G B; Atzori, M; Zotti, A

2018-05-01

An established deep neural network (DNN) based on transfer learning and a newly designed DNN were tested to predict the grade of meningiomas from magnetic resonance (MR) images in dogs and to determine the accuracy of classification of using pre- and post-contrast T1-weighted (T1W), and T2-weighted (T2W) MR images. The images were randomly assigned to a training set, a validation set and a test set, comprising 60%, 10% and 30% of images, respectively. The combination of DNN and MR sequence displaying the highest discriminating accuracy was used to develop an image classifier to predict the grading of new cases. The algorithm based on transfer learning using the established DNN did not provide satisfactory results, whereas the newly designed DNN had high classification accuracy. On the basis of classification accuracy, an image classifier built on the newly designed DNN using post-contrast T1W images was developed. This image classifier correctly predicted the grading of 8 out of 10 images not included in the data set. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

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

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

2015-06-21

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

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

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

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

2014-12-14

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

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

NASA Astrophysics Data System (ADS)

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

2006-07-01

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

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2011 CFR

2011-10-01

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

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2013 CFR

2013-10-01

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

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2014 CFR

2014-10-01

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

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2012 CFR

2012-10-01

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

48 CFR 25.504-4 - Group award basis.

Code of Federal Regulations, 2010 CFR

2010-10-01

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

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

PubMed

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

2015-10-01

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

Visualization and Nowcasting for Aviation using online verified ensemble weather radar extrapolation.

NASA Astrophysics Data System (ADS)

Kaltenboeck, Rudolf; Kerschbaum, Markus; Hennermann, Karin; Mayer, Stefan

2013-04-01

Nowcasting of precipitation events, especially thunderstorm events or winter storms, has high impact on flight safety and efficiency for air traffic management. Future strategic planning by air traffic control will result in circumnavigation of potential hazardous areas, reduction of load around efficiency hot spots by offering alternatives, increase of handling capacity, anticipation of avoidance manoeuvres and increase of awareness before dangerous areas are entered by aircraft. To facilitate this rapid update forecasts of location, intensity, size, movement and development of local storms are necessary. Weather radar data deliver precipitation analysis of high temporal and spatial resolution close to real time by using clever scanning strategies. These data are the basis to generate rapid update forecasts in a time frame up to 2 hours and more for applications in aviation meteorological service provision, such as optimizing safety and economic impact in the context of sub-scale phenomena. On the basis of tracking radar echoes by correlation the movement vectors of successive weather radar images are calculated. For every new successive radar image a set of ensemble precipitation fields is collected by using different parameter sets like pattern match size, different time steps, filter methods and an implementation of history of tracking vectors and plausibility checks. This method considers the uncertainty in rain field displacement and different scales in time and space. By validating manually a set of case studies, the best verification method and skill score is defined and implemented into an online-verification scheme which calculates the optimized forecasts for different time steps and different areas by using different extrapolation ensemble members. To get information about the quality and reliability of the extrapolation process additional information of data quality (e.g. shielding in Alpine areas) is extrapolated and combined with an extrapolation-quality-index. Subsequently the probability and quality information of the forecast ensemble is available and flexible blending to numerical prediction model for each subarea is possible. Simultaneously with automatic processing the ensemble nowcasting product is visualized in a new innovative way which combines the intensity, probability and quality information for different subareas in one forecast image.

ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-12-18

A 10-parameter, range-separated hybrid (RSH), generalized gradient approximation (GGA) density functional with nonlocal correlation (VV10) is presented in this paper. Instead of truncating the B97-type power series inhomogeneity correction factors (ICF) for the exchange, same-spin correlation, and opposite-spin correlation functionals uniformly, all 16 383 combinations of the linear parameters up to fourth order (m = 4) are considered. These functionals are individually fit to a training set and the resulting parameters are validated on a primary test set in order to identify the 3 optimal ICF expansions. Through this procedure, it is discovered that the functional that performs best onmore » the training and primary test sets has 7 linear parameters, with 3 additional nonlinear parameters from range-separation and nonlocal correlation. The resulting density functional, ωB97X-V, is further assessed on a secondary test set, the parallel-displaced coronene dimer, as well as several geometry datasets. Finally and furthermore, the basis set dependence and integration grid sensitivity of ωB97X-V are analyzed and documented in order to facilitate the use of the functional.« less

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

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

Talamini, Vittorino

2010-02-15

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

Use of Molecular Modeling to Determine the Interaction and Competition of Gases within Coal for Carbon Dioxide Sequestration

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

Jeffrey D. Evanseck; Jeffry D. Madura

A 3-dimensional coal structural model for the Argonne Premium Coal Pocahontas No. 3 has been generated. The model was constructed based on the wealth of structural information available in the literature with the enhancement that the structural diversity within the structure was represented implicitly (for the first time) based on image analysis of HRTEM in combination with LDMS data. The complex and large structural model (>10,000 carbon atoms) will serve as a basis for examining the interaction of gases within this low volatile bituminous coal. Simulations are of interest to permit reasonable simulations of the host-guest interactions with regard tomore » carbon dioxide sequestration within coal and methane displacement from coal. The molecular structure will also prove useful in examining other coal related behavior such as solvent swelling, liquefaction and other properties. Molecular models of CO{sub 2} have been evaluated with water to analyze which classical molecular force-field parameters are the most reasonable to predict the interactions of CO{sub 2} with water. The comparison of the molecular force field models was for a single CO{sub 2}-H{sub 2}O complex and was compared against first principles quantum mechanical calculations. The interaction energies and the electrostatic interaction distances were used as criteria in the comparison. The ab initio calculations included Hartree-Fock, B3LYP, and Moeller-Plesset 2nd, 3rd, and 4th order perturbation theories with basis sets up to the aug-cc-pvtz basis set. The Steele model was the best literature model, when compared to the ab initio data, however, our new CO{sub 2} model reproduces the QM data significantly better than the Steele force-field model.« less

Cone photoreceptor sensitivities and unique hue chromatic responses: correlation and causation imply the physiological basis of unique hues.

PubMed

Pridmore, Ralph W

2013-01-01

This paper relates major functions at the start and end of the color vision process. The process starts with three cone photoreceptors transducing light into electrical responses. Cone sensitivities were once expected to be Red Green Blue color matching functions (to mix colors) but microspectrometry proved otherwise: they instead peak in yellowish, greenish, and blueish hues. These physiological functions are an enigma, unmatched with any set of psychophysical (behavioral) functions. The end-result of the visual process is color sensation, whose essential percepts are unique (or pure) hues red, yellow, green, blue. Unique hues cannot be described by other hues, but can describe all other hues, e.g., that hue is reddish-blue. They are carried by four opponent chromatic response curves but the literature does not specify whether each curve represents a range of hues or only one hue (a unique) over its wavelength range. Here the latter is demonstrated, confirming that opponent chromatic responses define, and may be termed, unique hue chromatic responses. These psychophysical functions also are an enigma, unmatched with any physiological functions or basis. Here both enigmas are solved by demonstrating the three cone sensitivity curves and the three spectral chromatic response curves are almost identical sets (Pearson correlation coefficients r from 0.95-1.0) in peak wavelengths, curve shapes, math functions, and curve crossover wavelengths, though previously unrecognized due to presentation of curves in different formats, e.g., log, linear. (Red chromatic response curve is largely nonspectral and thus derives from two cones.) Close correlation combined with deterministic causation implies cones are the physiological basis of unique hues. This match of three physiological and three psychophysical functions is unique in color vision.

Energies and spin states of FeS(0/-), FeS2(0/-), Fe2S2(0/-), Fe3S4(0/-), and Fe4S4(0/-) clusters.

PubMed

Li, Yan-Ni; Wang, Shengguang; Wang, Tao; Gao, Rui; Geng, Chun-Yu; Li, Yong-Wang; Wang, Jianguo; Jiao, Haijun

2013-04-15

The structures and energies of the electronic ground states of the FeS(0/-), FeS2(0/-), Fe2S2(0/-), Fe3S4(0/-), and Fe4S4(0/-) neutral and anionic clusters have been computed systematically with nine computational methods in combination with seven basis sets. The computed adiabatic electronic affinities (AEA) have been compared with available experimental data. Most reasonable agreements between theory and experiment have been found for both hybrid B3LYP and B3PW91 functionals in conjugation with 6-311+G* and QZVP basis sets. Detailed comparisons between the available experimental and computed AEA data at the B3LYP/6-311+G* level identified the electronic ground state of (5)Δ for FeS, (4)Δ for FeS(-), (5)B2 for FeS2, (6)A1 for FeS2(-), (1)A1 for Fe2S2, (8)A' for Fe2S2(-), (5)A'' for Fe3S4, (6)A'' for Fe3S4(-), (1)A1 for Fe4S4, and (1)A2 for Fe4S4(-). In addition, Fe2S2, Fe3S4, Fe3S4(-), Fe4S4, and Fe4S4(-) are antiferromagnetic at the B3LYP/6-311+G* level. The magnetic properties are discussed on the basis of natural bond orbital analysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cone Photoreceptor Sensitivities and Unique Hue Chromatic Responses: Correlation and Causation Imply the Physiological Basis of Unique Hues

PubMed Central

Pridmore, Ralph W.

2013-01-01

This paper relates major functions at the start and end of the color vision process. The process starts with three cone photoreceptors transducing light into electrical responses. Cone sensitivities were once expected to be Red Green Blue color matching functions (to mix colors) but microspectrometry proved otherwise: they instead peak in yellowish, greenish, and blueish hues. These physiological functions are an enigma, unmatched with any set of psychophysical (behavioral) functions. The end-result of the visual process is color sensation, whose essential percepts are unique (or pure) hues red, yellow, green, blue. Unique hues cannot be described by other hues, but can describe all other hues, e.g., that hue is reddish-blue. They are carried by four opponent chromatic response curves but the literature does not specify whether each curve represents a range of hues or only one hue (a unique) over its wavelength range. Here the latter is demonstrated, confirming that opponent chromatic responses define, and may be termed, unique hue chromatic responses. These psychophysical functions also are an enigma, unmatched with any physiological functions or basis. Here both enigmas are solved by demonstrating the three cone sensitivity curves and the three spectral chromatic response curves are almost identical sets (Pearson correlation coefficients r from 0.95–1.0) in peak wavelengths, curve shapes, math functions, and curve crossover wavelengths, though previously unrecognized due to presentation of curves in different formats, e.g., log, linear. (Red chromatic response curve is largely nonspectral and thus derives from two cones.) Close correlation combined with deterministic causation implies cones are the physiological basis of unique hues. This match of three physiological and three psychophysical functions is unique in color vision. PMID:24204755

Application of the CC(P;Q) Hierarchy of Coupled-Cluster Methods to the Beryllium Dimer.

PubMed

Magoulas, Ilias; Bauman, Nicholas P; Shen, Jun; Piecuch, Piotr

2018-02-08

The performance of coupled-cluster approaches with higher-than-doubly excited clusters, including the CCSD(T), CCSD(2) T , CR-CC(2,3), CCSD(TQ), and CR-CC(2,4) corrections to CCSD, the active-space CCSDt, CCSDtq, and CCSDTq methods, and the CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) corrections to CCSDt, CCSDtq, and CCSDTq resulting from the CC(P;Q) formalism, in reproducing the CCSDT and CCSDTQ potential energy curves and vibrational term values characterizing Be 2 in its electronic ground state is assessed. The correlation-consistent aug-cc-pVnZ and aug-cc-pCVnZ (n = T and Q) basis sets are employed. Among the CCSD-based corrections, the completely renormalized CR-CC(2,3) and CR-CC(2,4) approaches perform the best. The CC(t;3), CC(t,q;3), CC(t,q;3,4), and CC(q;4) methods, especially CC(t;3) and CC(q;4), outperform other employed approaches in reproducing the CCSDT and CCSDTQ data. Composite schemes combining the all-electron CCSDT calculations extrapolated to the complete basis set limit with the frozen-core CC(q;4) and CCSDTQ computations using the aug-cc-pVTZ basis to account for connected quadruple excitations reproduce the latest experimental vibrational spectrum of Be 2 to within 4-5 cm -1 , when the vibrational spacings are examined, with typical errors being below 1-2 cm -1 . The resulting binding energies and equilibrium bond lengths agree with their experimentally derived counterparts to within ∼10 cm -1 and 0.01 Å.

The Objective Borderline method (OBM): a probability-based model for setting up an objective pass/fail cut-off score in medical programme assessments.

PubMed

Shulruf, Boaz; Turner, Rolf; Poole, Phillippa; Wilkinson, Tim

2013-05-01

The decision to pass or fail a medical student is a 'high stakes' one. The aim of this study is to introduce and demonstrate the feasibility and practicality of a new objective standard-setting method for determining the pass/fail cut-off score from borderline grades. Three methods for setting up pass/fail cut-off scores were compared: the Regression Method, the Borderline Group Method, and the new Objective Borderline Method (OBM). Using Year 5 students' OSCE results from one medical school we established the pass/fail cut-off scores by the abovementioned three methods. The comparison indicated that the pass/fail cut-off scores generated by the OBM were similar to those generated by the more established methods (0.840 ≤ r ≤ 0.998; p < .0001). Based on theoretical and empirical analysis, we suggest that the OBM has advantages over existing methods in that it combines objectivity, realism, robust empirical basis and, no less importantly, is simple to use.

New interplanetary proton fluence model

NASA Technical Reports Server (NTRS)

Feynman, Joan; Armstrong, T. P.; Dao-Gibner, L.; Silverman, S.

1990-01-01

A new predictive engineering model for the interplanetary fluence of protons with above 10 MeV and above 30 MeV is described. The data set used is a combination of observations made from the earth's surface and from above the atmosphere between 1956 and 1963 and observations made from spacecraft in the vicinity of earth between 1963 and 1985. The data cover a time period three times as long as the period used in earlier models. With the use of this data set the distinction between 'ordinary proton events' and 'anomalously large events' made in earlier work disappears. This permitted the use of statistical analysis methods developed for 'ordinary events' on the entire data set. The greater than 10 MeV fluences at 1 AU calculated with the new model are about twice those expected on the basis of models now in use. At energies above 30 MeV, the old and new models agree. In contrast to earlier models, the results do not depend critically on the fluence from any one event and are independent of sunspot number. Mission probability curves derived from the fluence distribution are presented.

Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

NASA Astrophysics Data System (ADS)

Huhn, William; Blum, Volker

2015-03-01

Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

Design, development, and clinical validation of therapeutic toys for autistic children

PubMed Central

Tseng, Kevin C.; Tseng, Sung-Hui; Cheng, Hsin-Yi Kathy

2016-01-01

[Purpose] One of the characteristics of autistic children is social interaction difficulties. Although therapeutic toys can promote social interaction, however its related research remains insufficient. The aim of the present study was to build a set of cooperative play toys that are suitable for autistic children. [Subjects and Methods] This study used an innovative product design and development approach as the basis for the creation of cooperative play toys. [Results] The present study has successfully developed cooperative play toys. Compared to the traditional game therapy for autism, cooperative play toy therapy can significantly improve the interactions between autistic children and their peers. [Conclusion] The most critical design theme of cooperative play toys focuses on captivating the interest of autistic children. Based on the needs of the individual cases, the design of the therapeutic toy set was specifically tailored, i.e., by reinforcing the sound and light effects to improve the attractiveness of the toys. In the future, different play modes can be combined with this toy set to further enhance the degree of interaction of autistic children and improve their quality of life and social skills. PMID:27512246

A group matrix representation relevant to scales of measurement of clinical disease states via stratified vectors.

PubMed

Sawamura, Jitsuki; Morishita, Shigeru; Ishigooka, Jun

2016-02-09

Previously, we applied basic group theory and related concepts to scales of measurement of clinical disease states and clinical findings (including laboratory data). To gain a more concrete comprehension, we here apply the concept of matrix representation, which was not explicitly exploited in our previous work. Starting with a set of orthonormal vectors, called the basis, an operator Rj (an N-tuple patient disease state at the j-th session) was expressed as a set of stratified vectors representing plural operations on individual components, so as to satisfy the group matrix representation. The stratified vectors containing individual unit operations were combined into one-dimensional square matrices [Rj]s. The [Rj]s meet the matrix representation of a group (ring) as a K-algebra. Using the same-sized matrix of stratified vectors, we can also express changes in the plural set of [Rj]s. The method is demonstrated on simple examples. Despite the incompleteness of our model, the group matrix representation of stratified vectors offers a formal mathematical approach to clinical medicine, aligning it with other branches of natural science.

Design, development, and clinical validation of therapeutic toys for autistic children.

PubMed

Tseng, Kevin C; Tseng, Sung-Hui; Cheng, Hsin-Yi Kathy

2016-07-01

[Purpose] One of the characteristics of autistic children is social interaction difficulties. Although therapeutic toys can promote social interaction, however its related research remains insufficient. The aim of the present study was to build a set of cooperative play toys that are suitable for autistic children. [Subjects and Methods] This study used an innovative product design and development approach as the basis for the creation of cooperative play toys. [Results] The present study has successfully developed cooperative play toys. Compared to the traditional game therapy for autism, cooperative play toy therapy can significantly improve the interactions between autistic children and their peers. [Conclusion] The most critical design theme of cooperative play toys focuses on captivating the interest of autistic children. Based on the needs of the individual cases, the design of the therapeutic toy set was specifically tailored, i.e., by reinforcing the sound and light effects to improve the attractiveness of the toys. In the future, different play modes can be combined with this toy set to further enhance the degree of interaction of autistic children and improve their quality of life and social skills.

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

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

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

2015-09-14

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

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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

PubMed

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

2013-12-28

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

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

PubMed

Zhao, Chunyu; Burge, James H

2007-12-24

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

Theoretical studies of the potential surface for the F - H2 greater than HF + H reaction

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Walch, Stephen, P.; Langhoff, Stephen R.; Taylor, Peter R.; Jaffe, Richard L.

1987-01-01

The F + H2 yields HF + H potential energy hypersurface was studied in the saddle point and entrance channel regions. Using a large (5s 5p 3d 2f 1g/4s 3p 2d) atomic natural orbital basis set, a classical barrier height of 1.86 kcal/mole was obtained at the CASSCF/multireference CI level (MRCI) after correcting for basis set superposition error and including a Davidson correction (+Q) for higher excitations. Based upon an analysis of the computed results, the true classical barrier is estimated to be about 1.4 kcal/mole. The location of the bottleneck on the lowest vibrationally adiabatic potential curve was also computed and the translational energy threshold determined from a one-dimensional tunneling calculation. Using the difference between the calculated and experimental threshold to adjust the classical barrier height on the computed surface yields a classical barrier in the range of 1.0 to 1.5 kcal/mole. Combining the results of the direct estimates of the classical barrier height with the empirical values obtained from the approximation calculations of the dynamical threshold, it is predicted that the true classical barrier height is 1.4 + or - 0.4 kcal/mole. Arguments are presented in favor of including the relatively large +Q correction obtained when nine electrons are correlated at the CASSCF/MRCI level.

Large-Scale Computation of Nuclear Magnetic Resonance Shifts for Paramagnetic Solids Using CP2K.

PubMed

Mondal, Arobendo; Gaultois, Michael W; Pell, Andrew J; Iannuzzi, Marcella; Grey, Clare P; Hutter, Jürg; Kaupp, Martin

2018-01-09

Large-scale computations of nuclear magnetic resonance (NMR) shifts for extended paramagnetic solids (pNMR) are reported using the highly efficient Gaussian-augmented plane-wave implementation of the CP2K code. Combining hyperfine couplings obtained with hybrid functionals with g-tensors and orbital shieldings computed using gradient-corrected functionals, contact, pseudocontact, and orbital-shift contributions to pNMR shifts are accessible. Due to the efficient and highly parallel performance of CP2K, a wide variety of materials with large unit cells can be studied with extended Gaussian basis sets. Validation of various approaches for the different contributions to pNMR shifts is done first for molecules in a large supercell in comparison with typical quantum-chemical codes. This is then extended to a detailed study of g-tensors for extended solid transition-metal fluorides and for a series of complex lithium vanadium phosphates. Finally, lithium pNMR shifts are computed for Li 3 V 2 (PO 4 ) 3 , for which detailed experimental data are available. This has allowed an in-depth study of different approaches (e.g., full periodic versus incremental cluster computations of g-tensors and different functionals and basis sets for hyperfine computations) as well as a thorough analysis of the different contributions to the pNMR shifts. This study paves the way for a more-widespread computational treatment of NMR shifts for paramagnetic materials.

Synthesis and structural study on (1E,2E,1'E,2'E)-3,3'-bis[(4-bromophenyl)-3,3'-(4-methy-1,2-phenylene diimine)] acetaldehyde dioxime: A combined experimental and theoretical study

NASA Astrophysics Data System (ADS)

Topal, T.; Kart, H. H.; Tunay Taşlı, P.; Karapınar, E.

2015-06-01

Tetradentate (1E,2E,1'E,2'E)-3,3'-bis[(4-bromophenyl)-3,3'-(4-methy-1,2-phenylene diimine)] acetaldehyde dioxime which possess N4 donor sets derived from the condensation of isonitroso- p-bromoacetophenone and 3,4-diaminotoluene are synthesized and characterized. The characterization of tetradentate Schiff base ligand has been deduced from LC-MS, FTIR, 13C and 1H NMR spectra and elemental analysis. Furthermore, the molecular geometry, infrared and NMR spectra of the title molecule in the ground state have been calculated by using the quantum chemical computational methods such as density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the 6-31G(d) and 6-311G(d) basis sets. The computed bond lengths and bond angles by using the both methods show the good agreement with each other. Moreover, the vibrational frequencies have been calculated and the scaled values have been compared with the experimental FTIR spectroscopic data. Assignments of the vibrational modes are made on the basis of potential energy distribution (PED) calculated from by using VEDA program. The correlations between the observed and calculated frequencies are in good agreement with each other as well as the correlation of the NMR data.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Simplified DFT methods for consistent structures and energies of large systems

NASA Astrophysics Data System (ADS)

Caldeweyher, Eike; Gerit Brandenburg, Jan

2018-05-01

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

A practical radial basis function equalizer.

PubMed

Lee, J; Beach, C; Tepedelenlioglu, N

1999-01-01

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

Tensor products of U{sub q}{sup Prime }sl-caret(2)-modules and the big q{sup 2}-Jacobi function transform

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

Gade, R. M.

2013-01-15

Four tensor products of evaluation modules of the quantum affine algebra U{sub q}{sup Prime }sl-caret(2) obtained from the negative and positive series, the complementary and the strange series representations are investigated. Linear operators R(z) satisfying the intertwining property on finite linear combinations of the canonical basis elements of the tensor products are described in terms of two sets of infinite sums {l_brace}{tau}{sup (r,t)}{r_brace}{sub r,t Element-Of Z{sub {>=}{sub 0}}} and {l_brace}{tau}{sup (r,t)}{r_brace}{sub r,t Element-Of Z{sub {>=}{sub 0}}} involving big q{sup 2}-Jacobi functions or related nonterminating basic hypergeometric series. Inhomogeneous recurrence relations can be derived for both sets. Evaluations of the simplestmore » sums provide the corresponding initial conditions. For the first set of sums the relations entail a big q{sup 2}-Jacobi function transform pair. An integral decomposition is obtained for the sum {tau}{sup (r,t)}. A partial description of the relation between the decompositions of the tensor products with respect to U{sub q}sl(2) or with respect to its complement in U{sub q}{sup Prime }sl-caret(2) can be formulated in terms of Askey-Wilson function transforms. For a particular combination of two tensor products, the occurrence of proper U{sub q}{sup Prime }sl-caret(2)-submodules is discussed.« less

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Self-Taught Learning Based on Sparse Autoencoder for E-Nose in Wound Infection Detection

PubMed Central

He, Peilin; Jia, Pengfei; Qiao, Siqi; Duan, Shukai

2017-01-01

For an electronic nose (E-nose) in wound infection distinguishing, traditional learning methods have always needed large quantities of labeled wound infection samples, which are both limited and expensive; thus, we introduce self-taught learning combined with sparse autoencoder and radial basis function (RBF) into the field. Self-taught learning is a kind of transfer learning that can transfer knowledge from other fields to target fields, can solve such problems that labeled data (target fields) and unlabeled data (other fields) do not share the same class labels, even if they are from entirely different distribution. In our paper, we obtain numerous cheap unlabeled pollutant gas samples (benzene, formaldehyde, acetone and ethylalcohol); however, labeled wound infection samples are hard to gain. Thus, we pose self-taught learning to utilize these gas samples, obtaining a basis vector θ. Then, using the basis vector θ, we reconstruct the new representation of wound infection samples under sparsity constraint, which is the input of classifiers. We compare RBF with partial least squares discriminant analysis (PLSDA), and reach a conclusion that the performance of RBF is superior to others. We also change the dimension of our data set and the quantity of unlabeled data to search the input matrix that produces the highest accuracy. PMID:28991154

Very high order discontinuous Galerkin method in elliptic problems

NASA Astrophysics Data System (ADS)

Jaśkowiec, Jan

2017-09-01

The paper deals with high-order discontinuous Galerkin (DG) method with the approximation order that exceeds 20 and reaches 100 and even 1000 with respect to one-dimensional case. To achieve such a high order solution, the DG method with finite difference method has to be applied. The basis functions of this method are high-order orthogonal Legendre or Chebyshev polynomials. These polynomials are defined in one-dimensional space (1D), but they can be easily adapted to two-dimensional space (2D) by cross products. There are no nodes in the elements and the degrees of freedom are coefficients of linear combination of basis functions. In this sort of analysis the reference elements are needed, so the transformations of the reference element into the real one are needed as well as the transformations connected with the mesh skeleton. Due to orthogonality of the basis functions, the obtained matrices are sparse even for finite elements with more than thousands degrees of freedom. In consequence, the truncation errors are limited and very high-order analysis can be performed. The paper is illustrated with a set of benchmark examples of 1D and 2D for the elliptic problems. The example presents the great effectiveness of the method that can shorten the length of calculation over hundreds times.

Very high order discontinuous Galerkin method in elliptic problems

NASA Astrophysics Data System (ADS)

Jaśkowiec, Jan

2018-07-01

The paper deals with high-order discontinuous Galerkin (DG) method with the approximation order that exceeds 20 and reaches 100 and even 1000 with respect to one-dimensional case. To achieve such a high order solution, the DG method with finite difference method has to be applied. The basis functions of this method are high-order orthogonal Legendre or Chebyshev polynomials. These polynomials are defined in one-dimensional space (1D), but they can be easily adapted to two-dimensional space (2D) by cross products. There are no nodes in the elements and the degrees of freedom are coefficients of linear combination of basis functions. In this sort of analysis the reference elements are needed, so the transformations of the reference element into the real one are needed as well as the transformations connected with the mesh skeleton. Due to orthogonality of the basis functions, the obtained matrices are sparse even for finite elements with more than thousands degrees of freedom. In consequence, the truncation errors are limited and very high-order analysis can be performed. The paper is illustrated with a set of benchmark examples of 1D and 2D for the elliptic problems. The example presents the great effectiveness of the method that can shorten the length of calculation over hundreds times.

The solitary wave solution of coupled Klein-Gordon-Zakharov equations via two different numerical methods

NASA Astrophysics Data System (ADS)

Dehghan, Mehdi; Nikpour, Ahmad

2013-09-01

In this research, we propose two different methods to solve the coupled Klein-Gordon-Zakharov (KGZ) equations: the Differential Quadrature (DQ) and Globally Radial Basis Functions (GRBFs) methods. In the DQ method, the derivative value of a function with respect to a point is directly approximated by a linear combination of all functional values in the global domain. The principal work in this method is the determination of weight coefficients. We use two ways for obtaining these coefficients: cosine expansion (CDQ) and radial basis functions (RBFs-DQ), the former is a mesh-based method and the latter categorizes in the set of meshless methods. Unlike the DQ method, the GRBF method directly substitutes the expression of the function approximation by RBFs into the partial differential equation. The main problem in the GRBFs method is ill-conditioning of the interpolation matrix. Avoiding this problem, we study the bases introduced in Pazouki and Schaback (2011) [44]. Some examples are presented to compare the accuracy and easy implementation of the proposed methods. In numerical examples, we concentrate on Inverse Multiquadric (IMQ) and second-order Thin Plate Spline (TPS) radial basis functions. The variable shape parameter (exponentially and random) strategies are applied in the IMQ function and the results are compared with the constant shape parameter.

Wick Product for Commutation Relations Connected with Yang-Baxter Operators and New Constructions of Factors

NASA Astrophysics Data System (ADS)

Krsolarlak, Ilona

We analyze a certain class of von Neumann algebras generated by selfadjoint elements , for satisfying the general commutation relations: Such algebras can be continuously embedded into some closure of the set of finite linear combinations of vectors , where is an orthonormal basis of a Hilbert space . The operator which represents the vector is denoted by and called the ``Wick product'' of the operators . We describe explicitly the form of this product. Also, we estimate the operator norm of for . Finally we apply these two results and prove that under the assumption all the von Neumann algebras considered are II1 factors.

The Solar Dynamic radiator with a historical perspective

NASA Technical Reports Server (NTRS)

Mclallin, K. L.; Fleming, M. L.; Hoehn, F. W.; Howerton, R.

1988-01-01

A historical perspective on pumped loop space radiators provides a basis for the design of the Space Station Solar Dynamic (SD) power module radiator. SD power modules, capable of generating 25 kWe each, are planned for growth Station power requirements. The Brayton (cycle) SD module configuration incorporates a pumped loop radiator that must reject up to 99 kW. The thermal/hydraulic design conditions in combination with required radiator orientation and packaging envelope form a unique set of constraints as compared to previous pumped loop radiator systems. Nevertheless, past program successes have demonstrated a technology base which can be applied to the SD radiator development program to ensure a low risk, low cost system.

Cracking mechanism of shale cracks during fracturing

NASA Astrophysics Data System (ADS)

Zhao, X. J.; Zhan, Q.; Fan, H.; Zhao, H. B.; An, F. J.

2018-06-01

In this paper, we set up a model for calculating the shale fracture pressure on the basis of Huang’s model by the theory of elastic-plastic mechanics, rock mechanics and the application of the maximum tensile stress criterion, which takes into account such factors as the crustal stress field, chemical field, temperature field, tectonic stress field, the porosity of shale and seepage of drilling fluid and so on. Combined with the experimental data of field fracturing and the experimental results of three axis compression of shale core with different water contents, the results show that the error between the present study and the measured value is 3.85%, so the present study can provide technical support for drilling engineering.

Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

PubMed

Koukounas, Constantine; Mavridis, Aristides

2008-11-06

The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

Analysis of facial motion patterns during speech using a matrix factorization algorithm

PubMed Central

Lucero, Jorge C.; Munhall, Kevin G.

2008-01-01

This paper presents an analysis of facial motion during speech to identify linearly independent kinematic regions. The data consists of three-dimensional displacement records of a set of markers located on a subject’s face while producing speech. A QR factorization with column pivoting algorithm selects a subset of markers with independent motion patterns. The subset is used as a basis to fit the motion of the other facial markers, which determines facial regions of influence of each of the linearly independent markers. Those regions constitute kinematic “eigenregions” whose combined motion produces the total motion of the face. Facial animations may be generated by driving the independent markers with collected displacement records. PMID:19062866

LETTER TO THE EDITOR: Two-centre exchange integrals for complex exponent Slater orbitals

NASA Astrophysics Data System (ADS)

Kuang, Jiyun; Lin, C. D.

1996-12-01

The one-dimensional integral representation for the Fourier transform of a two-centre product of B functions (finite linear combinations of Slater orbitals) with real parameters is generalized to include B functions with complex parameters. This one-dimensional integral representation allows for an efficient method of calculating two-centre exchange integrals with plane-wave electronic translational factors (ETF) over Slater orbitals of real/complex exponents. This method is a significant improvement on the previous two-dimensional quadrature method of the integrals. A new basis set of the form 0953-4075/29/24/005/img1 is proposed to improve the description of pseudo-continuum states in the close-coupling treatment of ion - atom collisions.

A hybrid linear/nonlinear training algorithm for feedforward neural networks.

PubMed

McLoone, S; Brown, M D; Irwin, G; Lightbody, A

1998-01-01

This paper presents a new hybrid optimization strategy for training feedforward neural networks. The algorithm combines gradient-based optimization of nonlinear weights with singular value decomposition (SVD) computation of linear weights in one integrated routine. It is described for the multilayer perceptron (MLP) and radial basis function (RBF) networks and then extended to the local model network (LMN), a new feedforward structure in which a global nonlinear model is constructed from a set of locally valid submodels. Simulation results are presented demonstrating the superiority of the new hybrid training scheme compared to second-order gradient methods. It is particularly effective for the LMN architecture where the linear to nonlinear parameter ratio is large.

Noble gas cluster ions

NASA Astrophysics Data System (ADS)

Kaya, Yunus; Kalkan, Yalçin; Veenhof, Rob

2018-02-01

In this work, a reaction mechanism of formation of noble gas (Ng) cluster ions has been theoretically investigated in detail. The kinetic studies of formation of Xe+Xe cluster in Xe, Ar+Ar cluster ions in Ar, and Ne+Ne cluster ions in Ne have been made as theoretically. The optimized structures in the ground state were calculated using the density functional theory (DFT) by the B3LYP method combined with the Stuttgart/Dresden effective core potential basis set (SDD). In addition, we calculated the rate constants of all cluster formations. The results are 1.15 × 10-31, 3.58 × 10-31, 0.23 × 10-31cm6/s, respectively for Neon, Argon, Xenon cluster ions.

Comparison of methods for the prediction of human clearance from hepatocyte intrinsic clearance for a set of reference compounds and an external evaluation set.

PubMed

Yamagata, Tetsuo; Zanelli, Ugo; Gallemann, Dieter; Perrin, Dominique; Dolgos, Hugues; Petersson, Carl

2017-09-01

1. We compared direct scaling, regression model equation and the so-called "Poulin et al." methods to scale clearance (CL) from in vitro intrinsic clearance (CL int ) measured in human hepatocytes using two sets of compounds. One reference set comprised of 20 compounds with known elimination pathways and one external evaluation set based on 17 compounds development in Merck (MS). 2. A 90% prospective confidence interval was calculated using the reference set. This interval was found relevant for the regression equation method. The three outliers identified were justified on the basis of their elimination mechanism. 3. The direct scaling method showed a systematic underestimation of clearance in both the reference and evaluation sets. The "Poulin et al." and the regression equation methods showed no obvious bias in either the reference or evaluation sets. 4. The regression model equation was slightly superior to the "Poulin et al." method in the reference set and showed a better absolute average fold error (AAFE) of value 1.3 compared to 1.6. A larger difference was observed in the evaluation set were the regression method and "Poulin et al." resulted in an AAFE of 1.7 and 2.6, respectively (removing the three compounds with known issues mentioned above). A similar pattern was observed for the correlation coefficient. Based on these data we suggest the regression equation method combined with a prospective confidence interval as the first choice for the extrapolation of human in vivo hepatic metabolic clearance from in vitro systems.

Increase of Short-Term Heart Rate Variability Induced by Blood Pressure Measurements during Ambulatory Blood Pressure Monitoring.

PubMed

Frigy, Attila; Magdás, Annamária; Moga, Victor-Dan; Coteț, Ioana Georgiana; Kozlovszky, Miklós; Szilágyi, László

2017-01-01

Objective. The possible effect of blood pressure measurements per se on heart rate variability (HRV) was studied in the setting of concomitant ambulatory blood pressure monitoring (ABPM) and Holter ECG monitoring (HM). Methods. In 25 hypertensive patients (14 women and 11 men, mean age: 58.1 years), 24-hour combined ABPM and HM were performed. For every blood pressure measurement, 2-minute ECG segments (before, during, and after measurement) were analyzed to obtain time domain parameters of HRV: SDNN and rMSSD. Mean of normal RR intervals (MNN), SDNN/MNN, and rMSSD/MNN were calculated, too. Parameter variations related to blood pressure measurements were analyzed using one-way ANOVA with multiple comparisons. Results. 2281 measurements (1518 during the day and 763 during the night) were included in the analysis. Both SDNN and SDNN/MNN had a constant (the same for 24-hour, daytime, and nighttime values) and significant change related to blood pressure measurements: an increase during measurements and a decrease after them ( p < 0.01 for any variation). Conclusion. In the setting of combined ABPM and HM, the blood pressure measurement itself produces an increase in short-term heart rate variability. Clarifying the physiological basis and the possible clinical value of this phenomenon needs further studies.

Remote Earth Sciences data collection using ACTS

NASA Technical Reports Server (NTRS)

Evans, Robert H.

1992-01-01

Given the focus on global change and the attendant scope of such research, we anticipate significant growth of requirements for investigator interaction, processing system capabilities, and availability of data sets. The increased complexity of global processes requires interdisciplinary teams to address them; the investigators will need to interact on a regular basis; however, it is unlikely that a single institution will house sufficient investigators with the required breadth of skills. The complexity of the computations may also require resources beyond those located within a single institution; this lack of sufficient computational resources leads to a distributed system located at geographically dispersed institutions. Finally the combination of long term data sets like the Pathfinder datasets and the data to be gathered by new generations of satellites such as SeaWiFS and MODIS-N yield extra-ordinarily large amounts of data. All of these factors combine to increase demands on the communications facilities available; the demands are generating requirements for highly flexible, high capacity networks. We have been examining the applicability of the Advanced Communications Technology Satellite (ACTS) to address the scientific, computational, and, primarily, communications questions resulting from global change research. As part of this effort three scenarios for oceanographic use of ACTS have been developed; a full discussion of this is contained in Appendix B.

[Research on discrimination of cabbage and weeds based on visible and near-infrared spectrum analysis].

PubMed

Zu, Qin; Zhao, Chun-Jiang; Deng, Wei; Wang, Xiu

2013-05-01

The automatic identification of weeds forms the basis for precision spraying of crops infest. The canopy spectral reflectance within the 350-2 500 nm band of two strains of cabbages and five kinds of weeds such as barnyard grass, setaria, crabgrass, goosegrass and pigweed was acquired by ASD spectrometer. According to the spectral curve characteristics, the data in different bands were compressed with different levels to improve the operation efficiency. Firstly, the spectrum was denoised in accordance with the different order of multiple scattering correction (MSC) method and Savitzky-Golay (SG) convolution smoothing method set by different parameters, then the model was built by combining the principal component analysis (PCA) method to extract principal components, finally all kinds of plants were classified by using the soft independent modeling of class analogy (SIMCA) taxonomy and the classification results were compared. The tests results indicate that after the pretreatment of the spectral data with the method of the combination of MSC and SG set with 3rd order, 5th degree polynomial, 21 smoothing points, and the top 10 principal components extraction using PCA as a classification model input variable, 100% correct classification rate was achieved, and it is able to identify cabbage and several kinds of common weeds quickly and nondestructively.

Dimensional analysis using toric ideals: primitive invariants.

PubMed

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

2014-01-01

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

42 CFR 457.700 - Basis, scope, and applicability.

Code of Federal Regulations, 2010 CFR

2010-10-01

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

42 CFR 457.700 - Basis, scope, and applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

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

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

Code of Federal Regulations, 2010 CFR

2010-10-01

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

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

NASA Astrophysics Data System (ADS)

Lombardini, Richard; Nowara, Ewa; Johnson, Bruce

2015-03-01

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

SRC Residual fuel oils

DOEpatents

Tewari, Krishna C.; Foster, Edward P.

1985-01-01

Coal solids (SRC) and distillate oils are combined to afford single-phase blends of residual oils which have utility as fuel oils substitutes. The components are combined on the basis of their respective polarities, that is, on the basis of their heteroatom content, to assure complete solubilization of SRC. The resulting composition is a fuel oil blend which retains its stability and homogeneity over the long term.

Optimally combined regional geoid models for the realization of height systems in developing countries - ORG4heights

NASA Astrophysics Data System (ADS)

Lieb, Verena; Schmidt, Michael; Willberg, Martin; Pail, Roland

2017-04-01

Precise height systems require high-resolution and high-quality gravity data. However, such data sets are sparse especially in developing or newly industrializing countries. Thus, we initiated the DFG-project "ORG4heights" for the formulation of a general scientific concept how to (1) optimally combine all available data sets and (2) estimate realistic errors. The resulting regional gravity field models then deliver the fundamental basis for (3) establishing physical national height systems. The innovative key aspects of the project incorporate the development of a method which links (low- up to mid-resolution) gravity satellite mission data and (high- down to low-quality) terrestrial data. Hereby, an optimal combination of the data utilizing their highest measure of information including uncertainty quantification and analyzing systematic omission errors is pursued. Regional gravity field modeling via Multi-Resolution Representation (MRR) and Least Squares Collocation (LSC) are studied in detail and compared based on their theoretical fundamentals. From the findings, MRR shall be further developed towards implementing a pyramid algorithm. Within the project, we investigate comprehensive case studies in Saudi Arabia and South America, i. e. regions with varying topography, by means of simulated data with heterogeneous distribution, resolution, quality and altitude. GPS and tide gauge records serve as complementary input or validation data. The resulting products include error propagation, internal and external validation. A generalized concept then is derived in order to establish physical height systems in developing countries. The recommendations may serve as guidelines for sciences and administration. We present the ideas and strategies of the project, which combines methodical development and practical applications with high socio-economic impact.

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

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

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

Multivariate Hermite interpolation on scattered point sets using tensor-product expo-rational B-splines

NASA Astrophysics Data System (ADS)

Dechevsky, Lubomir T.; Bang, Børre; Laksa˚, Arne; Zanaty, Peter

2011-12-01

At the Seventh International Conference on Mathematical Methods for Curves and Surfaces, To/nsberg, Norway, in 2008, several new constructions for Hermite interpolation on scattered point sets in domains in Rn,n∈N, combined with smooth convex partition of unity for several general types of partitions of these domains were proposed in [1]. All of these constructions were based on a new type of B-splines, proposed by some of the authors several years earlier: expo-rational B-splines (ERBS) [3]. In the present communication we shall provide more details about one of these constructions: the one for the most general class of domain partitions considered. This construction is based on the use of two separate families of basis functions: one which has all the necessary Hermite interpolation properties, and another which has the necessary properties of a smooth convex partition of unity. The constructions of both of these two bases are well-known; the new part of the construction is the combined use of these bases for the derivation of a new basis which enjoys having all above-said interpolation and unity partition properties simultaneously. In [1] the emphasis was put on the use of radial basis functions in the definitions of the two initial bases in the construction; now we shall put the main emphasis on the case when these bases consist of tensor-product B-splines. This selection provides two useful advantages: (A) it is easier to compute higher-order derivatives while working in Cartesian coordinates; (B) it becomes clear that this construction becomes a far-going extension of tensor-product constructions. We shall provide 3-dimensional visualization of the resulting bivariate bases, using tensor-product ERBS. In the main tensor-product variant, we shall consider also replacement of ERBS with simpler generalized ERBS (GERBS) [2], namely, their simplified polynomial modifications: the Euler Beta-function B-splines (BFBS). One advantage of using BFBS instead of ERBS is the simplified computation, since BFBS are piecewise polynomial, which ERBS are not. One disadvantage of using BFBS in the place of ERBS in this construction is that the necessary selection of the degree of BFBS imposes constraints on the maximal possible multiplicity of the Hermite interpolation.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

PubMed

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

2018-05-14

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

Volatility of organic aerosol and its components in the Megacity of Paris

NASA Astrophysics Data System (ADS)

Paciga, A.; Karnezi, E.; Kostenidou, E.; Hildebrandt, L.; Psichoudaki, M.; Engelhart, G. J.; Lee, B.-H.; Crippa, M.; Prévôt, A. S. H.; Baltensperger, U.; Pandis, S. N.

2015-08-01

Using a mass transfer model and the volatility basis set, we estimate the volatility distribution for the organic aerosol (OA) components during summer and winter in Paris, France as part of the collaborative project MEGAPOLI. The concentrations of the OA components as a function of temperature were measured combining data from a thermodenuder and an aerosol mass spectrometer (AMS) with Positive Matrix Factorization (PMF) analysis. The hydrocarbon-like organic aerosol (HOA) had similar volatility distributions for the summer and winter campaigns with half of the material in the saturation concentration bin of 10 μg m-3 and another 35-40 % consisting of low and extremely low volatility organic compounds (LVOCs and ELVOCs, respectively). The winter cooking OA (COA) was more than an order of magnitude less volatile than the summer COA. The low volatility oxygenated OA (LV-OOA) factor detected in the summer had the lowest volatility of all the derived factors and consisted almost exclusively of ELVOCs. The volatility for the semi-volatile oxygenated OA (SV-OOA) was significantly higher than that of the LV-OOA, containing both semi-volatile organic components (SVOCs) and LVOCs. The oxygenated OA (OOA) factor in winter consisted of SVOCs (45 %), LVOCs (25 %) and ELVOCs (30 %). The volatility of marine OA (MOA) was higher than that of the other factors containing around 60 % SVOCs. The biomass burning OA (BBOA) factor contained components with a wide range of volatilities with significant contributions from both SVOCs (50 %) and LVOCs (30 %). Finally, combining the O : C ratio and volatility distributions of the various factors, we incorporated our results into the two-dimensional volatility basis set (2D-VBS). Our results show that the factors cover a broad spectrum of volatilities with no direct link between the average volatility and average O : C of the OA components. Agreement between our findings and previous publications is encouraging for our understanding of the evolution of atmospheric OA.

Kinetics and Thermodynamics of the Reaction between the (•)OH Radical and Adenine: A Theoretical Investigation.

PubMed

Milhøj, Birgitte O; Sauer, Stephan P A

2015-06-18

The accessibility of all possible reaction paths for the reaction between the nucleobase adenine and the (•)OH radical is investigated through quantum chemical calculations of barrier heights and rate constants at the ωB97X-D/6-311++G(2df,2pd) level with Eckart tunneling corrections. First the computational method is validated by considering the hydrogen abstraction from the heterocyclic N9 nitrogen in adenine as a test system. Geometries for all molecules in the reaction are optimized with four different DFT exchange-correlation functionals (B3LYP, BHandHLYP, M06-2X, and ωB97X-D), in combination with Pople and Dunning basis sets, all of which have been employed in similar investigations in the literature. Improved energies are obtained through single point calculations with CCSD(T) and the same basis sets, and reaction rate constants are calculated for all methods both without tunneling corrections and with the Wigner, Bell, and Eckart corrections. In comparison to CCSD(T)//BHandHLYP/aug-cc-pVTZ reference results, the ωB97X-D/6-311++G(2df,2pd) method combined with Eckart tunneling corrections provides a sensible compromise between accuracy and time. Using this method, all subreactions of the reaction between adenine and the (•)OH radical are investigated. The total rate constants for hydrogen abstraction and addition for adenine are predicted with this method to be 1.06 × 10(-12) and 1.10 × 10(-12) cm(3) molecules(-1) s(-1), respectively. Abstractions of H61 and H62 contribute the most, while only addition to the C8 carbon is found to be of any significance, in contrast to previous claims that addition is the dominant reaction pathway. The overall rate constant for the complete reaction is found to be 2.17 × 10(-12) cm(3) molecules(-1) s(-1), which agrees exceptionally well with experimental results.

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

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

Classification of high-resolution multi-swath hyperspectral data using Landsat 8 surface reflectance data as a calibration target and a novel histogram based unsupervised classification technique to determine natural classes from biophysically relevant fit parameters

NASA Astrophysics Data System (ADS)

McCann, C.; Repasky, K. S.; Morin, M.; Lawrence, R. L.; Powell, S. L.

2016-12-01

Compact, cost-effective, flight-based hyperspectral imaging systems can provide scientifically relevant data over large areas for a variety of applications such as ecosystem studies, precision agriculture, and land management. To fully realize this capability, unsupervised classification techniques based on radiometrically-calibrated data that cluster based on biophysical similarity rather than simply spectral similarity are needed. An automated technique to produce high-resolution, large-area, radiometrically-calibrated hyperspectral data sets based on the Landsat surface reflectance data product as a calibration target was developed and applied to three subsequent years of data covering approximately 1850 hectares. The radiometrically-calibrated data allows inter-comparison of the temporal series. Advantages of the radiometric calibration technique include the need for minimal site access, no ancillary instrumentation, and automated processing. Fitting the reflectance spectra of each pixel using a set of biophysically relevant basis functions reduces the data from 80 spectral bands to 9 parameters providing noise reduction and data compression. Examination of histograms of these parameters allows for determination of natural splitting into biophysical similar clusters. This method creates clusters that are similar in terms of biophysical parameters, not simply spectral proximity. Furthermore, this method can be applied to other data sets, such as urban scenes, by developing other physically meaningful basis functions. The ability to use hyperspectral imaging for a variety of important applications requires the development of data processing techniques that can be automated. The radiometric-calibration combined with the histogram based unsupervised classification technique presented here provide one potential avenue for managing big-data associated with hyperspectral imaging.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

PubMed

Damas, Joana; O'Connor, Rebecca; Farré, Marta; Lenis, Vasileios Panagiotis E; Martell, Henry J; Mandawala, Anjali; Fowler, Katie; Joseph, Sunitha; Swain, Martin T; Griffin, Darren K; Larkin, Denis M

2017-05-01

Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon ( Columbia livia ) and peregrine falcon ( Falco peregrinus ) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome. © 2017 Damas et al.; Published by Cold Spring Harbor Laboratory Press.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

PubMed Central

O'Connor, Rebecca; Lenis, Vasileios Panagiotis E.; Martell, Henry J.; Mandawala, Anjali; Fowler, Katie; Joseph, Sunitha; Swain, Martin T.; Griffin, Darren K.; Larkin, Denis M.

2017-01-01

Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome. PMID:27903645

A new parallel algorithm of MP2 energy calculations.

PubMed

Ishimura, Kazuya; Pulay, Peter; Nagase, Shigeru

2006-03-01

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

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

PubMed

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

2012-02-17

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

A machine learning approach for efficient uncertainty quantification using multiscale methods

NASA Astrophysics Data System (ADS)

Chan, Shing; Elsheikh, Ahmed H.

2018-02-01

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

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

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

PubMed

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

2010-02-04

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

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

PubMed

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

2013-01-15

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

Probabilistic Open Set Recognition

NASA Astrophysics Data System (ADS)

Jain, Lalit Prithviraj

Real-world tasks in computer vision, pattern recognition and machine learning often touch upon the open set recognition problem: multi-class recognition with incomplete knowledge of the world and many unknown inputs. An obvious way to approach such problems is to develop a recognition system that thresholds probabilities to reject unknown classes. Traditional rejection techniques are not about the unknown; they are about the uncertain boundary and rejection around that boundary. Thus traditional techniques only represent the "known unknowns". However, a proper open set recognition algorithm is needed to reduce the risk from the "unknown unknowns". This dissertation examines this concept and finds existing probabilistic multi-class recognition approaches are ineffective for true open set recognition. We hypothesize the cause is due to weak adhoc assumptions combined with closed-world assumptions made by existing calibration techniques. Intuitively, if we could accurately model just the positive data for any known class without overfitting, we could reject the large set of unknown classes even under this assumption of incomplete class knowledge. For this, we formulate the problem as one of modeling positive training data by invoking statistical extreme value theory (EVT) near the decision boundary of positive data with respect to negative data. We provide a new algorithm called the PI-SVM for estimating the unnormalized posterior probability of class inclusion. This dissertation also introduces a new open set recognition model called Compact Abating Probability (CAP), where the probability of class membership decreases in value (abates) as points move from known data toward open space. We show that CAP models improve open set recognition for multiple algorithms. Leveraging the CAP formulation, we go on to describe the novel Weibull-calibrated SVM (W-SVM) algorithm, which combines the useful properties of statistical EVT for score calibration with one-class and binary support vector machines. Building from the success of statistical EVT based recognition methods such as PI-SVM and W-SVM on the open set problem, we present a new general supervised learning algorithm for multi-class classification and multi-class open set recognition called the Extreme Value Local Basis (EVLB). The design of this algorithm is motivated by the observation that extrema from known negative class distributions are the closest negative points to any positive sample during training, and thus should be used to define the parameters of a probabilistic decision model. In the EVLB, the kernel distribution for each positive training sample is estimated via an EVT distribution fit over the distances to the separating hyperplane between positive training sample and closest negative samples, with a subset of the overall positive training data retained to form a probabilistic decision boundary. Using this subset as a frame of reference, the probability of a sample at test time decreases as it moves away from the positive class. Possessing this property, the EVLB is well-suited to open set recognition problems where samples from unknown or novel classes are encountered at test. Our experimental evaluation shows that the EVLB provides a substantial improvement in scalability compared to standard radial basis function kernel machines, as well as P I-SVM and W-SVM, with improved accuracy in many cases. We evaluate our algorithm on open set variations of the standard visual learning benchmarks, as well as with an open subset of classes from Caltech 256 and ImageNet. Our experiments show that PI-SVM, WSVM and EVLB provide significant advances over the previous state-of-the-art solutions for the same tasks.

Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

NASA Astrophysics Data System (ADS)

Datta, Dipayan; Kossmann, Simone; Neese, Frank

2016-09-01

The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the threshold for the natural orbital occupation number cutoff by an order of magnitude compared to the DLPNO-CCSD energy calculations.

Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

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

Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy

2006-09-20

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

The accuracy of the Gaussian-and-finite-element-Coulomb (GFC) method for the calculation of Coulomb integrals.

PubMed

Przybytek, Michal; Helgaker, Trygve

2013-08-07

We analyze the accuracy of the Coulomb energy calculated using the Gaussian-and-finite-element-Coulomb (GFC) method. In this approach, the electrostatic potential associated with the molecular electronic density is obtained by solving the Poisson equation and then used to calculate matrix elements of the Coulomb operator. The molecular electrostatic potential is expanded in a mixed Gaussian-finite-element (GF) basis set consisting of Gaussian functions of s symmetry centered on the nuclei (with exponents obtained from a full optimization of the atomic potentials generated by the atomic densities from symmetry-averaged restricted open-shell Hartree-Fock theory) and shape functions defined on uniform finite elements. The quality of the GF basis is controlled by means of a small set of parameters; for a given width of the finite elements d, the highest accuracy is achieved at smallest computational cost when tricubic (n = 3) elements are used in combination with two (γ(H) = 2) and eight (γ(1st) = 8) Gaussians on hydrogen and first-row atoms, respectively, with exponents greater than a given threshold (αmin (G)=0.5). The error in the calculated Coulomb energy divided by the number of atoms in the system depends on the system type but is independent of the system size or the orbital basis set, vanishing approximately like d(4) with decreasing d. If the boundary conditions for the Poisson equation are calculated in an approximate way, the GFC method may lose its variational character when the finite elements are too small; with larger elements, it is less sensitive to inaccuracies in the boundary values. As it is possible to obtain accurate boundary conditions in linear time, the overall scaling of the GFC method for large systems is governed by another computational step-namely, the generation of the three-center overlap integrals with three Gaussian orbitals. The most unfavorable (nearly quadratic) scaling is observed for compact, truly three-dimensional systems; however, this scaling can be reduced to linear by introducing more effective techniques for recognizing significant three-center overlap distributions.

47 CFR 4.1 - Scope, basis and purpose.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

47 CFR 4.1 - Scope, basis and purpose.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Scope, basis and purpose. 4.1 Section 4.1 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL DISRUPTIONS TO COMMUNICATIONS General § 4.1 Scope, basis and purpose. In this part, the Federal Communications Commission is setting forth requirements...

Spatial Bayesian Latent Factor Regression Modeling of Coordinate-based Meta-analysis Data

PubMed Central

Montagna, Silvia; Wager, Tor; Barrett, Lisa Feldman; Johnson, Timothy D.; Nichols, Thomas E.

2017-01-01

Summary Now over 20 years old, functional MRI (fMRI) has a large and growing literature that is best synthesised with meta-analytic tools. As most authors do not share image data, only the peak activation coordinates (foci) reported in the paper are available for Coordinate-Based Meta-Analysis (CBMA). Neuroimaging meta-analysis is used to 1) identify areas of consistent activation; and 2) build a predictive model of task type or cognitive process for new studies (reverse inference). To simultaneously address these aims, we propose a Bayesian point process hierarchical model for CBMA. We model the foci from each study as a doubly stochastic Poisson process, where the study-specific log intensity function is characterised as a linear combination of a high-dimensional basis set. A sparse representation of the intensities is guaranteed through latent factor modeling of the basis coefficients. Within our framework, it is also possible to account for the effect of study-level covariates (meta-regression), significantly expanding the capabilities of the current neuroimaging meta-analysis methods available. We apply our methodology to synthetic data and neuroimaging meta-analysis datasets. PMID:28498564

Academic procrastination and academic performance: An initial basis for intervention.

PubMed

Goroshit, Marina

2018-01-01

Academic procrastination is a prevalent phenomenon with a range of negative outcomes. Many studies focused on causes and correlates of academic procrastination; however, the study of interventions for academic procrastination is scarce. The present study is an initial effort to study the relationship between academic procrastination, online course participation, and achievement, as a basis for developing an intervention for academic procrastination. Findings indicated that studying procrastination was negatively associated with final exam grade as well as with the three online course participation measures. Final exam grade was positively associated with two of the online course participation measures, and they positively correlated with each other. In addition, results indicated that studying procrastination, in combination with online course participation measures, explained about 50% of variance in final exam's grade. Frequency of activities in course Web site had the strongest positive effect on final exam's grade. These findings strengthen the notion that studying procrastination is an impediment to students' academic performance and outcomes and clarifies the need to develop and study academic interventions for academic procrastination as a means to decrease its prevalence in academic settings.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

Color constancy: enhancing von Kries adaption via sensor transformations

NASA Astrophysics Data System (ADS)

Finlayson, Graham D.; Drew, Mark S.; Funt, Brian V.

1993-09-01

Von Kries adaptation has long been considered a reasonable vehicle for color constancy. Since the color constancy performance attainable via the von Kries rule strongly depends on the spectral response characteristics of the human cones, we consider the possibility of enhancing von Kries performance by constructing new `sensors' as linear combinations of the fixed cone sensitivity functions. We show that if surface reflectances are well-modeled by 3 basis functions and illuminants by 2 basis functions then there exists a set of new sensors for which von Kries adaptation can yield perfect color constancy. These new sensors can (like the cones) be described as long-, medium-, and short-wave sensitive; however, both the new long- and medium-wave sensors have sharpened sensitivities -- their support is more concentrated. The new short-wave sensor remains relatively unchanged. A similar sharpening of cone sensitivities has previously been observed in test and field spectral sensitivities measured for the human eye. We present simulation results demonstrating improved von Kries performance using the new sensors even when the restrictions on the illumination and reflectance are relaxed.

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates

PubMed Central

Tamura, Koichiro; Tao, Qiqing; Kumar, Sudhir

2018-01-01

Abstract RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits. PMID:29893954

Robust representation and recognition of facial emotions using extreme sparse learning.

PubMed

Shojaeilangari, Seyedehsamaneh; Yau, Wei-Yun; Nandakumar, Karthik; Li, Jun; Teoh, Eam Khwang

2015-07-01

Recognition of natural emotions from human faces is an interesting topic with a wide range of potential applications, such as human-computer interaction, automated tutoring systems, image and video retrieval, smart environments, and driver warning systems. Traditionally, facial emotion recognition systems have been evaluated on laboratory controlled data, which is not representative of the environment faced in real-world applications. To robustly recognize the facial emotions in real-world natural situations, this paper proposes an approach called extreme sparse learning, which has the ability to jointly learn a dictionary (set of basis) and a nonlinear classification model. The proposed approach combines the discriminative power of extreme learning machine with the reconstruction property of sparse representation to enable accurate classification when presented with noisy signals and imperfect data recorded in natural settings. In addition, this paper presents a new local spatio-temporal descriptor that is distinctive and pose-invariant. The proposed framework is able to achieve the state-of-the-art recognition accuracy on both acted and spontaneous facial emotion databases.

On the Flow of a Compressible Fluid by the Hodograph Method. II - Fundamental Set of Particular Flow Solutions of the Chaplygin Differential Equation

NASA Technical Reports Server (NTRS)

Garrick, I. E.; Kaplan, Carl

1944-01-01

The differential equation of Chaplygin's jet problem is utilized to give a systematic development of particular solutions of the hodograph flow equations, which extends the treatment of Chaplygin into the supersonic range and completes the set of particular solutions. The particular solutions serve to place on a reasonable basis the use of velocity correction formulas for the comparison of incompressible and compressible flows. It is shown that the geometric-mean type of velocity correction formula introduced in part I has significance as an over-all type of approximation in the subsonic range. A brief review of general conditions limiting the potential flow of an adiabatic compressible fluid is given and application is made to the particular solutions, yielding conditions for the existence of singular loci in the supersonic range. The combining of particular solutions in accordance with prescribed boundary flow conditions is not treated in the present paper.

National, holistic, watershed-scale approach to understand the sources, transport, and fate of agricultural chemicals

USGS Publications Warehouse

Capel, P.D.; McCarthy, K.A.; Barbash, J.E.

2008-01-01

This paper is an introduction to the following series of papers that report on in-depth investigations that have been conducted at five agricultural study areas across the United States in order to gain insights into how environmental processes and agricultural practices interact to determine the transport and fate of agricultural chemicals in the environment. These are the first study areas in an ongoing national study. The study areas were selected, based on the combination of cropping patterns and hydrologic setting, as representative of nationally important agricultural settings to form a basis for extrapolation to unstudied areas. The holistic, watershed-scale study design that involves multiple environmental compartments and that employs both field observations and simulation modeling is presented. This paper introduces the overall study design and presents an overview of the hydrology of the five study areas. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

On-line diagnosis of sequential systems, 2

NASA Technical Reports Server (NTRS)

Sundstrom, R. J.

1974-01-01

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

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

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

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

Computational studies of metal-metal and metal-ligand interactions

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.

1992-01-01

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

An imputed genotype resource for the laboratory mouse

PubMed Central

Szatkiewicz, Jin P.; Beane, Glen L.; Ding, Yueming; Hutchins, Lucie; de Villena, Fernando Pardo-Manuel; Churchill, Gary A.

2009-01-01

We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 49 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrate that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains. The data are available for bulk download or query at http://cgd.jax.org/. PMID:18301946

Comparison of the effectiveness of alternative feature sets in shape retrieval of multicomponent images

NASA Astrophysics Data System (ADS)

Eakins, John P.; Edwards, Jonathan D.; Riley, K. Jonathan; Rosin, Paul L.

2001-01-01

Many different kinds of features have been used as the basis for shape retrieval from image databases. This paper investigates the relative effectiveness of several types of global shape feature, both singly and in combination. The features compared include well-established descriptors such as Fourier coefficients and moment invariants, as well as recently-proposed measures of triangularity and ellipticity. Experiments were conducted within the framework of the ARTISAN shape retrieval system, and retrieval effectiveness assessed on a database of over 10,000 images, using 24 queries and associated ground truth supplied by the UK Patent Office . Our experiments revealed only minor differences in retrieval effectiveness between different measures, suggesting that a wide variety of shape feature combinations can provide adequate discriminating power for effective shape retrieval in multi-component image collections such as trademark registries. Marked differences between measures were observed for some individual queries, suggesting that there could be considerable scope for improving retrieval effectiveness by providing users with an improved framework for searching multi-dimensional feature space.

Comparison of the effectiveness of alternative feature sets in shape retrieval of multicomponent images

NASA Astrophysics Data System (ADS)

Eakins, John P.; Edwards, Jonathan D.; Riley, K. Jonathan; Rosin, Paul L.

2000-12-01

Many different kinds of features have been used as the basis for shape retrieval from image databases. This paper investigates the relative effectiveness of several types of global shape feature, both singly and in combination. The features compared include well-established descriptors such as Fourier coefficients and moment invariants, as well as recently-proposed measures of triangularity and ellipticity. Experiments were conducted within the framework of the ARTISAN shape retrieval system, and retrieval effectiveness assessed on a database of over 10,000 images, using 24 queries and associated ground truth supplied by the UK Patent Office . Our experiments revealed only minor differences in retrieval effectiveness between different measures, suggesting that a wide variety of shape feature combinations can provide adequate discriminating power for effective shape retrieval in multi-component image collections such as trademark registries. Marked differences between measures were observed for some individual queries, suggesting that there could be considerable scope for improving retrieval effectiveness by providing users with an improved framework for searching multi-dimensional feature space.

Rotational and Infrared Spectroscopy of Ethanimine: A Route toward Its Astrophysical and Planetary Detection

NASA Astrophysics Data System (ADS)

Melli, Alessio; Melosso, Mattia; Tasinato, Nicola; Bosi, Giulio; Spada, Lorenzo; Bloino, Julien; Mendolicchio, Marco; Dore, Luca; Barone, Vincenzo; Puzzarini, Cristina

2018-03-01

Ethanimine, a possible precursor of amino acids, is considered an important prebiotic molecule and thus may play important roles in the formation of biological building blocks in the interstellar medium. In addition, its identification in Titan’s atmosphere would be important for understanding the abiotic synthesis of organic species. An accurate computational characterization of the molecular structure, energetics, and spectroscopic properties of the E and Z isomers of ethanimine, CH3CHNH, has been carried out by means of a composite scheme based on coupled-cluster techniques, which also account for extrapolation to the complete basis-set limit and core-valence correlation correction, combined with density functional theory for the treatment of vibrational anharmonic effects. By combining the computational results with new millimeter-wave measurements up to 300 GHz, the rotational spectrum of both isomers can be accurately predicted up to 500 GHz. Furthermore, our computations allowed us to revise the infrared spectrum of both E- and Z-CH3CHNH, thus predicting all fundamental bands with high accuracy.

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

NASA Astrophysics Data System (ADS)

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

1995-05-01

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

A case for restricted-domain relational learning.

PubMed

Wright, Anthony A; Katz, Jeffrey S

2009-10-01

Monkeys and pigeons learned a same/different task with pairs that were selected from a training set of eight picture stimuli. They showed no novel-stimulus transfer and hence no abstract-concept learning. They were also tested with novel pairs of the eight training pictures (i.e., combinations that had not been used in training) and with inverted pictures of the training pairs. If the subjects had learned the task item-specifically (e.g., if-then or configural learning), they should have failed these tests, but they performed well with novel combinations of training pictures and inverted pictures, suggesting that they learned the task relationally (i.e., on the basis of the relationship between the two pictures that were presented in each trial). This somewhat paradoxical conclusion of relational learning in the absence of abstract-concept learning is contrary to most theories of abstract-concept learning. The implications of this conclusion are discussed in the context of restricted-domain relational learning.

Extremity movements help occupational therapists identify stress responses in preterm infants in the neonatal intensive care unit: a systematic review.

PubMed

Holsti, Liisa; Grunau, Ruth E

2007-06-01

Accurate assessment and treatment of pain and stress in preterm infants in neonatal intensive care units (NICU) is vital because pain and stress responses have been linked to long-term alterations in development in this population. To review the evidence of specific extremity movements in preterm infants as observed during stressful procedures. Five on-line databases were searched for relevant studies. For each study, levels of evidence were determined and effect size estimates were calculated. Each study was also evaluated for specific factors that presented potential threats to its validity. Eighteen studies were identified and seven comprised the review. The combined sample included 359 preterm infants. Six specific movements were associated with painful and intrusive procedures. A set of specific extremity movements, when combined with other reliable biobehavioural measures of pain and stress, can form the basis for future research and development of a clinical stress scale for preterm infants.

[Midazolam sedation in the general dental practice].

PubMed

Bertens, J; Abraham-Inpijn, L; Meuwissen, P J

1994-03-01

The general dental practitioner is occasionally confronted with patients who, on the basis of psychological--and often somatic--criteria, are difficult to treat. Medicinal sedation in combination with anxiety reduction may be deemed appropriate for such patients. In the Netherlands inhalation sedation by means of a combination of oxygen and nitrous oxide is generally used. The limitations and disadvantages of this method have directed attention towards sedation by means of midazolam, a quick-acting benzodiazepine. In view of the complications which may accompany the administration of midazolam, the general practitioner working alone or in a group practice is advised against using midazolam sedation. Such use should be reserved for a dentist working in a hospital setting, who is able to consult with a physician regarding the advisability of administering midazolam. Even then, the safety of the patient requires that the practitioners have a proper insight into the physical state of the patient, work according to a protocol and in accordance with clearly defined responsibilities, and provide adequate accommodation during and after treatment.

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

PubMed

Naden, Levi N; Shirts, Michael R

2016-04-12

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

Electronic and spectroscopic characterizations of SNP isomers

NASA Astrophysics Data System (ADS)

Trabelsi, Tarek; Al Mogren, Muneerah Mogren; Hochlaf, Majdi; Francisco, Joseph S.

2018-02-01

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ˜2.4 eV above the linear SNP isomer. The low-lying singlet and triplet electronic states of the linear SNP and SPN isomers were investigated using a multi-reference configuration interaction method and large basis set. Several bound electronic states were identified. However, their upper rovibrational levels were predicted to pre-dissociate, leading to S + PN, P + NS products, and multi-step pathways were discovered. For the ground states, a set of spectroscopic parameters were derived using standard and explicitly correlated coupled-cluster methods in conjunction with augmented correlation-consistent basis sets extrapolated to the complete basis set limit. We also considered scalar and core-valence effects. For linear isomers, the rovibrational spectra were deduced after generation of their 3D-potential energy surfaces along the stretching and bending coordinates and variational treatments of the nuclear motions.

Hybrid Wavelet De-noising and Rank-Set Pair Analysis approach for forecasting hydro-meteorological time series

NASA Astrophysics Data System (ADS)

WANG, D.; Wang, Y.; Zeng, X.

2017-12-01

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

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

PubMed

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

2015-07-15

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

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

NASA Astrophysics Data System (ADS)

Ohnishi, Yu-ya; Ten-no, Seiichiro

2013-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

High-precision horizontally directed force measurements for high dead loads based on a differential electromagnetic force compensation system

NASA Astrophysics Data System (ADS)

Vasilyan, Suren; Rivero, Michel; Schleichert, Jan; Halbedel, Bernd; Fröhlich, Thomas

2016-04-01

In this paper, we present an application for realizing high-precision horizontally directed force measurements in the order of several tens of nN in combination with high dead loads of about 10 N. The set-up is developed on the basis of two identical state-of-the-art electromagnetic force compensation (EMFC) high precision balances. The measurement resolution of horizontally directed single-axis quasi-dynamic forces is 20 nN over the working range of  ±100 μN. The set-up operates in two different measurement modes: in the open-loop mode the mechanical deflection of the proportional lever is an indication of the acting force, whereas in the closed-loop mode it is the applied electric current to the coil inside the EMFC balance that compensates deflection of the lever to the offset zero position. The estimated loading frequency (cutoff frequency) of the set-up in the open-loop mode is about 0.18 Hz, in the closed-loop mode it is 0.7 Hz. One of the practical applications that the set-up is suitable for is the flow rate measurements of low electrically conducting electrolytes by applying the contactless technique of Lorentz force velocimetry. Based on a previously developed set-up which uses a single EMFC balance, experimental, theoretical and numerical analyses of the thermo-mechanical properties of the supporting structure are presented.

[Research on spectra recognition method for cabbages and weeds based on PCA and SIMCA].

PubMed

Zu, Qin; Deng, Wei; Wang, Xiu; Zhao, Chun-Jiang

2013-10-01

In order to improve the accuracy and efficiency of weed identification, the difference of spectral reflectance was employed to distinguish between crops and weeds. Firstly, the different combinations of Savitzky-Golay (SG) convolutional derivation and multiplicative scattering correction (MSC) method were applied to preprocess the raw spectral data. Then the clustering analysis of various types of plants was completed by using principal component analysis (PCA) method, and the feature wavelengths which were sensitive for classifying various types of plants were extracted according to the corresponding loading plots of the optimal principal components in PCA results. Finally, setting the feature wavelengths as the input variables, the soft independent modeling of class analogy (SIMCA) classification method was used to identify the various types of plants. The experimental results of classifying cabbages and weeds showed that on the basis of the optimal pretreatment by a synthetic application of MSC and SG convolutional derivation with SG's parameters set as 1rd order derivation, 3th degree polynomial and 51 smoothing points, 23 feature wavelengths were extracted in accordance with the top three principal components in PCA results. When SIMCA method was used for classification while the previously selected 23 feature wavelengths were set as the input variables, the classification rates of the modeling set and the prediction set were respectively up to 98.6% and 100%.

CCSDT calculations of molecular equilibrium geometries

NASA Astrophysics Data System (ADS)

Halkier, Asger; Jørgensen, Poul; Gauss, Jürgen; Helgaker, Trygve

1997-08-01

CCSDT equilibrium geometries of CO, CH 2, F 2, HF, H 2O and N 2 have been calculated using the correlation-consistent cc-pVXZ basis sets. Similar calculations have been performed for SCF, CCSD and CCSD(T). In general, bond lengths decrease when improving the basis set and increase when improving the N-electron treatment. CCSD(T) provides an excellent approximation to CCSDT for bond lengths as the largest difference between CCSDT and CCSD(T) is 0.06 pm. At the CCSDT/cc-pVQZ level, basis set deficiencies, neglect of higher-order excitations, and incomplete treatment of core-correlation all give rise to errors of a few tenths of a pm, but to a large extent, these errors cancel. The CCSDT/cc-pVQZ bond lengths deviate on average only by 0.11 pm from experiment.

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

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

Sorella, S., E-mail: sorella@sissa.it; Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr

2015-12-28

We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wavemore » function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.« less

Scanning tunneling microscopy image simulation of the rutile (110) TiO2 surface with hybrid functionals and the localized basis set approach

NASA Astrophysics Data System (ADS)

Di Valentin, Cristiana

2007-10-01

In this work we present a simplified procedure to use hybrid functionals and localized atomic basis sets to simulate scanning tunneling microscopy (STM) images of stoichiometric, reduced and hydroxylated rutile (110) TiO2 surface. For the two defective systems it is necessary to introduce some exact Hartree-Fock exchange in the exchange functional in order to correctly describe the details of the electronic structure. Results are compared to the standard density functional theory and planewave basis set approach. Both methods have advantages and drawbacks that are analyzed in detail. In particular, for the localized basis set approach, it is necessary to introduce a number of Gaussian function in the vacuum region above the surface in order to correctly describe the exponential decay of the integrated local density of states from the surface. In the planewave periodic approach, a thick vacuum region is required to achieve correct results. Simulated STM images are obtained for both the reduced and hydroxylated surface which nicely compare with experimental findings. A direct comparison of the two defects as displayed in the simulated STM images indicates that the OH groups should appear brighter than oxygen vacancies in perfect agreement with the experimental STM data.

The Value of Diffusion-Weighted Imaging in Combination With Conventional Magnetic Resonance Imaging for Improving Tumor Detection for Early Cervical Carcinoma Treated With Fertility-Sparing Surgery.

PubMed

Li, Xiulei; Wang, Ling; Li, Yong; Song, Peiji

2017-10-01

This study aimed to investigate the value of diffusion-weighted imaging (DWI) in combination with conventional magnetic resonance imaging (MRI) for improving tumor detection in young patients treated with fertility-sparing surgery because of early cervical carcinoma. Fifty-four patients with stage Ia or Ib1 cervical carcinoma were enrolled into this study. Magnetic resonance examinations were performed for these patients using conventional MRI (including T1-weighted imaging, T2-weighted imaging, and dynamic contrast-enhanced MRI) and DWI. The apparent diffusion coefficient (ADC) values of cervical carcinoma were analyzed quantitatively and compared with that of adjacent epithelium. Sensitivity, positive predictive value, and accuracy of 2 sets of MRI sequences were calculated on the basis of histologic results, and the diagnostic ability of conventional MRI/DWI combinations was compared with that of conventional MRI. The mean ADC value from cervical carcinoma (mean, 786 × 10 mm/s ± 100) was significantly lower than that from adjacent epithelium (mean, 1352 × 10 mm/s ± 147) (P = 0.01). When the threshold ADC value set as 1010 × 10 mm/s, the sensitivity and specificity for differentiating cervical carcinoma from nontumor epithelium were 78.2% and 67.2%, respectively. The sensitivity and accuracy of conventional MRI for tumor detection were 76.0% and 70.4%, whereas the sensitivity and accuracy of conventional MRI/DWI combinations were 91.7% and 90.7%, respectively. Conventional MRI/DWI combinations revealed a positive predictive value of 97.8% and only 4 false-negative findings. The addition of DWI to conventional MRI considerably improves the sensitivity and accuracy of tumor detection in young patients treated with fertility-sparing surgery, which supports the inclusion quantitative analysis of ADC value in routine MRI protocol before fertility-sparing surgery.

[Phenomenology of multiculturalism and intercultural pluralism].

PubMed

Hoyos, Guillermo

2012-01-01

Multiculturalism is defined as the combination, within a given territory, of a social unit and a cultural plurality by way of exchanges and communications among actors who use different categories of expression, analysis and interpretation. A multiculturalist project should not promote a society that is split up into closed groups; on the contrary, it should set forth policies based on communication and cooperation processes among the cultural communities. To understand this concept, we will present the ontological basis of this phenomenonin the search for a communicational solution, with our startpoint being a phenomenological description of the way in which multiculturalism manifests to us in life; to later deepen into the meaning of the phenomenon,and finally offer a pluralist solution to the problems and challenges cultural differences bring about.

[3D imaging benefits in clinical pratice of orthodontics].

PubMed

Frèrejouand, Emmanuel

2016-12-01

3D imaging possibilities raised up in the last few years in the orthodontic field. In 2016, it can be used for diagnosis improvement and treatment planning by using digital set up combined to CBCT. It is relevant for orthodontic mechanic updating by creating visible or invisible customised appliances. It forms the basis of numerous scientific researches. The author explains the progress 3D imaging brings to diagnosis and clinics but also highlights the requirements it creates. The daily use of these processes in orthodontic clinical practices needs to be regulated regarding the benefit/risk ratio and the patient satisfaction. The command of the digital work flow created by these technics requires habits modifications from the orthodontist and his staff. © EDP Sciences, SFODF, 2016.

Impact of computer use on children's vision.

PubMed

Kozeis, N

2009-10-01

Today, millions of children use computers on a daily basis. Extensive viewing of the computer screen can lead to eye discomfort, fatigue, blurred vision and headaches, dry eyes and other symptoms of eyestrain. These symptoms may be caused by poor lighting, glare, an improper work station set-up, vision problems of which the person was not previously aware, or a combination of these factors. Children can experience many of the same symptoms related to computer use as adults. However, some unique aspects of how children use computers may make them more susceptible than adults to the development of these problems. In this study, the most common eye symptoms related to computer use in childhood, the possible causes and ways to avoid them are reviewed.

A nomogram for interpreting slope stability of fine-grained deposits in modern and ancient-marine environments.

USGS Publications Warehouse

Booth, J.S.; Sangrey, D.A.; Fugate, J.K.

1985-01-01

This nomogram was designed to aid in interpreting the causes of mass movement in modern and ancient settings, to provide a basis for evaluating and predicting slope stability under given conditions and to further the understanding of the relationships among the several key factors that control slope stability. Design of the nomogram is based on effective stress and combines consolidation theory as applicable to depositional environments with the infinite-slope model of slope-stability analysis. If infinite-slope conditions are assumed to exist, the effective overburden stress can be used to derive a factor of safety against static slope failure by using the angle of internal friction and the slope angle. -from Authors

Basic materials physics of transparent conducting oxides.

PubMed

Edwards, P P; Porch, A; Jones, M O; Morgan, D V; Perks, R M

2004-10-07

Materials displaying the remarkable combination of high electrical conductivity and optical transparency already from the basis of many important technological applications, including flat panel displays, solar energy capture and other opto-electronic devices. Here we present the basic materials physics of these important materials centred on the nature of the doping process to generate n-type conductivity in transparent conducting oxides, the associated transition to the metallic (conducting) state and the detailed properties of the degenerate itinerant electron gas. The aim is to fully understand the origins of the basic performance limits of known materials and to set the scene for new or improved materials which will breach those limits for new-generation transparent conducting materials, either oxides, or beyond oxides.

A quantum chemistry study of Qinghaosu

NASA Astrophysics Data System (ADS)

Gu, Jian-De; Chen, Kai-Xian; Jiang, Hua-Liang; Zhu, Wei-Liang; Chen, Jian-Zhong; Ji, Ru-Yun

1997-10-01

The powerful anti-malarial drug, Qinghaosu (Artemisinin), has been studied using ab initio methods. The DFT B3LYP method with the 6-31G ∗ basis set gives an excellent geometry compared to experiments, especially for the OO bond length and the 1,2,4-Trioxane ring subsystem. The R(OO) bond length predicted at this level is 1.460 Å, only 0.018 Å shorter than the experimental measurement. The vibrational analysis shows that the OO stretching mode is combined with the OC vibration mode, having the character of an OOC entity. The OO vibrational band at 722 cm -1 suggested in the experimental studies has been assigned as 1,2,4-trioxane ring breathing.

A periodic table of coiled-coil protein structures.

PubMed

Moutevelis, Efrosini; Woolfson, Derek N

2009-01-23

Coiled coils are protein structure domains with two or more alpha-helices packed together via interlacing of side chains known as knob-into-hole packing. We analysed and classified a large set of coiled-coil structures using a combination of automated and manual methods. This led to a systematic classification that we termed a "periodic table of coiled coils," which we have made available at http://coiledcoils.chm.bris.ac.uk/ccplus/search/periodic_table. In this table, coiled-coil assemblies are arranged in columns with increasing numbers of alpha-helices and in rows of increased complexity. The table provides a framework for understanding possibilities in and limits on coiled-coil structures and a basis for future prediction, engineering and design studies.

The solar dynamic radiator with a historical perspective

NASA Technical Reports Server (NTRS)

Mclallin, K. L.; Fleming, M. L.; Hoehn, F. W.; Howerton, R. L.

1988-01-01

A historical perspective on pumped-fluid loop space radiators provides a basis for the design of the Space Station Solar Dynamic (SD) power module radiator. SD power modules, capable of generating 25 kW (electrical) each, are planned for growth in Station power requirements. The Brayton cycle SD module configuration incorporates a pumped-fluid loop radiator that must reject up to 99 kW (thermal). The thermal/hydraulic design conditions in combination with required radiator orientation and packaging envelope form a unique set of constraints as compared to previous pumped-fluid loop radiator systems. Nevertheless, past program successes have demonstrated a technology base that can be applied to the SD radiator development program to ensure a low risk, low cost system.

Computational investigation of rearrangements in huisgen cycloadducts of azolium N-dicyanomethanide 1,3-dipoles with alkynes: a mechanistic panoply.

PubMed

Burke, Luke A; Butler, Richard N

2009-08-07

The reaction surfaces leading to rearrangements and ring expansions of azapentalene cycloadducts of imidazolo- and triazolodicyanomethanide 1,3-dipoles with alkynes are studied with the B3LYP DFT method using the 6-31G(d) and 6-311+G(2d,p) basis sets. The surprisingly complex surface involves (1) consecutive but not combined pericyclic steps, a coarctate TS, and pseudopericyclic mechanisms, (2) anchimerically assisted H-atom transfer competing effectively with concerted symmetry-allowed sigmatropic steps, and (3) azolium methanide zwitterions and ketenimines as key intermediates. The azolium methanide is identified as the intermediate detected previously in a variable-temperature NMR experiment that converted the unstable cycloadduct to product imine.

Modular thrust subsystem approaches to solar electric propulsion module design

NASA Technical Reports Server (NTRS)

Cake, J. E.; Sharp, G. R.; Oglebay, J. C.; Shaker, F. J.; Zavesky, R. J.

1976-01-01

Three approaches are presented for packaging the elements of a 30 cm ion thruster subsystem into a modular thrust subsystem. The individual modules, when integrated into a conceptual solar electric propulsion module are applicable to a multimission set of interplanetary flights with the space shuttle interim upper stage as the launch vehicle. The emphasis is on the structural and thermal integration of the components into the modular thrust subsystems. Thermal control for the power processing units is either by direct radiation through louvers in combination with heat pipes or an all heat pipe system. The propellant storage and feed system and thruster gimbal system concepts are presented. The three approaches are compared on the basis of mass, cost, testing, interfaces, simplicity, reliability, and maintainability.

Modular thrust subsystem approaches to solar electric propulsion module design

NASA Technical Reports Server (NTRS)

Cake, J. E.; Sharp, G. R.; Oglebay, J. C.; Shaker, F. J.; Zevesky, R. J.

1976-01-01

Three approaches are presented for packaging the elements of a 30 cm ion thrustor subsystem into a modular thrust subsystem. The individual modules, when integrated into a conceptual solar electric propulsion module are applicable to a multimission set of interplanetary flights with the Space Shuttle/Interim Upper Stage as the launch vehicle. The emphasis is on the structural and thermal integration of the components into the modular thrust subsystems. Thermal control for the power processing units is either by direct radiation through louvers in combination with heat pipes of an all heat pipe system. The propellant storage and feed system and thrustor gimbal system concepts are presented. The three approaches are compared on the basis of mass, cost, testing, interfaces, simplicity, reliability, and maintainability.

Proposal of a skin tests based approach for the prevention of recurrent hypersensitivity reactions to iodinated contrast media.

PubMed

Della-Torre, E; Berti, A; Yacoub, M R; Guglielmi, B; Tombetti, E; Sabbadini, M G; Voltolini, S; Colombo, G

2015-05-01

The purpose of the present work is to evaluate the efficacy of an approach that combines clinical history, skin tests results, and premedication, in preventing recurrent hypersensitivity reactions to iodinated contrast media (ICM). Skin Prick tests, Intradermal tests, and Patch tests were performed in 36 patients with a previous reaction to ICM. All patients underwent a second contrast enhanced radiological procedure with an alternative ICM selected on the basis of the proposed approach. After alternative ICM re-injection, only one patient presented a mild NIR. The proposed algorithm, validated in clinical settings where repeated radiological exams are needed, offers a safe and practical approach for protecting patients from recurrent hypersensitivity reactions to ICM.

Structural, spectral and NBO analysis of 3-(1-(3-hydroxypropylamino)ethylidene)chroman-2,4-dione

NASA Astrophysics Data System (ADS)

Avdović, Edina H.; Milenković, Dejan; Dimitrić-Marković, Jasmina M.; Vuković, Nenad; Trifunović, Srećko R.; Marković, Zoran

2017-11-01

The structure of the newly synthesized coumarin derivative, 3-(1-(3-hydroxypropylamino)-ethylidene)-chroman-2,4-dione, was investigated experimentally and theoretically. FTIR, 1H and 13C NMR spectroscopic methods along with the density functional theory calculations, with B3LYP functional (and with empirical dispersion corrections D3BJ) in combination with the 6-311+G(d,p) basis set, are performed in order to characterize the molecular structure and spectroscopic behavior of the investigated coumarin derivative. Molecular docking analysis was carried out in order to identify the potency of inhibition of the title molecule against human C-reactive protein. The inhibition activity was obtained for ten conformations of ligand inside protein.

Modeling the Losses of Dissolved CO(2) from Laser-Etched Champagne Glasses.

PubMed

Liger-Belair, Gérard

2016-04-21

Under standard champagne tasting conditions, the complex interplay between the level of dissolved CO2 found in champagne, its temperature, the glass shape, and the bubbling rate definitely impacts champagne tasting by modifying the neuro-physicochemical mechanisms responsible for aroma release and flavor perception. On the basis of theoretical principles combining heterogeneous bubble nucleation, ascending bubble dynamics, and mass transfer equations, a global model is proposed, depending on various parameters of both the wine and the glass itself, which quantitatively provides the progressive losses of dissolved CO2 from laser-etched champagne glasses. The question of champagne temperature was closely examined, and its role on the modeled losses of dissolved CO2 was corroborated by a set of experimental data.

Modeling global vector fields of chaotic systems from noisy time series with the aid of structure-selection techniques.

PubMed

Xu, Daolin; Lu, Fangfang

2006-12-01

We address the problem of reconstructing a set of nonlinear differential equations from chaotic time series. A method that combines the implicit Adams integration and the structure-selection technique of an error reduction ratio is proposed for system identification and corresponding parameter estimation of the model. The structure-selection technique identifies the significant terms from a pool of candidates of functional basis and determines the optimal model through orthogonal characteristics on data. The technique with the Adams integration algorithm makes the reconstruction available to data sampled with large time intervals. Numerical experiment on Lorenz and Rossler systems shows that the proposed strategy is effective in global vector field reconstruction from noisy time series.

The Molecular Structure of cis-FONO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

Vibrational spectroscopic analysis of 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione.

PubMed

Soliman, H S; Eid, Kh M; Ali, H A M; Atef, S M; El-Mansy, M A M

2012-11-01

In the present work, a combined experimental and computational study for the optimized molecular structural parameters, FT-IR spectra, thermo-chemical parameters, total dipole moment and HOMO-LUMO energy gap for 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione have been investigated using B3LYP/6-311G basis set. Our calculated results have showed that the investigated compound possesses a dipole moment of 4.9 Debye and HOMO-LUMO energy gap of 3 eV which indicate high recommendations for photovoltaic devices fabrication. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Theoretical calculations of Electron Paramagnetic Resonance parameters of liquid phase Orotic acid radical

NASA Astrophysics Data System (ADS)

Sarikaya, Ebru Karakaş; Dereli, Ömer

2017-02-01

To obtain liquid phase molecular structure, conformational analysis of Orotic acid was performed and six conformers were determined. For these conformations, eight possible radicals were modelled by using Density Functional Theory computations with respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were performed using Becke's three-parameter hybrid-exchange functional combined with the Lee-Yang-Parr correlation functional of Density Functional Theory and 6-311++G(d,p) basis sets in p-dioxane solution. Because Orotic acid can be mutagenic in mammalian somatic cells and it is also mutagenic for bacteria and yeast, it has been studied.

Seasonality in malaria transmission: implications for case-management with long-acting artemisinin combination therapy in sub-Saharan Africa.

PubMed

Cairns, Matthew E; Walker, Patrick G T; Okell, Lucy C; Griffin, Jamie T; Garske, Tini; Asante, Kwaku Poku; Owusu-Agyei, Seth; Diallo, Diadier; Dicko, Alassane; Cisse, Badara; Greenwood, Brian M; Chandramohan, Daniel; Ghani, Azra C; Milligan, Paul J

2015-08-19

Long-acting artemisinin-based combination therapy (LACT) offers the potential to prevent recurrent malaria attacks in highly exposed children. However, it is not clear where this advantage will be most important, and deployment of these drugs is not rationalized on this basis. To understand where post-treatment prophylaxis would be most beneficial, the relationship between seasonality, transmission intensity and the interval between malaria episodes was explored using data from six cohort studies in West Africa and an individual-based malaria transmission model. The total number of recurrent malaria cases per 1000 child-years at risk, and the fraction of the total annual burden that this represents were estimated for sub-Saharan Africa. In settings where prevalence is less than 10 %, repeat malaria episodes constitute a small fraction of the total burden, and few repeat episodes occur within the window of protection provided by currently available drugs. However, in higher transmission settings, and particularly in high transmission settings with highly seasonal transmission, repeat malaria becomes increasingly important, with up to 20 % of the total clinical burden in children estimated to be due to repeat episodes within 4 weeks of a prior attack. At a given level of transmission intensity and annual incidence, the concentration of repeat malaria episodes in time, and consequently the protection from LACT is highest in the most seasonal areas. As a result, the degree of seasonality, in addition to the overall intensity of transmission, should be considered by policy makers when deciding between ACT that differ in their duration of post-treatment prophylaxis.

Ethical considerations in HIV prevention and vaccine research in resource-limited settings.

PubMed

Garner, Samual A; Anude, Chuka J; Adams, Elizabeth; Dawson, Liza

2014-09-01

HIV prevention research has been facing increasing ethical and operational challenges. Factors influencing the design and conduct of HIV prevention trials include a rapidly changing evidence base, new biomedical prevention methods and modalities being tested, a large diversity of countries, sites and populations affected by HIV and participating in trials, and challenges of developing and making available products that will be feasible and affordable for at-risk populations. To discuss these challenges, a meeting, Ethical considerations around novel combination prevention modalities in HIV prevention and vaccine trials in resource-limited settings, was convened by NIH/NIAID/Division of AIDS on April 22-23, 2013. Several themes emerged from the meeting: (1) because of both trial design and ethical complexities, choosing prevention packages and designing combination prevention research trials will need to be evaluated on a case by case basis in different clinical trials, countries, and health systems; (2) multilevel stakeholder engagement from the beginning is vital to a fair and transparent process and also to designing ethical and relevant trials; (3) research should generally be responsive to a host country's needs, and sponsors and stakeholders should work together to address potential barriers to future access; and finally, (4) another meeting including a broader group of stakeholders is needed to address many of the outstanding ethical issues raised by this meeting. We offer an overview of the meeting and the key discussion points and recommendations to help guide the design and conduct of future HIV prevention and vaccine research in resource-limited settings.

Non-invasive prediction of hemoglobin levels by principal component and back propagation artificial neural network

PubMed Central

Ding, Haiquan; Lu, Qipeng; Gao, Hongzhi; Peng, Zhongqi

2014-01-01

To facilitate non-invasive diagnosis of anemia, specific equipment was developed, and non-invasive hemoglobin (HB) detection method based on back propagation artificial neural network (BP-ANN) was studied. In this paper, we combined a broadband light source composed of 9 LEDs with grating spectrograph and Si photodiode array, and then developed a high-performance spectrophotometric system. By using this equipment, fingertip spectra of 109 volunteers were measured. In order to deduct the interference of redundant data, principal component analysis (PCA) was applied to reduce the dimensionality of collected spectra. Then the principal components of the spectra were taken as input of BP-ANN model. On this basis we obtained the optimal network structure, in which node numbers of input layer, hidden layer, and output layer was 9, 11, and 1. Calibration and correction sample sets were used for analyzing the accuracy of non-invasive hemoglobin measurement, and prediction sample set was used for testing the adaptability of the model. The correlation coefficient of network model established by this method is 0.94, standard error of calibration, correction, and prediction are 11.29g/L, 11.47g/L, and 11.01g/L respectively. The result proves that there exist good correlations between spectra of three sample sets and actual hemoglobin level, and the model has a good robustness. It is indicated that the developed spectrophotometric system has potential for the non-invasive detection of HB levels with the method of BP-ANN combined with PCA. PMID:24761296