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.
Rossi, Tuomas P. Sakko, Arto; Puska, Martti J.; Lehtola, Susi; Nieminen, Risto M.
2015-03-07
We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.
Anacker, Tony; Hill, J Grant; Friedrich, Joachim
2016-04-21
Minimal basis sets, denoted DSBSenv, based on the segmented basis sets of Ahlrichs and co-workers have been developed for use as environmental basis sets for the domain-specific basis set (DSBS) incremental scheme with the aim of decreasing the CPU requirements of the incremental scheme. The use of these minimal basis sets within explicitly correlated (F12) methods has been enabled by the optimization of matching auxiliary basis sets for use in density fitting of two-electron integrals and resolution of the identity. The accuracy of these auxiliary sets has been validated by calculations on a test set containing small- to medium-sized molecules. The errors due to density fitting are about 2-4 orders of magnitude smaller than the basis set incompleteness error of the DSBSenv orbital basis sets. Additional reductions in computational cost have been tested with the reduced DSBSenv basis sets, in which the highest angular momentum functions of the DSBSenv auxiliary basis sets have been removed. The optimized and reduced basis sets are used in the framework of the domain-specific basis set of the incremental scheme to decrease the computation time without significant loss of accuracy. The computation times and accuracy of the previously used environmental basis and that optimized in this work have been validated with a test set of medium- to large-sized systems. The optimized and reduced DSBSenv basis sets decrease the CPU time by about 15.4% and 19.4% compared with the old environmental basis and retain the accuracy in the absolute energy with standard deviations of 0.99 and 1.06 kJ/mol, respectively.
NASA Astrophysics Data System (ADS)
Bhardwaj, Piyush; Dasgupta, Bhaskar; Deb, Kalyanmoy
2014-07-01
In the past few years, multi-objective optimization algorithms have been extensively applied in several fields including engineering design problems. A major reason is the advancement of evolutionary multi-objective optimization (EMO) algorithms that are able to find a set of non-dominated points spread on the respective Pareto-optimal front in a single simulation. Besides just finding a set of Pareto-optimal solutions, one is often interested in capturing knowledge about the variation of variable values over the Pareto-optimal front. Recent innovization approaches for knowledge discovery from Pareto-optimal solutions remain as a major activity in this direction. In this article, a different data-fitting approach for continuous parameterization of the Pareto-optimal front is presented. Cubic B-spline basis functions are used for fitting the data returned by an EMO procedure in a continuous variable space. No prior knowledge about the order in the data is assumed. An automatic procedure for detecting gaps in the Pareto-optimal front is also implemented. The algorithm takes points returned by the EMO as input and returns the control points of the B-spline manifold representing the Pareto-optimal set. Results for several standard and engineering, bi-objective and tri-objective optimization problems demonstrate the usefulness of the proposed procedure.
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
NASA Astrophysics Data System (ADS)
Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.
2015-12-01
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.
2015-12-28
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
NASA Astrophysics Data System (ADS)
Gidopoulos, Nikitas I.; Lathiotakis, Nektarios N.
2013-10-01
The Comment by Friedrich does not dispute the central result of our paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052508 85, 052508 (2012)] that nonanalytic behavior is present in long-established mathematical pathologies arising in the solution of finite basis optimized effective potential (OEP) equations. In the Comment, the terms “balancing of basis sets” and “basis-set convergence” imply a particular order towards the limit of a large orbital basis sets where the large-orbital-base limit is always taken first, before the large-auxiliary-base limit, until overall convergence is achieved, at a high computational cost. The authors claim that, on physical grounds, this order of limits is not only sufficient, but also necessary in order to avoid the mathematical pathologies. In response to the Comment, we remark that it is already written in our paper that the nonanalyticity trivially disappears with large orbital basis sets. We point out that the authors of the Comment give an incorrect proof of this statement. We also show that the order of limits towards convergence of the potential is immaterial. A recent paper by the authors of the Comment proposes a partial correction for the incomplete orbital basis error in the full-potential linearized augmented-plane-wave method. Similar to the correction developed in our paper, this correction also benefits from an effectively complete orbital basis, even though only a finite orbital basis is employed in the calculation. This shows that it is unnecessary to take, in practice, the limit of an infinite orbital basis in order to avoid mathematical pathologies in the OEP. Our paper is a significant contribution in that direction with general applicability to any choice of basis sets. Finally, contrary to an allusion in the abstract and assertions in the main text of the Comment that unphysical oscillations of the OEP are supposedly attributed to the common energy denominator approximation, in fact, such
Optimal composition of atomic orbital basis sets for recovering static correlation energies.
Wallace, Andrew J; Crittenden, Deborah L
2014-03-20
Static correlation energies (Estat) are calculated in a range of basis sets for a chemically diverse collection of atoms and molecules. The reliability of a basis set in capturing Estat is assessed according to the following: mean and maximum absolute deviations from near-exact Estat estimates, monotonic convergence to the complete basis set limit, and ability to capture Estat accurately independent of changes in geometry, molecular size, and electronic configuration. Within the polarization and correlation-consistent basis set series, triple-ζ basis sets are the smallest that can reliably capture Estat. The cc-pVTZ basis set performs particularly well, recovering Estat to chemical accuracy for all atoms and molecules in our data set. A series of customized basis sets are constructed by stripping polarization functions from, and swapping polarization functions among, existing basis sets. Basis sets without polarization functions are incapable of accurately recovering Estat. Basis sets with a near-complete set of s, p, and d functions can approach chemical accuracy in maximum absolute error. However, this may be achieved at lower computational cost by using a well balanced triple-ζ basis set including f functions, along with a smaller number of s, p, and d functions. Recommended basis sets for calculating Estat with increasing accuracy at increasing computational cost are 6-311G(2d,2p), cc-pVTZ, and cc-pVQZ stripped of g functions.
Complete Basis Set Model Chemistries
NASA Astrophysics Data System (ADS)
Ochterski, Joseph Wallace
1994-01-01
The major source of error in most ab initio calculations of molecular energies is the truncation of the one-electron basis set. Extrapolation to the complete basis set second -order (CBS2) limit using the N^{-1 } asymptotic convergence of N-configuration pair natural orbital (PNO) expansions can be combined with the use of relatively small basis sets for the higher-order correlation energy to develop cost effective computational models. Following this strategy, four new computational models denoted CBS-4, CBS-q, CBS-Q, and CBS-QCI/APNO are introduced. The mean absolute deviations (MAD) from experiment for the 125 energies of the G2 test set are 2.0, 1.7, 1.0 and 0.5 kcal/mol, respectively. The error distributions for all six models are indistinguishable from Gaussian distribution functions. Calculations on the cyclopropenyl radical and cyclopropenylidene provide new dissociation energies which are in accord with an interpretation of the thermochemistry emphasizing aromaticity. Several levels of theory are examined as candidates for the routine calculation of molecular geometries. The very simple UHF/3-21G* model gives bond lengths to an accuracy of +/-0.027 A compared with experiment for a test set of 69 small molecules. The commonly used MP2/6-31G* model (RMS error 0.025 A) offers virtually no improvement and use of the considerably more expensive QCISD calculations with the same basis set provides only a modest reduction to 0.020 A. However, spin projected MP3 calculations with a modified basis set including f -functions on Si, P, S, and Cl, reduce the RMS error to 0.010 A. This PMP3/6-31Gdf* model is recommended as a general scheme of geometry optimization for small molecules. The equilibrium structure and binding energy of the water dimer have been determined for several levels of ab initio theory. The basis set convergence of the SCF energy, the intramolecular and intermolecular MP2 energy, and higher-order effects, are examined separately and realistic error
López Arvizu, Gregorio; Calaminici, Patrizia
2007-05-21
Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (n
Rocca, Dario
2014-05-14
A new ab initio approach is introduced to compute the correlation energy within the adiabatic connection fluctuation dissipation theorem in the random phase approximation. First, an optimally small basis set to represent the response functions is obtained by diagonalizing an approximate dielectric matrix containing the kinetic energy contribution only. Then, the Lanczos algorithm is used to compute the full dynamical dielectric matrix and the correlation energy. The convergence issues with respect to the number of empty states or the dimension of the basis set are avoided and the dynamical effects are easily kept into account. To demonstrate the accuracy and efficiency of this approach the binding curves for three different configurations of the benzene dimer are computed: T-shaped, sandwich, and slipped parallel.
Feller, D; Schuchardt, Karen L.; Didier, Brett T.; Elsethagen, Todd; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared; Li, Jun
The Basis Set Exchange (BSE) provides a web-based user interface for downloading and uploading Gaussian-type (GTO) basis sets, including effective core potentials (ECPs), from the EMSL Basis Set Library. It provides an improved user interface and capabilities over its predecessor, the EMSL Basis Set Order Form, for exploring the contents of the EMSL Basis Set Library. The popular Basis Set Order Form and underlying Basis Set Library were originally developed by Dr. David Feller and have been available from the EMSL webpages since 1994. BSE not only allows downloading of the more than 500 Basis sets in various formats; it allows users to annotate existing sets and to upload new sets. (Specialized Interface)
Goerigk, Lars; Collyer, Charles A; Reimers, Jeffrey R
2014-12-18
We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.
Wu, Anan; Xu, Xin
2012-06-15
We present a method, named DCMB, for the calculations of large molecules. It is a combination of a parallel divide-and-conquer (DC) method and a mixed-basis (MB) set scheme. In this approach, atomic forces, total energy and vibrational frequencies are obtained from a series of MB calculations, which are derived from the target system utilizing the DC concept. Unlike the fragmentation based methods, all DCMB calculations are performed over the whole target system and no artificial caps are introduced so that it is particularly useful for charged and/or delocalized systems. By comparing the DCMB results with those from the conventional method, we demonstrate that DCMB is capable of providing accurate prediction of molecular geometries, total energies, and vibrational frequencies of molecules of general interest. We also demonstrate that the high efficiency of the parallel DCMB code holds the promise for a routine geometry optimization of large complex systems.
Harrison, Amabilis H; Noseworthy, Michael D; Reilly, James P; Connolly, John F
2014-01-01
Electroencephalography data recorded during functional magnetic resonance imaging acquisition are subject to large cardiac-related artifacts that must be corrected during postprocessing. This study compared two widely used ballistocardiogram (BCG) correction algorithms as implemented in two software programs. Reduction of BCG amplitude, correlation of corrected data with electrocardiogram traces, correlation of independent components with electrocardiogram traces, and event-related potential signal-to-noise ratio from each algorithm were compared. Both algorithms effectively reduced the BCG artifact, with a slight advantage of average artifact subtraction over the optimal basis set method (0.1-2.2%) when the quality of the correction was examined at the individual subject level. This study provides users of these software tools with an important, practical, and previously unavailable comparison of the performance of these two methods.
Spackman, Peter R.; Karton, Amir
2015-05-15
Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.
Wu, Xia; Wu, Tong; Zhan, Zhichao; Yao, Li; Wen, Xiaotong
2016-04-01
The simultaneous acquisition of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) provides both high temporal and spatial resolution when measuring brain activity. A real-time analysis during a simultaneous EEG-fMRI acquisition is essential when studying neurofeedback and conducting effective brain activity monitoring. However, the ballistocardiogram (BCG) artifacts which are induced by heartbeat-related electrode movements in an MRI scanner severely contaminate the EEG signals and hinder a reliable real-time analysis. The optimal basis sets (OBS) method is an effective candidate for removing BCG artifacts in a traditional offline EEG-fMRI analysis, but has yet to be applied to a real-time EEG-fMRI analysis. Here, a novel real-time technique based on OBS method (rtOBS) is proposed to remove BCG artifacts on a moment-to-moment basis. Real-time electrocardiogram R-peak detection procedure and sliding window OBS method were adopted. A series of simulated data was constructed to verify the feasibility of the rtOBS technique. Furthermore, this method was applied to real EEG-fMRI data to remove BCG artifacts. The results of both simulated data and real EEG-fMRI data from eight healthy human subjects demonstrate the effectiveness of rtOBS in both the time and frequency domains. A comparison between rtOBS and real-time averaged artifact subtraction (rtAAS) was conducted. The results suggest the efficacy and advantage of rtOBS in the real-time removal of BCG artifacts. In this study, a novel real-time OBS technique was proposed for the real-time removal of BCG artifacts. The proposed method was tested using simulated data and applied to real simultaneous EEG-fMRI data. The results suggest the effectiveness of this method. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Provasi, Patricio F; Sauer, Stephan P A
2010-08-07
The aug-cc-pVTZ-J series of basis sets for indirect nuclear spin-spin coupling constants has been extended to the atoms B, Al, Si, P, and Cl. The basis sets were obtained according to the scheme previously described by Provasi et al. [J. Chem. Phys. 115, 1324 (2001)]. First, the completely uncontracted correlation consistent aug-cc-pVTZ basis sets were extended with four tight s and three tight d functions. Second, the s and p basis functions were contracted with the molecular orbital coefficients of self-consistent-field calculations performed with the uncontracted basis sets on the simplest hydrides of each atom. As a first illustration, we have calculated the one-bond indirect spin-spin coupling constants in BH(4)(-), BF, AlH, AlF, SiH(4), SiF(4), PH(3), PF(3), H(2)S, SF(6), HCl, and ClF at the level of density functional theory using the Becke three parameter Lee-Yang-Parr and the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes.
Basis set dependence of the doubly hybrid XYG3 functional
NASA Astrophysics Data System (ADS)
Zhang, Igor Ying; Luo, Yi; Xu, Xin
2010-09-01
In the present study, we investigated the basis set dependence of XYG3, a newly developed doubly hybrid functional [Y. Zhang, X. Xu, and W. A. Goddard III, Proc. Natl. Acad. Sci. U.S.A. 106, 4963 (2009)], in prediction of (1) heats of formation (HOFs), (2) bond dissociation enthalpies (BDEs), (3) reaction barrier heights (RBHs), and (4) nonbonded interactions (NBIs). We used basis sets of triple-zeta quality starting from 6-311+G(d,p) with increasing completeness of the polarization functions to the largest Pople-type basis set 6-311++G(3df,3pd) and found that there was a continued improvement with larger basis sets. We showed that while HOF predictions were prone to basis set deficiencies, the basis set dependences in calculating BDEs, RBHs, and NBIs were mild. All of them converged fast with the increase of basis set size. We extended XYG3 to propose the XYG3o functional which was specifically optimized for a particular basis set in order to enhance its performance when using basis set of moderate size. With the 6-311+G(2df,p) basis set, XYG3o led to MADs of 2.56 kcal/mol for HOFs of the G3/99 set, 1.17 kcal/mol for BDEs of the BDE92/07 set, 1.11 kcal/mol for RBHs of the NHTBH38/04 and HTBH38/04 sets, and 0.40 kcal/mol for NBIs of the NCIE31/05 set, being comparable to those obtained by using XYG3/6-311++G(3df,3pd).
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.
Accurate basis set truncation for wavefunction embedding
NASA Astrophysics Data System (ADS)
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
Chopped random-basis quantum optimization
Caneva, Tommaso; Calarco, Tommaso; Montangero, Simone
2011-08-15
In this work, we describe in detail the chopped random basis (CRAB) optimal control technique recently introduced to optimize time-dependent density matrix renormalization group simulations [P. Doria, T. Calarco, and S. Montangero, Phys. Rev. Lett. 106, 190501 (2011)]. Here, we study the efficiency of this control technique in optimizing different quantum processes and we show that in the considered cases we obtain results equivalent to those obtained via different optimal control methods while using less resources. We propose the CRAB optimization as a general and versatile optimal control technique.
Shaw, Robert A; Hill, J Grant
2017-03-08
Auxiliary basis sets for use in the resolution of the identity (RI) approximation in explicitly correlated methods are presented for the elements H-Ar. These extend the cc-pVnZ-F12/OptRI (n = D-Q) auxiliary basis sets of Peterson and co-workers by the addition of a small number of s- and p-functions, optimized so as to yield the greatest complementary auxiliary basis set (CABS) singles correction to the Hartree-Fock energy. The new sets, denoted OptRI+, also lead to a reduction in errors due to the RI approximation and hence an improvement in correlation energies. The atomization energies and heats of formation for a test set of small molecules, and spectroscopic constants for 27 diatomics, calculated at the CCSD(T)-F12b level, are shown to have improved error distributions for the new auxiliary basis sets with negligible additional effort. The OptRI+ sets retain all of the desirable properties of the original OptRI, including the production of smooth potential energy surfaces, while maintaining a compact nature.
Entanglement patterns in mutually unbiased basis sets
Lawrence, Jay
2011-08-15
A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=p{sup N}), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (p{sup N}-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (p{sup N}-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.
Atomic Natural Orbital Basis Sets for Transition Metals
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Taylor, Peter R.
1993-01-01
We show that atomic natural orbitals are an excellent way to contract transition-metal basis sets, even though the different low-lying electronic states may have very different basis set requirements.
Basis Set Exchange: A Community Database for Computational Sciences
Schuchardt, Karen L.; Didier, Brett T.; Elsethagen, Todd O.; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared M.; Li, Jun; Windus, Theresa L.
2007-05-01
Basis sets are one of the most important input data for computational models in the chemistry, materials, biology and other science domains that utilize computational quantum mechanics methods. Providing a shared, web accessible environment where researchers can not only download basis sets in their required format, but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.
Hill, J Grant; Platts, James A
2009-03-10
Auxiliary basis sets for use in density fitting second-order Møller-Plesset perturbation theory and other correlated ab initio methods have been developed for the 4d transition metal elements Y-Tc and Rh-Pd (sets for Ru, Ag, and Cd are already available), to be used in conjunction with the correlation consistent basis sets with pseudopotentials cc-pVnZ-PP and aug-cc-pVnZ-PP. Correlation energy calculations for a test set of small- to medium-sized transition metal complexes encompassing a variety of oxidation states show that the error in using these auxiliary basis sets is around 3-4 orders of magnitude smaller than the error due to orbital basis set size. The effect of truncating the auxiliary basis sets to remove higher angular momentum functions is also considered.
Optimality for set-valued optimization in the sense of vector and set criteria.
Kong, Xiangyu; Yu, GuoLin; Liu, Wei
2017-01-01
The vector criterion and set criterion are two defining approaches of solutions for the set-valued optimization problems. In this paper, the optimality conditions of both criteria of solutions are established for the set-valued optimization problems. By using Studniarski derivatives, the necessary and sufficient optimality conditions are derived in the sense of vector and set optimization.
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.
Localized basis sets for unbound electrons in nanoelectronics.
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.
Hill, J Grant
2011-07-28
Auxiliary basis sets specifically matched to the correlation consistent cc-pVnZ-PP, cc-pwCVnZ-PP, aug-cc-pVnZ-PP, and aug-cc-pwCVnZ-PP orbital basis sets (used in conjunction with pseudopotentials) for the 5d transition metal elements Hf-Pt have been optimized for use in density fitting second-order Møller-Plesset perturbation theory and other correlated ab initio methods. Calculations of the second-order Møller-Plesset perturbation theory correlation energy, for a test set of small to medium sized molecules, indicate that the density fitting error when utilizing these sets is negligible at three to four orders of magnitude smaller than the orbital basis set incompleteness error. © 2011 American Institute of Physics
Hill, J Grant; Peterson, Kirk A
2014-09-07
New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga-Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of the spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.
Claudot, Julien; Lebègue, Sébastien; Rocca, Dario
2017-01-01
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. PMID:28595409
NASA Astrophysics Data System (ADS)
Dixit, Anant; Claudot, Julien; Lebègue, Sébastien; Rocca, Dario
2017-06-01
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.
Point Set Denoising Using Bootstrap-Based Radial Basis Function.
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.
Accurate universal Gaussian basis set for all atoms of the Periodic Table
NASA Astrophysics Data System (ADS)
de Castro, E. V. R.; Jorge, F. E.
1998-04-01
We have applied a discretized version of the generator coordinate Hartree-Fock method to generate a universal Gaussian basis set for the atoms from H through Lr. In general, for He to Rn the ground state Hartree-Fock total energy results obtained with our universal Gaussian basis set are lower than the corresponding ones obtained by Clementi et al. using larger atom-optimized geometrical Gaussian basis sets. For the atoms from H through Lr we have obtained ground state energy values with at least seven digits of accuracy (except for Pm, with six digits), in comparison with the corresponding ten digits of the numerical Hartree-Fock total energy results.
Accurate extrapolation of electron correlation energies from small basis sets.
Bakowies, Dirk
2007-10-28
A new two-point scheme is proposed for the extrapolation of electron correlation energies obtained with small basis sets. Using the series of correlation-consistent polarized valence basis sets, cc-pVXZ, the basis set truncation error is expressed as deltaE(X) proportional, variant(X + xi(i))(-gamma). The angular momentum offset xi(i) captures differences in effective rates of convergence previously observed for first-row molecules. It is based on simple electron counts and tends to values close to 0 for hydrogen-rich compounds and values closer to 1 for pure first-row compounds containing several electronegative atoms. The formula is motivated theoretically by the structure of correlation-consistent basis sets which include basis functions up to angular momentum L = X-1 for hydrogen and helium and up to L = X for first-row atoms. It contains three parameters which are calibrated against a large set of 105 reference molecules (H, C, N, O, F) for extrapolations of MP2 and CCSD valence-shell correlation energies from double- and triple-zeta (DT) and triple- and quadruple-zeta (TQ) basis sets. The new model is shown to be three to five times more accurate than previous two-point schemes using a single parameter, and (TQ) extrapolations are found to reproduce a small set of available R12 reference data better than even (56) extrapolations using the conventional asymptotic limit formula deltaE(X) proportional, variantX(-3). Applications to a small selection of boron compounds and to neon show very satisfactory results as well. Limitations of the model are discussed.
A new basis set for molecular bending degrees of freedom
NASA Astrophysics Data System (ADS)
Jutier, Laurent
2010-07-01
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 θ ɛ[0:π]. 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.
Accurate Coulomb-fitting basis sets for H to Rn.
Weigend, Florian
2006-03-07
A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented. For each element only one auxiliary basis set is needed to approximate Coulomb energies in conjunction with orbital basis sets of split valence, triple zeta valence and quadruple zeta valence quality with errors of typically below ca. 0.15 kJ mol(-1) per atom; this was demonstrated in conjunction with the recently developed orbital basis sets of types def2-SV(P), def2-TZVP and def2-QZVPP for a large set of small molecules representing (nearly) each element in all of its common oxidation states. These auxiliary bases are slightly more than three times larger than orbital bases of split valence quality. Compared to non-approximated treatments, computation times for the Coulomb part are reduced by a factor of ca. 8 for def2-SV(P) orbital bases, ca. 25 for def2-TZVP and ca. 100 for def2-QZVPP orbital bases.
Improved Segmented All-Electron Relativistically Contracted Basis Sets for the Lanthanides.
Aravena, Daniel; Neese, Frank; Pantazis, Dimitrios A
2016-03-08
Improved versions of the segmented all-electron relativistically contracted (SARC) basis sets for the lanthanides are presented. The second-generation SARC2 basis sets maintain efficient construction of their predecessors and their individual adaptation to the DKH2 and ZORA Hamiltonians, but feature exponents optimized with a completely new orbital shape fitting procedure and a slightly expanded f space that results in sizable improvement in CASSCF energies and in significantly more accurate prediction of spin-orbit coupling parameters. Additionally, an extended set of polarization/correlation functions is constructed that is appropriate for multireference correlated calculations and new auxiliary basis sets for use in resolution-of-identity (density-fitting) approximations in combination with both DFT and wave function based treatments. Thus, the SARC2 basis sets extend the applicability of the first-generation DFT-oriented basis sets to routine all-electron wave function-based treatments of lanthanide complexes. The new basis sets are benchmarked with respect to excitation energies, radial distribution functions, optimized geometries, orbital eigenvalues, ionization potentials, and spin-orbit coupling parameters of lanthanide systems and are shown to be suitable for the description of magnetic and spectroscopic properties using both DFT and multireference wave function-based methods.
The Neural Basis of Optimism and Pessimism
2013-01-01
Our survival and wellness require a balance between optimism and pessimism. Undue pessimism makes life miserable; however, excessive optimism can lead to dangerously risky behaviors. A review and synthesis of the literature on the neurophysiology subserving these two worldviews suggests that optimism and pessimism are differentially associated with the two cerebral hemispheres. High self-esteem, a cheerful attitude that tends to look at the positive aspects of a given situation, as well as an optimistic belief in a bright future are associated with physiological activity in the left-hemisphere (LH). In contrast, a gloomy viewpoint, an inclination to focus on the negative part and exaggerate its significance, low self-esteem as well as a pessimistic view on what the future holds are interlinked with neurophysiological processes in the right-hemisphere (RH). This hemispheric asymmetry in mediating optimistic and pessimistic outlooks is rooted in several biological and functional differences between the two hemispheres. The RH mediation of a watchful and inhibitive mode weaves a sense of insecurity that generates and supports pessimistic thought patterns. Conversely, the LH mediation of an active mode and the positive feedback it receives through its motor dexterity breed a sense of confidence in one's ability to manage life's challenges, and optimism about the future. PMID:24167413
The neural basis of optimism and pessimism.
Hecht, David
2013-09-01
Our survival and wellness require a balance between optimism and pessimism. Undue pessimism makes life miserable; however, excessive optimism can lead to dangerously risky behaviors. A review and synthesis of the literature on the neurophysiology subserving these two worldviews suggests that optimism and pessimism are differentially associated with the two cerebral hemispheres. High self-esteem, a cheerful attitude that tends to look at the positive aspects of a given situation, as well as an optimistic belief in a bright future are associated with physiological activity in the left-hemisphere (LH). In contrast, a gloomy viewpoint, an inclination to focus on the negative part and exaggerate its significance, low self-esteem as well as a pessimistic view on what the future holds are interlinked with neurophysiological processes in the right-hemisphere (RH). This hemispheric asymmetry in mediating optimistic and pessimistic outlooks is rooted in several biological and functional differences between the two hemispheres. The RH mediation of a watchful and inhibitive mode weaves a sense of insecurity that generates and supports pessimistic thought patterns. Conversely, the LH mediation of an active mode and the positive feedback it receives through its motor dexterity breed a sense of confidence in one's ability to manage life's challenges, and optimism about the future.
Szalay, Viktor
2006-10-21
The method of optimal generalized finite basis and discrete variable representations (FBR and DVR) generalizes the standard, Gaussian quadrature grid-classical orthonormal polynomial basis-based FBR/DVR method to general sets of grid points and to general, nondirect product, and/or nonpolynomial bases. Here, it is shown how an optimal set of grid points can be obtained for an optimal generalized FBR/DVR calculation with a given truncated basis. Basis set optimized and potential optimized grids are defined. The optimized grids are shown to minimize a function of grid points derived by relating the optimal generalized FBR of a Hamiltonian operator to a non-Hermitian effective Hamiltonian matrix. Locating the global minimum of this function can be reduced to finding the zeros of a function in the case of one dimensional problems and to solving a system of D nonlinear equations repeatedly in the case of D>1 dimensional problems when there is an equal number of grid points and basis functions. Gaussian quadrature grids are shown to be basis optimized grids. It is demonstrated by a numerical example that an optimal generalized FBR/DVR calculation of the eigenvalues of a Hamiltonian operator with potential optimized grids can have orders of magnitude higher accuracy than a variational calculation employing the same truncated basis. Nevertheless, for numerical integration with the optimal generalized FBR quadrature rule basis optimized grids are the best among grids of the same number of points. The notions of Gaussian quadrature and Gaussian quadrature accuracy are extended to general, multivariable basis functions.
NASA Astrophysics Data System (ADS)
Balabin, Roman M.
2011-03-01
The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.
Scar Functions, Barriers for Chemical Reactivity, and Vibrational Basis Sets.
Revuelta, F; Vergini, E; Benito, R M; Borondo, F
2016-07-14
The performance of a recently proposed method to efficiently calculate scar functions is analyzed in problems of chemical interest. An application to the computation of wave functions associated with barriers relevant for the LiNC ⇄ LiCN isomerization reaction is presented as an illustration. These scar functions also constitute excellent elements for basis sets suitable for quantum calculation of vibrational energy levels. To illustrate their efficiency, a calculation of the LiNC/LiCN eigenfunctions is also presented.
NASA Astrophysics Data System (ADS)
Spackman, Peter R.; Jayatilaka, Dylan; Karton, Amir
2016-09-01
We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H—X, 49 X—Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ˜4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0
Spackman, Peter R; Jayatilaka, Dylan; Karton, Amir
2016-09-14
We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H-X, 49 X-Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ∼4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0.0019 (D
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).
Large Atomic Natural Orbital Basis Sets for the First Transition Row Atoms
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)
1994-01-01
Large atomic natural orbital (ANO) basis sets are tabulated for the Sc to Cu. The primitive sets are taken from the large sets optimized by Partridge, namely (21s 13p 8d) for Sc and Ti and (20s 12p 9d) for V to Cu. These primitive sets are supplemented with three p, one d, six f, and four g functions. The ANO sets are derived from configuration interaction density matrices constructed as the average of the lowest states derived from the 3d(sup n)4s(sup 2) and 3d(sup n+1)4s(sup 1) occupations. For Ni, the 1S(3d(sup 10)) state is included in the averaging. The choice of basis sets for molecular calculations is discussed.
Hellweg, Arnim; Rappoport, Dmitrij
2015-01-14
We report optimized auxiliary basis sets for use with the Karlsruhe segmented contracted basis sets including moderately diffuse basis functions (Rappoport and Furche, J. Chem. Phys., 2010, 133, 134105) in resolution-of-the-identity (RI) post-self-consistent field (post-SCF) computations for the elements H-Rn (except lanthanides). The errors of the RI approximation using optimized auxiliary basis sets are analyzed on a comprehensive test set of molecules containing the most common oxidation states of each element and do not exceed those of the corresponding unaugmented basis sets. During these studies an unsatisfying performance of the def2-SVP and def2-QZVPP auxiliary basis sets for Barium was found and improved sets are provided. We establish the versatility of the def2-SVPD, def2-TZVPPD, and def2-QZVPPD basis sets for RI-MP2 and RI-CC (coupled-cluster) energy and property calculations. The influence of diffuse basis functions on correlation energy, basis set superposition error, atomic electron affinity, dipole moments, and computational timings is evaluated at different levels of theory using benchmark sets and showcase examples.
Coupled-cluster based basis sets for valence correlation calculations
NASA Astrophysics Data System (ADS)
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via
The local electron affinity for non-minimal basis sets.
Clark, Timothy
2010-07-01
A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EA(L). Intensity filtering allows EA(L) to be calculated using semiempirical molecular orbital techniques that include polarisation functions. Without intensity filtering, such techniques yield spurious EA(L) values that are dominated by the polarisation functions. As intensity filtering should also be applicable for ab initio or density functional theory calculations with large basis sets, it also makes EA(L) available for these techniques.
Semiclassical basis sets for the computation of molecular vibrational states.
Revuelta, F; Vergini, E; Benito, R M; Borondo, F
2017-01-07
In this paper, we extend a method recently reported [F. Revuelta et al., Phys. Rev. E 87, 042921 (2013)] for the calculation of the eigenstates of classically highly chaotic systems to cases of mixed dynamics, i.e., those presenting regular and irregular motions at the same energy. The efficiency of the method, which is based on the use of a semiclassical basis set of localized wave functions, is demonstrated by applying it to the determination of the vibrational states of a realistic molecular system, namely, the LiCN molecule.
Gauge origin independence in finite basis sets and perturbation theory
NASA Astrophysics Data System (ADS)
Sørensen, Lasse Kragh; Lindh, Roland; Lundberg, Marcus
2017-09-01
We show that origin independence in finite basis sets for the oscillator strengths is possibly in any gauge contrary to what is stated in literature. This is proved from a discussion of the consequences in perturbation theory when the exact eigenfunctions and eigenvalues to the zeroth order Hamiltonian H0 cannot be found. We demonstrate that the erroneous conclusion for the lack of gauge origin independence in the length gauge stems from not transforming the magnetic terms in the multipole expansion leading to the use of a mixed gauge. Numerical examples of exact origin dependence are shown.
Optimal ratio between phase basis and bit basis in quantum key distributions
NASA Astrophysics Data System (ADS)
Hayashi, Masahito
2009-02-01
In the original Bennett-Brassard 1984 protocol, the bit basis and the phase basis are used with equal probability. Lo [J. Cryptology 18, 133 (2005)] proposed modifying the ratio between the two bases by increasing the final key generation rate. However, the optimum ratio has not yet been derived. In this Rapid Communication, in order to examine this problem, the ratio between the two bases is optimized for exponential constraints, given Eve’s information distinguishability and the final error probability.
Optimal Piecewise Linear Basis Functions in Two Dimensions
Brooks III, E D; Szoke, A
2009-01-26
We use a variational approach to optimize the center point coefficients associated with the piecewise linear basis functions introduced by Stone and Adams [1], for polygonal zones in two Cartesian dimensions. Our strategy provides optimal center point coefficients, as a function of the location of the center point, by minimizing the error induced when the basis function interpolation is used for the solution of the time independent diffusion equation within the polygonal zone. By using optimal center point coefficients, one expects to minimize the errors that occur when these basis functions are used to discretize diffusion equations, or transport equations in optically thick zones (where they approach the solution of the diffusion equation). Our optimal center point coefficients satisfy the requirements placed upon the basis functions for any location of the center point. We also find that the location of the center point can be optimized, but this requires numerical calculations. Curiously, the optimum center point location is independent of the values of the dependent variable on the corners only for quadrilaterals.
An efficient basis set representation for calculating electrons in molecules
Jones, Jeremiah R.; Rouet, Francois -Henry; Lawler, Keith V.; ...
2016-04-27
The method of McCurdy, Baertschy, and Rescigno, is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. Themore » calculation of contracted two-electron matrix elements among orbitals requires only O(Nlog (N)) multiplication operations, not O(N4), where N is the number of basis functions; N = n3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He+, H+2), 2- (H2, He), 10- (CH4), and 56-electron (C8H8) systems.« less
An efficient basis set representation for calculating electrons in molecules
Jones, Jeremiah R.; Rouet, Francois -Henry; Lawler, Keith V.; Vecharynski, Eugene; Ibrahim, Khaled Z.; Williams, Samuel; Abeln, Brant; Yang, Chao; McCurdy, William; Haxton, Daniel J.; Li, Xiaoye S.; Rescigno, Thomas N.
2016-04-27
The method of McCurdy, Baertschy, and Rescigno, is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O(Nlog (N)) multiplication operations, not O(N^{4}), where N is the number of basis functions; N = n^{3} on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He^{+}, H^{+}_{2}), 2- (H_{2}, He), 10- (CH_{4}), and 56-electron (C_{8}H_{8}) systems.
Roscioni, Otello M; Lee, Edmond P F; Dyke, John M
2012-10-05
We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium. They were also tested by computing the electronic ground state geometry and harmonic frequencies of [Rh(CO)(2) μ-Cl](2) , Rh(CO)(2) ClPy, and RhCO (neutral and its positive, and negative ions) as well as the enthalpy of the reaction of [Rh(CO)(2) μ-Cl](2) with pyridine (Py) to give Rh(CO)(2) ClPy, at different levels of theory. Good agreement with experimental values was obtained. Although the number of basis functions used in our ECP basis sets is smaller than those of other ECP basis sets of comparable quality, we show that the newly developed ECP basis sets provide the flexibility and precision required to reproduce a wide range of chemical and physical properties of rhodium compounds. Therefore, we recommend the use of these compact yet accurate ECP basis sets for electronic structure calculations on molecules involving rhodium atoms. Copyright © 2012 Wiley Periodicals, Inc.
Near Hartree-Fock quality Gaussian type orbital basis sets for the first- and third-row atoms
NASA Technical Reports Server (NTRS)
Partridge, Harry
1989-01-01
Energy-optimized, near Hartree-Fock (NHF) quality Gaussian type orbital (GTO) basis sets are reported for the second-row (Li to Ne) and fourth-row (K to Kr) atoms. The most accurate basis sets reported for the second row are (18s 13p) sets which are with 4 micro E(H) of the numerical Hartree-Fock (NHF) results. For B to Ne basis sets with more than 15s functions are quadruple zeta in the valence space. For the second-row transition metal atoms the (20s 12p 9d) basis sets are triple zeta in the valence space and are approximately equivalent to Clementi and Roetti's accurate Slater type orbital sets. Supplementing the (20s 12p 9d) basis sets optimized for the lowest state with the 4s(2)3d(n) occupation with a diffuse d function gives self-consistent-field energy separations to the 4s(1)3d(n+1) and 3d(n+2) states which are within 100 micro E(H) of the NHF results. The most accurate basis sets for the transition metal atoms are with 30 micro E(H) of the NHF results. In addition, energy optimized sets are reported for He(3P), Li(2P) and Be(3P).
NASA Astrophysics Data System (ADS)
Plascencia, Cesar; Wang, Jiaqi; Wilson, Angela K.
2017-10-01
The impact of basis set choice has been considered for a series of transition metal (TM) species. The need for higher level correlation consistent basis sets on both the metal and ligand has been investigated, and permutations in the pairings of basis set used for TM's and basis set used for ligands can lead to effective routes to complete basis set (CBS) limit extrapolations of thermochemical energetics with little change in thermochemical predictions as compared to those resulting from the use of traditional basis set pairings, while enabling computational cost savings. Basis set superposition errors (BSSE) that can arise have also been considered.
Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin
2016-07-28
Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.
NASA Astrophysics Data System (ADS)
Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin
2016-07-01
Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.
Hättig, Christof; Schmitz, Gunnar; Kossmann, Jörg
2012-05-14
We report optimised auxiliary basis sets for the resolution-of-the-identity (or density-fitting) approximation of two-electron integrals in second-order Møller-Plesset perturbation theory (MP2) and similar electronic structure calculations with correlation-consistent basis sets for the post-d elements Ga-Kr, In-Xe, and Tl-Rn. The auxiliary basis sets are optimised such that the density-fitting error is negligible compared to the one-electron basis set error. To check to which extent this criterion is fulfilled we estimated for a test set of 80 molecules the basis set limit of the correlation energy at the MP2 level and evaluated the remaining density-fitting and the one-electron basis set errors. The resulting auxiliary basis sets are only 2-6 times larger than the corresponding one-electron basis sets and lead in MP2 calculations to speed-ups of the integral evaluation by one to three orders of magnitude. The density-fitting errors in the correlation energy are at least hundred times smaller than the one-electron basis set error, i.e. in the order of only 1-100 μH per atom. This journal is © the Owner Societies 2012
Basis set expansion for inverse problems in plasma diagnostic analysis
NASA Astrophysics Data System (ADS)
Jones, B.; Ruiz, C. L.
2013-07-01
A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)], 10.1063/1.1482156 is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20-25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.
Basis set expansion for inverse problems in plasma diagnostic analysis
Jones, B.; Ruiz, C. L.
2013-07-15
A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)] is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20–25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.
First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.
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.
Behavior and neural basis of near-optimal visual search
Ma, Wei Ji; Navalpakkam, Vidhya; Beck, Jeffrey M; van den Berg, Ronald; Pouget, Alexandre
2013-01-01
The ability to search efficiently for a target in a cluttered environment is one of the most remarkable functions of the nervous system. This task is difficult under natural circumstances, as the reliability of sensory information can vary greatly across space and time and is typically a priori unknown to the observer. In contrast, visual-search experiments commonly use stimuli of equal and known reliability. In a target detection task, we randomly assigned high or low reliability to each item on a trial-by-trial basis. An optimal observer would weight the observations by their trial-to-trial reliability and combine them using a specific nonlinear integration rule. We found that humans were near-optimal, regardless of whether distractors were homogeneous or heterogeneous and whether reliability was manipulated through contrast or shape. We present a neural-network implementation of near-optimal visual search based on probabilistic population coding. The network matched human performance. PMID:21552276
NASA Astrophysics Data System (ADS)
Nikolaev, A. V.; Lamoen, D.; Partoens, B.
2016-07-01
In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the u ˙ l -component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.
Is there an optimal basis to maximise optical information transfer?
Chen, Mingzhou; Dholakia, Kishan; Mazilu, Michael
2016-01-01
We establish the concept of the density of the optical degrees of freedom that may be applied to any photonics based system. As a key example of this versatile approach we explore information transfer using optical communication. We demonstrate both experimentally, theoretically and numerically that the use of a basis set with fields containing optical vortices does not increase the telecommunication capacity of an optical system. PMID:26976626
Evaluation of Density Functionals and Basis Sets for Carbohydrates
USDA-ARS?s Scientific Manuscript database
Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...
Accurate Electron Densities at Nuclei Using Small Ramp-Gaussian Basis Sets.
McKemmish, Laura K; Gilbert, Andrew T B
2015-08-11
Electron densities at nuclei are difficult to calculate accurately with all-Gaussian basis sets because they lack an electron-nuclear cusp. The newly developed mixed ramp-Gaussian basis sets, such as R-31G, possess electron-nuclear cusps due to the presence of ramp functions in the basis. The R-31G basis set is a general-purpose mixed ramp-Gaussian basis set modeled on the 6-31G basis set. The prediction of electron densities at nuclei using R-31G basis sets for Li-F outperforms Dunning, Pople, and Jensen general purpose all-Gaussian basis sets of triple-ζ quality or lower and the cc-pVQZ basis set. It is of similar quality to the specialized pcJ-0 basis set which was developed with partial decontraction of core functions and extra high exponent s-Gaussians to predict electron density at the nucleus. These results show significant advantages in the properties of mixed ramp-Gaussian basis sets compared to all-Gaussian basis sets.
Time-domain semi-parametric estimation based on a metabolite basis set.
Ratiney, H; Sdika, M; Coenradie, Y; Cavassila, S; van Ormondt, D; Graveron-Demilly, D
2005-02-01
A novel and fast time-domain quantitation algorithm--quantitation based on semi-parametric quantum estimation (QUEST)--invoking optimal prior knowledge is proposed and tested. This nonlinear least-squares algorithm fits a time-domain model function, made up from a basis set of quantum-mechanically simulated whole-metabolite signals, to low-SNR in vivo data. A basis set of in vitro measured signals can be used too. The simulated basis set was created with the software package NMR-SCOPE which can invoke various experimental protocols. Quantitation of 1H short echo-time signals is often hampered by a background signal originating mainly from macromolecules and lipids. Here, we propose and compare three novel semi-parametric approaches to handle such signals in terms of bias-variance trade-off. The performances of our methods are evaluated through extensive Monte-Carlo studies. Uncertainty caused by the background is accounted for in the Cramér-Rao lower bounds calculation. Valuable insight about quantitation precision is obtained from the correlation matrices. Quantitation with QUEST of 1H in vitro data, 1H in vivo short echo-time and 31P human brain signals at 1.5 T, as well as 1H spectroscopic imaging data of human brain at 1.5 T, is demonstrated.
Basis set convergence of electric properties in HF and DFT calculations of nucleic acid bases
NASA Astrophysics Data System (ADS)
Campos, C. T.; Jorge, F. E.
Recently, a hierarchical sequence of augmented basis sets of double, triple, and quadruple zeta valence quality plus polarization functions (AXZP, X = D, T, and Q) for the atoms from H to Ar were presented by Jorge et al. We report a systematic study of basis sets required to obtain accurate values of several electric properties for benzene, pyridine, the five common nucleic acid bases (uracil, cytosine, thymine, guanine, and adenine), and three related bases (fluorouracil, 5-methylcytosine, and hypoxanthine) at their full optimized geometries. Two methods were examined: Hartree-Fock (HF) and density functional theory (DFT). Including electron correlation decreases the magnitude of the dipole moment and increases the mean polarizability and also the polarizability anisotropy for every molecule. Calculated B3LYP/ADZP dipole moments and dipole polarizabilities show good agreement with both experimental and ab initio results based on second-order Møller-Plesset perturbation theory calculations. We have also showed that a basis set of double zeta quality is enough to obtain reliable and accurate electric property results for this kind of compounds.
Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr
NASA Astrophysics Data System (ADS)
Feng, Rulin; Peterson, Kirk A.
2017-08-01
New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal
Nuclear second analytical derivative calculations using auxiliary basis set expansions
NASA Astrophysics Data System (ADS)
Deglmann, Peter; May, Klaus; Furche, Filipp; Ahlrichs, Reinhart
2004-01-01
We present an efficient implementation of second order analytical derivatives (force constants) within density functional theory which applies to non-hybrid functionals. The dominant step in force constant treatments concerns the solution of the coupled perturbed Kohn-Sham equations (CPKS). We employ an auxiliary basis expansion, the RI- J technique (resolution of the identity for the interelectronic Couomb energy J), to accelerate the solution of the CPKS equations. This results in pronounced reductions of computational work and implies insignificant losses in accuracy as is shown by extensive tests. A force constant calculation of cyanocobalamin is reported as a demonstrative application.
Sensory irritation as a basis for setting occupational exposure limits.
Brüning, Thomas; Bartsch, Rüdiger; Bolt, Hermann Maximillian; Desel, Herbert; Drexler, Hans; Gundert-Remy, Ursula; Hartwig, Andrea; Jäckh, Rudolf; Leibold, Edgar; Pallapies, Dirk; Rettenmeier, Albert W; Schlüter, Gerhard; Stropp, Gisela; Sucker, Kirsten; Triebig, Gerhard; Westphal, Götz; van Thriel, Christoph
2014-10-01
There is a need of guidance on how local irritancy data should be incorporated into risk assessment procedures, particularly with respect to the derivation of occupational exposure limits (OELs). Therefore, a board of experts from German committees in charge of the derivation of OELs discussed the major challenges of this particular end point for regulatory toxicology. As a result, this overview deals with the question of integrating results of local toxicity at the eyes and the upper respiratory tract (URT). Part 1 describes the morphology and physiology of the relevant target sites, i.e., the outer eye, nasal cavity, and larynx/pharynx in humans. Special emphasis is placed on sensory innervation, species differences between humans and rodents, and possible effects of obnoxious odor in humans. Based on this physiological basis, Part 2 describes a conceptual model for the causation of adverse health effects at these targets that is composed of two pathways. The first, "sensory irritation" pathway is initiated by the interaction of local irritants with receptors of the nervous system (e.g., trigeminal nerve endings) and a downstream cascade of reflexes and defense mechanisms (e.g., eyeblinks, coughing). While the first stages of this pathway are thought to be completely reversible, high or prolonged exposure can lead to neurogenic inflammation and subsequently tissue damage. The second, "tissue irritation" pathway starts with the interaction of the local irritant with the epithelial cell layers of the eyes and the URT. Adaptive changes are the first response on that pathway followed by inflammation and irreversible damages. Regardless of these initial steps, at high concentrations and prolonged exposures, the two pathways converge to the adverse effect of morphologically and biochemically ascertainable changes. Experimental exposure studies with human volunteers provide the empirical basis for effects along the sensory irritation pathway and thus, "sensory
Feller, David
2013-02-21
Simple modifications of complete basis set extrapolation formulas chosen from the literature are examined with respect to their abilities to reproduce a diverse set of 183 reference atomization energies derived primarily from very large basis set standard, frozen core coupled-cluster singles, doubles plus perturbative triples (CCSD(T)) with the aug-cc-pVnZ basis sets. This reference set was augmented with a few larger chemical systems treated with explicitly correlated CCSD(T)-F12b using a quadruple zeta quality basis set followed by extrapolation to complete basis set limit. Tuning the extrapolation formula parameters for the present reference set resulted in substantial reductions in the error metrics. In the case of the best performing approach, the aVnZ extrapolated results are equivalent to or better than results obtained from raw aV(n + 3)Z basis set calculations. To the extent this behavior holds for molecules outside the reference set, it represents an improvement of at least one basis set level over the original formulations and a further significant reduction in the amount of computer time needed to accurately approximate the basis set limit.
Lovastatin production: From molecular basis to industrial process optimization.
Mulder, Kelly C L; Mulinari, Flávia; Franco, Octávio L; Soares, Maria S F; Magalhães, Beatriz S; Parachin, Nádia S
2015-11-01
Lovastatin, composed of secondary metabolites produced by filamentous fungi, is the most frequently used drug for hypercholesterolemia treatment due to the fact that lovastatin is a competitive inhibitor of HMG-CoA reductase. Moreover, recent studies have shown several important applications for lovastatin including antimicrobial agents and treatments for cancers and bone diseases. Studies regarding the lovastatin biosynthetic pathway have also demonstrated that lovastatin is synthesized from two-chain reactions using acetate and malonyl-CoA as a substrate. It is also known that there are two key enzymes involved in the biosynthetic pathway called polyketide synthases (PKS). Those are characterized as multifunctional enzymes and are encoded by specific genes organized in clusters on the fungal genome. Since it is a secondary metabolite, cultivation process optimization for lovastatin biosynthesis has included nitrogen limitation and non-fermentable carbon sources such as lactose and glycerol. Additionally, the influences of temperature, pH, agitation/aeration, and particle and inoculum size on lovastatin production have been also described. Although many reviews have been published covering different aspects of lovastatin production, this review brings, for the first time, complete information about the genetic basis for lovastatin production, detection and quantification, strain screening and cultivation process optimization. Moreover, this review covers all the information available from patent databases covering each protected aspect during lovastatin bio-production. Copyright © 2015 Elsevier Inc. All rights reserved.
Brechet, Laurent; Lucas, Marie-Françoise; Doncarli, Christian; Farina, Dario
2007-12-01
We propose a novel scheme for signal compression based on the discrete wavelet packet transform (DWPT) decompositon. The mother wavelet and the basis of wavelet packets were optimized and the wavelet coefficients were encoded with a modified version of the embedded zerotree algorithm. This signal dependant compression scheme was designed by a two-step process. The first (internal optimization) was the best basis selection that was performed for a given mother wavelet. For this purpose, three additive cost functions were applied and compared. The second (external optimization) was the selection of the mother wavelet based on the minimal distortion of the decoded signal given a fixed compression ratio. The mother wavelet was parameterized in the multiresolution analysis framework by the scaling filter, which is sufficient to define the entire decomposition in the orthogonal case. The method was tested on two sets of ten electromyographic (EMG) and ten electrocardiographic (ECG) signals that were compressed with compression ratios in the range of 50%-90%. For 90% compression ratio of EMG (ECG) signals, the percent residual difference after compression decreased from (mean +/- SD) 48.6 +/- 9.9% (21.5 +/- 8.4%) with discrete wavelet transform (DWT) using the wavelet leading to poorest performance to 28.4 +/- 3.0% (6.7 +/- 1.9%) with DWPT, with optimal basis selection and wavelet optimization. In conclusion, best basis selection and optimization of the mother wavelet through parameterization led to substantial improvement of performance in signal compression with respect to DWT and randon selection of the mother wavelet. The method provides an adaptive approach for optimal signal representation for compression and can thus be applied to any type of biomedical signal.
Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.
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.
Basis set effects on the geometry of C96H24
NASA Astrophysics Data System (ADS)
Bauschlicher, Charles W.
2016-11-01
C96H24 has D6h symmetry using the 4-31G, 6-31G, cc-pVDZ, or cc-pVTZ basis sets, but has lower symmetry if the 6-31G∗∗ or 6-311G∗∗ basis sets are used. Changing the carbon 3d exponent in the 6-31G∗∗ basis set can restore the D6h symmetry, but raises the total energy. The question of geometry vs basis set is discussed.
New Slater-type orbital basis sets for first row transition elements
NASA Astrophysics Data System (ADS)
Bernardo, L. A. G.; Sordo, J. A.
1986-08-01
A comparative study, at the atomic level, of the quality of eight Slater-type orbitals (STO) basis sets has been carried out for the first row transition elements. Two new basis sets are proposed for these elements: the β1 basis set (small-size-type) and the α2 basis set (intermediate-size-type). Both basis sets have been developed according to the so-called δ test [J. A. Sordo and L. Pueyo, Int. J. Quantum Chem. XXVIII, 687 (1985)]. The results suggest that the errors detected by means of the δ test could be responsible for the wrong ordering predicted by 2-ζ (and lower quality basis sets) for the 4s13d10 (2S) and 4s23d9(2D) states in Cu. All the quality tests used indicated that β1 basis sets would be very appropriate for performing economical molecular calculations and that α2 basis sets, with only one STO more than 2-ζ basis sets, would provide atomic results near the Hartree-Fock limit.
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The atomization energies of the 55 G2 molecules are computed using the B3LYP approach with a variety of basis sets. The 6-311 + G(3df) basis set is found to yield superior results to those obtained using the augmented - correlation - consistent valence-polarized triple-zeta set. The atomization energy of SO2 is found to be the most sensitive to basis set and is studied in detail. Including tight d functions is found to be important for obtaining good atomization energies. The results for SO2 are compared with those obtained using the coupled-cluster singles and doubles approach including a perturbational estimate of the triple excitations.
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex
Shirkov, Leonid; Makarewicz, Jan
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
Miliordos, Evangelos; Xantheas, Sotiris S.
2015-03-07
We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.
Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.
Siiskonen, Antti; Priimagi, Arri
2017-02-01
In recent years, halogen bonding has become an important design tool in crystal engineering, supramolecular chemistry and biosciences. The fundamentals of halogen bonding have been studied extensively with high-accuracy computational methods. Due to its non-covalency, the use of triple-zeta (or larger) basis sets is often recommended when studying halogen bonding. However, in the large systems often encountered in supramolecular chemistry and biosciences, large basis sets can make the calculations far too slow. Therefore, small basis sets, which would combine high computational speed and high accuracy, are in great demand. This study focuses on comparing how well density functional theory (DFT) methods employing small, double-zeta basis sets can estimate halogen-bond strengths. Several methods with triple-zeta basis sets are included for comparison. Altogether, 46 DFT methods were tested using two data sets of 18 and 33 halogen-bonded complexes for which the complexation energies have been previously calculated with the high-accuracy CCSD(T)/CBS method. The DGDZVP basis set performed far better than other double-zeta basis sets, and it even outperformed the triple-zeta basis sets. Due to its small size, it is well-suited to studying halogen bonding in large systems.
Generation of basis sets with high degree of fulfillment of the Hellmann-Feynman theorem.
Rico, J Fernández; López, R; Ema, I; Ramírez, G
2007-03-01
A direct relationship is established between the degree of fulfillment of the Hellman-Feynman (electrostatic) theorem, measured as the difference between energy derivatives and electrostatic forces, and the stability of the basis set, measured from the indices that characterize the distance of the space generated by the basis functions to the space of their derivatives with respect to the nuclear coordinates. On the basis of this relationship, a criterion for obtaining basis sets of moderate size with a high degree of fulfillment of the theorem is proposed. As an illustrative application, previously reported Slater basis sets are extended by using this criterion. The resulting augmented basis sets are tested on several molecules finding that the differences between energy gradient and electrostatic forces are reduced by at least one order of magnitude.
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.
Method/basis set dependence of NICS values among metallic nano-clusters and hydrocarbons.
Badri, Zahra; Foroutan-Nejad, Cina; Rashidi-Ranjbar, Parviz
2012-03-14
The influence of various all-electron basis sets and effective core potentials employed along with several DFT functionals (B3LYP, B3PW91, BLYP, BP86 and M06) on the magnitude of nucleus independent chemical shift (NICS) values in different metallic nano-clusters and hydrocarbons is studied. In general, it is demonstrated that the NICS values are very sensitive to the applied method/basis set; however, the method/basis set dependence is more prominent for computed NICS values in transition metal clusters. In hydrocarbons, medium-size basis sets perform roughly similar to large basis sets in most cases. It is also found that NICS(0) values are more sensitive to the method/basis set variation compared to the NICS values computed at 1 or 2 Å above the ring plane. However, in many cases, no broad-spectrum regulation is found for the effect of basis set/method on the magnitude of NICS values. A detailed study showed that bond length alternation in a molecule has an insignificant effect on the magnitude of NICS values so the influence of method/basis sets on the magnitude of NICS values mostly arises from the different predicted ring current intensities at various computational levels.
NASA Astrophysics Data System (ADS)
Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta
2015-02-01
The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91 kJ/mol and 114.32 kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99 kJ/mol and 117.08 kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29 Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22 Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions
Mizera, Mikołaj; Lewadowska, Kornelia; Talaczyńska, Alicja; Cielecka-Piontek, Judyta
2015-02-25
The work was aimed at investigating the influence of diffusion of basis functions on the geometry optimization of molecule of losartan in acidic and salt form. Spectroscopic properties of losartan potassium were also calculated and compared with experiment. Density functional theory method with various basis sets: 6-31G(d,p) and its diffused variations 6-31G(d,p)+ and 6-31G(d,p)++ was used. Application of diffuse basis functions in geometry optimization resulted in significant change of total molecule energy. Total molecule energy of losartan potassium decreased by 112.91kJ/mol and 114.32kJ/mol for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets, respectively. Almost the same decrease was observed for losartan: 114.99kJ/mol and 117.08kJ/mol respectively for 6-31G(d,p)+ and 6-31G(d,p)++ basis sets. Further investigation showed significant difference within geometries of losartan potassium optimized with investigated basis sets. Application of diffused basis functions resulted in average 1.29Å difference in relative position between corresponding atoms of three obtained geometries. Similar study taken on losartan resulted in only average 0.22Å of dislocation. Extensive analysis of geometry changes in molecules obtained with diffused and non-diffuse basis functions was carried out in order to elucidate observed changes. The analysis was supported by electrostatic potential maps and calculation of natural atomic charges. UV, FT-IR and Raman spectra of losartan potassium were calculated and compared with experimental results. No crucial differences between Raman spectra obtained with different basis sets were observed. However, FT-IR spectra of geometry of losartan potassium optimized with 6-31G(d,p)++ basis set resulted in 40% better correlation with experimental FT-IR spectra than FT-IR calculated with geometry optimized with 6-31G(d,p) basis set. Therefore, it is highly advisable to optimize geometry of molecules with ionic interactions using diffuse basis functions when
On the effectiveness of CCSD(T) complete basis set extrapolations for atomization energies.
Feller, David; Peterson, Kirk A; Hill, J Grant
2011-07-28
The leading cause of error in standard coupled cluster theory calculations of thermodynamic properties such as atomization energies and heats of formation originates with the truncation of the one-particle basis set expansion. Unfortunately, the use of finite basis sets is currently a computational necessity. Even with basis sets of quadruple zeta quality, errors can easily exceed 8 kcal/mol in small molecules, rendering the results of little practical use. Attempts to address this serious problem have led to a wide variety of proposals for simple complete basis set extrapolation formulas that exploit the regularity in the correlation consistent sequence of basis sets. This study explores the effectiveness of six formulas for reproducing the complete basis set limit. The W4 approach was also examined, although in lesser detail. Reference atomization energies were obtained from standard coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) calculations involving basis sets of 6ζ or better quality for a collection of 141 molecules. In addition, a subset of 51 atomization energies was treated with explicitly correlated CCSD(T)-F12b calculations and very large basis sets. Of the formulas considered, all proved reliable at reducing the one-particle expansion error. Even the least effective formulas cut the error in the raw values by more than half, a feat requiring a much larger basis set without the aid of extrapolation. The most effective formulas cut the mean absolute deviation by a further factor of two. Careful examination of the complete body of statistics failed to reveal a single choice that out performed the others for all basis set combinations and all classes of molecules. © 2011 American Institute of Physics
Derivation of a formula for the resonance integral for a nonorthogonal basis set
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
Confidence sets for optimal factor levels of a response surface.
Wan, Fang; Liu, Wei; Bretz, Frank; Han, Yang
2016-12-01
Construction of confidence sets for the optimal factor levels is an important topic in response surfaces methodology. In Wan et al. (2015), an exact (1-α) confidence set has been provided for a maximum or minimum point (i.e., an optimal factor level) of a univariate polynomial function in a given interval. In this article, the method has been extended to construct an exact (1-α) confidence set for the optimal factor levels of response surfaces. The construction method is readily applied to many parametric and semiparametric regression models involving a quadratic function. A conservative confidence set has been provided as an intermediate step in the construction of the exact confidence set. Two examples are given to illustrate the application of the confidence sets. The comparison between confidence sets indicates that our exact confidence set is better than the only other confidence set available in the statistical literature that guarantees the (1-α) confidence level.
NASA Astrophysics Data System (ADS)
Hill, J. Grant; Mazumder, Shivnath; Peterson, Kirk A.
2010-02-01
Correlation consistent basis sets have been optimized for accurately describing core-core and core-valence correlation effects with explicitly correlated F12 methods. The new sets, denoted cc-pCVnZ-F12 (n =D, T, Q) and aug-cc-pCF12VnZ (n =D, T, Q, 5), were developed by augmenting the cc-pVnZ-F12 and aug-cc-pVnZ families of basis sets with additional functions whose exponents were optimized based on the difference between all-electron and valence-electron correlation energies. The number of augmented functions added is fewer, in general, than in the standard cc-pCVnZ and cc-pwCVnZ families of basis sets. Optimal values of the geminal Slater exponent for use with these basis sets in MP2-F12 calculations are presented and are also recommended for CCSD-F12b calculations. Auxiliary basis sets for use in the resolution of the identity approximation in explicitly correlated calculations have also been optimized and matched to the new cc-pCVnZ-F12 series of orbital basis sets. The cc-pCVnZ-F12 basis sets, along with the new auxiliary sets, were benchmarked in CCSD(T)-F12b calculations of spectroscopic properties on a series of homo- and heteronuclear first and second row diatomic molecules. Comparing the effects of correlating the outer core electrons in these molecules with those from conventional CCSD(T) at the complete basis set limit, which involved calculations with new cc-pCV6Z basis sets for the second row elements that were also developed in the course of this work, it is observed that the F12 values are reasonably well converged already at just the triple-ζ level.
Melicherčík, Miroslav; Pitoňák, Michal; Kellö, Vladimír; Hobza, Pavel; Neogrády, Pavel
2013-12-10
Proper description of noncovalent interactions requires, among other things, the use of diffuse atomic orbital (AO) basis sets. However, the presence of diffuse functions, especially in extended molecular systems, can lead to linear dependent AO basis sets. This in turn results, for example, in molecular orbital optimization problems or, when dependencies are removed in unpredictable and possibly geometry-dependent accuracy fluctuations. In this work, an alternative approach is proposed which suffers no linear dependence problems and delivers comparably accurate noncovalent interaction energies. An algorithm is proposed and implemented to construct a grid of off-center s-type Gaussian functions surrounding the molecule; substituting the presence of atom-centered diffuse basis functions. While the number of basis functions in the grid is comparable to the number of diffuse basis functions in aug-cc-pVXZ (for each cardinality number "X") basis sets for small molecular systems, the ratio becomes more favorable with increasing system size. The grid is constructed in a way that it is unique for a molecule (monomer) and, thus, independent of noncovalent complex/cluster geometry. The grid parameters, such as the density of grid points and s-function exponents, are obtained via optimization toward the S22 data set on the MP2 level. The quality, transferability, and versatility of the grid is tested on the S66 data set as well as on several cuts through the potential energy surface for noncovalent complexes, such as methyl-guanine···methyl-cytosine conversion from stacked to hydrogen-bonded structure.
Vicinal proton—proton coupling constants. Basis set dependence in SCF ab initio calculations
NASA Astrophysics Data System (ADS)
San-Fabián, Jesús; Guilleme, Joaquín; Díez, Ernesto; Lazzeretti, Paolo; Malagoli, Massimo; Zanasi, Riccardo
1993-04-01
An SCF ab initio study of the angular dependence and substituent effects upon the vicinal coupling constants has been carried out for the molecules CH 3CH 3, CH 2FCH 3 and CHF 2CH 3. The four contributions to 3JHH ( JFC, JSD, JOD and JOP) have been computed using the STO-3G, 6-31G, 6-31G * and 6-31G ** basis sets. The major contributions arise from the FC term. The magnitude of the SD contributions is very small and near independent of the size of the basis set. The magnitude of the orbital contributions OR (=OD+OP) decreases as the size of the basis set increases. The FC term slightly overestimates both the individual and the interaction substituent effects for basis sets larger than the STO-3G one. For this basis such effects are underestimated.
Basis set generation for quantum dynamics simulations using simple trajectory-based methods.
Saller, Maximilian A C; Habershon, Scott
2015-01-13
Methods for solving the time-dependent Schrödinger equation generally employ either a global static basis set, which is fixed at the outset, or a dynamic basis set, which evolves according to classical-like or variational equations of motion; the former approach results in the well-known exponential scaling with system size, while the latter can suffer from challenging numerical problems, such as singular matrices, as well as violation of energy conservation. Here, we suggest a middle road: building a basis set using trajectories to place time-independent basis functions in the regions of phase space relevant to wave function propagation. This simple approach, which potentially circumvents many of the problems traditionally associated with global or dynamic basis sets, is successfully demonstrated for two challenging benchmark problems in quantum dynamics, namely, relaxation dynamics following photoexcitation in pyrazine, and the spin Boson model.
Bi-directional evolutionary level set method for topology optimization
NASA Astrophysics Data System (ADS)
Zhu, Benliang; Zhang, Xianmin; Fatikow, Sergej; Wang, Nianfeng
2015-03-01
A bi-directional evolutionary level set method for solving topology optimization problems is presented in this article. The proposed method has three main advantages over the standard level set method. First, new holes can be automatically generated in the design domain during the optimization process. Second, the dependency of the obtained optimized configurations upon the initial configurations is eliminated. Optimized configurations can be obtained even being started from a minimum possible initial guess. Third, the method can be easily implemented and is computationally more efficient. The validity of the proposed method is tested on the mean compliance minimization problem and the compliant mechanisms topology optimization problem.
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.
NASA Astrophysics Data System (ADS)
Richard, Ryan M.; Herbert, John M.
2013-06-01
Previous electronic structure studies that have relied on fragmentation have been primarily interested in those methods' abilities to replicate the supersystem energy (or a related energy difference) without recourse to the ability of those supersystem results to replicate experiment or high accuracy benchmarks. Here we focus on replicating accurate ab initio benchmarks, that are suitable for comparison to experimental data. In doing this it becomes imperative that we correct our methods for basis-set superposition errors (BSSE) in a computationally feasible way. This criterion leads us to develop a new method for BSSE correction, which we term the many-body counterpoise correction, or MBn for short. MBn is truncated at order n, in much the same manner as a normal many-body expansion leading to a decrease in computational time. Furthermore, its formulation in terms of fragments makes it especially suitable for use with pre-existing fragment codes. A secondary focus of this study is directed at assessing fragment methods' abilities to extrapolate to the complete basis set (CBS) limit as well as compute approximate triples corrections. Ultimately, by analysis of (H_2O)_6 and (H_2O)_{10}F^- systems, it is concluded that with large enough basis-sets (triple or quad zeta) fragment based methods can replicate high level benchmarks in a fraction of the time.
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.
Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets.
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.
Pseudospectral sampling of Gaussian basis sets as a new avenue to high-dimensional quantum dynamics
NASA Astrophysics Data System (ADS)
Heaps, Charles
This thesis presents a novel approach to modeling quantum molecular dynamics (QMD). Theoretical approaches to QMD are essential to understanding and predicting chemical reactivity and spectroscopy. We implement a method based on a trajectory-guided basis set. In this case, the nuclei are propagated in time using classical mechanics. Each nuclear configuration corresponds to a basis function in the quantum mechanical expansion. Using the time-dependent configurations as a basis set, we are able to evolve in time using relatively little information at each time step. We use a basis set of moving frozen (time-independent width) Gaussian functions that are well-known to provide a simple and efficient basis set for nuclear dynamics. We introduce a new perspective to trajectory-guided Gaussian basis sets based on existing numerical methods. The distinction is based on the Galerkin and collocation methods. In the former, the basis set is tested using basis functions, projecting the solution onto the functional space of the problem and requiring integration over all space. In the collocation method, the Dirac delta function tests the basis set, projecting the solution onto discrete points in space. This effectively reduces the integral evaluation to function evaluation, a fundamental characteristic of pseudospectral methods. We adopt this idea for independent trajectory-guided Gaussian basis functions. We investigate a series of anharmonic vibrational models describing dynamics in up to six dimensions. The pseudospectral sampling is found to be as accurate as full integral evaluation, while the former method is fully general and integration is only possible on very particular model potential energy surfaces. Nonadiabatic dynamics are also investigated in models of photodissociation and collinear triatomic vibronic coupling. Using Ehrenfest trajectories to guide the basis set on multiple surfaces, we observe convergence to exact results using hundreds of basis functions
Zaleśny, Robert; Baranowska-Łączkowska, Angelika; Medveď, Miroslav; Luis, Josep M
2015-09-08
In the present work, we perform an assessment of several property-oriented atomic basis sets in computing (hyper)polarizabilities with a focus on the vibrational contributions. Our analysis encompasses the Pol and LPol-ds basis sets of Sadlej and co-workers, the def2-SVPD and def2-TZVPD basis sets of Rappoport and Furche, and the ORP basis set of Baranowska-Łączkowska and Łączkowski. Additionally, we use the d-aug-cc-pVQZ and aug-cc-pVTZ basis sets of Dunning and co-workers to determine the reference estimates of the investigated electric properties for small- and medium-sized molecules, respectively. We combine these basis sets with ab initio post-Hartree-Fock quantum-chemistry approaches (including the coupled cluster method) to calculate electronic and nuclear relaxation (hyper)polarizabilities of carbon dioxide, formaldehyde, cis-diazene, and a medium-sized Schiff base. The primary finding of our study is that, among all studied property-oriented basis sets, only the def2-TZVPD and ORP basis sets yield nuclear relaxation (hyper)polarizabilities of small molecules with average absolute errors less than 5.5%. A similar accuracy for the nuclear relaxation (hyper)polarizabilites of the studied systems can also be reached using the aug-cc-pVDZ basis set (5.3%), although for more accurate calculations of vibrational contributions, i.e., average absolute errors less than 1%, the aug-cc-pVTZ basis set is recommended. It was also demonstrated that anharmonic contributions to first and second hyperpolarizabilities of a medium-sized Schiff base are particularly difficult to accurately predict at the correlated level using property-oriented basis sets. For instance, the value of the nuclear relaxation first hyperpolarizability computed at the MP2/def2-TZVPD level of theory is roughly 3 times larger than that determined using the aug-cc-pVTZ basis set. We link the failure of the def2-TZVPD basis set with the difficulties in predicting the first-order field
Trail-Needs pseudopotentials in quantum Monte Carlo calculations with plane-wave/blip basis sets
NASA Astrophysics Data System (ADS)
Drummond, N. D.; Trail, J. R.; Needs, R. J.
2016-10-01
We report a systematic analysis of the performance of a widely used set of Dirac-Fock pseudopotentials for quantum Monte Carlo (QMC) calculations. We study each atom in the periodic table from hydrogen (Z =1 ) to mercury (Z =80 ), with the exception of the 4 f elements (57 ≤Z ≤70 ). We demonstrate that ghost states are a potentially serious problem when plane-wave basis sets are used in density functional theory (DFT) orbital-generation calculations, but that this problem can be almost entirely eliminated by choosing the s channel to be local in the DFT calculation; the d channel can then be chosen to be local in subsequent QMC calculations, which generally leads to more accurate results. We investigate the achievable energy variance per electron with different levels of trial wave function and we determine appropriate plane-wave cutoff energies for DFT calculations for each pseudopotential. We demonstrate that the so-called "T-move" scheme in diffusion Monte Carlo is essential for many elements. We investigate the optimal choice of spherical integration rule for pseudopotential projectors in QMC calculations. The information reported here will prove crucial in the planning and execution of QMC projects involving beyond-first-row elements.
Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness.
Kulik, Heather J; Seelam, Natasha; Mar, Brendan D; Martínez, Todd J
2016-07-28
Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.
Basis set limit coupled-cluster studies of hydrogen-bonded systems
NASA Astrophysics Data System (ADS)
Boese, A. Daniel
2015-07-01
As hydrogen-bonded systems are of utmost importance in especially biological and chemical systems, a new set of highly accurate reference dissociation energies, denoted HB49, is devised. For the molecules in this set, the basis set convergence of post-Hartree-Fock methods, including F12 methods, is investigated. Using combined Møller-Plesset perturbation theory (MP2) and CCSD(T) approaches for energies and MP2 and QCISD(T) for gradients, we achieve CCSD(T) accuracy, which has been determined before to yield an accuracy of 0.2 kJ/mol for a subset of HB49. Both conventional extrapolation techniques and F12 techniques are competitive with each other. By using MP2+ΔCCSD(T), a rather fast basis set convergence is obtained when both basis sets are carefully chosen. In memory of a great supervisor Prof. Nicholas C. Handy
Peterson, Kirk A.; Figgen, Detlev; Goll, Erich; Stoll, Hermann; Dolg, Michael F.
2003-12-01
Series of correlation consistent basis sets have been developed for the post-d group 16-18 elements in conjunction with small-core relativistic pseudopotentials (PPs) of the energy-consistent variety. The latter were adjusted to multiconfiguration Dirac-Hartree-Fock data based on the Dirac-Coulomb-Breit Hamiltonian. The outer-core (n-1)spd shells are explicitly treated together with the nsp valence shell with these PPs. The accompanying cc-pVnZ-PP and aug-cc-pVnZ-PP basis sets range in size from DZ to 5Z quality and yield systematic convergence of both Hartree-Fock and correlated total energies. In addition to the calculation of atomic electron affinities and dipole polarizabilities of the rare gas atoms, numerous molecular benchmark calculations (HBr, HI, HAt, Br2, I2, At2, SiSe, SiTe, SiPo, KrH+, XeH+, and RnH+) are also reported at the coupled cluster level of theory. For the purposes of comparison, all-electron calculations using the Douglas-Kroll-Hess Hamiltonian have also been carried out for the halogen-containing molecules using basis sets of 5Z quality.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.
2015-08-14
A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.
Magnetic properties with multiwavelets and DFT: the complete basis set limit achieved.
Jensen, Stig Rune; Flå, Tor; Jonsson, Dan; Monstad, Rune Sørland; Ruud, Kenneth; Frediani, Luca
2016-08-03
Multiwavelets are emerging as an attractive alternative to traditional basis sets such as Gaussian-type orbitals and plane waves. One of their distinctive properties is the ability to reach the basis set limit (often a chimera for traditional approaches) reliably and consistently by fixing the desired precision ε. We present our multiwavelet implementation of the linear response formalism, applied to static magnetic properties, at the self-consistent field level of theory (both for Hartree-Fock and density functional theories). We demonstrate that the multiwavelets consistently improve the accuracy of the results when increasing the desired precision, yielding results that have four to five digits precision, thus providing a very useful benchmark which could otherwise only be estimated by extrapolation methods. Our results show that magnetizabilities obtained with the augmented quadruple-ζ basis (aug-cc-pCVQZ) are practically at the basis set limit, whereas absolute nuclear magnetic resonance shielding tensors are more challenging: even by making use of a standard extrapolation method, the accuracy is not substantially improved. In contrast, our results provide a benchmark that: (1) confirms the validity of the extrapolation ansatz; (2) can be used as a reference to achieve a property-specific extrapolation scheme, thus providing a means to obtain much better extrapolated results; (3) allows us to separate functional-specific errors from basis-set ones and thus to assess the level of cancellation between basis set and functional errors often exploited in density functional theory.
Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.
Steele, Ryan P
2015-12-17
This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.
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.
Holden, Zachary C.; Richard, Ryan M.; Herbert, John M.
2013-12-28
An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.
NASA Astrophysics Data System (ADS)
Park, R.; Jo, D.; Kim, M.; Spracklen, D. V.; Hodzic, A.
2014-12-01
Organic aerosol (OA) constitutes significant mass fractions (20-90%) of total dry fine aerosols in the atmosphere. However, global models of OA have shown large discrepancies when compared to the observations because of the limited capability to simulate secondary OA (SOA). For reducing the discrepancies between observations and models, recent studies have shown that chemical aging reactions in the atmosphere are important because they can lead to decreases in organic volatility, resulting in increase of SOA mass yields. To efficiently simulate chemical aging of SOA in the atmosphere, we implemented the volatility basis set approach in a global 3-D chemical transport model (GEOS-Chem). We present full-year simulations and their comparisons with multiple observations - global aerosol mass spectrometer dataset, the Interagency Monitoring of Protected Visual Environments from the United States, the European Monitoring and Evaluation Programme dataset and water-soluble organic carbon observation data collected over East Asia. Using different input parameters in the model, we also explore the uncertainty of the SOA simulation for which we use an observational constraint to find the optimized values with which the model reduces the discrepancy from the observations. Finally, we estimate the effect of OA on climate using our best simulation results.
Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.
NASA Astrophysics Data System (ADS)
Barclay, V. J.
"Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations
Representability of Bloch states on Projector-augmented-wave (PAW) basis sets
NASA Astrophysics Data System (ADS)
Agapito, Luis; Ferretti, Andrea; Curtarolo, Stefano; Buongiorno Nardelli, Marco
2015-03-01
Design of small, yet `complete', localized basis sets is necessary for an efficient dual representation of Bloch states on both plane-wave and localized basis. Such simultaneous dual representation permits the development of faster more accurate (beyond DFT) electronic-structure methods for atomistic materials (e.g. the ACBN0 method.) by benefiting from algorithms (real and reciprocal space) and hardware acceleration (e.g. GPUs) used in the quantum-chemistry and solid-state communities. Finding a `complete' atomic-orbital basis (partial waves) is also a requirement in the generation of robust and transferable PAW pseudopotentials. We have employed the atomic-orbital basis from available PAW data sets, which extends through most of the periodic table, and tested the representability of Bloch states on such basis. Our results show that PAW data sets allow systematic and accurate representability of the PAW Bloch states, better than with traditional quantum-chemistry double-zeta- and double-zeta-polarized-quality basis sets.
Efficient calculation of integrals in mixed ramp-Gaussian basis sets
McKemmish, Laura K.
2015-04-07
Algorithms for the efficient calculation of two-electron integrals in the newly developed mixed ramp-Gaussian basis sets are presented, alongside a Fortran90 implementation of these algorithms, RAMPITUP. These new basis sets have significant potential to (1) give some speed-up (estimated at up to 20% for large molecules in fully optimised code) to general-purpose Hartree-Fock (HF) and density functional theory quantum chemistry calculations, replacing all-Gaussian basis sets, and (2) give very large speed-ups for calculations of core-dependent properties, such as electron density at the nucleus, NMR parameters, relativistic corrections, and total energies, replacing the current use of Slater basis functions or very large specialised all-Gaussian basis sets for these purposes. This initial implementation already demonstrates roughly 10% speed-ups in HF/R-31G calculations compared to HF/6-31G calculations for large linear molecules, demonstrating the promise of this methodology, particularly for the second application. As well as the reduction in the total primitive number in R-31G compared to 6-31G, this timing advantage can be attributed to the significant reduction in the number of mathematically complex intermediate integrals after modelling each ramp-Gaussian basis-function-pair as a sum of ramps on a single atomic centre.
Evolutionary optimization of radial basis function classifiers for data mining applications.
Buchtala, Oliver; Klimek, Manuel; Sick, Bernhard
2005-10-01
In many data mining applications that address classification problems, feature and model selection are considered as key tasks. That is, appropriate input features of the classifier must be selected from a given (and often large) set of possible features and structure parameters of the classifier must be adapted with respect to these features and a given data set. This paper describes an evolutionary algorithm (EA) that performs feature and model selection simultaneously for radial basis function (RBF) classifiers. In order to reduce the optimization effort, various techniques are integrated that accelerate and improve the EA significantly: hybrid training of RBF networks, lazy evaluation, consideration of soft constraints by means of penalty terms, and temperature-based adaptive control of the EA. The feasibility and the benefits of the approach are demonstrated by means of four data mining problems: intrusion detection in computer networks, biometric signature verification, customer acquisition with direct marketing methods, and optimization of chemical production processes. It is shown that, compared to earlier EA-based RBF optimization techniques, the runtime is reduced by up to 99% while error rates are lowered by up to 86%, depending on the application. The algorithm is independent of specific applications so that many ideas and solutions can be transferred to other classifier paradigms.
Basis set effects on the Hartree-Fock description of confined many-electron atoms
NASA Astrophysics Data System (ADS)
Garza, Jorge; Hernández-Pérez, Julio M.; Ramírez, José-Zeferino; Vargas, Rubicelia
2012-01-01
In this work, the basis sets designed by Clementi, Bunge and Thakkar, for atomic systems, have been used to obtain the electronic structure of confined many-electron atoms by using Roothaan's approach in the Hartree-Fock context with a new code written in C, which uses the message-passing interface library. The confinement was imposed as Ludeña suggested to simulate walls with infinity potential. For closed-shell atoms, the Thakkar basis set functions give the best total energies (TE) as a function of the confinement radius, obtaining the following ordering: TE(Thakkar) < TE(Bunge) < TE(Clementi). However, for few open-shell atoms this ordering is not preserved and a trend, for the basis sets, is not observed. Although there are differences between the TE predicted by these basis set functions, the corresponding pressures are similar to each other; it means that changes in the total energy are described almost in the same way by using any of these basis sets. By analysing the total energy as a function of the inverse of the volume we propose an equation of state; for regions of small volumes, this equation predicts that the pressure is inversely proportional to the square of the volume.
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.
Macedo, Luiz Guilherme M de Borin, Antonio Carlos; Silva, Alberico B.F. da
2007-11-15
Prolapse-free basis sets suitable for four-component relativistic quantum chemical calculations are presented for the superheavy elements up to {sub 118}Uuo ({sub 104}Rf, {sub 105}Db, {sub 106}Sg, {sub 107}Bh, {sub 108}Hs, {sub 109}Mt, {sub 110}Ds, {sub 111}Rg, {sub 112}Uub, {sub 113}Uut, {sub 114}Uuq, {sub 115}Uup, {sub 116}Uuh, {sub 117}Uus, {sub 118}Uuo) and {sub 103}Lr. These basis sets were optimized by minimizing the absolute values of the energy difference between the Dirac-Fock-Roothaan total energy and the corresponding numerical value at a milli-Hartree order of magnitude, resulting in a good balance between cost and accuracy. Parameters for generating exponents and new numerical data for some superheavy elements are also presented.
Woon, D.E.; Dunning, T.H. Jr. )
1994-02-15
An accurate description of the electrical properties of atoms and molecules is critical for quantitative predictions of the nonlinear properties of molecules and of long-range atomic and molecular interactions between both neutral and charged species. We report a systematic study of the basis sets required to obtain accurate correlated values for the static dipole ([alpha][sub 1]), quadrupole ([alpha][sub 2]), and octopole ([alpha][sub 3]) polarizabilities and the hyperpolarizability ([gamma]) of the rare gas atoms He, Ne, and Ar. Several methods of correlation treatment were examined, including various orders of Moller--Plesset perturbation theory (MP2, MP3, MP4), coupled-cluster theory with and without perturbative treatment of triple excitations [CCSD, CCSD(T)], and singles and doubles configuration interaction (CISD). All of the basis sets considered here were constructed by adding even-tempered sets of diffuse functions to the correlation consistent basis sets of Dunning and co-workers. With multiply-augmented sets we find that the electrical properties of the rare gas atoms converge smoothly to values that are in excellent agreement with the available experimental data and/or previously computed results. As a further test of the basis sets presented here, the dipole polarizabilities of the F[sup [minus
Influence of basis sets and electron correlation on theoretically predicted infrared intensities
Miller, M.D. ); Jensen, F. ); Chapman, O.L.; Houk, K.N. )
1989-06-01
A systematic study of the effects of basis sets and electron correlation on calculated infrared intensities has been performed with ab initio molecular orbital calculations and Moeller-Plesset perturbation theory. Absolute IR intensities of hydrogen fluoride, hydroxy radical, carbon monoxide, hydrogen cyanide, and formaldehyde have been calculated with basis sets ranging from 3-21G to 6-311++G(2dd{prime},2pp{prime}) and with electron correlation corrections up through MP4(SDTQ). A basis set with polarization and diffuse functions is necessary to obtain reasonably accurate intensities. Electron correlation significantly improves the agreement between experimental and calculated values. Except for carbon monoxide, the intensities calculated at the MP4 level compare favorably with experimental intensities, the errors being less than the measured difference between those obtained from inert-gas matrices at low temperature and those reported for the gas phase.
Balabin, Roman M
2010-06-21
The accuracy of quantum chemical treatment of biopolymers by means of density functional theory is brought into question in terms of intramolecular basis set superposition error (BSSE). Secondary structure forms--beta-strands (C5; fully extended conformation), repeated gamma-turns (C7), 3(10)-helices (C10), and alpha-helices (C13)--of homopolypeptides (polyglycine and polyalanine) are used as representative examples. The studied molecules include Ace(Gly)(5)NH(2), Ace(Gly)(10)NH(2), Ace(Ala)(5)NH(2), and Ace(Ala)(10)NH(2). The counterpoise correction procedure was found to produce reliable estimations for the BSSE values (other methods of BSSE correction are discussed). The calculations reported here used the B3LYP, PBE0 (PBE1PBE), and BMK density functionals with different basis sets [from 6-31G(d) to 6-311+G(3df,3pd)] to estimate the influence of basis set size on intramolecular BSSE. Calculation of BSSE was used to determine the deviation of the current results from the complete basis set limit. Intramolecular BSSE was found to be nonadditive with respect to biopolymer size, in contrast to claims in recent literature. The error, which is produced by a basis set superposition, was found to exceed 4 kcal mol(-1) when a medium-sized basis set was used. This indicates that this error has the same order of magnitude as the relative energy differences of secondary structure elements of biopolymers. This result makes all recent reports on the gas-phase stability of homopolypeptides and their analogs questionable.
On the basis set convergence of electron–electron entanglement measures: helium-like systems
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
Wright, J.S.; Kruus, E.
1986-12-15
The utility of midbond functions in molecular calculations was tested in two cases where the correct results are known: the H/sub 2/ potential curve and the collinear H/sub 3/ potential surface. For H/sub 2/, a variety of basis sets both with and without bond functions was compared to the exact nonrelativistic potential curve of Kolos and Wolniewicz (J. Chem. Phys. 43, 2429 (1965)). It was found that optimally balanced basis sets at two levels of quality were the double zeta single polarization plus sp bond function basis (BF1) and the triple zeta double polarization plus two sets of sp bond function basis (BF2). These gave bond dissociation energies D/sub e/ = 4.7341 and 4.7368 eV, respectively (expt. 4.7477 eV). Four basis sets were tested for basis set superposition errors, which were found to be small relative to basis set incompleteness and therefore did not affect any conclusions regarding basis set balance. Basis sets BF1 and BF2 were used to construct potential surfaces for collinear H/sub 3/, along with the corresponding basis sets DZ*P and TZ*PP which contain no bond functions. Barrier heights of 12.52, 10.37, 10.06, and 9.96 kcal/mol were obtained for basis sets DZ*P, TZ*PP, BF1, and BF2, respectively, compared to an estimated limiting value of 9.60 kcal/mol. Difference maps, force constants, and relative rms deviations show that the bond functions improve the surface shape as well as the barrier height.
Papajak, Ewa; Truhlar, Donald G.
2011-01-11
We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”, “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.
Energy-optimal path planning by stochastic dynamically orthogonal level-set optimization
NASA Astrophysics Data System (ADS)
Subramani, Deepak N.; Lermusiaux, Pierre F. J.
2016-04-01
A stochastic optimization methodology is formulated for computing energy-optimal paths from among time-optimal paths of autonomous vehicles navigating in a dynamic flow field. Based on partial differential equations, the methodology rigorously leverages the level-set equation that governs time-optimal reachability fronts for a given relative vehicle-speed function. To set up the energy optimization, the relative vehicle-speed and headings are considered to be stochastic and new stochastic Dynamically Orthogonal (DO) level-set equations are derived. Their solution provides the distribution of time-optimal reachability fronts and corresponding distribution of time-optimal paths. An optimization is then performed on the vehicle's energy-time joint distribution to select the energy-optimal paths for each arrival time, among all stochastic time-optimal paths for that arrival time. Numerical schemes to solve the reduced stochastic DO level-set equations are obtained, and accuracy and efficiency considerations are discussed. These reduced equations are first shown to be efficient at solving the governing stochastic level-sets, in part by comparisons with direct Monte Carlo simulations. To validate the methodology and illustrate its accuracy, comparisons with semi-analytical energy-optimal path solutions are then completed. In particular, we consider the energy-optimal crossing of a canonical steady front and set up its semi-analytical solution using a energy-time nested nonlinear double-optimization scheme. We then showcase the inner workings and nuances of the energy-optimal path planning, considering different mission scenarios. Finally, we study and discuss results of energy-optimal missions in a wind-driven barotropic quasi-geostrophic double-gyre ocean circulation.
A basis set convergence study of conventional and HSF electron densities in the Li 2 molecule
NASA Astrophysics Data System (ADS)
Challacombe, Matt; Cioslowski, Jerzy
1994-07-01
Calculations of nonnuclear, Hartree-Fock HSF and CHSF electron densities are reported for the first time. The positions of critical points in the conventional, HSF, and CHSF electron densities of the Li 2 molecule (including the nonnuclear maximum) and corresponding values of the electron density are computed for a sequence of systematically improved basis sets. The basis set convergence of these topological properties, as well as that of the densities at nuclei, are examined. Quantities derived from HSF and CHSF electron densities are found to converge more rapidly than their conventional counterparts.
Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.
Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F
2016-10-05
Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.
An extended basis set {ital ab} {ital initio} study of alkali metal cation--water clusters
Feller, D.; Glendening, E.D.; Woon, D.E.; Feyereisen, M.W.
1995-09-01
Ionic clusters comprised of a single alkali metal cation and up to eight water molecules were studied at the Hartree--Fock and correlated levels of theory using the correlation consistent sequence of basis sets. Estimates of the degree of convergence in the computed properties with respect to the complete basis set limit were facilitated by the underlying systematic manner in which the correlation consistent sets approach completeness. In favorable cases, improved property values could be obtained by fitting finite basis set results with a simple analytical expression in order to extrapolate to the complete basis set limit. The sensitivity of structures and binding energies were analyzed with regard to the inclusion of valence and core-valence correlation recovery at the MP2, MP4, and CCSD(T) levels of theory. The replacement of metal core electrons and the introduction of relativistic contributions via effective core potentials was compared to corresponding all-electron results. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.
Molecular Dipole Moments within the Incremental Scheme Using the Domain-Specific Basis-Set Approach.
Fiedler, Benjamin; Coriani, Sonia; Friedrich, Joachim
2016-07-12
We present the first implementation of the fully automated incremental scheme for CCSD unrelaxed dipole moments using the domain-specific basis-set approach. Truncation parameters are varied, and the accuracy of the method is statistically analyzed for a test set of 20 molecules. The local approximations introduce small errors at second order and negligible ones at third order. For a third-order incremental CCSD expansion with a CC2 error correction, a cc-pVDZ/SV domain-specific basis set (tmain = 3.5 Bohr), and the truncation parameter f = 30 Bohr, we obtain a mean error of 0.00 mau (-0.20 mau) and a standard deviation of 1.95 mau (2.17 mau) for the total dipole moments (Cartesian components of the dipole vectors). By analyzing incremental CCSD energies, we demonstrate that the MP2 and CC2 error correction schemes are an exclusive correction for the domain-specific basis-set error. Our implementation of the incremental scheme provides fully automated computations of highly accurate dipole moments at reduced computational cost and is fully parallelized in terms of the calculation of the increments. Therefore, one can utilize the incremental scheme, on the same hardware, to extend the basis set in comparison to standard CCSD and thus obtain a better total accuracy.
How to spoil a good basis set for Rayleigh-Ritz calculations
Pupyshev, Vladimir I.; Montgomery, H. E. Jr.
2013-08-15
For model quantum mechanical systems such as the harmonic oscillator and a particle in an impenetrable box, we consider the set of exact discrete spectrum functions and define the modified basis set by subtraction of the ground state wavefunction from all the other wavefunctions with some real weights. It is demonstrated that the modified set of functions is complete in the space of square integrable functions if and only if the series of the squared weights diverges. A similar, but nonequivalent criterion is derived for convergence of Rayleigh-Ritz ground state energy calculations to the exact ground state energy value with the basis set extension. Some numerical illustrations are provided which demonstrate a wide variety of possible situations for model systems.
A minimization method on the basis of embedding the feasible set and the epigraph
NASA Astrophysics Data System (ADS)
Zabotin, I. Ya; Shulgina, O. N.; Yarullin, R. S.
2016-11-01
We propose a conditional minimization method of the convex nonsmooth function which belongs to the class of cutting-plane methods. During constructing iteration points a feasible set and an epigraph of the objective function are approximated by the polyhedral sets. In this connection, auxiliary problems of constructing iteration points are linear programming problems. In optimization process there is some opportunity of updating sets which approximate the epigraph. These updates are performed by periodically dropping of cutting planes which form embedding sets. Convergence of the proposed method is proved, some realizations of the method are discussed.
Correlation consistent basis sets for actinides. I. The Th and U atoms
Peterson, Kirk A.
2015-02-21
New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than the DKH2
Correlation consistent basis sets for actinides. I. The Th and U atoms.
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.
NASA Astrophysics Data System (ADS)
Borges, A.; Solomon, G. C.
2016-05-01
Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and -π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems.
Determination of a natural basis function set on thick, structured slabs using Prony's method
NASA Technical Reports Server (NTRS)
Jorgenson, Roy E.; Epp, Larry; Mittra, Raj
1991-01-01
The calculation of currents on a thick, structured slab such as a thick slab of honeycomb is discussed. Unfortunately, for certain applications, the slab can be on the order of several wavelengths, so that the straightforward application of the method of moments using subdomain basis functions is too expensive. The authors discuss how to apply Prony's method to the currents calculated for a thin, structured slab to obtain a natural set of basis functions to represent the currents in the interior of a thick slab. Prony's method represents the currents as a series of complex exponential functions. The thick slab problem is then solved by the method of moments using subdomain basis functions near the slab interfaces and one or two of the complex exponentials as basis functions within the slab.
Sun, Yaping; Zhang, Jinyu; Wang, Yan; Yu, Zhiping
2014-12-01
Finer grid representation is required for a more accurate description of mask patterns in inverse lithography techniques, thus resulting in a large-size mask representation and heavy computational cost. To mitigate the computation problem caused by intensive convolutions in mask optimization, a new method called convolution using basis expansion (CBE) is discussed in this paper. Matrices defined in fine grid are projected on coarse gird under a base matrix set. The new matrices formed by the expansion coefficients are used to perform convolution on the coarse grid. The convolution on fine grid can be approximated by the sum of a few convolutions on coarse grid following an interpolation procedure. The CBE is verified by random matrix convolutions and intensity calculation in lithography simulation. Results show that the use of the CBE method results in similar image quality with significant running speed enhancement compared with traditional convolution method.
Training set optimization under population structure in genomic selection
USDA-ARS?s Scientific Manuscript database
The optimization of the training set (TRS) in genomic selection (GS) has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the Coefficient of D...
Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets.
Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost
2009-11-10
Hartree-Fock exchange with a truncated Coulomb operator has recently been discussed in the context of periodic plane-waves calculations [Spencer, J.; Alavi, A. Phys. Rev. B: Solid State, 2008, 77, 193110]. In this work, this approach is extended to Gaussian basis sets, leading to a stable and accurate procedure for evaluating Hartree-Fock exchange at the Γ-point. Furthermore, it has been found that standard hybrid functionals can be transformed into short-range functionals without loss of accuracy. The well-defined short-range nature of the truncated exchange operator can naturally be exploited in integral screening procedures and makes this approach interesting for both condensed phase and gas phase systems. The presented Hartree-Fock implementation is massively parallel and scales up to ten thousands of cores. This makes it feasible to perform highly accurate calculations on systems containing thousands of atoms or ten thousands of basis functions. The applicability of this scheme is demonstrated by calculating the cohesive energy of a LiH crystal close to the Hartree-Fock basis set limit and by performing an electronic structure calculation of a complete protein (rubredoxin) in solution with a large and flexible basis set.
Heats of formation for third-period hydrides: test of an extended basis set
Gordon, M.S.; Heitzinger, J.
1987-04-23
The extended basis set developed by McLean and Chandler for third-period atoms is combined with the -311G hydrogen basis and augmented by polarization functions to predict the heats of formation of third-period hydrides at the full MP4 computational level. The calculated heats of formation are at least as accurate as those predicted for second-row hydrides by using MP4/6-311G(d,p) wave functions, with a root mean square error of approximately 4 kcal/mol.
Level-Set Topology Optimization with Aeroelastic Constraints
NASA Technical Reports Server (NTRS)
Dunning, Peter D.; Stanford, Bret K.; Kim, H. Alicia
2015-01-01
Level-set topology optimization is used to design a wing considering skin buckling under static aeroelastic trim loading, as well as dynamic aeroelastic stability (flutter). The level-set function is defined over the entire 3D volume of a transport aircraft wing box. Therefore, the approach is not limited by any predefined structure and can explore novel configurations. The Sequential Linear Programming (SLP) level-set method is used to solve the constrained optimization problems. The proposed method is demonstrated using three problems with mass, linear buckling and flutter objective and/or constraints. A constraint aggregation method is used to handle multiple buckling constraints in the wing skins. A continuous flutter constraint formulation is used to handle difficulties arising from discontinuities in the design space caused by a switching of the critical flutter mode.
Constructing DNA Barcode Sets based on Particle Swarm Optimization.
Waang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi
2017-03-07
Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.
Parameterization of Model Validating Sets for Uncertainty Bound Optimizations. Revised
NASA Technical Reports Server (NTRS)
Lim, K. B.; Giesy, D. P.
2000-01-01
Given measurement data, a nominal model and a linear fractional transformation uncertainty structure with an allowance on unknown but bounded exogenous disturbances, easily computable tests for the existence of a model validating uncertainty set are given. Under mild conditions, these tests are necessary and sufficient for the case of complex, nonrepeated, block-diagonal structure. For the more general case which includes repeated and/or real scalar uncertainties, the tests are only necessary but become sufficient if a collinearity condition is also satisfied. With the satisfaction of these tests, it is shown that a parameterization of all model validating sets of plant models is possible. The new parameterization is used as a basis for a systematic way to construct or perform uncertainty tradeoff with model validating uncertainty sets which have specific linear fractional transformation structure for use in robust control design and analysis. An illustrative example which includes a comparison of candidate model validating sets is given.
S H bond dissociation enthalpies: The importance of a complete basis set approach
NASA Astrophysics Data System (ADS)
Cabral do Couto, P.; Costa Cabral, Benedito J.; Martinho Simões, José A.
2006-04-01
The S-H homolytic bond dissociation enthalpies (BDEs) for several compounds of reference were estimated by different theoretical methods including CCSD(T), CBS-QB3, and the multi-coefficient extrapolated density functional theory multi-level approaches, MCG3-MPWB and MCG3-TS. Emphasis was placed on the importance of extrapolating theoretical BDEs to complete basis set. A very good agreement between S-H BDEs from CCSD(T) calculations and experiment is observed when a simple dual extrapolation scheme to complete basis set proposed by Truhlar is adopted. For thiophenol, our CCSD(T) estimate for the S-H BDE (347.2 kJ mol -1) supports a recent experimental value obtained from time-resolved photoacoustic calorimetry (349 ± 5 kJ mol -1).
Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets
NASA Technical Reports Server (NTRS)
Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.
1990-01-01
Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.
Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets.
Jacobsen, Ruth L; Johnson, Russell D; Irikura, Karl K; Kacker, Raghu N
2013-02-12
Anharmonic calculations using vibrational perturbation theory are known to provide near-spectroscopic accuracy when combined with high-level ab initio potential energy functions. However, performance with economical, popular electronic structure methods is less well characterized. We compare the accuracy of harmonic and anharmonic predictions from Hartree-Fock, second-order perturbation, and density functional theories combined with 6-31G(d) and 6-31+G(d,p) basis sets. As expected, anharmonic frequencies are closer than harmonic frequencies to experimental fundamentals. However, common practice is to correct harmonic predictions using multiplicative scaling. The surprising conclusion is that scaled anharmonic calculations are no more accurate than scaled harmonic calculations for the basis sets we used. The data used are from the Computational Chemistry Comparison and Benchmark Database (CCCBDB), maintained by the National Institute of Standards and Technology, which includes more than 3939 independent vibrations for 358 molecules.
Comment on ``Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets''
NASA Astrophysics Data System (ADS)
Civalleri, Bartolomeo; Orlando, Roberto; Zicovich-Wilson, Claudio M.; Roetti, Carla; Saunders, Victor R.; Pisani, Cesare; Dovesi, Roberto
2010-03-01
In a recent paper on Hartree-Fock (HF) calculations on solid LiH with large Gaussian-type basis sets, Paier [Phys. Rev. B 80, 174114 (2009)] report a comment that we dispute: that similar calculations appear unlikely to be feasible using the CRYSTAL code. Here we show that using a full HF approach within periodic boundary conditions as implemented in the CRYSTAL code the same total energy is obtained as from the schemes adopted by Paier
Basis-set expansion and truncation approach to interacting Bose particles problem
NASA Astrophysics Data System (ADS)
Sze, Michelle Wynne; Sykes, Andrew; Corson, John; Bohn, John
2014-05-01
As ultracold gases push into regimes beyond mean-field physics, alternative approaches are required to follow their behavior. To this end, we investigate a basis set expansion and truncation scheme based on perturbation theory to obtain approximate ground state energies as a function of interaction parameter. We explore the ability of this approach to describe interacting Bose particles in 1D and 3D. AFOSR MURI, US DoD through the NDSEG Fellowship Program, and JILA PFC.
NASA Astrophysics Data System (ADS)
Poirier, Vincent
Mesh deformation schemes play an important role in numerical aerodynamic optimization. As the aerodynamic shape changes, the computational mesh must adapt to conform to the deformed geometry. In this work, an extension to an existing fast and robust Radial Basis Function (RBF) mesh movement scheme is presented. Using a reduced set of surface points to define the mesh deformation increases the efficiency of the RBF method; however, at the cost of introducing errors into the parameterization by not recovering the exact displacement of all surface points. A secondary mesh movement is implemented, within an adjoint-based optimization framework, to eliminate these errors. The proposed scheme is tested within a 3D Euler flow by reducing the pressure drag while maintaining lift of a wing-body configured Boeing-747 and an Onera-M6 wing. As well, an inverse pressure design is executed on the Onera-M6 wing and an inverse span loading case is presented for a wing-body configured DLR-F6 aircraft.
An ab initio investigation of disiloxane using extended basis sets and electron correlation
Nicholas, J.B.; Hopfinger, A.J.; Winans, R.E.
1992-10-01
The ab initio structure of disiloxane (H{sub 3}Si-O-SiH{sub 3}) is studied with a series of basis sets of increasing quality, including extended basis sets and explicit electron correlation at the single-reference single-and double-excitation configuration interaction (SDCI) level. The calculated molecular geometry and barrier to linearization of the Si-O-Si bond angle are compared to experimental and previous theoretical values. Results show that the rigorous expansion of the basis set leads to a good agreement with experimental data at the restricted Hartree-Fock (RHF) level. The potential energy curves and force constants for variation of the Si-O-Si angle and the Si-H and Si-O bond lengths are calculated and discussed in relationship to molecular modeling of zeolites and clays. The authors also investigated coupling between the Si-O bond and Si-O bond angle. They discuss the effects of temperature on the comparison between theoretical and experimental results. 46 refs., 4 figs., 4 tabs.
Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting
Das Sarma, Akash; Parameswaran, Aditya; Widom, Jennifer
2017-01-01
We study crowdsourcing quality management, that is, given worker responses to a set of tasks, our goal is to jointly estimate the true answers for the tasks, as well as the quality of the workers. Prior work on this problem relies primarily on applying Expectation-Maximization (EM) on the underlying maximum likelihood problem to estimate true answers as well as worker quality. Unfortunately, EM only provides a locally optimal solution rather than a globally optimal one. Other solutions to the problem (that do not leverage EM) fail to provide global optimality guarantees as well. In this paper, we focus on filtering, where tasks require the evaluation of a yes/no predicate, and rating, where tasks elicit integer scores from a finite domain. We design algorithms for finding the global optimal estimates of correct task answers and worker quality for the underlying maximum likelihood problem, and characterize the complexity of these algorithms. Our algorithms conceptually consider all mappings from tasks to true answers (typically a very large number), leveraging two key ideas to reduce, by several orders of magnitude, the number of mappings under consideration, while preserving optimality. We also demonstrate that these algorithms often find more accurate estimates than EM-based algorithms. This paper makes an important contribution towards understanding the inherent complexity of globally optimal crowdsourcing quality management. PMID:28149000
Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting.
Das Sarma, Akash; Parameswaran, Aditya; Widom, Jennifer
2016-01-01
We study crowdsourcing quality management, that is, given worker responses to a set of tasks, our goal is to jointly estimate the true answers for the tasks, as well as the quality of the workers. Prior work on this problem relies primarily on applying Expectation-Maximization (EM) on the underlying maximum likelihood problem to estimate true answers as well as worker quality. Unfortunately, EM only provides a locally optimal solution rather than a globally optimal one. Other solutions to the problem (that do not leverage EM) fail to provide global optimality guarantees as well. In this paper, we focus on filtering, where tasks require the evaluation of a yes/no predicate, and rating, where tasks elicit integer scores from a finite domain. We design algorithms for finding the global optimal estimates of correct task answers and worker quality for the underlying maximum likelihood problem, and characterize the complexity of these algorithms. Our algorithms conceptually consider all mappings from tasks to true answers (typically a very large number), leveraging two key ideas to reduce, by several orders of magnitude, the number of mappings under consideration, while preserving optimality. We also demonstrate that these algorithms often find more accurate estimates than EM-based algorithms. This paper makes an important contribution towards understanding the inherent complexity of globally optimal crowdsourcing quality management.
NASA Astrophysics Data System (ADS)
Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin
2017-06-01
With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.
Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook; Kim, Woo Youn
2015-03-07
We developed a self-consistent field program based on Kohn-Sham density functional theory using Lagrange-sinc functions as a basis set and examined its numerical accuracy for atoms and molecules through comparison with the results of Gaussian basis sets. The result of the Kohn-Sham inversion formula from the Lagrange-sinc basis set manifests that the pseudopotential method is essential for cost-effective calculations. The Lagrange-sinc basis set shows faster convergence of the kinetic and correlation energies of benzene as its size increases than the finite difference method does, though both share the same uniform grid. Using a scaling factor smaller than or equal to 0.226 bohr and pseudopotentials with nonlinear core correction, its accuracy for the atomization energies of the G2-1 set is comparable to all-electron complete basis set limits (mean absolute deviation ≤1 kcal/mol). The same basis set also shows small mean absolute deviations in the ionization energies, electron affinities, and static polarizabilities of atoms in the G2-1 set. In particular, the Lagrange-sinc basis set shows high accuracy with rapid convergence in describing density or orbital changes by an external electric field. Moreover, the Lagrange-sinc basis set can readily improve its accuracy toward a complete basis set limit by simply decreasing the scaling factor regardless of systems.
Using symmetry-adapted optimized sum-of-products basis functions to calculate vibrational spectra
NASA Astrophysics Data System (ADS)
Leclerc, Arnaud; Carrington, Tucker
2016-01-01
Vibrational spectra can be computed without storing full-dimensional vectors by using low-rank sum-of-products (SOP) basis functions. We introduce symmetry constraints in the SOP basis functions to make it possible to separately calculate states in different symmetry subgroups. This is done using a power method to compute eigenvalues and an alternating least squares method to optimize basis functions. Owing to the fact that the power method favours the convergence of the lowest states, one must be careful not to exclude basis functions of some symmetries. Exploiting symmetry facilitates making assignments and improves the accuracy. The method is applied to the acetonitrile molecule.
An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification.
Wang, Jun; Samal, Ashok; Rong, Panying; Green, Jordan R
2016-02-01
The authors sought to determine an optimal set of flesh points on the tongue and lips for classifying speech movements. 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. 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). 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.
Ghost transmission: How large basis sets can make electron transport calculations worse
Herrmann, Carmen; Solomon, Gemma C.; Subotnik, Joseph E.; Mujica, Vladimiro; Ratner, Mark A.
2010-01-01
The Landauer approach has proven to be an invaluable tool for calculating the electron transport properties of single molecules, especially when combined with a nonequilibrium Green’s function approach and Kohn–Sham density functional theory. However, when using large nonorthogonal atom-centered basis sets, such as those common in quantum chemistry, one can find erroneous results if the Landauer approach is applied blindly. In fact, basis sets of triple-zeta quality or higher sometimes result in an artificially high transmission and possibly even qualitatively wrong conclusions regarding chemical trends. In these cases, transport persists when molecular atoms are replaced by basis functions alone (“ghost atoms”). The occurrence of such ghost transmission is correlated with low-energy virtual molecular orbitals of the central subsystem and may be interpreted as a biased and thus inaccurate description of vacuum transmission. An approximate practical correction scheme is to calculate the ghost transmission and subtract it from the full transmission. As a further consequence of this study, it is recommended that sensitive molecules be used for parameter studies, in particular those whose transmission functions show antiresonance features such as benzene-based systems connected to the electrodes in meta positions and other low-conducting systems such as alkanes and silanes.
NASA Astrophysics Data System (ADS)
Wang, Yingjun; Benson, David J.
2016-12-01
In this paper, an approach based on the fast point-in-polygon (PIP) algorithm and trimmed elements is proposed for isogeometric topology optimization (TO) with arbitrary geometric constraints. The isogeometric parameterized level-set-based TO method, which directly uses the non-uniform rational basis splines (NURBS) for both level set function (LSF) parameterization and objective function calculation, provides higher accuracy and efficiency than previous methods. The integration of trimmed elements is completed by the efficient quadrature rule that can design the quadrature points and weights for arbitrary geometric shape. Numerical examples demonstrate the efficiency and flexibility of the method.
Kinetically balanced Gaussian basis-set approach to relativistic Compton profiles of atoms
Jaiswal, Prerit; Shukla, Alok
2007-02-15
Atomic Compton profiles (CPs) are a very important property which provide us information about the momentum distribution of atomic electrons. Therefore, for CPs of heavy atoms, relativistic effects are expected to be important, warranting a relativistic treatment of the problem. In this paper, we present an efficient approach aimed at ab initio calculations of atomic CPs within a Dirac-Hartree-Fock (DHF) formalism, employing kinetically balanced Gaussian basis functions. The approach is used to compute the CPs of noble gases ranging from He to Rn, and the results have been compared to the experimental and other theoretical data, wherever possible. The influence of the quality of the basis set on the calculated CPs has also been systematically investigated.
Optimal power settings for Holmium:YAG lithotripsy.
Sea, Jason; Jonat, Lee M; Chew, Ben H; Qiu, Jinze; Wang, Bingqing; Hoopman, John; Milner, Thomas; Teichman, Joel M H
2012-03-01
We determined the optimal Ho:YAG lithotripsy power settings to achieve maximal fragmentation, minimal fragment size and minimal retropulsion. Stone phantoms were irradiated in water with a Ho:YAG laser using a 365 μm optical fiber. Six distinct power settings were tested, including 0.2 to 2.0 J and 10 to 40 Hz. For all cohorts 500 J total radiant energy were delivered. A seventh cohort (0.2 J 40 Hz) was tested post hoc to a total energy of 1,250 J. Two experimental conditions were tested, including with and without phantom stabilization. Total fragmentation, fragment size and retropulsion were characterized. In mechanism experiments using human calculi we measured crater volume by optical coherence tomography and pressure transients by needle hydrophone across similar power settings. Without stabilization increased pulse energy settings produced increased total fragmentation and increased retropulsion (each p <0.0001). Fragment size was smallest for the 0.2 J cohorts (p <0.02). With stabilization increased pulse energy settings produced increased total fragmentation and increased retropulsion but also increased fragment size (each p <0.0001). Craters remained symmetrical and volume increased as pulse energy increased. Pressure transients remained modest at less than 30 bars even at 2.0 J pulse energy. Holmium:YAG lithotripsy varies as pulse energy settings vary. At low pulse energy (0.2 J) less fragmentation and retropulsion occur and small fragments are produced. At high pulse energy (2.0 J) more fragmentation and retropulsion occur with larger fragments. Anti-retropulsion devices produce more efficient lithotripsy, particularly at high pulse energy. Optimal lithotripsy laser dosimetry depends on the desired outcome. Copyright © 2012 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.
Grimme, Stefan Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-07
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-07
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods
NASA Astrophysics Data System (ADS)
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-01
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods
Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz
2014-02-01
Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.
NASA Astrophysics Data System (ADS)
Hübener, H.; Pérez-Osorio, M. A.; Ordejón, P.; Giustino, F.
2012-09-01
We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81, 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices of silicon and diamond calculated using our method fall within 1% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional ζ's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods.
An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification
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
FDR-FET: an optimizing gene set enrichment analysis method.
Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E
2011-01-01
Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher's exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications.
Variational Trajectory Optimization Tool Set: Technical description and user's manual
NASA Technical Reports Server (NTRS)
Bless, Robert R.; Queen, Eric M.; Cavanaugh, Michael D.; Wetzel, Todd A.; Moerder, Daniel D.
1993-01-01
The algorithms that comprise the Variational Trajectory Optimization Tool Set (VTOTS) package are briefly described. The VTOTS is a software package for solving nonlinear constrained optimal control problems from a wide range of engineering and scientific disciplines. The VTOTS package was specifically designed to minimize the amount of user programming; in fact, for problems that may be expressed in terms of analytical functions, the user needs only to define the problem in terms of symbolic variables. This version of the VTOTS does not support tabular data; thus, problems must be expressed in terms of analytical functions. The VTOTS package consists of two methods for solving nonlinear optimal control problems: a time-domain finite-element algorithm and a multiple shooting algorithm. These two algorithms, under the VTOTS package, may be run independently or jointly. The finite-element algorithm generates approximate solutions, whereas the shooting algorithm provides a more accurate solution to the optimization problem. A user's manual, some examples with results, and a brief description of the individual subroutines are included.
Extrapolation of G0W0 energy levels from small basis sets for elements from H to Cl
NASA Astrophysics Data System (ADS)
Zhu, Tong; Blum, Volker
G0W0 calculations based on orbitals from a density-functional theory reference are widely used to predict carrier levels in molecular and inorganic materials. Their computational feasibility, however, is limited by the need to evaluate slow-converging sums over unoccupied states, requiring large basis sets paired with unfavorable scaling exponents to evaluate the self-energy. In the quantum chemistry literature, complete basis set (CBS) extrapolation strategies have been used successfully to overcome this problem for total energies. We here apply the principle of basis set extrapolation to G0W0 energy levels. For a set of 49 small molecules and clusters containing the elements H, Li through F, and Na through Cl, we test established extrapolation strategies based on Dunning's correlation-consistent (cc) basis sets (aug)-cc-pVNZ (N=2-5), as well as numeric atom-centered NAO-VCC-nZ (n=2-5) basis sets in the FHI-aims all-electron code. For the occupied and lowest unoccupied levels, different extrapolation strategies agree within +/-50 meV based on large 4Z and 5Z basis sets. We show that extrapolation based on much smaller 2Z and 3Z basis sets with largest errors +/- 100 meV based on a refinement of the NAO-VCC-nZ basis sets.
Optimizing antibiotic therapy in the intensive care unit setting
Kollef, Marin H
2001-01-01
Antibiotics are one of the most common therapies administered in the intensive care unit setting. In addition to treating infections, antibiotic use contributes to the emergence of resistance among pathogenic microorganisms. Therefore, avoiding unnecessary antibiotic use and optimizing the administration of antimicrobial agents will help to improve patient outcomes while minimizing further pressures for resistance. This review will present several strategies aimed at achieving optimal use of antimicrobial agents. It is important to note that each intensive care unit should have a program in place which monitors antibiotic utilization and its effectiveness. Only in this way can the impact of interventions aimed at improving antibiotic use (e.g. antibiotic rotation, de-escalation therapy) be evaluated at the local level. PMID:11511331
NASA Technical Reports Server (NTRS)
Lewis, Robert Michael
1995-01-01
This paper discusses certain connections between nonlinear programming algorithms and the formulation of optimization problems for systems governed by state constraints. The major points of this paper are the detailed calculation of the sensitivities associated with different formulations of optimization problems and the identification of some useful relationships between different formulations. These relationships have practical consequences; if one uses a reduced basis nonlinear programming algorithm, then the implementations for the different formulations need only differ in a single step.
Chacon-Madrid, Heber J; Murphy, Benjamin N; Pandis, Spyros N; Donahue, Neil M
2012-10-16
We use a two-dimensional volatility basis set (2D-VBS) box model to simulate secondary organic aerosol (SOA) mass yields of linear oxygenated molecules: n-tridecanal, 2- and 7-tridecanone, 2- and 7-tridecanol, and n-pentadecane. A hybrid model with explicit, a priori treatment of the first-generation products for each precursor molecule, followed by a generic 2D-VBS mechanism for later-generation chemistry, results in excellent model-measurement agreement. This strongly confirms that the 2D-VBS mechanism is a predictive tool for SOA modeling but also suggests that certain important first-generation products for major primary SOA precursors should be treated explicitly for optimal SOA predictions.
FDR-FET: an optimizing gene set enrichment analysis method
Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E
2011-01-01
Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as “gene sets”. Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher’s exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications. PMID:21918636
Optimization of the generator settings for endobiliary radiofrequency ablation.
Barret, Maximilien; Leblanc, Sarah; Vienne, Ariane; Rouquette, Alexandre; Beuvon, Frederic; Chaussade, Stanislas; Prat, Frederic
2015-11-10
To determine the optimal generator settings for endobiliary radiofrequency ablation. Endobiliary radiofrequency ablation was performed in live swine on the ampulla of Vater, the common bile duct and in the hepatic parenchyma. Radiofrequency ablation time, "effect", and power were allowed to vary. The animals were sacrificed two hours after the procedure. Histopathological assessment of the depth of the thermal lesions was performed. Twenty-five radiofrequency bursts were applied in three swine. In the ampulla of Vater (n = 3), necrosis of the duodenal wall was observed starting with an effect set at 8, power output set at 10 W, and a 30 s shot duration, whereas superficial mucosal damage of up to 350 μm in depth was recorded for an effect set at 8, power output set at 6 W and a 30 s shot duration. In the common bile duct (n = 4), a 1070 μm, safe and efficient ablation was obtained for an effect set at 8, a power output of 8 W, and an ablation time of 30 s. Within the hepatic parenchyma (n = 18), the depth of tissue damage varied from 1620 μm (effect = 8, power = 10 W, ablation time = 15 s) to 4480 μm (effect = 8, power = 8 W, ablation time = 90 s). The duration of the catheter application appeared to be the most important parameter influencing the depth of the thermal injury during endobiliary radiofrequency ablation. In healthy swine, the currently recommended settings of the generator may induce severe, supratherapeutic tissue damage in the biliary tree, especially in the high-risk area of the ampulla of Vater.
Asynchronous parallel generating set search for linearly-constrained optimization.
Lewis, Robert Michael; Griffin, Joshua D.; Kolda, Tamara Gibson
2006-08-01
Generating set search (GSS) is a family of direct search methods that encompasses generalized pattern search and related methods. We describe an algorithm for asynchronous linearly-constrained GSS, which has some complexities that make it different from both the asynchronous bound-constrained case as well as the synchronous linearly-constrained case. The algorithm has been implemented in the APPSPACK software framework and we present results from an extensive numerical study using CUTEr test problems. We discuss the results, both positive and negative, and conclude that GSS is a reliable method for solving small-to-medium sized linearly-constrained optimization problems without derivatives.
Analytic basis set for high-Z atomic QED calculations: Heavy He-like ions
Hylton, D.J.; Snyderman, N.J.
1997-04-01
A relativistic Sturmian analytic basis set representation for the Coulomb-Dirac Green function, previously studied by Zapryagaev, Manakov, and Pal{close_quote}chikov [Opt. Spectrosc. {bold 52}, 248 (1982)], is investigated for application to high-Z atomic QED calculations. This pseudoeigenfunction representation follows from exact identities starting from the Whittaker function representation. It eliminates the radial ordering problem of that representation, and so is particularly useful for numerical calculation of the perturbation theory Feynman diagrams with more than one electron Green function. While the Green function represents discrete bound states, and both positive and negative energy continuum states, the Sturmian (bound-state-like) form for the pseudoeigenfunctions makes it possible to more analytically calculate matrix elements for full photon exchange, reducing numerical problems for high photon frequency. For He-like Fm (Z=100) we calculate the perturbation theory equivalent of the Dirac-Fock-Breit ground-state energy, agreeing well with the Grant code and with the numerical B-spline basis set approach results of Blundell, Mohr, Johnson, and Sapirstein [Phys. Rev. A {bold 48}, 2615 (1993)]. Preliminary results on the relativistic and QED correlation are also reported. {copyright} {ital 1997} {ital The American Physical Society}
Analytic basis set for high-Z atomic QED calculations: Heavy He-like ions
NASA Astrophysics Data System (ADS)
Hylton, D. J.; Snyderman, N. J.
1997-04-01
A relativistic Sturmian analytic basis set representation for the Coulomb-Dirac Green function, previously studied by Zapryagaev, Manakov, and Pal'chikov [Opt. Spectrosc. 52, 248 (1982)], is investigated for application to high-Z atomic QED calculations. This pseudoeigenfunction representation follows from exact identities starting from the Whittaker function representation. It eliminates the radial ordering problem of that representation, and so is particularly useful for numerical calculation of the perturbation theory Feynman diagrams with more than one electron Green function. While the Green function represents discrete bound states, and both positive and negative energy continuum states, the Sturmian (bound-state-like) form for the pseudoeigenfunctions makes it possible to more analytically calculate matrix elements for full photon exchange, reducing numerical problems for high photon frequency. For He-like Fm (Z=100) we calculate the perturbation theory equivalent of the Dirac-Fock-Breit ground-state energy, agreeing well with the Grant code and with the numerical B-spline basis set approach results of Blundell, Mohr, Johnson, and Sapirstein [Phys. Rev. A 48, 2615 (1993)]. Preliminary results on the relativistic and QED correlation are also reported.
Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.
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.
An active set algorithm for treatment planning optimization.
Hristov, D H; Fallone, B G
1997-09-01
An active set algorithm for optimization of radiation therapy dose planning by intensity modulated beams has been developed. The algorithm employs a conjugate-gradient routine for subspace minimization in order to achieve a higher rate of convergence than the widely used constrained steepest-descent method at the expense of a negligible amount of overhead calculations. The performance of the new algorithm has been compared to that of the constrained steepest-descent method for various treatment geometries and two different objectives. The active set algorithm is found to be superior to the constrained steepest descent, both in terms of its convergence properties and the residual value of the cost functions at termination. Its use can significantly accelerate the design of conformal plans with intensity modulated beams by decreasing the number of time-consuming dose calculations.
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 H2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less
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.
Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism
Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.
2014-11-04
Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number L_{max} = (l,m)_{max}, while scattering matrices, which determine spectral properties, are truncated at L_{tr} = (l,m)_{tr} where phase shifts δl>l_{tr} are negligible. Historically, L_{max} is set equal to L_{tr}, which is correct for large enough L_{max} but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for L_{max} > L_{tr} with δl>l_{tr} set to zero [Zhang and Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R^{3} process with rank N(l_{tr} + 1)^{2}] and includes higher-L contributions via linear algebra [R^{2} process with rank N(l_{max} +1)^{2}]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L1_{0} CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus L_{max} for a given L_{tr}.
Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism
Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; ...
2014-11-04
Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an ecient sitecentered, electronic-structure technique for addressing an assembly of N scatterers. Wave-functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax = (l,m)max, while scattering matrices, which determine spectral properties, are truncated at Ltr = (l,m)tr where phase shifts δl>ltr are negligible. Historically, Lmax is set equal to Ltr, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax > Ltr with δl>ltr set to zero [Zhang andmore » Butler, Phys. Rev. B 46, 7433]. We present a numerically ecient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N(ltr + 1)2] and includes higher-L contributions via linear algebra [R2 process with rank N(lmax +1)2]. Augmented-KKR approach yields properly normalized wave-functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe and L10 CoPt, and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Ltr.« less
Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism
NASA Astrophysics Data System (ADS)
Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.
2014-11-01
The Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an efficient site-centered, electronic-structure technique for addressing an assembly of N scatterers. Wave functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax=(l,mmax), while scattering matrices, which determine spectral properties, are truncated at Lt r=(l,mt r) where phase shifts δl >ltr are negligible. Historically, Lmax is set equal to Lt r, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax>Lt r with δl >ltr set to zero [X.-G. Zhang and W. H. Butler, Phys. Rev. B 46, 7433 (1992), 10.1103/PhysRevB.46.7433]. We present a numerically efficient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N (ltr+1 ) 2 ] and includes higher-L contributions via linear algebra [R2 process with rank N (lmax+1) 2 ]. The augmented-KKR approach yields properly normalized wave functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe, and L 1 0 CoPt and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Lt r.
Optimal sets of measurement data for profile reconstruction in scatterometry
NASA Astrophysics Data System (ADS)
Gross, H.; Rathsfeld, A.; Scholze, F.; Bär, M.; Dersch, U.
2007-06-01
We discuss numerical algorithms for the determination of periodic surface structures from light diffraction patterns. With decreasing feature sizes of lithography masks, increasing demands on metrology techniques arise. Scatterometry as a non-imaging indirect optical method is applied to simple periodic line structures in order to determine parameters like side-wall angles, heights, top and bottom widths and to evaluate the quality of the manufacturing process. The numerical simulation of diffraction is based on the finite element solution of the Helmholtz equation. The inverse problem seeks to reconstruct the grating geometry from measured diffraction patterns. Restricting the class of gratings and the set of measurements, this inverse problem can be reformulated as a non-linear operator equation in Euclidean spaces. The operator maps the grating parameters to special efficiencies of diffracted plane wave modes. We employ a Gauss-Newton type iterative method to solve this operator equation. The reconstruction properties and the convergence of the algorithm, however, is controlled by the local conditioning of the non-linear mapping. To improve reconstruction and convergence, we determine optimal sets of efficiencies optimizing the condition numbers of the corresponding Jacobians. Numerical examples are presented for "chrome on glass" masks under the wavelength 632.8 nm and for EUV masks.
Qualitative optimization of image processing systems using random set modeling
NASA Astrophysics Data System (ADS)
Kelly, Patrick A.; Derin, Haluk; Vaidya, Priya G.
2000-08-01
Many decision-making systems involve image processing that converts input sensor data into output images having desirable features. Typically, the system user selects some processing parameters. The processor together with the input image can then be viewed as a system that maps the processing parameters into output features. However, the most significant output features often are not numerical quantities, but instead are subjective measures of image quality. It can be a difficult task for a user to find the processing parameters that give the 'best' output. We wish to automate this qualitative optimization task. The key to this is incorporation linguistic operating rules and qualitative output parameters in a numerical optimization scheme. In this paper, we use the test system of input parameter selection for 2D Wiener filtering to restore noisy and blurred images. Operating rules represented with random sets are used to generate a nominal input-output system model, which is then used to select initial Wiener filter input parameters. Whenthe nominally optimal Wiener filter is applied to an observed image, the operator's assessment of output image quality is used in an adaptive filtering algorithm to adjust the model and select new input parameters. Test on several images have confirmed that with a few such iterations, a significant improvement in output quality is achieved.
TiCl, TiH and TiH+ Bond Energies, a Test of a Correlation Consistent Ti Basis Set
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)
1999-01-01
Correlation consistent basis sets are developed for Ti atom. The polarization functions are optimized for the average of the 3F and 5F states. One series of correlation consistent basis sets is for 3d and 4s correlation, while the second series includes 3s and 3p correlation as well as 3d and 4s correlation. These basis sets are tested using the Ti 3F-5F separation and the dissociation energies of TiCl X4Phi, TiH X4Phi, and TiH(+) X3Phi. The CCSD(T) complete basis set limit values are determined by extrapolation. The Douglas Kroll approach is used to compute the scalar relativistic effect. Spin-orbit effects are taken from experiment and/or computed at the CASSCF level. The Ti 3F-5F separation is in excellent agreement with experiment, while the TiCl, TiH, and TiH(+) bond energies are in good agreement with experiment. Extrapolation with the valence basis set is consistent with other atoms, while including 3s and 3p correlation appears to make extrapolation.
Nada, R.; Nicholas, J.B.; McCarthy, M.I.; Hess, A.C.
1996-11-15
Silica sodalite is an ideal model system to establish base-line computer requirements of ab initio periodic Hartree-Fock (PHF) calculations of zeolites. In this article, the authors investigate the effect of various basis sets on the structural and electronic properties of bulk silica sodalite. They also study the interaction of He, Ne, and Ar with the sodalite cage. This work shows that basis-set superposition errors (BSSE) in calculations using STO-3G and 6-21G(*) basis sets are as large as the interaction energies, leading to poor confidence in the results. To cure this problem, the authors present high-quality basis sets for si, O, He, Ne, and Ar, optimized for use with PHF methods, and demonstrate that the new basis set greatly reduces BSSE. The theoretical barriers for transfer of the rare gases between sodalite cages are 5.6, 13.2, and 62.1 kcal/mol for He, Ne, and Ar. 27 refs., 6 figs., 8 tabs.
A restricted-open-shell complete-basis-set model chemistry
NASA Astrophysics Data System (ADS)
Wood, Geoffrey P. F.; Radom, Leo; Petersson, George A.; Barnes, Ericka C.; Frisch, Michael J.; Montgomery, John A.
2006-09-01
A restricted-open-shell model chemistry based on the complete basis set-quadratic Becke3 (CBS-QB3) model is formulated and denoted ROCBS-QB3. As the name implies, this method uses spin-restricted wave functions, both for the direct calculations of the various components of the electronic energy and for extrapolating the correlation energy to the complete-basis-set limit. These modifications eliminate the need for empirical corrections that are incorporated in standard CBS-QB3 to compensate for spin contamination when spin-unrestricted wave functions are used. We employ an initial test set of 19 severely spin-contaminated species including doublet radicals and both singlet and triplet biradicals. The mean absolute deviation (MAD) from experiment for the new ROCBS-QB3 model (3.6±1.5kJmol-1) is slightly smaller than that of the standard unrestricted CBS-QB3 version (4.8±1.5kJmol-1) and substantially smaller than the MAD for the unrestricted CBS-QB3 before inclusion of the spin correction (16.1±1.5kJmol-1). However, when applied to calculate the heats of formation at 298K for the moderately spin-contaminated radicals in the G2/97 test set, ROCBS-QB3 does not perform quite as well as the standard unrestricted CBS-QB3, with a MAD from experiment of 3.8±1.6kJmol-1 (compared with 2.9±1.6kJmol-1 for standard CBS-QB3). ROCBS-QB3 performs marginally better than standard CBS-QB3 for the G2/97 set of ionization energies with a MAD of 4.1±0.1kJmol-1 (compared with 4.4±0.1kJmol-1) and electron affinities with a MAD of 3.9±0.2kJmol-1 (compared with 4.3±0.2kJmol-1), but the differences in MAD values are comparable to the experimental uncertainties. Our overall conclusion is that ROCBS-QB3 eliminates the spin correction in standard CBS-QB3 with no loss in accuracy.
A restricted-open-shell complete-basis-set model chemistry.
Wood, Geoffrey P F; Radom, Leo; Petersson, George A; Barnes, Ericka C; Frisch, Michael J; Montgomery, John A
2006-09-07
A restricted-open-shell model chemistry based on the complete basis set-quadratic Becke3 (CBS-QB3) model is formulated and denoted ROCBS-QB3. As the name implies, this method uses spin-restricted wave functions, both for the direct calculations of the various components of the electronic energy and for extrapolating the correlation energy to the complete-basis-set limit. These modifications eliminate the need for empirical corrections that are incorporated in standard CBS-QB3 to compensate for spin contamination when spin-unrestricted wave functions are used. We employ an initial test set of 19 severely spin-contaminated species including doublet radicals and both singlet and triplet biradicals. The mean absolute deviation (MAD) from experiment for the new ROCBS-QB3 model (3.6+/-1.5 kJ mol(-1)) is slightly smaller than that of the standard unrestricted CBS-QB3 version (4.8+/-1.5 kJ mol(-1)) and substantially smaller than the MAD for the unrestricted CBS-QB3 before inclusion of the spin correction (16.1+/-1.5 kJ mol(-1)). However, when applied to calculate the heats of formation at 298 K for the moderately spin-contaminated radicals in the G2/97 test set, ROCBS-QB3 does not perform quite as well as the standard unrestricted CBS-QB3, with a MAD from experiment of 3.8+/-1.6 kJ mol(-1) (compared with 2.9+/-1.6 kJ mol(-1) for standard CBS-QB3). ROCBS-QB3 performs marginally better than standard CBS-QB3 for the G2/97 set of ionization energies with a MAD of 4.1+/-0.1 kJ mol(-1) (compared with 4.4+/-0.1 kJ mol(-1)) and electron affinities with a MAD of 3.9+/-0.2 kJ mol(-1) (compared with 4.3+/-0.2 kJ mol(-1)), but the differences in MAD values are comparable to the experimental uncertainties. Our overall conclusion is that ROCBS-QB3 eliminates the spin correction in standard CBS-QB3 with no loss in accuracy.
CONORBIT: constrained optimization by radial basis function interpolation in trust regions
Regis, Rommel G.; Wild, Stefan M.
2016-09-26
Here, this paper presents CONORBIT (CONstrained Optimization by Radial Basis function Interpolation in Trust regions), a derivative-free algorithm for constrained black-box optimization where the objective and constraint functions are computationally expensive. CONORBIT employs a trust-region framework that uses interpolating radial basis function (RBF) models for the objective and constraint functions, and is an extension of the ORBIT algorithm. It uses a small margin for the RBF constraint models to facilitate the generation of feasible iterates, and extensive numerical tests confirm that such a margin is helpful in improving performance. CONORBIT is compared with other algorithms on 27 test problems, a chemical process optimization problem, and an automotive application. Numerical results show that CONORBIT performs better than COBYLA, a sequential penalty derivative-free method, an augmented Lagrangian method, a direct search method, and another RBF-based algorithm on the test problems and on the automotive application.
Optimization of head movement recognition using Augmented Radial Basis Function Neural Network.
Yuwono, Mitchell; Handojoseno, A M Ardi; Nguyen, H T
2011-01-01
For people with severe spine injury, head movement recognition control has been proven to be one of the most convenient and intuitive ways to control a power wheelchair. While substantial research has been done in this area, the challenge to improve system reliability and accuracy remains due to the diversity in movement tendencies and the presence of movement artifacts. We propose a Neural-Network Configuration which we call Augmented Radial Basis Function Neural-Network (ARBF-NN). This network is constructed as a Radial Basis Function Neural-Network (RBF-NN) with a Multilayer Perceptron (MLP) augmentation layer to negate optimization limitation posed by linear classifiers in conventional RBF-NN. The RBF centroid is optimized through Regrouping Particle Swarm Optimization (RegPSO) seeded with K-Means. The trial results of ARBF-NN on Head-movement show a significant improvement on recognition accuracy up to 98.1% in sensitivity.
CONORBIT: constrained optimization by radial basis function interpolation in trust regions
Regis, Rommel G.; Wild, Stefan M.
2016-09-26
Here, this paper presents CONORBIT (CONstrained Optimization by Radial Basis function Interpolation in Trust regions), a derivative-free algorithm for constrained black-box optimization where the objective and constraint functions are computationally expensive. CONORBIT employs a trust-region framework that uses interpolating radial basis function (RBF) models for the objective and constraint functions, and is an extension of the ORBIT algorithm. It uses a small margin for the RBF constraint models to facilitate the generation of feasible iterates, and extensive numerical tests confirm that such a margin is helpful in improving performance. CONORBIT is compared with other algorithms on 27 test problems, amore » chemical process optimization problem, and an automotive application. Numerical results show that CONORBIT performs better than COBYLA, a sequential penalty derivative-free method, an augmented Lagrangian method, a direct search method, and another RBF-based algorithm on the test problems and on the automotive application.« less
States that "look the same" with respect to every basis in a mutually unbiased set
NASA Astrophysics Data System (ADS)
Amburg, Ilya; Sharma, Roshan; Sussman, Daniel M.; Wootters, William K.
2014-12-01
A complete set of mutually unbiased bases (MUBs) in a Hilbert space of dimension d defines a set of d + 1 orthogonal measurements. Relative to such a set, we define a MUB-balanced state to be a pure state for which the list of probabilities of the d outcomes of any of these measurements is independent of the choice of measurement, up to permutations. In this paper, we explicitly construct a MUB-balanced state for each prime power dimension d for which d = 3 (mod 4). These states have already been constructed by Appleby in unpublished notes, but our presentation here is different in that both the expression for the states themselves and the proof of MUB-balancedness are given in terms of the discrete Wigner function, rather than the density matrix or state vector. The discrete Wigner functions of these states are "rotationally symmetric" in a sense roughly analogous to the rotational symmetry of the energy eigenstates of a harmonic oscillator in the continuous two-dimensional phase space. Upon converting the Wigner function to a density matrix, we find that the states are expressible as real state vectors in the standard basis. We observe numerically that when d is large (and not a power of 3), a histogram of the components of such a state vector appears to form a semicircular distribution.
Relativistic correlating basis sets for actinide atoms from 90Th to 103Lr.
Noro, Takeshi; Sekiya, Masahiro; Osanai, You; Koga, Toshikatsu; Matsuyama, Hisashi
2007-12-01
For 14 actinide atoms from (90)Th to (103)Lr, contracted Gaussian-type function sets are developed for the description of correlations of the 5f, 6d, and 7s electrons. Basis sets for the 6d orbitals are also prepared, since the orbitals are important in molecular environments despite their vacancy in the ground state of some actinides. A segmented contraction scheme is employed for the compactness and efficiency. Contraction coefficients and exponents are so determined as to minimize the deviation from accurate natural orbitals of the lowest term arising from the 5f(n-1)6d(1)7s(2) configuration. The spin-free relativistic effects are considered through the third-order Douglas-Kroll approximation. To test the present correlating sets, all-electron calculations are performed on the ground state of (90)ThO molecule. The calculated spectroscopic constants are in excellent agreement with experimental values. (c) 2007 Wiley Periodicals, Inc.
Kawashima, Yukio; Hirao, Kimihiko
2017-03-09
We introduced two methods to correct the singularity in the calculation of long-range Hartree-Fock (HF) exchange for long-range-corrected density functional theory (LC-DFT) calculations in plane-wave basis sets. The first method introduces an auxiliary function to cancel out the singularity. The second method introduces a truncated long-range Coulomb potential, which has no singularity. We assessed the introduced methods using the LC-BLYP functional by applying it to isolated systems of naphthalene and pyridine. We first compared the total energies and the HOMO energies of the singularity-corrected and uncorrected calculations and confirmed that singularity correction is essential for LC-DFT calculations using plane-wave basis sets. The LC-DFT calculation results converged rapidly with respect to the cell size as the other functionals, and their results were in good agreement with the calculated results obtained using Gaussian basis sets. LC-DFT succeeded in obtaining accurate orbital energies and excitation energies. We next applied LC-DFT with singularity correction methods to the electronic structure calculations of the extended systems, Si and SiC. We confirmed that singularity correction is important for calculations of extended systems as well. The calculation results of the valence and conduction bands by LC-BLYP showed good convergence with respect to the number of k points sampled. The introduced methods succeeded in overcoming the singularity problem in HF exchange calculation. We investigated the effect of the singularity correction on the excitation state calculation and found that careful treatment of the singularities is required compared to ground-state calculations. We finally examined the excitonic effect on the band gap of the extended systems. We calculated the excitation energies to the first excited state of the extended systems using a supercell model at the Γ point and found that the excitonic binding energy, supposed to be small for
Mathieson, Luke; Mendes, Alexandre; Marsden, John; Pond, Jeffrey; Moscato, Pablo
2017-01-01
This chapter introduces a new method for knowledge extraction from databases for the purpose of finding a discriminative set of features that is also a robust set for within-class classification. Our method is generic and we introduce it here in the field of breast cancer diagnosis from digital mammography data. The mathematical formalism is based on a generalization of the k-Feature Set problem called (α, β)-k-Feature Set problem, introduced by Cotta and Moscato (J Comput Syst Sci 67(4):686-690, 2003). This method proceeds in two steps: first, an optimal (α, β)-k-feature set of minimum cardinality is identified and then, a set of classification rules using these features is obtained. We obtain the (α, β)-k-feature set in two phases; first a series of extremely powerful reduction techniques, which do not lose the optimal solution, are employed; and second, a metaheuristic search to identify the remaining features to be considered or disregarded. Two algorithms were tested with a public domain digital mammography dataset composed of 71 malignant and 75 benign cases. Based on the results provided by the algorithms, we obtain classification rules that employ only a subset of these features.
Li, Z.; Pan, Y.K.; Tao, F.M.
1996-01-15
Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.
AgH, Ag/sub 2/, and AgO revisited: Basis set extensions
Martin, R.L.
1987-05-01
An extended basis set has been developed for Ag which significantly improves the agreement between theoretical and experimental spectroscopic parameters for AgH, AgO, and Ag/sub 2/. The major improvement comes about as a result of the improved treatment of electron correlation in the Ag d shell upon the introduction of f functions. Their inclusion produces very slight differences at the SCF level, but significant reductions in r/sub e/ and increases in ..omega../sub e/ and D/sub e/ in the Mo-dash-barller--Plesset perturbation theory expansion. At the MP4(SDTQ) level, typical results are 0.02 A too long for r/sub e/, 4% too low for ..omega../sub e/, and 10 kcal too small for D/sub e/. From a pragmatic standpoint, MP2 give results very similar to this at a much reduced level of effort.
Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets
NASA Astrophysics Data System (ADS)
Paier, Joachim; Diaconu, Cristian V.; Scuseria, Gustavo E.; Guidon, Manuel; Vandevondele, Joost; Hutter, Jürg
2009-11-01
Calculating highly accurate thermochemical properties of condensed matter via wave-function-based approaches (such as, e.g., Hartree-Fock or hybrid functionals) has recently attracted much interest. We here present two strategies providing accurate Hartree-Fock energies for solid LiH in a large Gaussian basis set and applying periodic boundary conditions. The total energies were obtained using two different approaches, namely, a supercell evaluation of Hartree-Fock exchange using a truncated Coulomb operator and an extrapolation toward the full-range Hartree-Fock limit of a Padé fit to a series of short-range screened Hartree-Fock calculations. These two techniques agreed to significant precision. We also present the Hartree-Fock cohesive energy of LiH (converged to within sub-millielectron volt) at the experimental equilibrium volume as well as the Hartree-Fock equilibrium lattice constant and bulk modulus.
Phosgene at the complete basis set limit of CCSDT(Q): Molecular structure and rovibrational analysis
NASA Astrophysics Data System (ADS)
Murphy, Kevin V.; Schaefer, Henry F.; Agarwal, Jay
2017-09-01
The ground-state (X∼1A″) equilibrium geometry of phosgene is examined with coupled-cluster theory, using derivatives extrapolated to the complete basis set (CBS) limit of CCSDT(Q). The C-O and C-Cl bond lengths are predicted to be 1.1768 Å and 1.7374 Å, respectively; the Cl-C-Cl bond angle is 124.03° and the O-C-Cl bond angle is 111.93°. Anharmonic frequencies are determined with VPT2, using CCSD(T)/cc-pCVQZ cubic and quartic force-fields and a CCSDT(Q)/CBS quadratic force field: ν1 = 1832.9 ; ν2 = 570.5 ; ν3 = 301.2 ; ν4 = 576.3 ; ν5 = 849.4 ; and ν6 = 438.9 cm-1.
A two-dimensional volatility basis set - Part 3: Prognostic modeling and NOx dependence
NASA Astrophysics Data System (ADS)
Chuang, W. K.; Donahue, N. M.
2016-01-01
When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2D-VBS) to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in Aerosol Mass Spectrometer (AMS) measurements. We also discuss the mathematical methods underlying the implementation of the 2D-VBS and provide the complete code in the Supplement. A developer version is available on Bitbucket, an online community repository.
A two-dimensional volatility basis set - Part 3: Prognostic modeling and NOx dependence
NASA Astrophysics Data System (ADS)
Chuang, W. K.; Donahue, N. M.
2015-06-01
When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2-D-VBS) to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in AMS measurements. We also discuss the mathematical methods underlying the implementation of the 2-D-VBS and provide the complete code in the Supplemental material. A developer version is available on Bitbucket, an online community repository.
Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem.
Nichols, Patrick; Govind, Niranjan; Bylaska, Eric J; de Jong, W A
2009-03-10
Relativistic spin-orbit density functional theory (DFT) methods have been implemented in the molecular Gaussian DFT and pseudopotential planewave DFT modules of the NWChem electronic-structure program. The Gaussian basis set implementation is based upon the zeroth-order regular approximation (ZORA) while the planewave implementation uses spin-orbit pseudopotentials that are directly generated from the atomic Dirac-Kohn-Sham wave functions or atomic ZORA-Kohn-Sham wave functions. Compared to solving the full Dirac equation these methods are computationally efficient but robust enough for a realistic description of relativistic effects such as spin-orbit splitting, molecular orbital hybridization, and core effects. Both methods have been applied to a variety of small molecules, including I2, IF, HI, Br2, Bi2, AuH, and Au2, using various exchange-correlation functionals. Our results are in good agreement with experiment and previously reported calculations.
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.
Tsuzuki, Seiji; Tanabe, Kazutoshi )
1991-03-21
Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.
A complete basis set model chemistry. V. Extensions to six or more heavy atoms
NASA Astrophysics Data System (ADS)
Ochterski, Joseph W.; Petersson, G. A.; Montgomery, J. A., Jr.
1996-02-01
The major source of error in most ab initio calculations of molecular energies is the truncation of the one-electron basis set. Extrapolation to the complete basis set second-order (CBS2) limit using the N-1 asymptotic convergence of N-configuration pair natural orbital (PNO) expansions can be combined with the use of relatively small basis sets for the higher-order (i.e., MP3, MP4, and QCI) correlation energy to develop cost effective computational models. Following this strategy, three new computational models denoted CBS-4, CBS-q, and CBS-Q, are introduced. The mean absolute deviations (MAD) from experiment for the 125 energies of the G2 test set are 2.0, 1.7, and 1.0 kcal/mol, respectively. These results compare favorably with the MAD for the more costly G2(MP2), G2, and CBS-QCI/APNO models (1.6, 1.2, and 0.5 kcal/mol, respectively). The error distributions over the G2 test set are indistinguishable from Gaussian distribution functions for all six models, indicating that the rms errors can be interpreted in the same way that experimental uncertainties are used to assess reliability. However, a broader range of examples reveals special difficulties presented by spin contamination, high molecular symmetry, and localization problems in molecules with multiple lone pairs on the same atom. These characteristics can occasionally result in errors several times the size expected from the Gaussian distributions. Each of the CBS models has a range of molecular size for which it is the most accurate computational model currently available. The largest calculations reported for these models include: The CBS-4 heat of formation of tetranitrohydrazine (91.5±5 kcal/mol), the CBS-4 and CBS-q isomerization energies for the conversion of azulene to naphthalene (ΔHcalc=-35.2±1.0 kcal/mol, ΔHexp=-35.3±2.2 kcal/mol), and the CBS-Q heat of formation of SF6 (ΔHcalc=-286.6±1.3 kcal/mol, ΔHexp=-288.3±0.2 kcal/mol). The CBS-Q value for the dissociation energy of a C-H bond in
NASA Astrophysics Data System (ADS)
Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo
2014-03-01
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo
2014-03-14
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
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.
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.
Evolutionary optimization of PAW data-sets for accurate high pressure simulations
NASA Astrophysics Data System (ADS)
Sarkar, Kanchan; Topsakal, Mehmet; Holzwarth, N. A. W.; Wentzcovitch, Renata M.
2017-10-01
We examine the challenge of performing accurate electronic structure calculations at high pressures by comparing the results of all-electron full potential linearized augmented-plane-wave calculations, as implemented in the WIEN2k code, with those of the projector augmented wave (PAW) method, as implemented in Quantum ESPRESSO or Abinit code. In particular, we focus on developing an automated and consistent way of generating transferable PAW data-sets that can closely produce the all electron equation of state defined from zero to arbitrary high pressures. The technique we propose is an evolutionary search procedure that exploits the ATOMPAW code to generate atomic data-sets and the Quantum ESPRESSO software suite for total energy calculations. We demonstrate different aspects of its workability by optimizing PAW basis functions of some elements relatively abundant in planetary interiors. In addition, we introduce a new measure of atomic data-set goodness by considering their performance uniformity over an extended pressure range.
Tellgren, Erik I; Reine, Simen S; Helgaker, Trygve
2012-07-14
Analytical integral evaluation is a central task of modern quantum chemistry. Here we present a general method for evaluating differentiated integrals over standard Gaussian and mixed Gaussian/plane-wave hybrid orbitals. The main idea is to have a representation of basis sets that is flexible enough to enable differentiated integrals to be reinterpreted as standard integrals over modified basis functions. As an illustration of the method, we report a very simple implementation of Hartree-Fock level geometrical derivatives in finite magnetic fields for gauge-origin independent atomic orbitals, within the London program. As a quantum-chemical application, we optimize the structure of helium clusters and some well-known covalently bound molecules (water, ammonia and benzene) subject to strong magnetic fields.
Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit.
Lemke, Kono H
2017-06-21
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.
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.
Optimization of global model composed of radial basis functions using the term-ranking approach
Cai, Peng; Tao, Chao Liu, Xiao-Jun
2014-03-15
A term-ranking method is put forward to optimize the global model composed of radial basis functions to improve the predictability of the model. The effectiveness of the proposed method is examined by numerical simulation and experimental data. Numerical simulations indicate that this method can significantly lengthen the prediction time and decrease the Bayesian information criterion of the model. The application to real voice signal shows that the optimized global model can capture more predictable component in chaos-like voice data and simultaneously reduce the predictable component (periodic pitch) in the residual signal.
Optimization of global model composed of radial basis functions using the term-ranking approach
Cai, Peng; Tao, Chao Liu, Xiao-Jun
2014-03-15
A term-ranking method is put forward to optimize the global model composed of radial basis functions to improve the predictability of the model. The effectiveness of the proposed method is examined by numerical simulation and experimental data. Numerical simulations indicate that this method can significantly lengthen the prediction time and decrease the Bayesian information criterion of the model. The application to real voice signal shows that the optimized global model can capture more predictable component in chaos-like voice data and simultaneously reduce the predictable component (periodic pitch) in the residual signal.
Optimal gate-width setting for passive neutrons multiplicity counting
Croft, Stephen; Evans, Louise G; Schear, Melissa A
2010-01-01
When setting up a passive neutron coincidence counter it is natural to ask what coincidence gate settings should be used to optimize the counting precision. If the gate width is too short then signal is lost and the precision is compromised because in a given period only a few coincidence events will be observed. On the other hand if the gate is too large the signal will be maximized but it will also be compromised by the high level of random pile-up or Accidental coincidence events which must be subtracted. In the case of shift register electronics connected to an assay chamber with an exponential dieaway profile operating in the regime where the Accidentals rate dominates the Reals coincidence rate but where dead-time is not a concern, simple arguments allow one to show that the relative precision on the net Reals rate is minimized when the coincidence gate is set to about 1.2 times the lie dieaway time of the system. In this work we show that making the same assumptions it is easy to show that the relative precision on the Triples rates is also at a minimum when the relative precision of the Doubles (or Reals) is at a minimum. Although the analysis is straightforward to our knowledge such a discussion has not been documented in the literature before. Actual measurement systems do not always behave in the ideal we choose to model them. Fortunately however the variation in the relative precision as a function of gate width is rather flat for traditional safeguards counters and so the performance is somewhat forgiving of the exact choice. The derivation further serves to delineate the important parameters which determine the relative counting precision of the Doubles and Triples rates under the regime considered. To illustrate the similarities and differences we consider the relative standard deviation that might be anticipated for a passive correlation count of an axial section of a spent nuclear fuel assembly under practically achievable conditions.
NASA Astrophysics Data System (ADS)
Coccia, Emanuele; Assaraf, Roland; Luppi, Eleonora; Toulouse, Julien
2017-07-01
We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.
European air quality modelled by CAMx including the volatility basis set scheme
NASA Astrophysics Data System (ADS)
Ciarelli, G.; Aksoyoglu, S.; Crippa, M.; Jimenez, J. L.; Nemitz, E.; Sellegri, K.; Äijälä, M.; Carbone, S.; Mohr, C.; O'Dowd, C.; Poulain, L.; Baltensperger, U.; Prévôt, A. S. H.
2015-12-01
Four periods of EMEP (European Monitoring and Evaluation Programme) intensive measurement campaigns (June 2006, January 2007, September-October 2008 and February-March 2009) were modelled using the regional air quality model CAMx with VBS (Volatility Basis Set) approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February-March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosols (OA). Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database Airbase. Sulfur dioxide (SO2) and ozone (O3) were found to be overestimated for all the four periods with O3 having the largest mean bias during June 2006 and January-February 2007 periods (8.93 and 12.30 ppb mean biases, respectively). In contrast, nitrogen dioxide (NO2) and carbon monoxide (CO) were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 very well for all the four periods with average biases ranging from -2.13 to 1.04 μg m-3. Comparisons with AMS (Aerosol Mass Spectrometer) measurements at different sites in Europe during February-March 2009, showed that in general the model over-predicts the inorganic aerosol fraction and under-predicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of volatility basis set scheme (VBS) on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February-March 2009 the chamber-case reduced the total OA concentrations by about 43 % on average. On the other hand, a test based on ambient measurement data increased OA concentrations by about 47 % for the same period bringing model
NASA Astrophysics Data System (ADS)
Jakšić, Nikola
2015-03-01
The optimality of the procedure of parameter identification is scrutinized in this paper. It was shown, with the relations between the mathematical theory of function approximation, three parameter probability distributions, which can adjust their shape, and the maximum-likelihood method, that the optimal expression of the distance between measured data and model fitting it can be established by using the three parameter probability distributions on the basis of iteration procedure, where the noise contained in the measured signal is extracted as well. The iterative method for optimal system/model parameter identification is presented and tested by the numerical experimentation. Four types of noise added to the simple single-degree-of-freedom system response are considered: Gauss, Cauchy, Laplace and Uniform. The method performs well for the noise types at relatively high noise content in the signal.
NASA Astrophysics Data System (ADS)
Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon
2017-06-01
Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.
Numerical Aspects of Atomic Physics: Helium Basis Sets and Matrix Diagonalization
NASA Astrophysics Data System (ADS)
Jentschura, Ulrich; Noble, Jonathan
2014-03-01
We present a matrix diagonalization algorithm for complex symmetric matrices, which can be used in order to determine the resonance energies of auto-ionizing states of comparatively simple quantum many-body systems such as helium. The algorithm is based in multi-precision arithmetic and proceeds via a tridiagonalization of the complex symmetric (not necessarily Hermitian) input matrix using generalized Householder transformations. Example calculations involving so-called PT-symmetric quantum systems lead to reference values which pertain to the imaginary cubic perturbation (the imaginary cubic anharmonic oscillator). We then proceed to novel basis sets for the helium atom and present results for Bethe logarithms in hydrogen and helium, obtained using the enhanced numerical techniques. Some intricacies of ``canned'' algorithms such as those used in LAPACK will be discussed. Our algorithm, for complex symmetric matrices such as those describing cubic resonances after complex scaling, is faster than LAPACK's built-in routines, for specific classes of input matrices. It also offer flexibility in terms of the calculation of the so-called implicit shift, which is used in order to ``pivot'' the system toward the convergence to diagonal form. We conclude with a wider overview.
Optimality Conditions in Differentiable Vector Optimization via Second-Order Tangent Sets
Jimenez, Bienvenido Novo, Vicente
2004-03-15
We provide second-order necessary and sufficient conditions for a point to be an efficient element of a set with respect to a cone in a normed space, so that there is only a small gap between necessary and sufficient conditions. To this aim, we use the common second-order tangent set and the asymptotic second-order cone utilized by Penot. As an application we establish second-order necessary conditions for a point to be a solution of a vector optimization problem with an arbitrary feasible set and a twice Frechet differentiable objective function between two normed spaces. We also establish second-order sufficient conditions when the initial space is finite-dimensional so that there is no gap with necessary conditions. Lagrange multiplier rules are also given.
Parallel axes gear set optimization in two-parameter space
NASA Astrophysics Data System (ADS)
Theberge, Y.; Cardou, A.; Cloutier, L.
1991-05-01
This paper presents a method for optimal spur and helical gear transmission design that may be used in a computer aided design (CAD) approach. The design objective is generally taken as obtaining the most compact set for a given power input and gear ratio. A mixed design procedure is employed which relies both on heuristic considerations and computer capabilities. Strength and kinematic constraints are considered in order to define the domain of feasible designs. Constraints allowed include: pinion tooth bending strength, gear tooth bending strength, surface stress (resistance to pitting), scoring resistance, pinion involute interference, gear involute interference, minimum pinion tooth thickness, minimum gear tooth thickness, and profile or transverse contact ratio. A computer program was developed which allows the user to input the problem parameters, to select the calculation procedure, to see constraint curves in graphic display, to have an objective function level curve drawn through the design space, to point at a feasible design point and to have constraint values calculated at that point. The user can also modify some of the parameters during the design process.
Multivariate Parameter Sets for Optimal Synthesis of Compliant Mechanisms
NASA Technical Reports Server (NTRS)
Shibakov, Alex; Hull, Patrick V.; Canfield, Stephen L.; Tinker, Mike
2005-01-01
This paper will propose the use of control maps along with discretized elements or meshes in the design parameter set for optimizing compliant mechanisms. The use of control maps will be demonstrated to encode the motion of groups of nodes or control points within a compliant mechanism design with simple mapping rules. The technique will serve as an alternative to increased mesh size or node wandering techniques that have been proposed to increase the number of alternative design shapes that may be considered. As an alternative approach, the proposed control map parameterization has the significant benefit that it minimizes the number of design parameters necessary (parameters increase linearly with the mesh size) in describing a given design making it computationally efficient. A limited number of tiles can produce a map that has a significant effect on the final shape. If the tiles are chosen appropriately, the problems such as material overlap and non-convex mesh elements are avoided automatically. This paper will describe the implementation of these control maps and provide several examples showing their implementation in the compliant mechanism topology synthesis process.
The Scientific Basis of Uncertainty Factors Used in Setting Occupational Exposure Limits
Dankovic, D. A.; Naumann, B. D.; Maier, A.; Dourson, M. L.; Levy, L. S.
2015-01-01
The uncertainty factor concept is integrated into health risk assessments for all aspects of public health practice, including by most organizations that derive occupational exposure limits. The use of uncertainty factors is predicated on the assumption that a sufficient reduction in exposure from those at the boundary for the onset of adverse effects will yield a safe exposure level for at least the great majority of the exposed population, including vulnerable subgroups. There are differences in the application of the uncertainty factor approach among groups that conduct occupational assessments; however, there are common areas of uncertainty which are considered by all or nearly all occupational exposure limit-setting organizations. Five key uncertainties that are often examined include interspecies variability in response when extrapolating from animal studies to humans, response variability in humans, uncertainty in estimating a no-effect level from a dose where effects were observed, extrapolation from shorter duration studies to a full life-time exposure, and other insufficiencies in the overall health effects database indicating that the most sensitive adverse effect may not have been evaluated. In addition, a modifying factor is used by some organizations to account for other remaining uncertainties—typically related to exposure scenarios or accounting for the interplay among the five areas noted above. Consideration of uncertainties in occupational exposure limit derivation is a systematic process whereby the factors applied are not arbitrary, although they are mathematically imprecise. As the scientific basis for uncertainty factor application has improved, default uncertainty factors are now used only in the absence of chemical-specific data, and the trend is to replace them with chemical-specific adjustment factors whenever possible. The increased application of scientific data in the development of uncertainty factors for individual chemicals also
The Scientific Basis of Uncertainty Factors Used in Setting Occupational Exposure Limits.
Dankovic, D A; Naumann, B D; Maier, A; Dourson, M L; Levy, L S
2015-01-01
The uncertainty factor concept is integrated into health risk assessments for all aspects of public health practice, including by most organizations that derive occupational exposure limits. The use of uncertainty factors is predicated on the assumption that a sufficient reduction in exposure from those at the boundary for the onset of adverse effects will yield a safe exposure level for at least the great majority of the exposed population, including vulnerable subgroups. There are differences in the application of the uncertainty factor approach among groups that conduct occupational assessments; however, there are common areas of uncertainty which are considered by all or nearly all occupational exposure limit-setting organizations. Five key uncertainties that are often examined include interspecies variability in response when extrapolating from animal studies to humans, response variability in humans, uncertainty in estimating a no-effect level from a dose where effects were observed, extrapolation from shorter duration studies to a full life-time exposure, and other insufficiencies in the overall health effects database indicating that the most sensitive adverse effect may not have been evaluated. In addition, a modifying factor is used by some organizations to account for other remaining uncertainties-typically related to exposure scenarios or accounting for the interplay among the five areas noted above. Consideration of uncertainties in occupational exposure limit derivation is a systematic process whereby the factors applied are not arbitrary, although they are mathematically imprecise. As the scientific basis for uncertainty factor application has improved, default uncertainty factors are now used only in the absence of chemical-specific data, and the trend is to replace them with chemical-specific adjustment factors whenever possible. The increased application of scientific data in the development of uncertainty factors for individual chemicals also has
Findlay, Barbara; Verhoef, Marja
2004-01-01
Creation of an optimal healing environment (OHE) in a clinical setting is a multifaceted undertaking and subject to a wide variety of developmental influences. While comprehensive definitions for OHE might provide sufficient guidance for communicating philosophy and values and developing patient-practitioner processes, direction for creating a supportive administrative structure or establishing an evaluation/research strategy is less defined. Operationalizing the concept of OHE by breaking it down into components such as values, structure, process, and measurement of outcomes, proved to be a useful framework for analyzing the evolution of our integrated care program. Future OHE initiatives may benefit from using this type of framework to assess readiness among cocreators prior to development and implementation, as a guide for ongoing evaluation of an OHE postimplementation and as a basis for comparing OHEs across a variety of clinical settings.
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.
Optimization of people evacuation plans on the basis of wireless sensor networks
NASA Astrophysics Data System (ADS)
Amirgaliyev, Yedilkhan; Yunussov, Rassul; Mamyrbayev, Orken
2016-01-01
This paper introduces the optimization process for people salvation in critical situations by organizing their evacuation plan from enclosed areas using modern approaches of data acquisition on the basis of wireless sensor networks. The proposed technology allows the ability to gather information about people density on the surveyed area by the usage of wireless sensor networks, consistently covering the enclosed territory. It enables the update of the evacuation plan on the basis of people density information inside the enclosed areas online. It is proposed to use common video surveillance cameras as sensors. The advantage of visual surveillance using cameras is that it does not require additional technological equipment for the area and much more important does not impose rules and restriction on the surveillance objects (people in this case). Next tasks are to be solved: creation of mathematical model of optimal enclosed area surveillance by wireless sensors, database and data interrogation modelling of wireless sensor network, creation of algorithmic model for automated people counting using video signal for the covering area; creation of dynamic people evacuation model on the basis of maximum flow problem [1, 2].
Wang, Yang; Liu, Qingzhu; Qiu, Ling; Wang, Tengfei; Yuan, Haoliang; Lin, Jianguo; Luo, Shineng
2015-01-01
Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N-H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.
Roper, Zachary J J; Vecera, Shaun P
2012-12-01
Recent work has demonstrated that attention can be configured to multiple potential targets in spatial search. However, this previous work relied on a fixed set of targets across multiple trials, allowing observers to offload attentional control settings to longer-term representations. In the present experiments, we demonstrate multiple attentional control settings that operate independently of space (Experiments 1 and 2). More important, we show that observers can be cued to different control settings on a trial-by-trial basis (Experiment 3). The latter result suggests that observers were capable of maintaining multiple control settings when the demands of the task required an attentional search for specific feature values. Attention can be configured to extract multiple feature values in a goal-directed manner, and this configuration can be can be dynamically engaged on a trial-by-trial basis. These results support recent findings that reveal the high precision, complexity, and flexibility of attentional control settings.
Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors
Kamiya, Muneaki; Hirata, So; Valiev, Marat
2008-02-19
Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of the cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.
Expressing clinical data sets with openEHR archetypes: a solid basis for ubiquitous computing.
Garde, Sebastian; Hovenga, Evelyn; Buck, Jasmin; Knaup, Petra
2007-12-01
The purpose of this paper is to analyse the feasibility and usefulness of expressing clinical data sets (CDSs) as openEHR archetypes. For this, we present an approach to transform CDS into archetypes, and outline typical problems with CDS and analyse whether some of these problems can be overcome by the use of archetypes. Literature review and analysis of a selection of existing Australian, German, other European and international CDSs; transfer of a CDS for Paediatric Oncology into openEHR archetypes; implementation of CDSs in application systems. To explore the feasibility of expressing CDS as archetypes an approach to transform existing CDSs into archetypes is presented in this paper. In case of the Paediatric Oncology CDS (which consists of 260 data items) this lead to the definition of 48 openEHR archetypes. To analyse the usefulness of expressing CDS as archetypes, we identified nine problems with CDS that currently remain unsolved without a common model underpinning the CDS. Typical problems include incompatible basic data types and overlapping and incompatible definitions of clinical content. A solution to most of these problems based on openEHR archetypes is motivated. With regard to integrity constraints, further research is required. While openEHR cannot overcome all barriers to Ubiquitous Computing, it can provide the common basis for ubiquitous presence of meaningful and computer-processable knowledge and information, which we believe is a basic requirement for Ubiquitous Computing. Expressing CDSs as openEHR archetypes is feasible and advantageous as it fosters semantic interoperability, supports ubiquitous computing, and helps to develop archetypes that are arguably of better quality than the original CDS.
NASA Astrophysics Data System (ADS)
Jo, D. S.; Park, R. J.; Kim, M. J.; Spracklen, D. V.
2013-12-01
A global 3-D chemical transport model (GEOS-Chem) is used with the volatility basis set (VBS) approach to examine the effects of chemical aging on global secondary organic aerosol (SOA) concentrations and budgets. We present full-year simulations and their comparisons with the global aerosol mass spectrometer (AMS) dataset, the Interagency Monitoring of Protected Visual Environments (IMPROVE) dataset from the United States, the European Monitoring and Evaluation Programme (EMEP) dataset from Europe, and water-soluble organic carbon observation data collected over East Asia. Using different chemical aging constants, we find that the model results with 4 × 10-11 cm3 molecule-1 s-1 are in better agreement with all observations relative to the model results with other aging constants, without aging, and with the two-product approach. The model simulations are improved when chemical aging is considered, especially for rural regions. However, the simulations still underestimate observed oxygenated organic aerosol (OOA) in urban areas. Two sensitivity simulations including semi-volatile primary organic aerosol (POA) were conducted. We find that including semi-volatile POA improves the model in terms of the hydrogen-like organic aerosol (HOA) to OOA ratio. However, the total OA concentrations are not improved. The total SOA production is considerably increased by 53%, from 26.0 to 39.9 Tg yr-1, after considering chemical aging, remaining lower than top-down estimates of SOA production. Direct radiative forcing (DRF) increases by -0.07 W m-2 due to the chemical aging of SOA, which is comparable to the mean DRF (-0.13 W m-2) of OA from the AeroCom multi-model study. This result indicates considerable global and, more importantly, regional climate implications. For example, the regional DRF change due to chemical aging of SOA in the eastern US is -0.29 W m-2, which is 4 times greater in magnitude than the global mean value.
Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.
Bielecki, Jakub; Lipiec, Ewelina
2016-02-01
Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.
Correction of the basis set superposition error in SCF and MP2 interaction energies. The water dimer
NASA Astrophysics Data System (ADS)
Szcześniak, M. M.; Scheiner, Steve
1986-06-01
There has been some discussion concerning whether basis set superposition error is more correctly evaluated using the full set of ghost orbitals of the partner molecule or some subset thereof. A formal treatment is presented, arguing that the full set is required at the Møller-Plesset level. Numerical support for this position is provided by calculation of the interaction energy between a pair of water molecules, using a series of moderate sized basis sets ranging from 6-31G** to the [432/21] contraction suggested by Clementi and Habitz. These energies, at both the SCF and MP2 levels, behave erratically with respect to changes in details of the basis set, e.g., H p-function exponent. On the other hand, after counterpoise correction using the full set of partner ghost orbitals, the interaction energies are rather insensitive to basis set and behave in a manner consistent with calculated monomer properties. For long intersystem separations, the contribution of correlation to the interaction is repulsive despite the attractive influence of dispersion. This effect is attributed to partial account of intrasystem correlation and can be approximated at long distances via electrostatic terms linear in MP2-induced changes in the monomer moments.
Optimization of massive countermeasure design in complex rockfall settings
NASA Astrophysics Data System (ADS)
Agliardi, Federico; Crosta, Giovanni B.
2015-04-01
Rockfall protection is a major need in areas impended by subvertical rockwalls with complex 3D morphology and little or no talus to provide natural rockfall attenuation. The design of massive embankments, usually required to ensure such protection, is particularly difficult in complex rockfall settings, due to: widespread occurrence of rockfall sources; difficult characterization of size distribution and location of unstable volumes; variability of failure mechanisms; spatial scattering of rockfall trajectories; high expected kinetic energies. Moreover, rockwalls in complex lithological and structural settings are often prone to mass falls related to rock mass sector collapses. All these issues may hamper a safe application of classic embankment analysis approaches, using empirical rules or 2D-based height/energy statistics, and point to the need of integrated analyses of rock slope instability and rockfall runout in 3D. We explore the potential of combining advanced rock mass characterisation techniques and 3D rockfall modelling to support challenging countermeasure design at a site near Lecco (Southern Alps, Italy). Here subvertical cliffs up to 600 m high impend on a narrow (< 150 m) strip of flat land along the Como Lake shore. Rock is thickly bedded limestone (Dolomia Principale Fm) involved in a ENE-trending, S-verging kilometre-scale anticline fold. The spatial variability of bedding attitude and fracture intensity is strongly controlled by the geological structure, with individual block sizes varying in the range 0.2-15 m3. This results in spatially variable rockfall susceptibility and mechanisms, from single block falls to mass falls. Several rockfall events occurred between 1981 and 2010 motivated the design of slope benching and a massive embankment. To support reliable design verification and optimization we performed a 3D assessment of both rock slope instability and rockfall runout. We characterised fracture patterns and rock mass quality associated
NASA Astrophysics Data System (ADS)
Petković, Dalibor; Gocic, Milan; Shamshirband, Shahaboddin; Qasem, Sultan Noman; Trajkovic, Slavisa
2016-08-01
Accurate estimation of the reference evapotranspiration (ET0) is important for the water resource planning and scheduling of irrigation systems. For this purpose, the radial basis function network with particle swarm optimization (RBFN-PSO) and radial basis function network with back propagation (RBFN-BP) were used in this investigation. The FAO-56 Penman-Monteith equation was used as reference equation to estimate ET0 for Serbia during the period of 1980-2010. The obtained simulation results confirmed the proposed models and were analyzed using the root mean-square error (RMSE), the mean absolute error (MAE), and the coefficient of determination ( R 2). The analysis showed that the RBFN-PSO had better statistical characteristics than RBFN-BP and can be helpful for the ET0 estimation.
Optimal embeddings of Bessel and Riesz type potentials on the basis of weighted Lorentz spaces
NASA Astrophysics Data System (ADS)
Karshygina, Gulden Zh.
2017-09-01
We study a space of potentials on the n-dimensional Euclidean space. They are constructed on the basis of rearrangement invariant spaces (RISs) by means of convolutions with kernels of general form. In particular, the spaces of classical potentials of Bessel and Riesz are included in the discussion. We establish the integral properties of potentials. For them the criteria for embedding in the RIS are found and explicit descriptions of the optimal RIS for these embeddings are obtained in case of the basic weighted Lorentz space. The aim of this paper is to give an explicit description of the optimal RIS X(Rn) for embeddings HEG(Rn)⊂X (Rn) in the case when the base RIS E(Rn) coincides with the weighted Lorentz space Λp(u).
Dong, Li-Yang; Zhou, Wei-Zhong; Ni, Jun-Wei; Xiang, Wei; Hu, Wen-Hao; Yu, Chang; Li, Hai-Yan
2017-02-01
The objective of this study was to identify the optimal gene and gene set for hepatocellular carcinoma (HCC) utilizing differential expression and differential co-expression (DEDC) algorithm. The DEDC algorithm consisted of four parts: calculating differential expression (DE) by absolute t-value in t-statistics; computing differential co-expression (DC) based on Z-test; determining optimal thresholds on the basis of Chi-squared (χ2) maximization and the corresponding gene was the optimal gene; and evaluating functional relevance of genes categorized into different partitions to determine the optimal gene set with highest mean minimum functional information (FI) gain (Δ*G). The optimal thresholds divided genes into four partitions, high DE and high DC (HDE-HDC), high DE and low DC (HDE-LDC), low DE and high DC (LDE‑HDC), and low DE and low DC (LDE-LDC). In addition, the optimal gene was validated by conducting reverse transcription-polymerase chain reaction (RT-PCR) assay. The optimal threshold for DC and DE were 1.032 and 1.911, respectively. Using the optimal gene, the genes were divided into four partitions including: HDE-HDC (2,053 genes), HED-LDC (2,822 genes), LDE-HDC (2,622 genes), and LDE-LDC (6,169 genes). The optimal gene was microtubule‑associated protein RP/EB family member 1 (MAPRE1), and RT-PCR assay validated the significant difference between the HCC and normal state. The optimal gene set was nucleoside metabolic process (GO\\GO:0009116) with Δ*G = 18.681 and 24 HDE-HDC partitions in total. In conclusion, we successfully investigated the optimal gene, MAPRE1, and gene set, nucleoside metabolic process, which may be potential biomarkers for targeted therapy and provide significant insight for revealing the pathological mechanism underlying HCC.
Optimal control of the sweeping process over polyhedral controlled sets
NASA Astrophysics Data System (ADS)
Colombo, G.; Henrion, R.; Nguyen, D. Hoang; Mordukhovich, B. S.
2016-02-01
The paper addresses a new class of optimal control problems governed by the dissipative and discontinuous differential inclusion of the sweeping/Moreau process while using controls to determine the best shape of moving convex polyhedra in order to optimize the given Bolza-type functional, which depends on control and state variables as well as their velocities. Besides the highly non-Lipschitzian nature of the unbounded differential inclusion of the controlled sweeping process, the optimal control problems under consideration contain intrinsic state constraints of the inequality and equality types. All of this creates serious challenges for deriving necessary optimality conditions. We develop here the method of discrete approximations and combine it with advanced tools of first-order and second-order variational analysis and generalized differentiation. This approach allows us to establish constructive necessary optimality conditions for local minimizers of the controlled sweeping process expressed entirely in terms of the problem data under fairly unrestrictive assumptions. As a by-product of the developed approach, we prove the strong W 1 , 2-convergence of optimal solutions of discrete approximations to a given local minimizer of the continuous-time system and derive necessary optimality conditions for the discrete counterparts. The established necessary optimality conditions for the sweeping process are illustrated by several examples.
Simulating the oxygen content of ambient organic aerosol with the 2D volatility basis set
NASA Astrophysics Data System (ADS)
Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Pandis, S. N.
2011-08-01
A module predicting the oxidation state of organic aerosol (OA) has been developed using the two-dimensional volatility basis set (2D-VBS) framework. This model is an extension of the 1D-VBS framework and tracks saturation concentration and oxygen content of organic species during their atmospheric lifetime. The host model, a one-dimensional Lagrangian transport model, is used to simulate air parcels arriving at Finokalia, Greece during the Finokalia Aerosol Measurement Experiment in May 2008 (FAME-08). Extensive observations were collected during this campaign using an aerosol mass spectrometer (AMS) and a thermodenuder to determine the chemical composition and volatility, respectively, of the ambient OA. Although there are several uncertain model parameters, the consistently high oxygen content of OA measured during FAME-08 (O:C = 0.8) can help constrain these parameters and elucidate OA formation and aging processes that are necessary for achieving the high degree of oxygenation observed. The base-case model reproduces observed OA mass concentrations (measured mean = 3.1 μg m-3, predicted mean = 3.3 μg m-3) and O:C (predicted O:C = 0.78) accurately. A suite of sensitivity studies explore uncertainties due to (1) the anthropogenic secondary OA (SOA) aging rate constant, (2) assumed enthalpies of vaporization, (3) the volatility change and number of oxygen atoms added for each generation of aging, (4) heterogeneous chemistry, (5) the oxidation state of the first generation of compounds formed from SOA precursor oxidation, and (6) biogenic SOA aging. Perturbations in most of these parameters do impact the ability of the model to predict O:C well throughout the simulation period. By comparing measurements of the O:C from FAME-08, several sensitivity cases including a high oxygenation case, a low oxygenation case, and biogenic SOA aging case are found to unreasonably depict OA aging, keeping in mind that this study does not consider possibly important processes
Evaluation of European air quality modelled by CAMx including the volatility basis set scheme
NASA Astrophysics Data System (ADS)
Ciarelli, Giancarlo; Aksoyoglu, Sebnem; Crippa, Monica; Jimenez, Jose-Luis; Nemitz, Eriko; Sellegri, Karine; Äijälä, Mikko; Carbone, Samara; Mohr, Claudia; O'Dowd, Colin; Poulain, Laurent; Baltensperger, Urs; Prévôt, André S. H.
2016-08-01
Four periods of EMEP (European Monitoring and Evaluation Programme) intensive measurement campaigns (June 2006, January 2007, September-October 2008 and February-March 2009) were modelled using the regional air quality model CAMx with VBS (volatility basis set) approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February-March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosol (OA). Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database AirBase. Sulfur dioxide (SO2) and ozone (O3) were found to be overestimated for all the four periods, with O3 having the largest mean bias during June 2006 and January-February 2007 periods (8.9 pbb and 12.3 ppb mean biases respectively). In contrast, nitrogen dioxide (NO2) and carbon monoxide (CO) were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 for all the four periods with average biases ranging from -2.1 to 1.0 µg m-3. Comparisons with AMS (aerosol mass spectrometer) measurements at different sites in Europe during February-March 2009 showed that in general the model overpredicts the inorganic aerosol fraction and underpredicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of VBS scheme on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February-March 2009 the chamber case reduced the total OA concentrations by about 42 % on average. In contrast, a test based on ambient measurement data increased OA concentrations by about 42 % for the same period bringing model and observations into better agreement
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.
NASA Astrophysics Data System (ADS)
Brorsen, Kurt R.; Sirjoosingh, Andrew; Pak, Michael V.; Hammes-Schiffer, Sharon
2015-06-01
The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF- and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN+, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.
Brorsen, Kurt R; Sirjoosingh, Andrew; Pak, Michael V; Hammes-Schiffer, Sharon
2015-06-07
The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF(-) and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN(+), and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.
Brorsen, Kurt R.; Sirjoosingh, Andrew; Pak, Michael V.; Hammes-Schiffer, Sharon
2015-06-07
The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF{sup −} and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN{sup +}, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.
NASA Astrophysics Data System (ADS)
Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.
Locally dense basis sets (
Reuter, Matthew G; Harrison, Robert J
2013-09-21
We revisit the derivation of electron transport theories with a focus on the projection operators chosen to partition the system. The prevailing choice of assigning each computational basis function to a region causes two problems. First, this choice generally results in oblique projection operators, which are non-Hermitian and violate implicit assumptions in the derivation. Second, these operators are defined with the physically insignificant basis set and, as such, preclude a well-defined basis set limit. We thus advocate for the selection of physically motivated, orthogonal projection operators (which are Hermitian) and present an operator-based derivation of electron transport theories. Unlike the conventional, matrix-based approaches, this derivation requires no knowledge of the computational basis set. In this process, we also find that common transport formalisms for nonorthogonal basis sets improperly decouple the exterior regions, leading to a short circuit through the system. We finally discuss the implications of these results for first-principles calculations of electron transport.
Kong, Liguo; Valeev, Edward F
2010-11-07
To reduce the basis set incompleteness of the complete-active-space self-consistent field (CASSCF) wave function and energy we develop a second-order perturbation correction due to single excitations to complete set of unoccupied states. Other than the one- and two-electron integrals, only one- and two-particle reduced density matrices are required to compute the correction, denoted as [2](S). Benchmark calculations on prototypical ground-state bond-breaking problems show that only the aug-cc-pVXZ basis is needed with the [2](S) correction to match the accuracy of CASSCF energies of the aug-cc-pV(X+1)Z quality.
Optimized virtual orbital subspace for faster GW calculations in localized basis
NASA Astrophysics Data System (ADS)
Bruneval, Fabien
2016-12-01
The popularity of the GW approximation to the self-energy to access the quasiparticle energies of molecules is constantly increasing. As the other methods addressing the electronic correlation, the GW self-energy unfortunately shows a very slow convergence with respect to the basis complexity, which precludes the calculation of accurate quasiparticle energies for large molecules. Here we propose a method to mitigate this issue that relies on two steps: (i) the definition of a reduced virtual orbital subspace, thanks to a much smaller basis set; (ii) the account of the remainder through the simpler one-ring approximation to the self-energy. We assess the quality of the corrected quasiparticle energies for simple molecules, and finally we show an application to large graphene chunks to demonstrate the numerical efficiency of the scheme.
NASA Astrophysics Data System (ADS)
Renaud, Rémi; Bendahmane, Mounir; Chery, Romain; Martin, Claire; Gurden, Hirac; Pain, Frederic
2012-06-01
Wide field multispectral imaging of light backscattered by brain tissues provides maps of hemodynamics changes (total blood volume and oxygenation) following activation. This technique relies on the fit of the reflectance images obtain at two or more wavelengths using a modified Beer-Lambert law1,2. It has been successfully applied to study the activation of several sensory cortices in the anesthetized rodent using visible light1-5. We have carried out recently the first multispectral imaging in the olfactory bulb6 (OB) of anesthetized rats. However, the optimization of wavelengths choice has not been discussed in terms of cross talk and uniqueness of the estimated parameters (blood volume and saturation maps) although this point was shown to be crucial for similar studies in Diffuse Optical Imaging in humans7-10. We have studied theoretically and experimentally the optimal sets of wavelength for multispectral imaging of rodent brain activation in the visible. Sets of optimal wavelengths have been identified and validated in vivo for multispectral imaging of the OB of rats following odor stimulus. We studied the influence of the wavelengths sets on the magnitude and time courses of the oxy- and deoxyhemoglobin concentration variations as well as on the spatial extent of activated brain areas following stimulation. Beyond the estimation of hemodynamic parameters from multispectral reflectance data, we observed repeatedly and for all wavelengths a decrease of light reflectance. For wavelengths longer than 590 nm, these observations differ from those observed in the somatosensory and barrel cortex and question the basis of the reflectance changes during activation in the OB. To solve this issue, Monte Carlo simulations (MCS) have been carried out to assess the relative contribution of absorption, scattering and anisotropy changes to the intrinsic optical imaging signals in somatosensory cortex (SsC) and OB model.
Optimizing Design Parameters for Sets of Concentric Tube Robots using Sampling-based Motion Planning
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
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.
NASA Astrophysics Data System (ADS)
Ehlers, A. W.; Böhme, M.; Dapprich, S.; Gobbi, A.; Höllwarth, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Frenking, G.
1993-06-01
A Set of seven-component f-type polarization functions has been optimized for use with the pseudo-potentials of Hay and Wadt at the CISD level of theory for the transition metals ScCu, YAg, LaAu in the energetically lowest-lying s 1 d n electronic state.
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.
NASA Astrophysics Data System (ADS)
Malli, G. L.; Da Silva, A. B. F.; Ishikawa, Yasuyuki
1994-10-01
A universal Gaussian basis set is developed that leads to relativistic Dirac-Fock SCF energies of comparable accuracy as that obtained by the accurate numerical finite-difference method (GRASP2 package) [J. Phys. B 25, 1 (1992)]. The Gaussian-type functions of our universal basis set satisfy the relativistic boundary conditions associated with the finite nuclear model for a finite speed of light and conform to the so-called kinetic balance at the nonrelativistic limit. We attribute the exceptionally high accuracy obtained in our calculations to the fact that the representation of the relativistic dynamics of an electron in a spherical ball finite nucleus near the origin in terms of our universal Gaussian basis set is as accurate as that provided by the numerical finite-difference method. Results of the Dirac-Fock-Coulomb energies for a number of atoms up to No (Z=102) and some negative ions are presented and compared with the recent results obtained with the numerical finite-difference method and geometrical Gaussian basis sets by Parpia, Mohanty, and Clementi [J. Phys. B 25, 1 (1992)]. The accuracy of our calculations is estimated to be within a few parts in 109 for all the atomic systems studied.
Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model
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 structure of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.
Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin
2016-05-21
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Holocene sea level variations on the basis of integration of independent data sets
Sahagian, D.; Berkman, P. . Dept. of Geological Sciences and Byrd Polar Research Center)
1992-01-01
Variations in sea level through earth history have occurred at a wide variety of time scales. Sea level researchers have attacked the problem of measuring these sea level changes through a variety of approaches, each relevant only to the time scale in question, and usually only relevant to the specific locality from which a specific type of data are derived. There is a plethora of different data types that can and have been used (locally) for the measurement of Holocene sea level variations. The problem of merging different data sets for the purpose of constructing a global eustatic sea level curve for the Holocene has not previously been adequately addressed. The authors direct the efforts to that end. Numerous studies have been published regarding Holocene sea level changes. These have involved exposed fossil reef elevations, elevation of tidal deltas, elevation of depth of intertidal peat deposits, caves, tree rings, ice cores, moraines, eolian dune ridges, marine-cut terrace elevations, marine carbonate species, tide gauges, and lake level variations. Each of these data sets is based on particular set of assumptions, and is valid for a specific set of environments. In order to obtain the most accurate possible sea level curve for the Holocene, these data sets must be merged so that local and other influences can be filtered out of each data set. Since each data set involves very different measurements, each is scaled in order to define the sensitivity of the proxy measurement parameter to sea level, including error bounds. This effectively determines the temporal and spatial resolution of each data set. The level of independence of data sets is also quantified, in order to rule out the possibility of a common non-eustatic factor affecting more than one variety of data. The Holocene sea level curve is considered to be independent of other factors affecting the proxy data, and is taken to represent the relation between global ocean water and basin volumes.
Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan
2013-09-26
We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.
Optimal continuous variable quantum teleportation protocol for realistic settings
NASA Astrophysics Data System (ADS)
Luiz, F. S.; Rigolin, Gustavo
2015-03-01
We show the optimal setup that allows Alice to teleport coherent states | α > to Bob giving the greatest fidelity (efficiency) when one takes into account two realistic assumptions. The first one is the fact that in any actual implementation of the continuous variable teleportation protocol (CVTP) Alice and Bob necessarily share non-maximally entangled states (two-mode finitely squeezed states). The second one assumes that Alice's pool of possible coherent states to be teleported to Bob does not cover the whole complex plane (| α | < ∞). The optimal strategy is achieved by tuning three parameters in the original CVTP, namely, Alice's beam splitter transmittance and Bob's displacements in position and momentum implemented on the teleported state. These slight changes in the protocol are currently easy to be implemented and, as we show, give considerable gain in performance for a variety of possible pool of input states with Alice.
NASA Astrophysics Data System (ADS)
Gerist, Saleheh; Maheri, Mahmoud R.
2016-12-01
In order to solve structural damage detection problem, a multi-stage method using particle swarm optimization is presented. First, a new spars recovery method, named Basis Pursuit (BP), is utilized to preliminarily identify structural damage locations. The BP method solves a system of equations which relates the damage parameters to the structural modal responses using the sensitivity matrix. Then, the results of this stage are subsequently enhanced to the exact damage locations and extents using the PSO search engine. Finally, the search space is reduced by elimination of some low damage variables using micro search (MS) operator embedded in the PSO algorithm. To overcome the noise present in structural responses, a method known as Basis Pursuit De-Noising (BPDN) is also used. The efficiency of the proposed method is investigated by three numerical examples: a cantilever beam, a plane truss and a portal plane frame. The frequency response is used to detect damage in the examples. The simulation results demonstrate the accuracy and efficiency of the proposed method in detecting multiple damage cases and exhibit its robustness regarding noise and its advantages compared to other reported solution algorithms.
Vázquez, Carlos; Mitiche, Amar; Laganière, Robert
2006-05-01
The purpose of this study is to investigate a variational method for joint segmentation and parametric estimation of image motion by basis function representation of motion and level set evolution. The functional contains three terms. One term is of classic regularization to bias the solution toward a segmentation with smooth boundaries. A second term biases the solution toward a segmentation with boundaries which coincide with motion discontinuities, following a description of motion discontinuities by a function of the image spatio-temporal variations. The third term refers to region information and measures conformity of the parametric representation of the motion of each region of segmentation to the image spatio-temporal variations. The components of motion in each region of segmentation are represented as functions in a space generated by a set of basis functions. The coefficients of the motion components considered combinations of the basis functions are the parameters of representation. The necessary conditions for a minimum of the functional, which are derived taking into consideration the dependence of the motion parameters on segmentation, lead to an algorithm which condenses to concurrent curve evolution, implemented via level sets, and estimation of the parameters by least squares within each region of segmentation. The algorithm and its implementation are verified on synthetic and real images using a basis of cosine transforms.
NASA Astrophysics Data System (ADS)
Pavese, Christian; Tibaldi, Carlo; Larsen, Torben J.; Kim, Taeseong; Thomsen, Kenneth
2016-09-01
The aim is to provide a fast and reliable approach to estimate ultimate blade loads for a multidisciplinary design optimization (MDO) framework. For blade design purposes, the standards require a large amount of computationally expensive simulations, which cannot be efficiently run each cost function evaluation of an MDO process. This work describes a method that allows integrating the calculation of the blade load envelopes inside an MDO loop. Ultimate blade load envelopes are calculated for a baseline design and a design obtained after an iteration of an MDO. These envelopes are computed for a full standard design load basis (DLB) and a deterministic reduced DLB. Ultimate loads extracted from the two DLBs with the two blade designs each are compared and analyzed. Although the reduced DLB supplies ultimate loads of different magnitude, the shape of the estimated envelopes are similar to the one computed using the full DLB. This observation is used to propose a scheme that is computationally cheap, and that can be integrated inside an MDO framework, providing a sufficiently reliable estimation of the blade ultimate loading. The latter aspect is of key importance when design variables implementing passive control methodologies are included in the formulation of the optimization problem. An MDO of a 10 MW wind turbine blade is presented as an applied case study to show the efficacy of the reduced DLB concept.
Non-homogeneous solutions of a Coulomb Schrödinger equation as basis set for scattering problems
Del Punta, J. A.; Ambrosio, M. J.; Gasaneo, G.; Zaytsev, S. A.; Ancarani, L. U.
2014-05-15
We introduce and study two-body Quasi Sturmian functions which are proposed as basis functions for applications in three-body scattering problems. They are solutions of a two-body non-homogeneous Schrödinger equation. We present different analytic expressions, including asymptotic behaviors, for the pure Coulomb potential with a driven term involving either Slater-type or Laguerre-type orbitals. The efficiency of Quasi Sturmian functions as basis set is numerically illustrated through a two-body scattering problem.
Linear scaling calculation of maximally localized Wannier functions with atomic basis set.
Xiang, H J; Li, Zhenyu; Liang, W Z; Yang, Jinlong; Hou, J G; Zhu, Qingshi
2006-06-21
We have developed a linear scaling algorithm for calculating maximally localized Wannier functions (MLWFs) using atomic orbital basis. An O(N) ground state calculation is carried out to get the density matrix (DM). Through a projection of the DM onto atomic orbitals and a subsequent O(N) orthogonalization, we obtain initial orthogonal localized orbitals. These orbitals can be maximally localized in linear scaling by simple Jacobi sweeps. Our O(N) method is validated by applying it to water molecule and wurtzite ZnO. The linear scaling behavior of the new method is demonstrated by computing the MLWFs of boron nitride nanotubes.
Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set
NASA Astrophysics Data System (ADS)
Bennie, Simon J.; Stella, Martina; Miller, Thomas F.; Manby, Frederick R.
2015-07-01
Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O ( N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.
Depression screening optimization in an academic rural setting.
Aleem, Sohaib; Torrey, William C; Duncan, Mathew S; Hort, Shoshana J; Mecchella, John N
2015-01-01
Primary care plays a critical role in screening and management of depression. The purpose of this paper is to focus on leveraging the electronic health record (EHR) as well as work flow redesign to improve the efficiency and reliability of the process of depression screening in two adult primary care clinics of a rural academic institution in USA. The authors utilized various process improvement tools from lean six sigma methodology including project charter, swim lane process maps, critical to quality tree, process control charts, fishbone diagrams, frequency impact matrix, mistake proofing and monitoring plan in Define-Measure-Analyze-Improve-Control format. Interventions included change in depression screening tool, optimization of data entry in EHR. EHR data entry optimization; follow up of positive screen, staff training and EHR redesign. Depression screening rate for office-based primary care visits improved from 17.0 percent at baseline to 75.9 percent in the post-intervention control phase (p<0.001). Follow up of positive depression screen with Patient History Questionnaire-9 data collection remained above 90 percent. Duplication of depression screening increased from 0.6 percent initially to 11.7 percent and then decreased to 4.7 percent after optimization of data entry by patients and flow staff. Impact of interventions on clinical outcomes could not be evaluated. Successful implementation, sustainability and revision of a process improvement initiative to facilitate screening, follow up and management of depression in primary care requires accounting for voice of the process (performance metrics), system limitations and voice of the customer (staff and patients) to overcome various system, customer and human resource constraints.
Optimal tooth numbers for compact standard spur gear sets
NASA Technical Reports Server (NTRS)
Savage, M.; Coy, J. J.; Townsend, D. P.
1981-01-01
The design of a standard gear mesh is treated with the objective of minimizing the gear size for a given ratio, pinion torque, and allowable tooth strength. Scoring, pitting fatigue, bending fatigue, and the kinematic limits of contact ratio and interference are considered. A design space is defined in terms of the number of teeth on the pinion and the diametral pitch. This space is then combined with the objective function of minimum center distance to obtain an optimal design region. This region defines the number of pinion teeth for the most compact design. The number is a function of the gear ratio only. A design example illustrating this procedure is also given.
An optimal period for setting sustained variability levels.
Stokes, P D; Balsam, P
2001-03-01
In two experiments, we investigated how explicit reinforcement of highly variable behavior at different points in training affected performance after the requirement was eliminated. Two versions of a computer game, differing in the number of possible solution paths, were used. In each, an optimal period of training for producing sustained high variability was found. Exposure to a high lag requirement shortly after acquisition sustained variability. Rewarding variability at other times did not have a sustained effect. The implications for learning and problem solving are discussed.
NASA Astrophysics Data System (ADS)
Purwanto, Wirawan; Krakauer, Henry; Zhang, Shiwei; Virgus, Yudistira
2011-03-01
Weak H2 physisorption energies present a significant challenge to first-principle theoretical modeling and prediction of materials for H storage. There has been controversy regarding the accuracy of DFT on systems involving Ca cations. We use the auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca + , - 4{H}2 . AFQMC scales as Nbasis3and has demonstrated accuracy similar to or better than the gold-standard coupled cluster CCSD(T) method. We apply a modified Cholesky decomposition to achieve efficient Hubbard-Stratonovich transformation in AFQMC at large basis sizes. We employ the largest correlation consistent basis sets available, up to Ca/cc-pCV5Z, to extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure. Supported by DOE and NSF. Calculations were performed at OLCF Jaguar and CPD.
On the Kohn-Sham density response in a localized basis set
NASA Astrophysics Data System (ADS)
Foerster, Dietrich; Koval, Peter
2009-07-01
We construct the Kohn-Sham density response function χ0 in a previously described basis of the space of orbital products. The calculational complexity of our construction is O(N2Nω) for a molecule of N atoms and in a spectroscopic window of Nω frequency points. As a first application, we use χ0 to calculate the molecular spectra from the Petersilka-Gossmann-Gross equation. With χ0 as input, we obtain the correct spectra with an extra computational effort that grows also as O(N2Nω) and, therefore, less steeply in N than the O(N3) complexity of solving Casida's equations. Our construction should be useful for the study of excitons in molecular physics and in related areas where χ0 is a crucial ingredient.
Optimizing distance-based methods for large data sets
NASA Astrophysics Data System (ADS)
Scholl, Tobias; Brenner, Thomas
2015-10-01
Distance-based methods for measuring spatial concentration of industries have received an increasing popularity in the spatial econometrics community. However, a limiting factor for using these methods is their computational complexity since both their memory requirements and running times are in {{O}}(n^2). In this paper, we present an algorithm with constant memory requirements and shorter running time, enabling distance-based methods to deal with large data sets. We discuss three recent distance-based methods in spatial econometrics: the D&O-Index by Duranton and Overman (Rev Econ Stud 72(4):1077-1106, 2005), the M-function by Marcon and Puech (J Econ Geogr 10(5):745-762, 2010) and the Cluster-Index by Scholl and Brenner (Reg Stud (ahead-of-print):1-15, 2014). Finally, we present an alternative calculation for the latter index that allows the use of data sets with millions of firms.
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.
Optimal Target Region for Subject Classification on the Basis of Amyloid PET Images.
Carbonell, Felix; Zijdenbos, Alex P; Charil, Arnaud; Grand'Maison, Marilyn; Bedell, Barry J
2015-09-01
Classification of subjects on the basis of amyloid PET scans is increasingly being used in research studies and clinical practice. Although qualitative, visual assessment is currently the gold standard approach, automated classification techniques are inherently more reproducible and efficient. The objective of this work was to develop a statistical approach for the automated classification of subjects with different levels of cognitive impairment into a group with low amyloid levels (AβL) and a group with high amyloid levels (AβH) through the use of amyloid PET data from the Alzheimer Disease Neuroimaging Initiative study. In our framework, an iterative, voxelwise, regularized discriminant analysis is combined with a receiver operating characteristic approach that optimizes the selection of a region of interest (ROI) and a cutoff value for the automated classification of subjects into the AβL and AβH groups. The robustness, spatial stability, and generalization of the resulting target ROIs were evaluated by use of the standardized uptake value ratio for (18)F-florbetapir PET images from subjects who served as healthy controls, subjects who had mild cognitive impairment, and subjects who had Alzheimer disease and were participating in the Alzheimer Disease Neuroimaging Initiative study. We determined that several iterations of the discriminant analysis improved the classification of subjects into the AβL and AβH groups. We found that an ROI consisting of the posterior cingulate cortex/precuneus and the medial frontal cortex yielded optimal group separation and showed good stability across different reference regions and cognitive cohorts. A key step in this process was the automated determination of the cutoff value for group separation, which was dependent on the reference region used for the standardized uptake value ratio calculation and which was shown to have a relatively narrow range across subject groups. We developed a data-driven approach for the
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.
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.
Salvador, P; Mayer, I
2004-04-01
The basis set superposition error-free second-order Møller-Plesset perturbation theory of intermolecular interactions, based on the "chemical Hamiltonian approach," which has been introduced in Part I, is applied here to open-shell systems by using a new, effective computer realization. The results of the numerical examples considered (CH(4) em leader HO, NO em leader HF) showed again the perfect performance of the method. Striking agreement has again been found with the results of the a posteriori counterpoise correction (CP) scheme in the case of large, well-balanced basis sets, which is also in agreement with a most recent formal theoretical analysis. The difficulties of the CP correction in open-shell systems are also discussed.
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.
Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets.
Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo
2016-08-09
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.
Saravanan, Chandra; Shao, Yihan; Baer, Roi; Ross, Philip N; Head-Gordon, Martin
2003-04-15
A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 618-622, 2003
Perturbing engine performance measurements to determine optimal engine control settings
Jiang, Li; Lee, Donghoon; Yilmaz, Hakan; Stefanopoulou, Anna
2014-12-30
Methods and systems for optimizing a performance of a vehicle engine are provided. The method includes determining an initial value for a first engine control parameter based on one or more detected operating conditions of the vehicle engine, determining a value of an engine performance variable, and artificially perturbing the determined value of the engine performance variable. The initial value for the first engine control parameter is then adjusted based on the perturbed engine performance variable causing the engine performance variable to approach a target engine performance variable. Operation of the vehicle engine is controlled based on the adjusted initial value for the first engine control parameter. These acts are repeated until the engine performance variable approaches the target engine performance variable.
A decision support system to determine optimal ventilator settings.
Akbulut, Fatma Patlar; Akkur, Erkan; Akan, Aydin; Yarman, B Siddik
2014-01-10
Choosing the correct ventilator settings for the treatment of patients with respiratory tract disease is quite an important issue. Since the task of specifying the parameters of ventilation equipment is entirely carried out by a physician, physician's knowledge and experience in the selection of these settings has a direct effect on the accuracy of his/her decisions. Nowadays, decision support systems have been used for these kinds of operations to eliminate errors. Our goal is to minimize errors in ventilation therapy and prevent deaths caused by incorrect configuration of ventilation devices. The proposed system is designed to assist less experienced physicians working in the facilities without having lung mechanics like cottage hospitals. This article describes a decision support system proposing the ventilator settings required to be applied in the treatment according to the patients' physiological information. The proposed model has been designed to minimize the possibility of making a mistake and to encourage more efficient use of time in support of the decision making process while the physicians make critical decisions about the patient. Artificial Neural Network (ANN) is implemented in order to calculate frequency, tidal volume, FiO2 outputs, and this classification model has been used for estimation of pressure support / volume support outputs. For the obtainment of the highest performance in both models, different configurations have been tried. Various tests have been realized for training methods, and a number of hidden layers mostly affect factors regarding the performance of ANNs. The physiological information of 158 respiratory patients over the age of 60 and were treated in three different hospitals between the years 2010 and 2012 has been used in the training and testing of the system. The diagnosed disease, core body temperature, pulse, arterial systolic pressure, diastolic blood pressure, PEEP, PSO2, pH, pCO2, bicarbonate data as well as the
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.
Chitwood, Daniel H; Kumar, Ravi; Headland, Lauren R; Ranjan, Aashish; Covington, Michael F; Ichihashi, Yasunori; Fulop, Daniel; Jiménez-Gómez, José M; Peng, Jie; Maloof, Julin N; Sinha, Neelima R
2013-07-01
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations.
Masoli, Stefano; Rizza, Martina F; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio
2017-01-01
In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models.
Masoli, Stefano; Rizza, Martina F.; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio
2017-01-01
In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models. PMID:28360841
Aquilanti, Vincenzo; Tonzani, Stefano
2004-03-01
Elliptic coordinates within the hyperspherical formalism for three-body problems were proposed some time ago [V. Aquilanti, S. Cavalli, and G. Grossi, J. Chem. Phys. 85, 1362 (1986)] and recently have also found application, for example, in chemical reaction theory [see O. I. Tolstikhin and H. Nakamura, J. Chem. Phys. 108, 8899 (1998)]. Here we consider their role in providing a smooth transition between the known "symmetric" and "asymmetric" parametrizations, and focus on the corresponding hyperspherical harmonics. These harmonics, which will be called hyperspherical elliptic, involve products of two associated Lame polynomials. We will provide an expansion of these new sets in a finite series of standard hyperspherical harmonics, producing a powerful tool for future applications in the field of scattering and bound-state quantum-mechanical three-body problems.
Multi-objective particle swarm optimization using Pareto-based set and aggregation approach
NASA Astrophysics Data System (ADS)
Huang, Song; Wang, Yan; Ji, Zhicheng
2017-07-01
Multi-objective optimization problems (MOPs) need to be solved in real world recently. In this paper, a multi-objective particle swarm optimization based on Pareto set and aggregation approach was proposed to deal with MOPs. Firstly, velocities and positions were updated similar to PSO. Then, global-best set was defined in particle swarm optimizer to preserve Pareto-based set obtained by the population. Specifically, a hybrid updating strategy based on Pareto set and aggregation approach was introduced to update the global-best set and local search was carried on global-best set. Thirdly, personal-best positions were updated in decomposition way, and global-best position was selected from global-best set. Finally, ZDT instances and DTLZ instances were selected to evaluate the performance of MULPSO and the results show validity of the proposed algorithm for MOPs.
Huang, He; Harlé, Katia; Movellan, Javier; Paulus, Martin
2016-01-01
Differentiating the ability from the motivation to act is of central importance to psychiatric disorders in general and depression in particular. However, it has been difficult to develop quantitative approaches to relate depression to poor motor performance in goal-directed tasks. Here, we use an inverse optimal control approach to provide a computational framework that can be used to infer and factorize performance deficits into three components: sensorimotor speed, goal setting and motivation. Using a novel computer-simulated driving experiment, we found that (1) severity of depression is associated with both altered sensorimotor speed and motivational function; (2) moderately to severely depressed individuals show an increased distance from the stop sign indicating aversive learning affecting goal setting functions. Taken together, the inverse optimal control framework can disambiguate on an individual basis the sensorimotor from the motivational dysfunctions in depression, which may help to develop more precisely targeted interventions.
Huang, He; Harlé, Katia; Movellan, Javier; Paulus, Martin
2016-01-01
Differentiating the ability from the motivation to act is of central importance to psychiatric disorders in general and depression in particular. However, it has been difficult to develop quantitative approaches to relate depression to poor motor performance in goal-directed tasks. Here, we use an inverse optimal control approach to provide a computational framework that can be used to infer and factorize performance deficits into three components: sensorimotor speed, goal setting and motivation. Using a novel computer-simulated driving experiment, we found that (1) severity of depression is associated with both altered sensorimotor speed and motivational function; (2) moderately to severely depressed individuals show an increased distance from the stop sign indicating aversive learning affecting goal setting functions. Taken together, the inverse optimal control framework can disambiguate on an individual basis the sensorimotor from the motivational dysfunctions in depression, which may help to develop more precisely targeted interventions. PMID:27973592
Cameras and settings for optimal image capture from UAVs
NASA Astrophysics Data System (ADS)
Smith, Mike; O'Connor, James; James, Mike R.
2017-04-01
Aerial image capture has become very common within the geosciences due to the increasing affordability of low payload (<20 kg) Unmanned Aerial Vehicles (UAVs) for consumer markets. Their application to surveying has led to many studies being undertaken using UAV imagery captured from consumer grade cameras as primary data sources. However, image quality and the principles of image capture are seldom given rigorous discussion which can lead to experiments being difficult to accurately reproduce. In this contribution we revisit the underpinning concepts behind image capture, from which the requirements for acquiring sharp, well exposed and suitable imagery are derived. This then leads to discussion of how to optimise the platform, camera, lens and imaging settings relevant to image quality planning, presenting some worked examples as a guide. Finally, we challenge the community to make their image data open for review in order to ensure confidence in the outputs/error estimates, allow reproducibility of the results and have these comparable with future studies. We recommend providing open access imagery where possible, a range of example images, and detailed metadata to rigorously describe the image capture process.
[The BASYS observation system for the analysis of aggressive behavior in classroom-settings].
Wettstein, Alexander
2012-01-01
Educational or therapeutic measures of aggressive student behavior are often based on the judgments of teachers. However, empirical studies show that the objectivity of these judgments is generally low. In order to assess aggressive behavior in classroom settings, we developed a context-sensitive observational system. The observation system exists in a version for teachers in action as well as a version for the uninvolved observer. The teacher version allows categorizing aggressive behavior while teaching. The aim is to differentiate the perception and the judgments of teachers, so that the judgments can serve as trustable diagnostic information. The version for an independent observer, in addition, contains categories to collect information about the context in which aggressions take place. The behavior observation system was tested in four field-studies in regular and special classes. The empirical results show that, after training, teachers were able to make objective observations, and that aggressive behavior depends to a large extent on situational factors. The system allows identification of problematic people-environment relationships and the derivation of intervention measures.
NASA Astrophysics Data System (ADS)
Martin, Jan M. L.; El-Yazal, Jamal; François, Jean-Pierre
1995-12-01
The performance of the Becke three-parameter Lee-Yang-Parr (B3LYP) method for geometries and harmonic frequencies has been compared with other density functional methods and accurate coupled cluster calculations, and its basis set convergence investigated. In a basis of [3s2p1d] quality, B3LYP geometries are more accurate than CCSD(T) due to an error compensation. Using simple additivity corrections, B3LYP/[4s3p2d1f] calculations allow the prediction of geometries to within 0·002 Å, on average. Except for certain special cases where frequencies are especially sensitive to the basis set, B3LYP/[4s3p2d1f] frequencies do not represent a clear improvement over B3LYP/[3s2p1d], while the latter are of nearly the same quality as CCSD(T)/[3s2p1d]. Applications to ethylene, benzene, furan and pyrrole are presented. For the latter three molecules, our best structures and harmonic frequencies are believed to be the most accurate computed values available.
NASA Astrophysics Data System (ADS)
Kruse, Holger; Grimme, Stefan
2012-04-01
chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.
Small Al clusters. I - The effect of basis set and correlation on the geometry of small Al clusters
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Pettersson, Lars G. M.
1987-01-01
A detailed study is presented of the basis set requirements and effects of correlation on the geometry and structure of small Al(n) clusters n = 2, 4, and 13. An effective core potential (ECP) is developed from the Huzinaga basis which accurately reproduces the all-electron results. It is found that depolarization functions are very important in computing the bond length, and that the bond contraction obtained is about as large for a 13-atom cluster as for the Al(4) rhombus structure. With d functions on each center in Al(13), a bond distance shorter than the bulk is obtained, as expected. The inclusion of correlation in Al(4) is found to be less important than the addition of polarization functions for determining the bond length, but increases substantially the calculated atomization energy. These calibration calculations allow an accurate treatment for Al(n) clusters to be designed.
NASA Astrophysics Data System (ADS)
Filter, Eckhard; Steinborn, E. Otto
1980-12-01
The matrix elements of the translation operator with respect to a complete orthonormal basis set of the Hilbert space L2(R3) are given in closed form as functions of the displacement vector. The basis functions are composed of an exponential, a Laguerre polynomial, and a regular solid spherical harmonic. With this formalism, a function which is defined with respect to a certain origin, can be ''shifted'', i.e., expressed in terms of given functions which are defined with respect to another origin. In this paper we also demonstrate the feasibility of this method by applying it to problems that are of special interest in the theory of the electronic structure of molecules and solids. We present new one-center expansions for some exponential-type functions (ETF's), and a closed-form expression for a multicenter integral over ETF's is given and numerically tested.
The Study of the Optimal Parameter Settings in a Hospital Supply Chain System in Taiwan
Liao, Hung-Chang; Chen, Meng-Hao; Wang, Ya-huei
2014-01-01
This study proposed the optimal parameter settings for the hospital supply chain system (HSCS) when either the total system cost (TSC) or patient safety level (PSL) (or both simultaneously) was considered as the measure of the HSCS's performance. Four parameters were considered in the HSCS: safety stock, maximum inventory level, transportation capacity, and the reliability of the HSCS. A full-factor experimental design was used to simulate an HSCS for the purpose of collecting data. The response surface method (RSM) was used to construct the regression model, and a genetic algorithm (GA) was applied to obtain the optimal parameter settings for the HSCS. The results show that the best method of obtaining the optimal parameter settings for the HSCS is the simultaneous consideration of both the TSC and the PSL to measure performance. Also, the results of sensitivity analysis based on the optimal parameter settings were used to derive adjustable strategies for the decision-makers. PMID:25250397
Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c.
González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A
2015-08-11
Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin's transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ's histone chaperone activity.
Structural basis for inhibition of the histone chaperone activity of SET/TAF-Iβ by cytochrome c
González-Arzola, Katiuska; Díaz-Moreno, Irene; Cano-González, Ana; Díaz-Quintana, Antonio; Velázquez-Campoy, Adrián; Moreno-Beltrán, Blas; López-Rivas, Abelardo; De la Rosa, Miguel A.
2015-01-01
Chromatin is pivotal for regulation of the DNA damage process insofar as it influences access to DNA and serves as a DNA repair docking site. Recent works identify histone chaperones as key regulators of damaged chromatin’s transcriptional activity. However, understanding how chaperones are modulated during DNA damage response is still challenging. This study reveals that the histone chaperone SET/TAF-Iβ interacts with cytochrome c following DNA damage. Specifically, cytochrome c is shown to be translocated into cell nuclei upon induction of DNA damage, but not upon stimulation of the death receptor or stress-induced pathways. Cytochrome c was found to competitively hinder binding of SET/TAF-Iβ to core histones, thereby locking its histone-binding domains and inhibiting its nucleosome assembly activity. In addition, we have used NMR spectroscopy, calorimetry, mutagenesis, and molecular docking to provide an insight into the structural features of the formation of the complex between cytochrome c and SET/TAF-Iβ. Overall, these findings establish a framework for understanding the molecular basis of cytochrome c-mediated blocking of SET/TAF-Iβ, which subsequently may facilitate the development of new drugs to silence the oncogenic effect of SET/TAF-Iβ’s histone chaperone activity. PMID:26216969
NASA Astrophysics Data System (ADS)
Salmin, Vadim V.
2017-01-01
Flight mechanics with a low-thrust is a new chapter of mechanics of space flight, considered plurality of all problems trajectory optimization and movement control laws and the design parameters of spacecraft. Thus tasks associated with taking into account the additional factors in mathematical models of the motion of spacecraft becomes increasingly important, as well as additional restrictions on the possibilities of the thrust vector control. The complication of the mathematical models of controlled motion leads to difficulties in solving optimization problems. Author proposed methods of finding approximate optimal control and evaluating their optimality based on analytical solutions. These methods are based on the principle of extending the class of admissible states and controls and sufficient conditions for the absolute minimum. Developed procedures of the estimation enabling to determine how close to the optimal founded solution, and indicate ways to improve them. Authors describes procedures of estimate for approximately optimal control laws for space flight mechanics problems, in particular for optimization flight low-thrust between the circular non-coplanar orbits, optimization the control angle and trajectory movement of the spacecraft during interorbital flights, optimization flights with low-thrust between arbitrary elliptical orbits Earth satellites.
Zhao, Bin; Wang, Shuxiao; Donahue, Neil M; Chuang, Wayne; Hildebrandt Ruiz, Lea; Ng, Nga L; Wang, Yangjun; Hao, Jiming
2015-02-17
We evaluate the one-dimensional volatility basis set (1D-VBS) and two-dimensional volatility basis set (2D-VBS) in simulating the aging of SOA derived from toluene and α-pinene against smog-chamber experiments. If we simulate the first-generation products with empirical chamber fits and the subsequent aging chemistry with a 1D-VBS or a 2D-VBS, the models mostly overestimate the SOA concentrations in the toluene oxidation experiments. This is because the empirical chamber fits include both first-generation oxidation and aging; simulating aging in addition to this results in double counting of the initial aging effects. If the first-generation oxidation is treated explicitly, the base-case 2D-VBS underestimates the SOA concentrations and O:C increase of the toluene oxidation experiments; it generally underestimates the SOA concentrations and overestimates the O:C increase of the α-pinene experiments. With the first-generation oxidation treated explicitly, we could modify the 2D-VBS configuration individually for toluene and α-pinene to achieve good model-measurement agreement. However, we are unable to simulate the oxidation of both toluene and α-pinene with the same 2D-VBS configuration. We suggest that future models should implement parallel layers for anthropogenic (aromatic) and biogenic precursors, and that more modeling studies and laboratory research be done to optimize the "best-guess" parameters for each layer.
Lobmaier, S M; Cruz-Lemini, M; Valenzuela-Alcaraz, B; Ortiz, J U; Martinez, J M; Gratacos, E; Crispi, F
2014-06-01
To compare left myocardial performance index (MPI) values and reproducibility using different settings and ultrasound equipment in order to standardize optimal machine settings. Left MPI was prospectively evaluated by one observer performing conventional Doppler in 62 fetuses (28-36 weeks of gestational age) using different settings (changing sweep speed, gain and wall motion filter (WMF)) and two different ultrasound devices (Siemens Antares, Siemens; Voluson 730 Expert, GE Medical Systems). Intraclass coefficients of agreement (ICCs) were calculated using Bland-Altman analysis. Using baseline settings on the Siemens, mean (SD) MPI was 0.44 (0.05) with an ICC of 0.81. Decreasing the sweep speed resulted in decreasing average MPI values (0.43) and decreasing ICC (0.61). Lowering gain also influenced average MPI values (0.46) and ICC (0.76). Raising gain resulted in similar MPI values (0.45) with better ICC (0.90) compared with baseline settings. Raising wall motion filter (WMF) provided the best ICC (0.94) compared with the other settings. Changing the ultrasound equipment resulted in an ICC of 0.64. The optimal settings to achieve the highest reproducibility in measurement of MPI were sweep speed 8, gain 60 dB and WMF 281 Hz for Siemens Antares and sweep speed 5, gain -10 dB and WMF 210 Hz for Voluson 730 Expert. Changing ultrasound settings or equipment may affect the calculation and repeatability of measurement of MPI values. Strict standardization of methods decreases the variability of this parameter for fetal cardiac function assessment. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.
NASA Astrophysics Data System (ADS)
Simon, Sílvia; Duran, Miquel
1997-08-01
Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.
Full glowworm swarm optimization algorithm for whole-set orders scheduling in single machine.
Yu, Zhang; Yang, Xiaomei
2013-01-01
By analyzing the characteristics of whole-set orders problem and combining the theory of glowworm swarm optimization, a new glowworm swarm optimization algorithm for scheduling is proposed. A new hybrid-encoding schema combining with two-dimensional encoding and random-key encoding is given. In order to enhance the capability of optimal searching and speed up the convergence rate, the dynamical changed step strategy is integrated into this algorithm. Furthermore, experimental results prove its feasibility and efficiency.
Analysis of the optimal laminated target made up of discrete set of materials
NASA Technical Reports Server (NTRS)
Aptukov, Valery N.; Belousov, Valentin L.
1991-01-01
A new class of problems was analyzed to estimate an optimal structure of laminated targets fabricated from the specified set of homogeneous materials. An approximate description of the perforation process is based on the model of radial hole extension. The problem is solved by using the needle-type variation technique. The desired optimization conditions and quantitative/qualitative estimations of optimal targets were obtained and are discussed using specific examples.
NASA Astrophysics Data System (ADS)
Feller, David; Peterson, Kirk A.
2013-08-01
The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 Eh) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.
Feller, David; Peterson, Kirk A
2013-08-28
The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 E(h)) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.
NASA Astrophysics Data System (ADS)
Rach, N.; Müller, M. M.; Calarco, T.; Montangero, S.
2015-12-01
In quantum optimal control theory the success of an optimization algorithm is highly influenced by how the figure of merit to be optimized behaves as a function of the control field, i.e., by the control landscape. Constraints on the control field introduce local minima in the landscape—false traps—which might prevent an efficient solution of the optimal control problem. Rabitz et al. [Science 303, 1998 (2004), 10.1126/science.1093649] showed that local minima occur only rarely for unconstrained optimization. Here, we extend this result to the case of bandwidth-limited control pulses showing that in this case one can eliminate the false traps arising from the constraint. Based on this theoretical understanding, we modify the chopped-random-basis (CRAB) optimal control algorithm and show that this development exploits the advantages of both (unconstrained) gradient algorithms and of truncated basis methods, allowing one to always follow the gradient of the unconstrained landscape by bandwidth-limited control functions. We study the effects of additional constraints and show that for reasonable constraints the convergence properties are still maintained. Finally, we numerically show that this approach saturates the theoretical bound on the minimal bandwidth of the control needed to optimally drive the system.
Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties.
Browning, Nicholas J; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole; Roethlisberger, Ursula
2017-04-06
The training of molecular models of quantum mechanical properties based on statistical machine learning requires large data sets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of training examples is often difficult or impossible to achieve, as prior knowledge may be unavailable. Ordinarily representative selection of training molecules from such data sets is achieved through random sampling. We use genetic algorithms for the optimization of training set composition consisting of tens of thousands of small organic molecules. The resulting machine learning models are considerably more accurate: in the limit of small training sets, mean absolute errors for out-of-sample predictions are reduced by up to ∼75%. We discuss and present optimized training sets consisting of 10 molecular classes for all molecular properties studied. We show that these classes can be used to design improved training sets for the generation of machine learning models of the same properties in similar but unrelated molecular sets.
NASA Astrophysics Data System (ADS)
Lindh, R.; Liu, B.
1991-03-01
The quadrupole moment of acetylene has been studied at the multiconfiguration self-consistent field (MCSCF) and multireference single and double configuration interaction (MRSDCI) level of theory. At the MCSCF level the π-CI complete active space SCF (CASSCF) and the valence-CI CASSCF were employed. The subsequent MRSDCI calculations were continued until the reference space included all configuration state functions (CSFs) of the MCSCF wave function with a coefficient larger than 0.01 [MRSDCI(0.01)]. The higher level basis sets in this study were all based on van Duijneveldt's C(13s 8p) and H(6s) and extensions of that basis set. The study shows in a consistent way that both the one- and n-particle spaces are saturated at the highest level of theory. The study has revealed that in addition to the well known increase of the quadrupole moment due to the inclusion of polarizing functions in the basis (typically 0.20 a.u.), the inclusion of electronic correlation in the model wave function as well as vibrational corrections will decrease the quadrupole moment significantly more, -0.66, -0.49, and -0.36 a.u., for the correlation correction and zero-point correction for HCCH and DCCD, respectively. The most accurate computations predict the quadrupole moment of HCCH, including zero-point correction, to be 4.29±0.12 a.u., which discriminates the experimental estimates of 4.03±0.30, 4.28±0.30, and 4.57±0.30 a.u. (the first being the favored value). The quadrupole moment of DCCD is computed to 4.42±0.10 a.u. In the study it was observed that in contradiction to previous experiences the use of the model equilibrium geometries rather than the experimental geometry gives a smoother convergence as the level of theory is increased. The effects of basis set quality and electron correlation on the quadrupole moment are studied in detail. These effects are analyzed with reference to the redistribution of the electronic charge.
NASA Astrophysics Data System (ADS)
Van Houteghem, Marc; Verstraelen, Toon; Ghysels, An; Vanduyfhuys, Louis; Waroquier, Michel; Van Speybroeck, Veronique
2012-09-01
An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.
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 .
Kupka, Teobald; Stachów, Michał; Nieradka, Marzena; Kaminsky, Jakub; Pluta, Tadeusz; Sauer, Stephan P A
2011-05-01
It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n complete basis set calculations the prediction of nuclear shieldings at the CCSD(T) level of nearly similar accuracy as those, obtained by fitting results obtained from computationally demanding pcS-n calculations at the CCSD(T) limit. A significant saving of computational efforts can thus be achieved by scaling inexpensive CCSD(T)/aug-cc-pVTZ-J calculations of nuclear isotropic shieldings with affordable DFT complete basis set limit corrections. Copyright © 2011 John Wiley & Sons, Ltd.
An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification
ERIC Educational Resources Information Center
Wang, Jun; Samal, Ashok; Rong, Panying; Green, Jordan R.
2016-01-01
Purpose: The authors sought to determine an optimal set of flesh points on the tongue and lips for classifying speech movements. Method: The authors used electromagnetic articulographs (Carstens AG500 and NDI Wave) to record tongue and lip movements from 13 healthy talkers who articulated 8 vowels, 11 consonants, a phonetically balanced set of…
An Optimal Set of Flesh Points on Tongue and Lips for Speech-Movement Classification
ERIC Educational Resources Information Center
Wang, Jun; Samal, Ashok; Rong, Panying; Green, Jordan R.
2016-01-01
Purpose: The authors sought to determine an optimal set of flesh points on the tongue and lips for classifying speech movements. Method: The authors used electromagnetic articulographs (Carstens AG500 and NDI Wave) to record tongue and lip movements from 13 healthy talkers who articulated 8 vowels, 11 consonants, a phonetically balanced set of…
Aerostructural Level Set Topology Optimization for a Common Research Model Wing
NASA Technical Reports Server (NTRS)
Dunning, Peter D.; Stanford, Bret K.; Kim, H. Alicia
2014-01-01
The purpose of this work is to use level set topology optimization to improve the design of a representative wing box structure for the NASA common research model. The objective is to minimize the total compliance of the structure under aerodynamic and body force loading, where the aerodynamic loading is coupled to the structural deformation. A taxi bump case was also considered, where only body force loads were applied. The trim condition that aerodynamic lift must balance the total weight of the aircraft is enforced by allowing the root angle of attack to change. The level set optimization method is implemented on an unstructured three-dimensional grid, so that the method can optimize a wing box with arbitrary geometry. Fast matching and upwind schemes are developed for an unstructured grid, which make the level set method robust and efficient. The adjoint method is used to obtain the coupled shape sensitivities required to perform aerostructural optimization of the wing box structure.
NASA Astrophysics Data System (ADS)
Acharyya, Atanu; Paul, Goutam
2017-02-01
A general framework of optimal eavesdropping on BB84 protocol was provided by Fuchs et al. [Phys. Rev. A 56, 1163 (1997), 10.1103/PhysRevA.56.1163]. An upper bound on mutual information was derived, which could be achieved by a specific type of interaction and the corresponding measurement. However, uniqueness of optimal interaction was posed as an unsolved problem there and it has remained open for almost two decades now. In this paper, we solve this open problem and establish the uniqueness of optimal interaction up to rotation. The specific choice of optimal interaction by Fuchs et al. is shown to be a special case of the form derived in our work.
A mathematical basis for the design optimization of adaptive trusses in precision control
NASA Technical Reports Server (NTRS)
Das, S. K.; Utku, S.; Chen, G. S.; Wada, B. K.
1991-01-01
Optimal actuator placement schemes are presently studied for cases of adaptive truss precision control and prestressing control, with a view to the maximization of actuator efficiencies. In statically indeterminate truss structures, the optimal placement criteria and techniques differ, depending on whether the primary determinate structure is known. A suboptimal actuator-placement solution to the global optimization problem which combines displacement control and prestressing control is suggested, by combining the separate displacement control and prestressing control optimization results. Attention is given to the results obtained for the illustrative case of a two-bay, three-dimensional precision truss structure.
Zhang, Peng; Liu, Keping; Zhao, Bo; Li, Yuanchun
2015-01-01
Optimal guidance is essential for the soft landing task. However, due to its high computational complexities, it is hardly applied to the autonomous guidance. In this paper, a computationally inexpensive optimal guidance algorithm based on the radial basis function neural network (RBFNN) is proposed. The optimization problem of the trajectory for soft landing on asteroids is formulated and transformed into a two-point boundary value problem (TPBVP). Combining the database of initial states with the relative initial co-states, an RBFNN is trained offline. The optimal trajectory of the soft landing is determined rapidly by applying the trained network in the online guidance. The Monte Carlo simulations of soft landing on the Eros433 are performed to demonstrate the effectiveness of the proposed guidance algorithm. PMID:26367382
Zhang, Peng; Liu, Keping; Zhao, Bo; Li, Yuanchun
2015-01-01
Optimal guidance is essential for the soft landing task. However, due to its high computational complexities, it is hardly applied to the autonomous guidance. In this paper, a computationally inexpensive optimal guidance algorithm based on the radial basis function neural network (RBFNN) is proposed. The optimization problem of the trajectory for soft landing on asteroids is formulated and transformed into a two-point boundary value problem (TPBVP). Combining the database of initial states with the relative initial co-states, an RBFNN is trained offline. The optimal trajectory of the soft landing is determined rapidly by applying the trained network in the online guidance. The Monte Carlo simulations of soft landing on the Eros433 are performed to demonstrate the effectiveness of the proposed guidance algorithm.
Optimization of structures on the basis of fracture mechanics and reliability criteria
NASA Technical Reports Server (NTRS)
Heer, E.; Yang, J. N.
1973-01-01
Systematic summary of factors which are involved in optimization of given structural configuration is part of report resulting from study of analysis of objective function. Predicted reliability of performance of finished structure is sharply dependent upon results of coupon tests. Optimization analysis developed by study also involves expected cost of proof testing.
The enthalpy of formation of the pentane-2,4-dionate radical: A complete basis set approach
NASA Astrophysics Data System (ADS)
Cabral do Couto, P.; Costa Cabral, Benedito J.; Martinho Simões, José A.
2006-02-01
Thermochemical properties of pentane-2,4-dione (acetylacetone, Hacac) and its radical (acac) were investigated by DFT and ab initio calculations based on complete basis set (CBS) extrapolation procedures, including CBS-QB3 and a modified CBS procedure that we named CBS-QB3-tz. We provide evidence that the most stable acac radical conformer is generated by C-H bond homolysis. The enthalpy of formation of gaseous acac, Δ fH∘(acac,g), was estimated as -228.3 kJ/mol (CBS-QB3) and -226.7 kJ/mol (CBS-QB3-tz). Based on these results, our recommended value for Δ fH∘(acac,g) is -227 ± 8 kJ/mol, implying that many literature values reported for metal-acac bond dissociation enthalpies in coordination complexes should be revised.
NASA Astrophysics Data System (ADS)
Guan, Qingze; Blume, Doerte
2016-05-01
The explicit correlated Gaussian (ECG) basis set expansion approach is a variational approach that has been used in various areas, including molecular, nuclear, atomic, and chemical physics. In the world of cold atoms, e.g., the ECG approach has been used to calculate the eigenenergies and eigenstates of few-body systems governed by Efimov physics. Since the first experimental realization of synthesized gauge fields, few-body systems with spin-orbit coupling have attracted a great deal of attention. Here, the ECG approach is customized to few-body systems with both short-range interactions and spin-orbit couplings. Benchmark tests and a performance analysis will be presented. Support by the NSF is gratefully acknowledged.
Cost optimization for series-parallel execution of a collection of intersecting operation sets
NASA Astrophysics Data System (ADS)
Dolgui, Alexandre; Levin, Genrikh; Rozin, Boris; Kasabutski, Igor
2016-05-01
A collection of intersecting sets of operations is considered. These sets of operations are performed successively. The operations of each set are activated simultaneously. Operation durations can be modified. The cost of each operation decreases with the increase in operation duration. In contrast, the additional expenses for each set of operations are proportional to its time. The problem of selecting the durations of all operations that minimize the total cost under constraint on completion time for the whole collection of operation sets is studied. The mathematical model and method to solve this problem are presented. The proposed method is based on a combination of Lagrangian relaxation and dynamic programming. The results of numerical experiments that illustrate the performance of the proposed method are presented. This approach was used for optimization multi-spindle machines and machining lines, but the problem is common in engineering optimization and thus the techniques developed could be useful for other applications.
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
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.
Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine
2016-01-01
Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4–6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data. PMID:27471441
Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine
2016-01-01
Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4-6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data.
Oberhofer, Harald; Blumberger, Jochen
2010-12-28
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.
NASA Astrophysics Data System (ADS)
Lee, Hee-Seung; Tuckerman, Mark E.
2007-04-01
Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.
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.
Kim, D.S.; Seong, P.H. . Dept. of Nuclear Engineering)
1994-02-01
This paper describes the optimal testing input sets required for the fault diagnosis of the nuclear power plant digital electronic circuits. With the complicated systems such as very large scale integration (VLSI), nuclear power plant (NPP), and aircraft, testing is the major factor of the maintenance of the system. Particularly, diagnosis time grows quickly with the complexity of the component. In this research, for reduce diagnosis time the authors derived the optimal testing sets that are the minimal testing sets required for detecting the failure and for locating of the failed component. For reduced diagnosis time, the technique presented by Hayes fits best for the approach to testing sets generation among many conventional methods. However, this method has the following disadvantages: (a) it considers only the simple network (b) it concerns only whether the system is in failed state or not and does not provide the way to locate the failed component. Therefore the authors have derived the optimal testing input sets that resolve these problems by Hayes while preserving its advantages. When they applied the optimal testing sets to the automatic fault diagnosis system (AFDS) which incorporates the advanced fault diagnosis method of artificial intelligence technique, they found that the fault diagnosis using the optimal testing sets makes testing the digital electronic circuits much faster than that using exhaustive testing input sets; when they applied them to test the Universal (UV) Card which is a nuclear power plant digital input/output solid state protection system card, they reduced the testing time up to about 100 times.
Liu, Long; Sun, Jun; Xu, Wenbo; Du, Guocheng; Chen, Jian
2009-01-01
Hyaluronic acid (HA) is a natural biopolymer with unique physiochemical and biological properties and finds a wide range of applications in biomedical and cosmetic fields. It is important to increase HA production to meet the increasing HA market demand. This work is aimed to model and optimize the amino acids addition to enhance HA production of Streptococcus zooepidemicus with radial basis function (RBF) neural network coupling quantum-behaved particle swarm optimization (QPSO) algorithm. In the RBF-QPSO approach, RBF neural network is used as a bioprocess modeling tool and QPSO algorithm is applied to conduct the optimization with the established RBF neural network black model as the objective function. The predicted maximum HA yield was 6.92 g/L under the following conditions: arginine 0.062 g/L, cysteine 0.036 g/L, and lysine 0.043 g/L. The optimal amino acids addition allowed HA yield increased from 5.0 g/L of the control to 6.7 g/L in the validation experiments. Moreover, the modeling and optimization capacity of the RBF-QPSO approach was compared with that of response surface methodology (RSM). It was indicated that the RBF-QPSO approach gave a slightly better modeling and optimization result compared with RSM. The developed RBF-QPSO approach in this work may be helpful for the modeling and optimization of the other multivariable, nonlinear, time-variant bioprocesses.
NASA Astrophysics Data System (ADS)
Nicholas, John B.; Feyereisen, Martin
1995-11-01
We studied the structure of disiloxane (H3Si-O-SiH3), silanol (H3Si-OH), and the silanol anion (H3Si-O-) with ab initio molecular orbital theory and the correlation consistent polarized basis sets of Dunning and co-workers. We present results for the correlation consistent polarized valence double zeta (cc-pVDZ), triple zeta (cc-pVTZ), and quadruple zeta [cc-pVQZ(-g)] basis sets. Optimized geometries and energies are given at both the restricted Hartree-Fock (RHF) level and with the inclusion of electron correlation by second order Møller-Plesset perturbation theory (MP2). The correlation consistent basis sets provide a systematic expansion of the orbital basis set, with each set of additional functions adding a similar contribution to the correlation energy. We find that the calculated molecular properties show exponential convergence with increasing basis set size. These calculations answer long-standing questions regarding the structure and barrier to linearization of disiloxane. Results at the highest level of theory [MP2/cc-pVQZ(-g)] for disiloxane gave a Si-O-Si bond angle of 147.0°, a Si-O bond length of 1.641 Å, and a barrier to linearization of 0.4 kcal/mol. All of these values are in excellent agreement with experimental results. Similar calculations for silanol gave a Si-O bond length of 1.655 Å, an O-H bond of 0.955 Å, and a Si-O-H angle of 117.9°. The MP2/cc-pVQZ(-g) deprotonation energy (ΔE0) for silanol, calculated as the energy difference between silanol and its anion, is -366.6 kcal/mol. The effects of electron correlation at the MP4 level are studied in all three molecules using the cc-pVDZ and cc-pVTZ basis sets.
NASA Technical Reports Server (NTRS)
Decker, Arthur J.
2001-01-01
Artificial neural networks have been used for a number of years to process holography-generated characteristic patterns of vibrating structures. This technology depends critically on the selection and the conditioning of the training sets. A scaling operation called folding is discussed for conditioning training sets optimally for training feed-forward neural networks to process characteristic fringe patterns. Folding allows feed-forward nets to be trained easily to detect damage-induced vibration-displacement-distribution changes as small as 10 nm. A specific application to aerospace of neural-net processing of characteristic patterns is presented to motivate the conditioning and optimization effort.
Stacking sequence and shape optimization of laminated composite plates via a level-set method
NASA Astrophysics Data System (ADS)
Allaire, G.; Delgado, G.
2016-12-01
We consider the optimal design of composite laminates by allowing a variable stacking sequence and in-plane shape of each ply. In order to optimize both variables we rely on a decomposition technique which aggregates the constraints into one unique constraint margin function. Thanks to this approach, an exactly equivalent bi-level optimization problem is established. This problem is made up of an inner level represented by the combinatorial optimization of the stacking sequence and an outer level represented by the topology and geometry optimization of each ply. We propose for the stacking sequence optimization an outer approximation method which iteratively solves a set of mixed integer linear problems associated to the evaluation of the constraint margin function. For the topology optimization of each ply, we lean on the level set method for the description of the interfaces and the Hadamard method for boundary variations by means of the computation of the shape gradient. Numerical experiments are performed on an aeronautic test case where the weight is minimized subject to different mechanical constraints, namely compliance, reserve factor and buckling load.
Kashyap, Kanchan Lata; Bajpai, Manish Kumar; Khanna, Pritee
2017-08-01
Computer-aided detection systems play an important role for the detection of breast abnormalities using mammograms. Global segmentation of mass in mammograms is a complex process due to low contrast mammogram images, irregular shape of mass, speculated margins, and the presence of intensity variations of pixels. This work presents a new approach for mass detection in mammograms, which is based on the variational level set function. Mesh-free based radial basis function (RBF) collocation approach is employed for the evolution of level set function for segmentation of breast as well as suspicious mass region. The mesh-based finite difference method (FDM) is used in literature for evolution of level set function. This work also showcases a comparative study of mesh-free and mesh-based approaches. An anisotropic diffusion filter is employed for enhancement of mammograms. The performance of mass segmentation is analyzed by computing statistical measures. Binarized statistical image features (BSIF) and variants of local binary pattern (LBP) are computed from the segmented suspicious mass regions. These features are given as input to the supervised support vector machine (SVM) classifier to classify suspicious mass region as mass (abnormal) or non-mass (normal) region. Validation of the proposed algorithm is done on sample mammograms taken from publicly available Mini-mammographic image analysis society (MIAS) and Digital Database for Screening Mammography (DDSM) datasets. Combined BSIF features perform better as compared to LBP variants with the performance reported as 97.12% sensitivity, 92.43% specificity, and 98% AUC with 5.12 FP/I on DDSM dataset; and 95.12% sensitivity, 92.41% specificity, and 95% AUC with 4.01FP/I on MIAS dataset. Copyright © 2017 Elsevier Ltd. All rights reserved.
NASA Astrophysics Data System (ADS)
Villanueva Perez, Carlos Hernan
Computational design optimization provides designers with automated techniques to develop novel and non-intuitive optimal designs. Topology optimization is a design optimization technique that allows for the evolution of a broad variety of geometries in the optimization process. Traditional density-based topology optimization methods often lack a sufficient resolution of the geometry and physical response, which prevents direct use of the optimized design in manufacturing and the accurate modeling of the physical response of boundary conditions. The goal of this thesis is to introduce a unified topology optimization framework that uses the Level Set Method (LSM) to describe the design geometry and the eXtended Finite Element Method (XFEM) to solve the governing equations and measure the performance of the design. The methodology is presented as an alternative to density-based optimization approaches, and is able to accommodate a broad range of engineering design problems. The framework presents state-of-the-art methods for immersed boundary techniques to stabilize the systems of equations and enforce the boundary conditions, and is studied with applications in 2D and 3D linear elastic structures, incompressible flow, and energy and species transport problems to test the robustness and the characteristics of the method. A comparison of the framework against density-based topology optimization approaches is studied with regards to convergence, performance, and the capability to manufacture the designs. Furthermore, the ability to control the shape of the design to operate within manufacturing constraints is developed and studied. The analysis capability of the framework is validated quantitatively through comparison against previous benchmark studies, and qualitatively through its application to topology optimization problems. The design optimization problems converge to intuitive designs and resembled well the results from previous 2D or density-based studies.
Second-order lower radial tangent derivatives and applications to set-valued optimization.
Xu, Bihang; Peng, Zhenhua; Xu, Yihong
2017-01-01
We introduce the concepts of second-order radial composed tangent derivative, second-order radial tangent derivative, second-order lower radial composed tangent derivative, and second-order lower radial tangent derivative for set-valued maps by means of a radial tangent cone, second-order radial tangent set, lower radial tangent cone, and second-order lower radial tangent set, respectively. Some properties of second-order tangent derivatives are discussed, using which second-order necessary optimality conditions are established for a point pair to be a Henig efficient element of a set-valued optimization problem, and in the expressions the second-order tangent derivatives of the objective function and the constraint function are separated.
The FERMI @ Elettra Technical Optimization Study: PreliminaryParameter Set and Initial Studies
Byrd, John; Corlett, John; Doolittle, Larry; Fawley, William; Lidia, Steven; Penn, Gregory; Ratti, Alex; Staples, John; Wilcox,Russell; Wurtele, Jonathan; Zholents, Alexander
2005-08-01
The goal of the FERMI {at} Elettra Technical Optimization Study is to produce a machine design and layout consistent with user needs for radiation in the approximate ranges 100 nm to 40 nm, and 40 nm to 10 nm, using seeded FEL's. The Study will involve collaboration between Italian and US physicists and engineers, and will form the basis for the engineering design and the cost estimation.
Dunn, Meghan E; Pokon, Emma K; Shields, George C
2004-03-03
The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate Delta H degrees and Delta G degrees values for neutral clusters of water, (H(2)O)(n), where n = 2-6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 x 10(14) molecules/cm(3), water trimer concentrations of 2.6 x 10(12) molecules/cm(3), tetramer concentrations of approximately 5.8 x 10(11) molecules/cm(3), and pentamer concentrations of approximately 3.5 x 10(10) molecules/cm(3) in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.
A Sequential Optimization Sampling Method for Metamodels with Radial Basis Functions
Pan, Guang; Ye, Pengcheng; Yang, Zhidong
2014-01-01
Metamodels have been widely used in engineering design to facilitate analysis and optimization of complex systems that involve computationally expensive simulation programs. The accuracy of metamodels is strongly affected by the sampling methods. In this paper, a new sequential optimization sampling method is proposed. Based on the new sampling method, metamodels can be constructed repeatedly through the addition of sampling points, namely, extrema points of metamodels and minimum points of density function. Afterwards, the more accurate metamodels would be constructed by the procedure above. The validity and effectiveness of proposed sampling method are examined by studying typical numerical examples. PMID:25133206
The spectral basis of optimal error field correction on DIII-D
Paz-Soldan, Carlos A.; Buttery, Richard J.; Garofalo, Andrea M.; Hanson, Jeremy M.; La Haye, Robert J.; Lanctot, Matthew J.; Park, Jong -Ku; Solomon, Wayne M.; Strait, Edward J.
2014-04-28
Here, experimental optimum error field correction (EFC) currents found in a wide breadth of dedicated experiments on DIII-D are shown to be consistent with the currents required to null the poloidal harmonics of the vacuum field which drive the kink mode near the plasma edge. This allows the identification of empirical metrics which predict optimal EFC currents with accuracy comparable to that of first- principles modeling which includes the ideal plasma response. While further metric refinements are desirable, this work suggests optimal EFC currents can be effectively fed-forward based purely on knowledge of the vacuum error field and basic equilibrium properties which are routinely calculated in real-time.
Code of Federal Regulations, 2010 CFR
2010-01-01
... REGULATIONS PROCEDURES FOR REIMBURSEMENT OF GENERAL AVIATION OPERATORS AND SERVICE PROVIDERS IN THE WASHINGTON, DC AREA Set-Aside for Operators or Providers at Certain Airports § 331.35 What is the basis upon...
Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A; Żyła, Adriana
2016-01-01
In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies. Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit.
Mourik, Van Tonja; Wilson, Angela K.; Dunning, Thomas H.
1999-02-20
The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)].
Ant Colony Optimization Analysis on Overall Stability of High Arch Dam Basis of Field Monitoring
Liu, Xiaoli; Chen, Hong-Xin; Kim, Jinxie
2014-01-01
A dam ant colony optimization (D-ACO) analysis of the overall stability of high arch dams on complicated foundations is presented in this paper. A modified ant colony optimization (ACO) model is proposed for obtaining dam concrete and rock mechanical parameters. A typical dam parameter feedback problem is proposed for nonlinear back-analysis numerical model based on field monitoring deformation and ACO. The basic principle of the proposed model is the establishment of the objective function of optimizing real concrete and rock mechanical parameter. The feedback analysis is then implemented with a modified ant colony algorithm. The algorithm performance is satisfactory, and the accuracy is verified. The m groups of feedback parameters, used to run a nonlinear FEM code, and the displacement and stress distribution are discussed. A feedback analysis of the deformation of the Lijiaxia arch dam and based on the modified ant colony optimization method is also conducted. By considering various material parameters obtained using different analysis methods, comparative analyses were conducted on dam displacements, stress distribution characteristics, and overall dam stability. The comparison results show that the proposal model can effectively solve for feedback multiple parameters of dam concrete and rock material and basically satisfy assessment requirements for geotechnical structural engineering discipline. PMID:25025089
Ant colony optimization analysis on overall stability of high arch dam basis of field monitoring.
Lin, Peng; Liu, Xiaoli; Chen, Hong-Xin; Kim, Jinxie
2014-01-01
A dam ant colony optimization (D-ACO) analysis of the overall stability of high arch dams on complicated foundations is presented in this paper. A modified ant colony optimization (ACO) model is proposed for obtaining dam concrete and rock mechanical parameters. A typical dam parameter feedback problem is proposed for nonlinear back-analysis numerical model based on field monitoring deformation and ACO. The basic principle of the proposed model is the establishment of the objective function of optimizing real concrete and rock mechanical parameter. The feedback analysis is then implemented with a modified ant colony algorithm. The algorithm performance is satisfactory, and the accuracy is verified. The m groups of feedback parameters, used to run a nonlinear FEM code, and the displacement and stress distribution are discussed. A feedback analysis of the deformation of the Lijiaxia arch dam and based on the modified ant colony optimization method is also conducted. By considering various material parameters obtained using different analysis methods, comparative analyses were conducted on dam displacements, stress distribution characteristics, and overall dam stability. The comparison results show that the proposal model can effectively solve for feedback multiple parameters of dam concrete and rock material and basically satisfy assessment requirements for geotechnical structural engineering discipline.
NASA Technical Reports Server (NTRS)
Clancy, Daniel J.; Oezguener, Uemit; Graham, Ronald E.
1994-01-01
The potential for excessive plume impingement loads on Space Station Freedom solar arrays, caused by jet firings from an approaching Space Shuttle, is addressed. An artificial neural network is designed to determine commanded solar array beta gimbal angle for minimum plume loads. The commanded angle would be determined dynamically. The network design proposed involves radial basis functions as activation functions. Design, development, and simulation of this network design are discussed.
Keller, J.; Blarigan, P. Van
1998-08-01
In this manuscript the authors report on two projects each of which the goal is to produce cost effective hydrogen utilization technologies. These projects are: (1) the development of an electrical generation system using a conventional four-stroke spark-ignited internal combustion engine generator combination (SI-GenSet) optimized for maximum efficiency and minimum emissions, and (2) the development of a novel internal combustion engine concept. The SI-GenSet will be optimized to run on either hydrogen or hydrogen-blends. The novel concept seeks to develop an engine that optimizes the Otto cycle in a free piston configuration while minimizing all emissions. To this end the authors are developing a rapid combustion homogeneous charge compression ignition (HCCI) engine using a linear alternator for both power take-off and engine control. Targeted applications include stationary electrical power generation, stationary shaft power generation, hybrid vehicles, and nearly any other application now being accomplished with internal combustion engines.
Image segmentation using globally optimal growth in three dimensions with an adaptive feature set
NASA Astrophysics Data System (ADS)
Taylor, David C.; Barrett, William A.
1994-09-01
A globally optimal region growing algorithm for 3D segmentation of anatomical objects is developed. The notion of simple 3D connected component labelling is extended to enable the combination of arbitrary features in the segmentation process. This algorithm uses a hybrid octree-btree structure to segment an object of interest in an ordered fashion. This tree structure overcomes the computational complexity of global optimality in three dimensions. The segmentation process is controlled by a set of active features, which work in concert to extract the object of interest. The cost function used to enforce the order is based on the combination of active features. The characteristics of the data throughout the volume dynamically influences which features are active. A foundation for applying user interaction with the object directly to the feature set is established. The result is a system which analyzes user input and neighborhood data and optimizes the tools used in the segmentation process accordingly.
NASA Astrophysics Data System (ADS)
Hashimoto, Hiroshi; Kim, Min-Geun; Abe, Kazuhisa; Cho, Seonho
2013-10-01
This paper presents a level set-based topology optimization method for noise barriers formed from an assembly of scatterers. The scattering obstacles are modeled by elastic bodies arranged periodically along the wall. Due to the periodicity, the problem can be reduced to that in a unit cell. The interaction between the elastic scatterers and the acoustic field is described in the context of the level set analysis. The semi-infinite acoustic wave regions located on the both sides of the barrier are represented by impedance matrices. The objective function is defined by the energy transmission passing the barrier. The design sensitivity is evaluated analytically by the aid of adjoint equations. The dependency of the optimal profile on the stiffness of scatterers and on the target frequency band is examined. The feasibility of the developed optimization method is proved through numerical examples.
Garza, Jorge; Ramírez, José-Zeferino; Vargas, Rubicelia
2005-02-03
In this work the effect of the basis set superposition error (BSSE) is explored with the counterpoise method on the occupied and unoccupied Hartree-Fock (HF) and Kohn-Sham (KS) orbitals. Three different systems linked by hydrogen bonds, H(2)O...FH, H(2)O...H(2)O, and H(2)O...CFH(3), were studied by using the basis set families cc-pVXZ and aug-cc-pVXZ (X = D, T, Q). The basis sets were tested with the HF method and two approximations for the exchange-correlation functional of KS: a generalized gradient approximation and a hybrid approach. In addition to these methods, the second-order Møller-Plesset perturbation theory, MP2, was considered. It was found that the presence of the "ghost" basis set affects the orbitals in two ways: (1) The occupied KS orbitals are more sensitive to the presence of this "ghost" basis set than the occupied HF orbitals. For this reason the BSSE observed in HF is less than that obtained with KS. (2) The unoccupied HF orbitals are more sensitive to the presence of the "ghost" basis set than their corresponding occupied orbitals. Because the MP2 method uses both, occupied and unoccupied HF orbitals, to compute the total energy, the contribution of the BSSE is bigger than that obtained with HF or KS methodologies.
An Approach to Feature Selection Based on Ant Colony Optimization and Rough Set
NASA Astrophysics Data System (ADS)
Wu, Junyun; Qiu, Taorong; Wang, Lu; Huang, Haiquan
Feature selection plays an important role in many fields. This paper proposes a method for feature selection which combined the rough set method and ant colony optimization algorithm. The algorithm used the attribute dependence and the attribute importance as the inspiration factor which applied to the transfer rules. For further, the quality of classification based on rough set method and the length of the feature subset were used to build the pheromone update strategy. Through the test of data set, results show that the proposed method is feasible.
NASA Astrophysics Data System (ADS)
Yang, Yanchao; Jiang, Hong; Liu, Congbin; Lan, Zhongli
2013-03-01
Cognitive radio (CR) is an intelligent wireless communication system which can dynamically adjust the parameters to improve system performance depending on the environmental change and quality of service. The core technology for CR is the design of cognitive engine, which introduces reasoning and learning methods in the field of artificial intelligence, to achieve the perception, adaptation and learning capability. Considering the dynamical wireless environment and demands, this paper proposes a design of cognitive engine based on the rough sets (RS) and radial basis function neural network (RBF_NN). The method uses experienced knowledge and environment information processed by RS module to train the RBF_NN, and then the learning model is used to reconfigure communication parameters to allocate resources rationally and improve system performance. After training learning model, the performance is evaluated according to two benchmark functions. The simulation results demonstrate the effectiveness of the model and the proposed cognitive engine can effectively achieve the goal of learning and reconfiguration in cognitive radio.
NASA Astrophysics Data System (ADS)
Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel
The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.
Karlický, František; Zbořil, Radek; Otyepka, Michal
2012-07-21
Density functional theory calculations of the electronic structure of graphane and stoichiometrically halogenated graphene derivatives (fluorographene and other analogous graphene halides) show: (i) localized orbital basis sets can be successfully and effectively used for such two-dimensional materials; (ii) several functionals predict that the band gap of graphane is greater than that of fluorographene, whereas HSE06 gives the opposite trend; (iii) HSE06 functional predicts quite good values of band gaps with respect to benchmark theoretical and experimental data; (iv) the zero band gap of graphene is opened by hydrogenation and halogenation and strongly depends on the chemical composition of mixed graphene halides; (v) the stability of graphene halides decreases sharply with increasing size of the halogen atom--fluorographene is stable, whereas graphene iodide spontaneously decomposes. In terms of band gap and stability, the C(2)FBr and C(2)HBr derivatives seem to be promising materials, e.g., for (opto)electronics applications, because their band gaps are similar to those of conventional semiconductors, and they are expected to be stable under ambient conditions. The results indicate that other fluorinated compounds (C(a)H(b)F(c) and C(a)F(b)Y(c), Y = Cl, Br, I) are stable insulators.
NASA Astrophysics Data System (ADS)
Kitamura, Hikaru
2013-02-01
Photoabsorption cross-sections of simple metals are formulated through a solid-state band theory based on the orthogonalized-plane-wave (OPW) method in Slater’s local-exchange approximation, where interband transitions of core and conduction electrons are evaluated up to the soft x-ray regime by using large basis sets. The photoabsorption cross-sections of a sodium crystal are computed for a wide photon energy range from 3 to 1800 eV. It is found that the numerical results reproduce the existing x-ray databases fairly well for energies above the L2,3-edge (31 eV), verifying a consistency between solid-state and atomic models for inner-shell photoabsorption; additional oscillatory structures in the present spectra manifest solid-state effects. Our computed results in the vacuum ultraviolet regime (6-30 eV) are also in better agreement with experimental data compared to earlier theories, although some discrepancies remain in the range of 20-30 eV. The influence of the core eigenvalues on the absorption spectra is examined.
The spectral basis of optimal error field correction on DIII-D
Paz-Soldan, Carlos A.; Buttery, Richard J.; Garofalo, Andrea M.; ...
2014-04-28
Here, experimental optimum error field correction (EFC) currents found in a wide breadth of dedicated experiments on DIII-D are shown to be consistent with the currents required to null the poloidal harmonics of the vacuum field which drive the kink mode near the plasma edge. This allows the identification of empirical metrics which predict optimal EFC currents with accuracy comparable to that of first- principles modeling which includes the ideal plasma response. While further metric refinements are desirable, this work suggests optimal EFC currents can be effectively fed-forward based purely on knowledge of the vacuum error field and basic equilibriummore » properties which are routinely calculated in real-time.« less
Optimal Sensor Selection for Classifying a Set of Ginsengs Using Metal-Oxide Sensors.
Miao, Jiacheng; Zhang, Tinglin; Wang, You; Li, Guang
2015-07-03
The sensor selection problem was investigated for the application of classification of a set of ginsengs using a metal-oxide sensor-based homemade electronic nose with linear discriminant analysis. Samples (315) were measured for nine kinds of ginsengs using 12 sensors. We investigated the classification performances of combinations of 12 sensors for the overall discrimination of combinations of nine ginsengs. The minimum numbers of sensors for discriminating each sample set to obtain an optimal classification performance were defined. The relation of the minimum numbers of sensors with number of samples in the sample set was revealed. The results showed that as the number of samples increased, the average minimum number of sensors increased, while the increment decreased gradually and the average optimal classification rate decreased gradually. Moreover, a new approach of sensor selection was proposed to estimate and compare the effective information capacity of each sensor.
Optimal Sensor Selection for Classifying a Set of Ginsengs Using Metal-Oxide Sensors
Miao, Jiacheng; Zhang, Tinglin; Wang, You; Li, Guang
2015-01-01
The sensor selection problem was investigated for the application of classification of a set of ginsengs using a metal-oxide sensor-based homemade electronic nose with linear discriminant analysis. Samples (315) were measured for nine kinds of ginsengs using 12 sensors. We investigated the classification performances of combinations of 12 sensors for the overall discrimination of combinations of nine ginsengs. The minimum numbers of sensors for discriminating each sample set to obtain an optimal classification performance were defined. The relation of the minimum numbers of sensors with number of samples in the sample set was revealed. The results showed that as the number of samples increased, the average minimum number of sensors increased, while the increment decreased gradually and the average optimal classification rate decreased gradually. Moreover, a new approach of sensor selection was proposed to estimate and compare the effective information capacity of each sensor. PMID:26151212
NASA Astrophysics Data System (ADS)
Fillenwarth, Brian Albert
As large countries such as China begin to industrialize and concerns about global warming continue to grow, there is an increasing need for more environmentally friendly building materials. One promising material known as a geopolymer can be used as a portland cement replacement and in this capacity emits around 67% less carbon dioxide. In addition to potentially reducing carbon emissions, geopolymers can be synthesized with many industrial waste products such as fly ash. Although the benefits of geopolymers are substantial, there are a few difficulties with designing geopolymer mixes which have hindered widespread commercialization of the material. One such difficulty is the high variability of the materials used for their synthesis. In addition to this, interrelationships between mix design variables and how these interrelationships impact the set behavior and compressive strength are not well understood. A third complicating factor with designing geopolymer mixes is that the role of calcium in these systems is not well understood. In order to overcome these barriers, this study developed predictive optimization models through the use of genetic programming with experimentally collected set times and compressive strengths of several geopolymer paste mixes. The developed set behavior models were shown to predict the correct set behavior from the mix design over 85% of the time. The strength optimization model was shown to be capable of predicting compressive strengths of geopolymer pastes from their mix design to within about 1 ksi of their actual strength. In addition to this the optimization models give valuable insight into the key factors influencing strength development as well as the key factors responsible for flash set and long set behaviors in geopolymer pastes. A method for designing geopolymer paste mixes was developed from the generated optimization models. This design method provides an invaluable tool for use in future geopolymer research as well as
NASA Astrophysics Data System (ADS)
Brandbyge, Mads
2014-05-01
In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an "implicit decoupling assumption," leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, and that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.
NASA Astrophysics Data System (ADS)
Hatua, Kaushik; Mondal, Avijit; Nandi, Prasanta K.
2017-10-01
Present investigation reveals that diffuse electron compounds M2X predict large (106 a.u.) γav value. The basis set dependence of γav showed that the quality of basis function rather than its size is more important. Sadlej's Pol basis set which is nearly four times less in size than aug-cc-pVQZ can give reliable estimate of γav. MP2 method in conjunction with large basis sets can give comparable results of γav that could be obtained from CCSD or CCSD(T). Higher order energy correction to MP2 leads to oscillatory behavior but inclusion of triple excitations to CCSD improves the magnitude of γav.
Urquhart, B.; Sengupta, M.; Keller, J.
2012-09-01
A multi-objective optimization was performed to allocate 2MW of PV among four candidate sites on the island of Lanai such that energy was maximized and variability in the form of ramp rates was minimized. This resulted in an optimal solution set which provides a range of geographic allotment alternatives for the fixed PV capacity. Within the optimal set, a tradeoff between energy produced and variability experienced was found, whereby a decrease in variability always necessitates a simultaneous decrease in energy. A design point within the optimal set was selected for study which decreased extreme ramp rates by over 50% while only decreasing annual energy generation by 3% over the maximum generation allocation. To quantify the allotment mix selected, a metric was developed, called the ramp ratio, which compares ramping magnitude when all capacity is allotted to a single location to the aggregate ramping magnitude in a distributed scenario. The ramp ratio quantifies simultaneously how much smoothing a distributed scenario would experience over single site allotment and how much a single site is being under-utilized for its ability to reduce aggregate variability. This paper creates a framework for use by cities and municipal utilities to reduce variability impacts while planning for high penetration of PV on the distribution grid.
Go-ICP: A Globally Optimal Solution to 3D ICP Point-Set Registration.
Yang, Jiaolong; Li, Hongdong; Campbell, Dylan; Jia, Yunde
2016-11-01
The Iterative Closest Point (ICP) algorithm is one of the most widely used methods for point-set registration. However, being based on local iterative optimization, ICP is known to be susceptible to local minima. Its performance critically relies on the quality of the initialization and only local optimality is guaranteed. This paper presents the first globally optimal algorithm, named Go-ICP, for Euclidean (rigid) registration of two 3D point-sets under the L2 error metric defined in ICP. The Go-ICP method is based on a branch-and-bound scheme that searches the entire 3D motion space SE(3). By exploiting the special structure of SE(3) geometry, we derive novel upper and lower bounds for the registration error function. Local ICP is integrated into the BnB scheme, which speeds up the new method while guaranteeing global optimality. We also discuss extensions, addressing the issue of outlier robustness. The evaluation demonstrates that the proposed method is able to produce reliable registration results regardless of the initialization. Go-ICP can be applied in scenarios where an optimal solution is desirable or where a good initialization is not always available.
Paschoal, Diego; Marcial, Bruna L; Lopes, Juliana Fedoce; De Almeida, Wagner B; Dos Santos, Hélio F
2012-11-05
In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis-diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all-electron basis sets (ABS). In addition, a modified all-electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6-31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol(-1), which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol(-1). For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol(-1), respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree-Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6-31+G(d) or B3PW91/mDZP/6-31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP-DNA complex), the lower levels B3LYP/LANL2DZ/6-31+G(d) and B3LYP/SBKJC-VDZ/6-31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol(-1), respectively, which is only 13% higher than the actual value.
Kupka, Teobald; Stachów, Michał; Kaminsky, Jakub; Sauer, Stephan P A
2013-08-01
A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2 O, H2 O, HF, F2 , HCN, SiH4 and H2 S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T)), with affordable pcS-2 basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and shieldings obtained with the significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected set of 37 calculation methods. It was possible to formulate a practical approach of estimating the values of isotropic nuclear magnetic shielding constants at the CCSD(T)/CBS and MP2/CBS levels from affordable CCSD(T)/pcS-2, MP2/pcS-2 and DFT/CBS calculations with pcS-n basis sets. The proposed method leads to a fairly accurate estimation of nuclear magnetic shieldings and considerable saving of computational efforts.
Ramírez-Solís, A; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ochoa-Calle, A J
2017-01-25
The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε1 phase and a higher pressure NM ε0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O2 molecules in the (O2)4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O2)4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O2)4 unit cell for the low-pressure regime of the ε phase.
NASA Astrophysics Data System (ADS)
Ai, Yuewei; Shao, Xinyu; Jiang, Ping; Li, Peigen; Liu, Yang; Yue, Chen
2015-11-01
The welded joints of dissimilar materials have been widely used in automotive, ship and space industries. The joint quality is often evaluated by weld seam geometry, microstructures and mechanical properties. To obtain the desired weld seam geometry and improve the quality of welded joints, this paper proposes a process modeling and parameter optimization method to obtain the weld seam with minimum width and desired depth of penetration for laser butt welding of dissimilar materials. During the process, Taguchi experiments are conducted on the laser welding of the low carbon steel (Q235) and stainless steel (SUS301L-HT). The experimental results are used to develop the radial basis function neural network model, and the process parameters are optimized by genetic algorithm. The proposed method is validated by a confirmation experiment. Simultaneously, the microstructures and mechanical properties of the weld seam generated from optimal process parameters are further studied by optical microscopy and tensile strength test. Compared with the unoptimized weld seam, the welding defects are eliminated in the optimized weld seam and the mechanical properties are improved. The results show that the proposed method is effective and reliable for improving the quality of welded joints in practical production.
NASA Astrophysics Data System (ADS)
Petersson, G. A.; Malick, David K.; Wilson, William G.; Ochterski, Joseph W.; Montgomery, J. A.; Frisch, M. J.
1998-12-01
We have reexamined several high-accuracy Gaussian-2, complete basis set and density functional methods for computational thermochemistry (in order of increasing speed): G2, G2(MP2), CBS-Q, G2(MP2,SVP), CBS-q, CBS-4, and B3LYP/6-311+G(3df,2p). We have employed ΔfH2980 for the "extended G2 neutral test set" for this comparison. Several errors in previous studies have been corrected and experimental spin-orbit interactions have been included in all calculated atomic energies. The mean absolute deviations from experiment are 1.43, 1.76, 1.19, 1.64, 2.34, 2.66, and 3.43 kcal/mol, respectively. The maximum deviations from experiment are 10.6, 8.8, 8.1, 9.4, 11.4, 12.9, and 24.1 kcal/mol respectively. The species responsible for these maximum errors are in order: SiF4, SiF4, Cl2C=CCl2, F2C=CF2, ClF3, ClF3, and SiCl4. All seven methods have relatively large errors for bonds to halogens, but these errors are sufficiently systematic to benefit from empirical corrections. After a discussion of ill conditioning in the "bond separation reaction" implementation of isodesmic reactions, we determine "isodesmic bond additivity corrections" (BACs) for several types of bonds by least-squares fits to the heats of formation for 76 organic species with up to ten carbons and a variety of heteroatoms. The mean absolute deviations are reduced from 1.49, 1.93, 1.22, 1.53, 2.28, 3.09, and 3.45 kcal/mol to 0.55, 0.57, 0.77, 0.63, 1.03, 0.98, and 1.16 kcal/mol. The maximum errors are reduced to about 3 kcal/mol for all but the DFT method (4.2 kcal/mol). The BACs are especially useful for larger molecules with many similar bonds. For example, the CBS-Q error for Cl2C=CCl2 is reduced from 8.1 to 3.0 kcal/mol and the CBS-4 errors for benzene and naphthalene are reduced from 10.5 and 17.5 to 2.1 and 1.6 kcal/mol, respectively.
Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf
2013-03-12
The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.
The route to MBxNyCz molecular wheels: II. Results using accurate functionals and basis sets
NASA Astrophysics Data System (ADS)
Güthler, A.; Mukhopadhyay, S.; Pandey, R.; Boustani, I.
2014-04-01
Applying ab initio quantum chemical methods, molecular wheels composed of metal and light atoms were investigated. High quality basis sets 6-31G*, TZPV, and cc-pVTZ as well as exchange and non-local correlation functionals B3LYP, BP86 and B3P86 were used. The ground-state energy and structures of cyclic planar and pyramidal clusters TiBn (for n = 3-10) were computed. In addition, the relative stability and electronic structures of molecular wheels TiBxNyCz (for x, y, z = 0-10) and MBnC10-n (for n = 2 to 5 and M = Sc to Zn) were determined. This paper sustains a follow-up study to the previous one of Boustani and Pandey [Solid State Sci. 14 (2012) 1591], in which the calculations were carried out at the HF-SCF/STO3G/6-31G level of theory to determine the initial stability and properties. The results show that there is a competition between the 2D planar and the 3D pyramidal TiBn clusters (for n = 3-8). Different isomers of TiB10 clusters were also studied and a structural transition of 3D-isomer into 2D-wheel is presented. Substitution boron in TiB10 by carbon or/and nitrogen atoms enhances the stability and leads toward the most stable wheel TiB3C7. Furthermore, the computations show that Sc, Ti and V at the center of the molecular wheels are energetically favored over other transition metal atoms of the first row.
Optimized tumor cryptic peptides: the basis for universal neo-antigen-like tumor vaccines
Menez-Jamet, Jeanne; Gallou, Catherine; Rougeot, Aude
2016-01-01
The very impressive clinical results recently obtained in cancer patients treated with immune response checkpoint inhibitors boosted the interest in immunotherapy as a therapeutic choice in cancer treatment. However, these inhibitors require a pre-existing tumor specific immune response and the presence of tumor infiltrating T cells to be efficient. This immune response can be triggered by cancer vaccines. One of the main issues in tumor vaccination is the choice of the right antigen to target. All vaccines tested to date targeted tumor associated antigens (TAA) that are self-antigens and failed to show a clinical efficacy because of the immune self-tolerance to TAA. A new class of tumor antigens has recently been described, the neo-antigens that are created by point mutations of tumor expressing proteins and are recognized by the immune system as non-self. Neo-antigens exhibit two main properties: they are not involved in the immune self-tolerance process and are immunogenic. However, the majority of the neo-antigens are patient specific and their use as cancer vaccines requires their previous identification in each patient individualy that can be done only in highly specialized research centers. It is therefore evident that neo-antigens cannot be used for patient vaccination worldwide. This raises the question of whether we can find neo-antigen like vaccines, which would not be patient specific. In this review we show that optimized cryptic peptides from TAA are neo-antigen like peptides. Optimized cryptic peptides are recognized by the immune system as non-self because they target self-cryptic peptides that escape self-tolerance; in addition they are strongly immunogenic because their sequence is modified in order to enhance their affinity for the HLA molecule. The first vaccine based on the optimized cryptic peptide approach, Vx-001, which targets the widely expressed tumor antigen telomerase reverse transcriptase (TERT), has completed a large phase I clinical
Kreuter, Matthew W; Alcaraz, Kassandra I; Pfeiffer, Debra; Christopher, Kara
2008-01-01
Selecting appropriate community channels or settings for delivering evidence-based health promotion programs can be critical to successful dissemination. This article describes how five criteria--accessibility, opportunity, appropriateness, reach, and specificity--were applied in identifying and comparing seven community settings as host sites for a tailored breast cancer education computer kiosk for African American women. Data were gathered from 10,306 kiosk uses in 92 beauty salons, churches, neighborhood health centers, laundromats, social service agencies, health fairs, and public libraries between June 2003 and March 2007. Of the seven settings, only laundromats were found to provide both high reach (ie, frequent kiosk use) and high specificity (ie, a large proportion of users with no health insurance, unaware of where to get a mammogram, reporting no recent mammogram and barriers to getting one, and having little knowledge about breast cancer and mammography). Systematic, data-based evaluations of potential dissemination channels can help identify optimal settings for cancer control interventions.
Tang, Li-Juan; Zhou, Yan-Ping; Jiang, Jian-Hui; Zou, Hong-Yan; Wu, Hai-Long; Shen, Guo-Li; Yu, Ru-Qin
2007-01-01
The support vector machine (SVM) has been receiving increasing interest in an area of QSAR study for its ability in function approximation and remarkable generalization performance. However, selection of support vectors and intensive optimization of kernel width of a nonlinear SVM are inclined to get trapped into local optima, leading to an increased risk of underfitting or overfitting. To overcome these problems, a new nonlinear SVM algorithm is proposed using adaptive kernel transform based on a radial basis function network (RBFN) as optimized by particle swarm optimization (PSO). The new algorithm incorporates a nonlinear transform of the original variables to feature space via a RBFN with one input and one hidden layer. Such a transform intrinsically yields a kernel transform of the original variables. A synergetic optimization of all parameters including kernel centers and kernel widths as well as SVM model coefficients using PSO enables the determination of a flexible kernel transform according to the performance of the total model. The implementation of PSO demonstrates a relatively high efficiency in convergence to a desired optimum. Applications of the proposed algorithm to QSAR studies of binding affinity of HIV-1 reverse transcriptase inhibitors and activity of 1-phenylbenzimidazoles reveal that the new algorithm provides superior performance to the backpropagation neural network and a conventional nonlinear SVM, indicating that this algorithm holds great promise in nonlinear SVM learning.
Generated spiral bevel gears: Optimal machine-tool settings and tooth contact analysis
NASA Technical Reports Server (NTRS)
Litvin, F. L.; Tsung, W. J.; Coy, J. J.; Heine, C.
1985-01-01
Geometry and kinematic errors were studied for Gleason generated spiral bevel gears. A new method was devised for choosing optimal machine settings. These settings provide zero kinematic errors and an improved bearing contact. The kinematic errors are a major source of noise and vibration in spiral bevel gears. The improved bearing contact gives improved conditions for lubrication. A computer program for tooth contact analysis was developed, and thereby the new generation process was confirmed. The new process is governed by the requirement that during the generation process there is directional constancy of the common normal of the contacting surfaces for generator and generated surfaces of pinion and gear.
Generated spiral bevel gears - Optimal machine-tool settings and tooth contact analysis
NASA Technical Reports Server (NTRS)
Litvin, F. L.; Tsung, W.-J.; Coy, J. J.; Heine, C.
1985-01-01
Geometry and kinematic errors were studied for Gleason generated spiral bevel gears. A new method was devised for choosing optimal machine settings. These settings provide zero kinematic errors and an improved bearing contact. The kinematic errors are a major source of noise and vibration in spiral bevel gears. The improved bearing contact gives improved conditions for lubrication. A computer program for tooth contact analysis was developed, and thereby the new generation process was confirmed. The new process is governed by the requirement that during the generation process there is directional constancy of the common normal of the contacting surfaces for generator and generated surfaces of pinion and gear.
Generated spiral bevel gears - Optimal machine-tool settings and tooth contact analysis
NASA Technical Reports Server (NTRS)
Litvin, F. L.; Tsung, W.-J.; Coy, J. J.; Heine, C.
1985-01-01
Geometry and kinematic errors were studied for Gleason generated spiral bevel gears. A new method was devised for choosing optimal machine settings. These settings provide zero kinematic errors and an improved bearing contact. The kinematic errors are a major source of noise and vibration in spiral bevel gears. The improved bearing contact gives improved conditions for lubrication. A computer program for tooth contact analysis was developed, and thereby the new generation process was confirmed. The new process is governed by the requirement that during the generation process there is directional constancy of the common normal of the contacting surfaces for generator and generated surfaces of pinion and gear.
Classification improvement by optimal dimensionality reduction when training sets are of small size
NASA Technical Reports Server (NTRS)
Starks, S. A.; Defigueiredo, R. J. P.; Vanrooy, D. L.
1976-01-01
A computer simulation was performed to test the conjecture that, when the sizes of the training sets are small, classification in a subspace of the original data space may give rise to a smaller probability of error than the classification in the data space itself; this is because the gain in the accuracy of estimation of the likelihood functions used in classification in the lower dimensional space (subspace) offsets the loss of information associated with dimensionality reduction (feature extraction). A number of pseudo-random training and data vectors were generated from two four-dimensional Gaussian classes. A special algorithm was used to create an optimal one-dimensional feature space on which to project the data. When the sizes of the training sets are small, classification of the data in the optimal one-dimensional space is found to yield lower error rates than the one in the original four-dimensional space.
A candidate-set-free algorithm for generating D-optimal split-plot designs
Jones, Bradley; Goos, Peter
2007-01-01
We introduce a new method for generating optimal split-plot designs. These designs are optimal in the sense that they are efficient for estimating the fixed effects of the statistical model that is appropriate given the split-plot design structure. One advantage of the method is that it does not require the prior specification of a candidate set. This makes the production of split-plot designs computationally feasible in situations where the candidate set is too large to be tractable. The method allows for flexible choice of the sample size and supports inclusion of both continuous and categorical factors. The model can be any linear regression model and may include arbitrary polynomial terms in the continuous factors and interaction terms of any order. We demonstrate the usefulness of this flexibility with a 100-run polypropylene experiment involving 11 factors where we found a design that is substantially more efficient than designs that are produced by using other approaches. PMID:21197132
A jazz-based approach for optimal setting of pressure reducing valves in water distribution networks
NASA Astrophysics Data System (ADS)
De Paola, Francesco; Galdiero, Enzo; Giugni, Maurizio
2016-05-01
This study presents a model for valve setting in water distribution networks (WDNs), with the aim of reducing the level of leakage. The approach is based on the harmony search (HS) optimization algorithm. The HS mimics a jazz improvisation process able to find the best solutions, in this case corresponding to valve settings in a WDN. The model also interfaces with the improved version of a popular hydraulic simulator, EPANET 2.0, to check the hydraulic constraints and to evaluate the performances of the solutions. Penalties are introduced in the objective function in case of violation of the hydraulic constraints. The model is applied to two case studies, and the obtained results in terms of pressure reductions are comparable with those of competitive metaheuristic algorithms (e.g. genetic algorithms). The results demonstrate the suitability of the HS algorithm for water network management and optimization.
Code of Federal Regulations, 2014 CFR
2014-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a...
Code of Federal Regulations, 2013 CFR
2013-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a...
Code of Federal Regulations, 2012 CFR
2012-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE...) SERVICES FURNISHED BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a...
Code of Federal Regulations, 2011 CFR
2011-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule...
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...
Echenique, Pablo; Alonso, José Luis
2008-07-15
We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH(2). The model chemistries (MCs) investigated are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the most accurate PES in the literature. All data sets have been analyzed according to a general framework, which can be extended to other complex problems and which captures the nearness concept in the space of MCs. The great number of MCs evaluated has allowed us to significantly explore this space and show that the correlation between accuracy and computational cost of the methods is imperfect, thus justifying a systematic search for the combination of features in a MC that is optimal to deal with peptides. Regarding the particular MCs studied, the most important conclusion is that the potentially very cost-saving heterolevel approximation is a very efficient one to describe the whole PES of HCO-L-Ala-NH(2). Finally, we show that, although RHF may be used to calculate the geometry if a MP2 single-point energy calculation follows, pure RHF//RHF homolevels are not recommendable for this problem. (c) 2008 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Clenet, A.; Ravera, L.; Bertrand, B.; den Hartog, R.; Jackson, B.; van Leeuwen, B.-J.; van Loon, D.; Parot, Y.; Pointecouteau, E.; Sournac, A.
2014-11-01
IRAP is developing the readout electronics of the SPICA-SAFARI's TES bolometer arrays. Based on the frequency domain multiplexing technique the readout electronics provides the AC-signals to voltage-bias the detectors; it demodulates the data; and it computes a feedback to linearize the detection chain. The feedback is computed with a specific technique, so called baseband feedback (BBFB) which ensures that the loop is stable even with long propagation and processing delays (i.e. several μ s) and with fast signals (i.e. frequency carriers of the order of 5 MHz). To optimize the power consumption we took advantage of the reduced science signal bandwidth to decouple the signal sampling frequency and the data processing rate. This technique allowed a reduction of the power consumption of the circuit by a factor of 10. Beyond the firmware architecture the optimization of the instrument concerns the characterization routines and the definition of the optimal parameters. Indeed, to operate an array TES one has to properly define about 21000 parameters. We defined a set of procedures to automatically characterize these parameters and find out the optimal settings.
Baranowska-Łączkowska, Angelika; Fernández, Berta
2014-01-30
In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto.
Character Projection Mask Set Optimization for Enhancing Throughput of MCC Projection Systems
NASA Astrophysics Data System (ADS)
Sugihara, Makoto; Matsunaga, Yusuke; Murakami, Kazuaki
Character projection (CP) lithography is utilized for maskless lithography and is a potential for the future photomask manufacture because it can project ICs much faster than point beam projection or variable-shaped beam (VSB) projection. In this paper, we first present a projection mask set development methodology for multi-column-cell (MCC) systems, in which column-cells can project patterns in parallel with the CP and VSB lithographies. Next, we present an INLP (integer nonlinear programming) model as well as an ILP (integer linear programming) model for optimizing a CP mask set of an MCC projection system so that projection time is reduced. The experimental results show that our optimization has achieved 33.4% less projection time in the best case than a naive CP mask development approach. The experimental results indicate that our CP mask set optimization method has virtually increased cell pattern objects on CP masks and has decreased VSB projection so that it has achieved higher projection throughput than just parallelizing two column-cells with conventional CP masks.
An adaptive optimal bandwidth sensor for video imaging and sparsifying basis
NASA Astrophysics Data System (ADS)
Noor, Imama
Many compressive sensing architectures have shown promise towards reducing the bandwidth for image acquisition significantly. In order to use these architectures for video acquisition we need a scheme that is able to effectively exploit temporal redundancies in a sequence. In this thesis we study a method to efficiently sample and reconstruct specific video sequences. The method is suitable for implementation using a single pixel detector along with a digital micromirror device (DMD) or other forms of spatial light modulators (SLMs). Conventional implementations of single pixel cameras are able to spatially compress the signal but the compressed measurements make it difficult to exploit temporal redundancies directly. Moreover a single pixel camera needs to make measurements in a sequential manner before the scene changes making it inefficient for video imaging. In this thesis we discuss a measurement scheme that exploits sparsity along the time axis for video imaging. After acquiring all measurements required for the first frame, measurements are only acquired from the areas which change in subsequent frames. We segment the first frame and detect magnitude and direction of change for each segment and acquire compressed measurements for the changing segments in the predicted direction. TV minimization is used to reconstruct the dynamic areas and PSNR variation is studied against different parameters of proposed scheme. We show the reconstruction results for a few test sequences commonly used for performance analysis and demonstrate the practical utility of the scheme. A comparison is made with existing algorithms to show the effectiveness of proposed method for specific video sequences. We also discuss use of customized transform to improve reconstruction of submillimeter wave single pixel imager. We use a sparseness inducing transformation on the measurements and optimize the result using l1 minimization algorithms. We demonstrate improvement in result of several
NASA Astrophysics Data System (ADS)
Lowe, D.; Topping, D. O.; Archer-Nicholls, S.; Darbyshire, E.; Morgan, W.; Liu, D.; Allan, J. D.; Coe, H.; McFiggans, G.
2015-12-01
The burning of forests in the Amazonia region is a globally significant source of carbonaceous aerosol, containing both absorbing and scattering components [1]. In addition biomass burning aerosol (BBA) are also efficient cloud condensation nuclei (CCN), modifying cloud properties and influencing atmospheric circulation and precipitation tendencies [2]. The impacts of BBA are highly dependent on their size distribution and composition. A bottom-up emissions inventory, the Brazilian Biomass Burning Emissions Model (3BEM) [3], utilising satellite products to generate daily fire emission maps is used. Injection of flaming emissions within the atmospheric column is simulated using both a sub-grid plume-rise parameterisation [4], and simpler schemes, within the Weather Research and Forecasting Model with Chemistry (WRF-Chem, v3.4.1) [5]. Aerosol dynamics are simulated using the sectional MOSAIC scheme [6], incorporating a volatility basis set (VBS) treatment of organic aerosol [7]. For this work we have modified the 9-bin VBS to use the biomass burning specific scheme developed by May et al. [8]. The model has been run for September 2012 over South America (at a 25km resolution). We will present model results evaluating the modelled aerosol vertical distribution, size distribution, and composition against measurements taken by the FAAM BAe-146 research aircraft during the SAMBBA campaign. The main focus will be on investigating the factors controlling the vertical gradient of the organic mass to black carbon ratio of the measured aerosol. This work is supported by the Nature Environment Research Council (NERC) as part of the SAMBBA project under grant NE/J010073/1. [1] D. G. Streets et al., 2004, J. Geophys. Res., 109, D24212. [2] M. O. Andreae et al., 2004, Science, 303, 1337-1342. [3] K. Longo et al., 2010, Atmos. Chem. Phys., 10, 5,785-5,795. [4] S. Freitas et al., 2007, Atmos. Chem. Phys., 7, 3,385-3,398. [5] S. Archer-Nicholls et al., 2015, Geosci. Model Dev., 8
Shrivastava, ManishKumar B.; Fast, Jerome D.; Easter, Richard C.; Gustafson, William I.; Zaveri, Rahul A.; Jimenez, Jose L.; Saide, Pablo; Hodzic, Alma
2011-07-13
The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25%, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15% oxygen mass per generation of oxidation; however, all modeling cases still under
NASA Astrophysics Data System (ADS)
Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Dall'Osto, M.; O'Dowd, C.; Kiendler-Scharr, A.; Pandis, S. N.
2012-04-01
Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS) in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1) heterogeneous oxidation via OH uptake to the particle-phase and (2) aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA) mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE) lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and aqueous
NASA Astrophysics Data System (ADS)
Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Dall'Osto, M.; O'Dowd, C.; Kiendler-Scharr, A.; Pandis, S. N.
2012-11-01
Multigenerational oxidation chemistry of atmospheric organic compounds and its effects on aerosol loadings and chemical composition is investigated by implementing the Two-Dimensional Volatility Basis Set (2-D-VBS) in a Lagrangian host chemical transport model. Three model formulations were chosen to explore the complex interactions between functionalization and fragmentation processes during gas-phase oxidation of organic compounds by the hydroxyl radical. The base case model employs a conservative transformation by assuming a reduction of one order of magnitude in effective saturation concentration and an increase of oxygen content by one or two oxygen atoms per oxidation generation. A second scheme simulates functionalization in more detail using group contribution theory to estimate the effects of oxygen addition to the carbon backbone on the compound volatility. Finally, a fragmentation scheme is added to the detailed functionalization scheme to create a functionalization-fragmentation parameterization. Two condensed-phase chemistry pathways are also implemented as additional sensitivity tests to simulate (1) heterogeneous oxidation via OH uptake to the particle-phase and (2) aqueous-phase chemistry of glyoxal and methylglyoxal. The model is applied to summer and winter periods at three sites where observations of organic aerosol (OA) mass and O:C were obtained during the European Integrated Project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaigns. The base case model reproduces observed mass concentrations and O:C well, with fractional errors (FE) lower than 55% and 25%, respectively. The detailed functionalization scheme tends to overpredict OA concentrations, especially in the summertime, and also underpredicts O:C by approximately a factor of 2. The detailed functionalization model with fragmentation agrees well with the observations for OA concentration, but still underpredicts O:C. Both heterogeneous oxidation and aqueous
NASA Astrophysics Data System (ADS)
Shrivastava, M.; Fast, J.; Easter, R.; Gustafson, W. I., Jr.; Zaveri, R. A.; Jimenez, J. L.; Saide, P.; Hodzic, A.
2011-07-01
The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25 %, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15 % oxygen mass per generation of oxidation; however, all modeling cases still under
NASA Astrophysics Data System (ADS)
Shrivastava, M.; Fast, J.; Easter, R.; Gustafson, W. I., Jr.; Zaveri, R. A.; Jimenez, J. L.; Saide, P.; Hodzic, A.
2010-12-01
The Weather Research and Forecasting model coupled with chemistry (WRF-Chem) is modified to include a volatility basis set (VBS) treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS) is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25%, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC) precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15% oxygen mass per generation of oxidation; however, all modeling cases still under
Volkov, Anatoliy; Koritsanszky, Tibor; Chodkiewicz, Michal; King, Harry F
2009-07-15
A new computer program for post-processing analysis of quantum-chemical electron densities is described. The code can work with Slater- and Gaussian-type basis functions of arbitrary angular momentum. It has been applied to explore the basis-set dependence of the electron density and its Laplacian in terms of local and integrated topological properties. Our analysis, including Gaussian/Slater basis sets up to sextuple/quadruple-zeta order, shows that these properties considerably depend on the choice of type and number of primitives utilized in the wavefunction expansion. Basis sets with high angular momentum (l = 5 or l = 6) are necessary to achieve convergence for local properties of the density and the Laplacian. In agreement with previous studies, atomic charges defined within Bader's Quantum Theory of Atoms in Molecules appear to be much more basis-set dependent than the Hirshfeld's stockholder charges. The former ones converge only at the quadruple-zeta/higher level with Gaussian/Slater functions.
Barbosa, Valmir C.
2010-01-01
Background Given an undirected graph, we consider the two problems of combinatorial optimization, which ask that its chromatic and independence numbers be found. Although both problems are NP-hard, when either one is solved on the incrementally denser graphs of a random sequence, at certain critical values of the number of edges, it happens that the transition to the next value causes optimal solutions to be obtainable substantially more easily than right before it. Methodology/Principal Findings We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another. We demonstrate that the performance jumps of graph coloring and independent sets at the critical-value transitions in the number of edges can be understood by resorting to the network that represents the solution space of the problems for each graph and examining its conduciveness between the non-optimal solutions and the optimal ones. Right past each transition, this network becomes strikingly more conducive in the direction of the optimal solutions than it was just before it, while at the same time becoming less conducive in the opposite direction. Conclusions/Significance Network conduciveness provides a useful conceptual framework for explaining the performance jumps associated with graph coloring and independent sets. We believe it may also become instrumental in helping clarify further issues related to NP-hardness that remain poorly understood. Additionally, it may become useful also in other areas in which network theory has a role to play. PMID:20628597
Barbosa, Valmir C
2010-07-08
Given an undirected graph, we consider the two problems of combinatorial optimization, which ask that its chromatic and independence numbers be found. Although both problems are NP-hard, when either one is solved on the incrementally denser graphs of a random sequence, at certain critical values of the number of edges, it happens that the transition to the next value causes optimal solutions to be obtainable substantially more easily than right before it. We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another. We demonstrate that the performance jumps of graph coloring and independent sets at the critical-value transitions in the number of edges can be understood by resorting to the network that represents the solution space of the problems for each graph and examining its conduciveness between the non-optimal solutions and the optimal ones. Right past each transition, this network becomes strikingly more conducive in the direction of the optimal solutions than it was just before it, while at the same time becoming less conducive in the opposite direction. Network conduciveness provides a useful conceptual framework for explaining the performance jumps associated with graph coloring and independent sets. We believe it may also become instrumental in helping clarify further issues related to NP-hardness that remain poorly understood. Additionally, it may become useful also in other areas in which network theory has a role to play.
Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade
2013-10-15
Accurate relativistic adapted Gaussian basis sets (RAGBSs) for 87 Fr up to 118 Uuo atoms without variational prolapse were developed here with the use of a polynomial version of the Generator Coordinate Dirac-Fock method. Two finite nuclear models have been used, the Gaussian and uniform sphere models. The largest RAGBS error, with respect to numerical Dirac-Fock results, is 15.4 miliHartree for Ununoctium with a basis set size of 33s30p19d14f functions.
Reuter, Matthew G; Harrison, Robert J
2014-05-07
The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.
Deriche, Rachid; Calder, Jeff; Descoteaux, Maxime
2009-08-01
Diffusion MRI has become an established research tool for the investigation of tissue structure and orientation. Since its inception, Diffusion MRI has expanded considerably to include a number of variations such as diffusion tensor imaging (DTI), diffusion spectrum imaging (DSI) and Q-ball imaging (QBI). The acquisition and analysis of such data is very challenging due to its complexity. Recently, an exciting new Kalman filtering framework has been proposed for DTI and QBI reconstructions in real-time during the repetition time (TR) of the acquisition sequence. In this article, we first revisit and thoroughly analyze this approach and show it is actually sub-optimal and not recursively minimizing the intended criterion due to the Laplace-Beltrami regularization term. Then, we propose a new approach that implements the QBI reconstruction algorithm in real-time using a fast and robust Laplace-Beltrami regularization without sacrificing the optimality of the Kalman filter. We demonstrate that our method solves the correct minimization problem at each iteration and recursively provides the optimal QBI solution. We validate with real QBI data that our proposed real-time method is equivalent in terms of QBI estimation accuracy to the standard offline processing techniques and outperforms the existing solution. Last, we propose a fast algorithm to recursively compute gradient orientation sets whose partial subsets are almost uniform and show that it can also be applied to the problem of efficiently ordering an existing point-set of any size. This work enables a clinician to start an acquisition with just the minimum number of gradient directions and an initial estimate of the orientation distribution functions (ODF) and then the next gradient directions and ODF estimates can be recursively and optimally determined, allowing the acquisition to be stopped as soon as desired or at any iteration with the optimal ODF estimates. This opens new and interesting opportunities for
Time-optimal path planning in dynamic flows using level set equations: theory and schemes
NASA Astrophysics Data System (ADS)
Lolla, Tapovan; Lermusiaux, Pierre F. J.; Ueckermann, Mattheus P.; Haley, Patrick J.
2014-10-01
We develop an accurate partial differential equation-based methodology that predicts the time-optimal paths of autonomous vehicles navigating in any continuous, strong, and dynamic ocean currents, obviating the need for heuristics. The goal is to predict a sequence of steering directions so that vehicles can best utilize or avoid currents to minimize their travel time. Inspired by the level set method, we derive and demonstrate that a modified level set equation governs the time-optimal path in any continuous flow. We show that our algorithm is computationally efficient and apply it to a number of experiments. First, we validate our approach through a simple benchmark application in a Rankine vortex flow for which an analytical solution is available. Next, we apply our methodology to more complex, simulated flow fields such as unsteady double-gyre flows driven by wind stress and flows behind a circular island. These examples show that time-optimal paths for multiple vehicles can be planned even in the presence of complex flows in domains with obstacles. Finally, we present and support through illustrations several remarks that describe specific features of our methodology.
NASA Astrophysics Data System (ADS)
Oby, Emily R.; Perel, Sagi; Sadtler, Patrick T.; Ruff, Douglas A.; Mischel, Jessica L.; Montez, David F.; Cohen, Marlene R.; Batista, Aaron P.; Chase, Steven M.
2016-06-01
Objective. A traditional goal of neural recording with extracellular electrodes is to isolate action potential waveforms of an individual neuron. Recently, in brain-computer interfaces (BCIs), it has been recognized that threshold crossing events of the voltage waveform also convey rich information. To date, the threshold for detecting threshold crossings has been selected to preserve single-neuron isolation. However, the optimal threshold for single-neuron identification is not necessarily the optimal threshold for information extraction. Here we introduce a procedure to determine the best threshold for extracting information from extracellular recordings. We apply this procedure in two distinct contexts: the encoding of kinematic parameters from neural activity in primary motor cortex (M1), and visual stimulus parameters from neural activity in primary visual cortex (V1). Approach. We record extracellularly from multi-electrode arrays implanted in M1 or V1 in monkeys. Then, we systematically sweep the voltage detection threshold and quantify the information conveyed by the corresponding threshold crossings. Main Results. The optimal threshold depends on the desired information. In M1, velocity is optimally encoded at higher thresholds than speed; in both cases the optimal thresholds are lower than are typically used in BCI applications. In V1, information about the orientation of a visual stimulus is optimally encoded at higher thresholds than is visual contrast. A conceptual model explains these results as a consequence of cortical topography. Significance. How neural signals are processed impacts the information that can be extracted from them. Both the type and quality of information contained in threshold crossings depend on the threshold setting. There is more information available in these signals than is typically extracted. Adjusting the detection threshold to the parameter of interest in a BCI context should improve our ability to decode motor intent
NASA Technical Reports Server (NTRS)
Seldner, K.
1977-01-01
An algorithm was developed to optimally control the traffic signals at each intersection using a discrete time traffic model applicable to heavy or peak traffic. Off line optimization procedures were applied to compute the cycle splits required to minimize the lengths of the vehicle queues and delay at each intersection. The method was applied to an extensive traffic network in Toledo, Ohio. Results obtained with the derived optimal settings are compared with the control settings presently in use.
Gartner, Daniel; Zhang, Yiye; Padman, Rema
2017-05-27
Order sets are a critical component in hospital information systems that are expected to substantially reduce physicians' physical and cognitive workload and improve patient safety. Order sets represent time interval-clustered order items, such as medications prescribed at hospital admission, that are administered to patients during their hospital stay. In this paper, we develop a mathematical programming model and an exact and a heuristic solution procedure with the objective of minimizing physicians' cognitive workload associated with prescribing order sets. Furthermore, we provide structural insights into the problem which lead us to a valid lower bound on the order set size. In a case study using order data on Asthma patients with moderate complexity from a major pediatric hospital, we compare the hospital's current solution with the exact and heuristic solutions on a variety of performance metrics. Our computational results confirm our lower bound and reveal that using a time interval decomposition approach substantially reduces computation times for the mathematical program, as does a K -means clustering based decomposition approach which, however, does not guarantee optimality because it violates the lower bound. The results of comparing the mathematical program with the current order set configuration in the hospital indicates that cognitive workload can be reduced by about 20.2% by allowing 1 to 5 order sets, respectively. The comparison of the K -means based decomposition with the hospital's current configuration reveals a cognitive workload reduction of about 19.5%, also by allowing 1 to 5 order sets, respectively. We finally provide a decision support system to help practitioners analyze the current order set configuration, the results of the mathematical program and the heuristic approach.
Marangu, Diana; Mwaniki, Hannah; Nduku, Salome; Maleche-Obimbo, Elizabeth; Jaoko, Walter; Babigumira, Joseph; John-Stewart, Grace; Rao, Deepa
2017-01-01
Optimal tuberculosis contact investigation impacts TB prevention, timely case finding and linkage to care, however data on routine implementation in high burden contexts is limited. In a multi-method qualitative study based on individual interviews with TB patients, facility observations and focus group discussions with health workers (HWs) in 13 public health facilities, and key informant interviews with governmental and non-governmental experts, we describe TB contact investigation in the context of an urban setting in Kenya and identify opportunities for optimization. Invitation of TB patients to bring close contacts by HWs was key for all patient decisions that led to contact screening in addition to patients' understanding of TB transmission and desire to avoid contacts suffering from TB. Sub-optimal HW enquiry of TB patients and contacts presenting at the facility were missed opportunities which stemmed from lack of standardized operational procedures, documentation tools and HW training. Stakeholders proposed provision of fast tracked and holistic health packages for contacts seeking TB screening, and sustainable government led funding for the requisite infrastructure and workforce. TB contact invitation by HWs leading to contact screening occurs in this context. Stakeholder perspectives inform the design of an operational framework for optimized delivery.
NASA Astrophysics Data System (ADS)
Benaissa, B.; Köppen, M.; Abdel Wahab, M.; Khatir, S.
2017-05-01
Complex engineering problems require simulations, which are computationally expensive in cases of inverse identification tasks since they commonly requires hundreds of thousands of simulations. This paper propose a method based on model reduction for crack size estimation, combining the proper orthogonal decomposition method with radial basis functions. The reduced model is validated by comparing the obtained boundary displacements with the corresponding results from a finite element model. This inverse procedure is formulated as the minimization of the difference between the measured and computed values of displacement at selected boundary nodes, called sensor points, using particle swarm optimization algorithm. Convex and a non-convex specimens have been considered for investigations of crack presence, and identification of its size, different crack sizes have been tested to demonstrate the efficiency of the proposed approach.
Cybulski, Hubert; Baranowska-Łączkowska, Angelika; Henriksen, Christian; Fernández, Berta
2014-11-06
By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these
Bogle, Lee B; Boyd, Jeff J; McLaughlin, Kyle A
2010-03-01
As winter backcountry activity increases, so does exposure to avalanche danger. A complicated situation arises when multiple victims are caught in an avalanche and where medical and other rescue demands overwhelm resources in the field. These mass casualty incidents carry a high risk of morbidity and mortality, and there is no recommended approach to patient care specific to this setting other than basic first aid principles. The literature is limited with regard to triaging systems applicable to avalanche incidents. In conjunction with the development of an electronic avalanche rescue training module by the Canadian Avalanche Association, we have designed the Avalanche Survival Optimizing Rescue Triage algorithm to address the triaging of multiple avalanche victims to optimize survival and disposition decisions.
NASA Astrophysics Data System (ADS)
Provencher, Bill; Burt, Oscar
1994-03-01
This paper presents two methods for approximating the optimal groundwater pumping policy for several interrelated aquifers in a stochastic setting that also involves conjunctive use of surface water. The first method employs a policy iteration dynamic programming (DP) algorithm where the value function is estimated by Monte Carlo simulation combined with curve-fitting techniques. The second method uses a Taylor series approximation to the functional equation of DP which reduces the problem, for a given observed state, to solving a system of equations equal in number to the aquifers. The methods are compared using a four-state variable, stochastic dynamic programming model of Madera County, California. The two methods yield nearly identical estimates of the optimal pumping policy, as well as the steady state pumping depth, suggesting that either method can be used in similar applications.
Chen, Shyi-Ming; Hsin, Wen-Chyuan
2015-07-01
In this paper, we propose a new weighted fuzzy interpolative reasoning method for sparse fuzzy rule-based systems based on the slopes of fuzzy sets. We also propose a particle swarm optimization (PSO)-based weights-learning algorithm to automatically learn the optimal weights of the antecedent variables of fuzzy rules for weighted fuzzy interpolative reasoning. We apply the proposed weighted fuzzy interpolative reasoning method using the proposed PSO-based weights-learning algorithm to deal with the computer activity prediction problem, the multivariate regression problems, and the time series prediction problems. The experimental results show that the proposed weighted fuzzy interpolative reasoning method using the proposed PSO-based weights-learning algorithm outperforms the existing methods for dealing with the computer activity prediction problem, the multivariate regression problems, and the time series prediction problems.
Al-Saidi, W A; Krakauer, Henry; Zhang, Shiwei
2007-05-21
The authors present phaseless auxiliary-field (AF) quantum Monte Carlo (QMC) calculations of the ground states of some hydrogen-bonded systems. These systems were selected to test and benchmark different aspects of the new phaseless AF QMC method. They include the transition state of H+H(2) near the equilibrium geometry and in the van der Walls limit, as well as the H(2)O, OH, and H(2)O(2) molecules. Most of these systems present significant challenges for traditional independent-particle electronic structure approaches, and many also have exact results available. The phaseless AF QMC method is used either with a plane wave basis with pseudopotentials or with all-electron Gaussian basis sets. For some systems, calculations are done with both to compare and characterize the performance of AF QMC under different basis sets and different Hubbard-Stratonovich decompositions. Excellent results are obtained using as input single Slater determinant wave functions taken from independent-particle calculations. Comparisons of the Gaussian based AF QMC results with exact full configuration interaction show that the errors from controlling the phase problem with the phaseless approximation are small. At the large basis-size limit, the AF QMC results using both types of basis sets are in good agreement with each other and with experimental values.
On the optimal identification of tag sets in time-constrained RFID configurations.
Vales-Alonso, Javier; Bueno-Delgado, María Victoria; Egea-López, Esteban; Alcaraz, Juan José; Pérez-Mañogil, Juan Manuel
2011-01-01
In Radio Frequency Identification facilities the identification delay of a set of tags is mainly caused by the random access nature of the reading protocol, yielding a random identification time of the set of tags. In this paper, the cumulative distribution function of the identification time is evaluated using a discrete time Markov chain for single-set time-constrained passive RFID systems, namely those ones where a single group of tags is assumed to be in the reading area and only for a bounded time (sojourn time) before leaving. In these scenarios some tags in a set may leave the reader coverage area unidentified. The probability of this event is obtained from the cumulative distribution function of the identification time as a function of the sojourn time. This result provides a suitable criterion to minimize the probability of losing tags. Besides, an identification strategy based on splitting the set of tags in smaller subsets is also considered. Results demonstrate that there are optimal splitting configurations that reduce the overall identification time while keeping the same probability of losing tags.
NASA Astrophysics Data System (ADS)
Woodford, Curtis; Yartsev, Slav; Van Dyk, Jake
2007-04-01
This study aims to determine the settings that provide the optimal clinical accuracy and consistency for the registration of megavoltage CT (MVCT) with planning kilovoltage CT image sets on the Hi-ART tomotherapy system. The systematic offset between the MVCT and the planning kVCT was determined by registration of multiple MVCT scans of a head phantom aligned with the planning isocentre. Residual error vector lengths and components were used to quantify the alignment quality for the phantom shifted by 5 mm in different directions obtained by all 27 possible combinations of MVCT inter-slice spacing, registration techniques and resolution. MVCT scans with normal slices are superior to coarse slices for registration of shifts in the superior-inferior, lateral and anterior-posterior directions. Decreasing the scan length has no detrimental effect on registration accuracy as long as the scan lengths are larger than 24 mm. In the case of bone technique and fine resolution, normal and fine MVCT scan slice spacing options give similar accuracy, so normal mode is preferable due to shorter procedure and less delivered dose required for patient set-up. A superior-inferior field length of 24-30 mm, normal slice spacing, bone technique, and fine resolution is the optimum set of registration settings for MVCT scans of a Rando head phantom acquired with the Hi-ART tomotherapy system, provided the registration shifts are less than 5 mm.
Optimal design of measurement settings for quantum-state-tomography experiments
NASA Astrophysics Data System (ADS)
Li, Jun; Huang, Shilin; Luo, Zhihuang; Li, Keren; Lu, Dawei; Zeng, Bei
2017-09-01
Quantum state tomography is an indispensable but costly part of many quantum experiments. Typically, it requires measurements to be carried out in a number of different settings on a fixed experimental setup. The collected data are often informationally overcomplete, with the amount of information redundancy depending on the particular set of measurement settings chosen. This raises a question about how one should optimally take data so that the number of measurement settings necessary can be reduced. Here, we cast this problem in terms of integer programming. For a given experimental setup, standard integer-programming algorithms allow us to find the minimum set of readout operations that can realize a target tomographic task. We apply the method to certain basic and practical state-tomographic problems in nuclear-magnetic-resonance experimental systems. The results show that considerably fewer readout operations can be found using our technique than by using the previous greedy search strategy. Therefore, our method could be helpful for simplifying measurement schemes to minimize the experimental effort.
On the Optimal Identification of Tag Sets in Time-Constrained RFID Configurations
Vales-Alonso, Javier; Bueno-Delgado, María Victoria; Egea-López, Esteban; Alcaraz, Juan José; Pérez-Mañogil, Juan Manuel
2011-01-01
In Radio Frequency Identification facilities the identification delay of a set of tags is mainly caused by the random access nature of the reading protocol, yielding a random identification time of the set of tags. In this paper, the cumulative distribution function of the identification time is evaluated using a discrete time Markov chain for single-set time-constrained passive RFID systems, namely those ones where a single group of tags is assumed to be in the reading area and only for a bounded time (sojourn time) before leaving. In these scenarios some tags in a set may leave the reader coverage area unidentified. The probability of this event is obtained from the cumulative distribution function of the identification time as a function of the sojourn time. This result provides a suitable criterion to minimize the probability of losing tags. Besides, an identification strategy based on splitting the set of tags in smaller subsets is also considered. Results demonstrate that there are optimal splitting configurations that reduce the overall identification time while keeping the same probability of losing tags. PMID:22163777
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC).
Frost, H Robert; Moore, Jason H
2014-06-15
Gene set enrichment has become a critical tool for interpreting the results of high-throughput genomic experiments. Inconsistent annotation quality and lack of annotation specificity, however, limit the statistical power of enrichment methods and make it difficult to replicate enrichment results across biologically similar datasets. We propose a novel algorithm for optimizing gene set annotations to best match the structure of specific empirical data sources. Our proposed method, entropy minimization over variable clusters (EMVC), filters the annotations for each gene set to minimize a measure of entropy across disjoint gene clusters computed for a range of cluster sizes over multiple bootstrap resampled datasets. As shown using simulated gene sets with simulated data and Molecular Signatures Database collections with microarray gene expression data, the EMVC algorithm accurately filters annotations unrelated to the experimental outcome resulting in increased gene set enrichment power and better replication of enrichment results. http://cran.r-project.org/web/packages/EMVC/index.html. © The Author 2014. Published by Oxford University Press.
NASA Astrophysics Data System (ADS)
Hou, Zeyu; Lu, Wenxi; Xue, Haibo; Lin, Jin
2017-08-01
Surrogate-based simulation-optimization technique is an effective approach for optimizing the surfactant enhanced aquifer remediation (SEAR) strategy for clearing DNAPLs. The performance of the surrogate model, which is used to replace the simulation model for the aim of reducing computation burden, is the key of corresponding researches. However, previous researches are generally based on a stand-alone surrogate model, and rarely make efforts to improve the approximation accuracy of the surrogate model to the simulation model sufficiently by combining various methods. In this regard, we present set pair analysis (SPA) as a new method to build ensemble surrogate (ES) model, and conducted a comparative research to select a better ES modeling pattern for the SEAR strategy optimization problems. Surrogate models were developed using radial basis function artificial neural network (RBFANN), support vector regression (SVR), and Kriging. One ES model is assembling RBFANN model, SVR model, and Kriging model using set pair weights according their performance, and the other is assembling several Kriging (the best surrogate modeling method of three) models built with different training sample datasets. Finally, an optimization model, in which the ES model was embedded, was established to obtain the optimal remediation strategy. The results showed the residuals of the outputs between the best ES model and simulation model for 100 testing samples were lower than 1.5%. Using an ES model instead of the simulation model was critical for considerably reducing the computation time of simulation-optimization process and maintaining high computation accuracy simultaneously.
Friese, Daniel H.; Törk, Lisa; Hättig, Christof
2014-11-21
We present scaling factors for vibrational frequencies calculated within the harmonic approximation and the correlated wave-function methods coupled cluster singles and doubles model (CC2) and Møller-Plesset perturbation theory (MP2) with and without a spin-component scaling (SCS or spin-opposite scaling (SOS)). Frequency scaling factors and the remaining deviations from the reference data are evaluated for several non-augmented basis sets of the cc-pVXZ family of generally contracted correlation-consistent basis sets as well as for the segmented contracted TZVPP basis. We find that the SCS and SOS variants of CC2 and MP2 lead to a slightly better accuracy for the scaled vibrational frequencies. The determined frequency scaling factors can also be used for vibrational frequencies calculated for excited states through response theory with CC2 and the algebraic diagrammatic construction through second order and their spin-component scaled variants.
Pinheiro, J.C.; Jorge, F.E.; Castro, E.V.R. de
2000-05-15
Accurate Gaussian basis sets (18s for Li and Be and 20s11p for the atoms from B to Ne) for the first-row atoms, generated with an improved generator coordinate Hartree-Fock method, were contracted and enriched with polarization functions. These basis sets were tested for B{sub 2}, C{sub 2}, BeO, Cn{sup {minus}}, LiF, N{sub 2}, CO, BF, NO{sup +}, O{sub 2}, and F{sub 2}. At the Hartree-Fock (HP), second-order Moeller-Plesset (MP2), fourth-order Moeller-Plesset (MP4), and density functional theory (DFT) levels, the dipole moments, bond lengths, and harmonic vibrational frequencies were studied, and at the MP2, MP4, and DFT levels, the dissociation energies were evaluated and compared with the corresponding experimental values and with values obtained using other contracted Gaussian basis sets and numerical HF calculations. For all diatomic molecules studied, the differences between the total energies, obtained with the largest contracted basis set [6s5p3d1f], and those calculated with the numerical HF methods were always less than 3.2 mhartree.
NASA Astrophysics Data System (ADS)
Hu, Ching-Han; Chong, Delano P.
1997-03-01
Density functional theory and the unrestricted generalized transition state (uGTS) model were applied to study the core-electron binding energies (CEBEs) of open-shell molecules. Basis set scaling based on Clementi and Raimondi's rules for atomic screening was used along with the cc-pVTZ basis set. The scaled pVTZ basis set is almost as good as the cc-pV5Z and complete basis set limit in predicting CEBEs. For small molecules (O 2, NO, NF 2 and NO 2) the average absolute deviation (aad) of our prediction (scaled pVTZ) is only 0.29 eV. For the larger molecule (CF 3) 2NO the aad is 0.56 eV, compared with experimental uncertainty of 0.5 eV. Theoretical predicted multiplet splittings for the small molecules agree quite well with experiment: the average deviation is -0.33 eV. For (CF 3) 2NO the calculated multiplet splittings are much smaller than the experimental ones. We also predict the CEBEs of PO, SN and SO, which have not been observed experimentally.
NASA Technical Reports Server (NTRS)
Decker, Arthur J. (Inventor)
2006-01-01
An artificial neural network is disclosed that processes holography generated characteristic pattern of vibrating structures along with finite-element models. The present invention provides for a folding operation for conditioning training sets for optimally training forward-neural networks to process characteristic fringe pattern. The folding pattern increases the sensitivity of the feed-forward network for detecting changes in the characteristic pattern The folding routine manipulates input pixels so as to be scaled according to the location in an intensity range rather than the position in the characteristic pattern.
Kallel, Héla; Zaïri, Hind; Rourou, Samia; Essafi, Makram; Barbouche, Ridha; Dellagi, Koussay; Fathallah, Dahmani M
2002-05-01
Taguchi's methods were used for the design of an experimental strategy aimed at optimizing cell density and monoclonal antibody (mAb) production from a spinner flask hybridoma culture. 23G11 is an antibody to the human leukocyte adhesion molecule, CR3 or beta 2 integrin (CD11b/CD18). It recognizes specifically the A-domain of the alpha subunit CD11b. Anti beta 2 integrin monoclonal antibodies hold a great potential for preventing inflammation mediated tissue injuries. An L8 orthogonal experimental design was used to investigate four different culture components: stirring speed, nature of serum, concentration of serum and nature of media (RPMI 1640 or RPMI 1640 supplemented with glucose and glutamine). The experiments were conducted using two levels for each factor studied and a direct ELISA test was used to estimate the level of antibody production. Statistical analysis of the collected data pointed to the stirring speed and serum concentration, and the interaction between these parameters, as the components that affected cell growth. Antibody production was affected by these factors and by the nature of medium but also by the following two interactions: stirring speed/nature of serum and stirring speed/concentration of serum. This study emphasizes the value of using Taguchi's methods as a basis for optimization of mAb production from a hybridoma culture, in cost effective and significantly less labor intensive ways.
NASA Astrophysics Data System (ADS)
Regis, Rommel G.; Shoemaker, Christine A.
2013-05-01
This article presents the DYCORS (DYnamic COordinate search using Response Surface models) framework for surrogate-based optimization of HEB (High-dimensional, Expensive, and Black-box) functions that incorporates an idea from the DDS (Dynamically Dimensioned Search) algorithm. The iterate is selected from random trial solutions obtained by perturbing only a subset of the coordinates of the current best solution. Moreover, the probability of perturbing a coordinate decreases as the algorithm reaches the computational budget. Two DYCORS algorithms that use RBF (Radial Basis Function) surrogates are developed: DYCORS-LMSRBF is a modification of the LMSRBF algorithm while DYCORS-DDSRBF is an RBF-assisted DDS. Numerical results on a 14-D watershed calibration problem and on eleven 30-D and 200-D test problems show that DYCORS algorithms are generally better than EGO, DDS, LMSRBF, MADS with kriging, SQP, an RBF-assisted evolution strategy, and a genetic algorithm. Hence, DYCORS is a promising approach for watershed calibration and for HEB optimization.
NASA Astrophysics Data System (ADS)
Wigdahl, J.; Agurto, C.; Murray, V.; Barriga, S.; Soliz, P.
2013-03-01
Diabetic retinopathy (DR) affects more than 4.4 million Americans age 40 and over. Automatic screening for DR has shown to be an efficient and cost-effective way to lower the burden on the healthcare system, by triaging diabetic patients and ensuring timely care for those presenting with DR. Several supervised algorithms have been developed to detect pathologies related to DR, but little work has been done in determining the size of the training set that optimizes an algorithm's performance. In this paper we analyze the effect of the training sample size on the performance of a top-down DR screening algorithm for different types of statistical classifiers. Results are based on partial least squares (PLS), support vector machines (SVM), k-nearest neighbor (kNN), and Naïve Bayes classifiers. Our dataset consisted of digital retinal images collected from a total of 745 cases (595 controls, 150 with DR). We varied the number of normal controls in the training set, while keeping the number of DR samples constant, and repeated the procedure 10 times using randomized training sets to avoid bias. Results show increasing performance in terms of area under the ROC curve (AUC) when the number of DR subjects in the training set increased, with similar trends for each of the classifiers. Of these, PLS and k-NN had the highest average AUC. Lower standard deviation and a flattening of the AUC curve gives evidence that there is a limit to the learning ability of the classifiers and an optimal number of cases to train on.
NASA Astrophysics Data System (ADS)
Burton, P. G.
1983-08-01
The non-variational CEPA2 PNO ansatz, recently employed in detailed studies of the H 2-H 2 van der Waals interaction by Burton and Senff and the full CI extrapolation studies on the same system by Burton are discussed in relation to the explicit full CI study of Harrison and Handy for the planar T configuration of H 2-H 2 ( R = 6.5 ao) in a basis of 80 functions.
Wang, Wei; Slepčev, Dejan; Basu, Saurav; Ozolek, John A.
2012-01-01
Transportation-based metrics for comparing images have long been applied to analyze images, especially where one can interpret the pixel intensities (or derived quantities) as a distribution of ‘mass’ that can be transported without strict geometric constraints. Here we describe a new transportation-based framework for analyzing sets of images. More specifically, we describe a new transportation-related distance between pairs of images, which we denote as linear optimal transportation (LOT). The LOT can be used directly on pixel intensities, and is based on a linearized version of the Kantorovich-Wasserstein metric (an optimal transportation distance, as is the earth mover’s distance). The new framework is especially well suited for computing all pairwise distances for a large database of images efficiently, and thus it can be used for pattern recognition in sets of images. In addition, the new LOT framework also allows for an isometric linear embedding, greatly facilitating the ability to visualize discriminant information in different classes of images. We demonstrate the application of the framework to several tasks such as discriminating nuclear chromatin patterns in cancer cells, decoding differences in facial expressions, galaxy morphologies, as well as sub cellular protein distributions. PMID:23729991
Yang, Bo; Guo, Qing; Wang, Fei; Cai, Kemin; Bao, Xueli; Chu, Jiusheng
2017-01-01
The present study was performed to identify a gene set for predicting the relapse in laryngeal carcinoma using large data analysis methods. Two gene expression profile data of laryngeal carcinoma (GSE27020 and GSE25727) were downloaded from public database. Genes associated with tumor relapse, namely informative genes, were identified by Cox regression analysis. Then the protein-protein interaction (PPI) network consisting of informative genes was constructed. Afterwards, the optimized support vector machine (SVM) classifier was constructed to classify the relapsed laryngeal carcinoma samples based on genes in specific PPI network. Furthermore, the efficiency of the SVM classifier was verified by other two independent datasets. A total of 331 informative genes were obtained from GSE27020 and GSE25757 datasets. A PPI network specific to laryngeal carcinoma relapse was constructed which contained informative genes and critical non-informative genes. The top 10 genes in specific PPI network were APP, NTRK1, TP53, PTEN, FN1, ELAVL1, HSP90AA1, XPO1, LDHA and CDK2 ranked by BC (betweenness centrality) value. The optimized SVM classifier including top 80 genes showed accuracy of 100% to classify the relapsed cases from laryngeal carcinoma samples. Next, the efficiency of the SVM classifier to predict relapse samples was verified in another independent datasets, which showed accuracy of 97.47%. The informative genes in the optimized SVM classifier were enriched in several pathways associated with tumor progression. A 80-gene set was identified as biomarker to predict the relapse of laryngeal carcinoma, which would be potentially applied in decision of different treatments for patients with different relapse risks.
Singh, Parminder; Sahoo, Jhari; Talwar, Gopika; Chatli, Manish K; Biswas, Ashim K
2015-03-01
A three factor Box-Behnken design of response surface methodology was employed to optimize spent hen meat level (600-700 g kg(-1)), oil level (25-75 g kg(-1)) and cooking time (3-5 min) for development of ready-to-eat chicken meat caruncles on the basis of sensory attributes - colour/appearance, flavour, crispiness, after-taste, meat flavour intensity and overall acceptability. The analysis of variance showed that meat and cooking time interaction showed significant effect (p < 0.01; p < 0.05; p < 0.1) on colour/appearance and crispiness of chicken meat caruncles. Quadratically meat level showed significantly higher effect (p < 0.01; p < 0.05; p < 0.1) on crispiness; and oil level and cooking time (p < 0.05; p < 0.1) on after-taste of chicken meat caruncles. Linearly meat level showed significantly higher (p < 0.05; p < 0.1) effect on colour/appearance, after-taste, meat flavour intensity and overall acceptability of chicken meat caruncles. The optimized conditions were: 650 g kg(-1) meat level, 50 g kg(-1) oil level and cooking time as 4 min. Among all sensory parameters, crispiness is one of the most important sensory parameters for meat snacks, which was highest (6.68) at the optimized conditions in the final product. The other sensory parameters ranged from 6.33 to 6.68 on an eight point scale. Box-Behnken design of RSM performed well in the optimization process of development of chicken meat caruncles to produce product with very high degree of acceptability. 650 g kg(-1) of spent hen meat level produced the most acceptable product in terms of sensory profile.
NASA Astrophysics Data System (ADS)
Höllwarth, A.; Böhme, M.; Dapprich, S.; Ehlers, A. W.; Gobbi, A.; Jonas, V.; Köhler, K. F.; Stegmann, R.; Veldkamp, A.; Frenking, G.
1993-06-01
A set of five-component d-type polarization functions has been optimized for the main group elements AlBi at the energetically lowest lying s 2p n electronic states for use with the effective core potentials of Hay and Wadt at the CISD level of theory. Also a set of f-type polarization functions is suggested for the elements Zn, Cd and Hg.
Differential optimal dopamine levels for set-shifting and working memory in Parkinson's disease.
Fallon, Sean James; Smulders, Katrijn; Esselink, Rianne A; van de Warrenburg, Bart P; Bloem, Bastiaan R; Cools, Roshan
2015-10-01
Parkinson's disease (PD) is an important model for the role of dopamine in supporting human cognition. However, despite the uniformity of midbrain dopamine depletion only some patients experience cognitive impairment. The neurocognitive mechanisms of this heterogeneity remain unclear. A genetic polymorphism in the catechol O-methyltransferase (COMT) enzyme, predominantly thought to exert its cognitive effect through acting on prefrontal cortex (PFC) dopamine transmission, provides us with an experimental window onto dopamine's role in cognitive performance in PD. In a large cohort of PD patients (n=372), we examined the association between COMT genotype and two tasks known to implicate prefrontal dopamine (spatial working memory and attentional set-shifting) and on a task less sensitive to prefrontal dopamine (paired associates learning). Consistent with the known neuroanatomical locus of its effects, differences between the COMT genotype groups were observed on dopamine-dependant tasks, but not the paired associates learning task. However, COMT genotype had differential effects on the two prefrontal dopamine tasks. Putative prefrontal dopamine levels influenced spatial working memory in an 'Inverted-U'-shaped fashion, whereas a linear, dose-dependant pattern was observed for attentional set-shifting. Cumulatively, these results revise our understanding of when COMT genotype modulates cognitive functioning in PD patients by showing that the behavioural consequences of genetic variation vary according to task demands, presumably because set-shifting and working memory have different optimal dopamine levels.
Two-stage fan. 4: Performance data for stator setting angle optimization
NASA Technical Reports Server (NTRS)
Burger, G. D.; Keenan, M. J.
1975-01-01
Stator setting angle optimization tests were conducted on a two-stage fan to improve efficiency at overspeed, stall margin at design speed, and both efficiency and stall margin at partspeed. The fan has a design pressure ratio of 2.8, a flow rate of 184.2 lb/sec (83.55 kg/sec) and a 1st-stage rotor tip speed of 1450 ft/sec (441.96 in/sec). Performance was obtained at 70,100, and 105 percent of design speed with different combinations of 1st-stage and 2nd-stage stator settings. One combination of settings, other than design, was common to all three speeds. At design speed, a 2.0 percentage point increase in stall margin was obtained at the expense of a 1.3 percentage point efficiency decrease. At 105 percent speed, efficiency was improved by 1.8 percentage points but stall margin decreased 4.7 percentage points. At 70 percent speed, no change in stall margin or operating line efficiency was obtained with stator resets although considerable speed-flow requlation occurred.
Sherstyuk, A.I.
1995-03-01
To calculate the response of many-electron systems to an external perturbation, a modification of the coupled variant of perturbation theory was developed using an expansion in a complete set of the Hartree-Fock virtual orbitals of the Sturmian type. The orbitals are associated with the pure discrete spectrum of a generalized eigenvalue problem related to an effective one-particle operator that does not contain the self-action of electrons. 9 refs.
Synthetic enzyme mixtures for biomass deconstruction: production and optimization of a core set.
Banerjee, Goutami; Car, Suzana; Scott-Craig, John S; Borrusch, Melissa S; Aslam, Nighat; Walton, Jonathan D
2010-08-01
The high cost of enzymes is a major bottleneck preventing the development of an economically viable lignocellulosic ethanol industry. Commercial enzyme cocktails for the conversion of plant biomass to fermentable sugars are complex mixtures containing more than 80 proteins of suboptimal activities and relative proportions. As a step toward the development of a more efficient enzyme cocktail for biomass conversion, we have developed a platform, called GENPLAT, that uses robotic liquid handling and statistically valid experimental design to analyze synthetic enzyme mixtures. Commercial enzymes (Accellerase 1000 +/- Multifect Xylanase, and Spezyme CP +/- Novozyme 188) were used to test the system and serve as comparative benchmarks. Using ammonia-fiber expansion (AFEX) pretreated corn stover ground to 0.5 mm and a glucan loading of 0.2%, an enzyme loading of 15 mg protein/g glucan, and 48 h digestion at 50 degrees C, commercial enzymes released 53% and 41% of the available glucose and xylose, respectively. Mixtures of three, five, and six pure enzymes of Trichoderma species, expressed in Pichia pastoris, were systematically optimized. Statistical models were developed for the optimization of glucose alone, xylose alone, and the average of glucose + xylose for two digestion durations, 24 and 48 h. The resulting models were statistically significant (P < 0.0001) and indicated an optimum composition for glucose release (values for optimized xylose release are in parentheses) of 29% (5%) cellobiohydrolase 1, 5% (14%) cellobiohydrolase 2, 25% (25%) endo-beta1,4-glucanase 1, 14% (5%) beta-glucosidase, 22% (34%) endo-beta1,4-xylanase 3, and 5% (17%) beta-xylosidase in 48 h at a protein loading of 15 mg/g glucan. Comparison of two AFEX-treated corn stover preparations ground to different particle sizes indicated that particle size (100 vs. 500 microm) makes a large difference in total digestibility. The assay platform and the optimized "core" set together provide a starting
NASA Astrophysics Data System (ADS)
Heryadi, Dodi; Yeager, Danny L.; Golab, Joseph T.; Nichols, Jeffrey A.
1995-06-01
In a recent paper in The Journal of Chemical Physics, we showed the potential energy curves for several cation states of O2 obtained using the multiconfigurational spin tensor electron propagator method (MCSTEP) with a <5s4p3d> basis set. In this communication we present vertical ionization potential calculations to the same O2 states. However, for the results reported here, exactly the same basis sets and geometries are used that were used for two other forefront methods; the coupled-cluster reference electron propagator theory (CC-EPT) and the Fock space multireference coupled-cluster method (FSMRCC). Hence, more direct comparisons and contrasts among these methods are now available.
Roos, Björn O; Lindh, Roland; Malmqvist, Per-Ake; Veryazov, Valera; Widmark, Per-Olof; Borin, Antonio Carlos
2008-11-13
New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.1 eV in most cases. Two molecular applications are included as illustration: the cerium diatom and the LuF3 molecule. In both cases it is shown that 4f orbitals are not involved in the chemical bond in contrast to an earlier claim for the latter molecule.
Sure, Rebecca; Brandenburg, Jan Gerit
2015-01-01
Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Quantifying and visualizing variations in sets of images using continuous linear optimal transport
NASA Astrophysics Data System (ADS)
Kolouri, Soheil; Rohde, Gustavo K.
2014-03-01
Modern advancements in imaging devices have enabled us to explore the subcellular structure of living organisms and extract vast amounts of information. However, interpreting the biological information mined in the captured images is not a trivial task. Utilizing predetermined numerical features is usually the only hope for quantifying this information. Nonetheless, direct visual or biological interpretation of results obtained from these selected features is non-intuitive and difficult. In this paper, we describe an automatic method for modeling visual variations in a set of images, which allows for direct visual interpretation of the most significant differences, without the need for predefined features. The method is based on a linearized version of the continuous optimal transport (OT) metric, which provides a natural linear embedding for the image data set, in which linear combination of images leads to a visually meaningful image. This enables us to apply linear geometric data analysis techniques such as principal component analysis and linear discriminant analysis in the linearly embedded space and visualize the most prominent modes, as well as the most discriminant modes of variations, in the dataset. Using the continuous OT framework, we are able to analyze variations in shape and texture in a set of images utilizing each image at full resolution, that otherwise cannot be done by existing methods. The proposed method is applied to a set of nuclei images segmented from Feulgen stained liver tissues in order to investigate the major visual differences in chromatin distribution of Fetal-Type Hepatoblastoma (FHB) cells compared to the normal cells.
Optimizing the Choice of Filter Sets for Space Based Imaging Instruments
NASA Astrophysics Data System (ADS)
Elliott, Rachel E.; Farrah, Duncan; Petty, Sara M.; Harris, Kathryn Amy
2015-01-01
We investigate the challenge of selecting a limited number of filters for space based imaging instruments such that they are able to address multiple heterogeneous science goals. The number of available filter slots for a mission is bounded by factors such as instrument size and cost. We explore methods used to extract the optimal group of filters such that they complement each other most effectively. We focus on three approaches; maximizing the separation of objects in two-dimensional color planes, SED fitting to select those filter sets that give the finest resolution in fitted physical parameters, and maximizing the orthogonality of physical parameter vectors in N-dimensional color-color space. These techniques are applied to a test-case, a UV/optical imager with space for five filters, with the goal of measuring the properties of local stars through to distant galaxies.
Locally Advanced Lung Cancer: An Optimal Setting for Vaccines and Other Immunotherapies
Iyengar, Puneeth; Gerber, David E.
2013-01-01
Lung cancer has traditionally been considered relatively resistant to immunotherapies. However, recent advances in the understanding of tumor-associated antigens, anti-tumor immune responses, and tumor immunosuppression mechanisms have resulted in a number of promising immunomodulatory therapies such as vaccines and checkpoint inhibitors. Locally advanced non-small cell lung cancer (NSCLC) is an optimal setting for these treatments because standard therapies such as surgery, radiation, and chemotherapy may enhance anti-tumor immune effects by debulking the tumor, increasing tumor antigen presentation, and promoting T-cell response and trafficking. Clinical trials incorporating immunomodulatory agents into combined modality therapy of locally advanced NSCLC have shown promising results. Future challenges include identifying biomarkers to predict those patients most likely to benefit from this approach, radiographic assessment of treatment effects, the timing and dosing of combined modality treatment including immunotherapies, and avoidance of potentially overlapping toxicities. PMID:23708072
NASA Technical Reports Server (NTRS)
Briand, Lionel C.; Basili, Victor R.; Hetmanski, Christopher J.
1993-01-01
Applying equal testing and verification effort to all parts of a software system is not very efficient, especially when resources are limited and scheduling is tight. Therefore, one needs to be able to differentiate low/high fault frequency components so that testing/verification effort can be concentrated where needed. Such a strategy is expected to detect more faults and thus improve the resulting reliability of the overall system. This paper presents the Optimized Set Reduction approach for constructing such models, intended to fulfill specific software engineering needs. Our approach to classification is to measure the software system and build multivariate stochastic models for predicting high risk system components. We present experimental results obtained by classifying Ada components into two classes: is or is not likely to generate faults during system and acceptance test. Also, we evaluate the accuracy of the model and the insights it provides into the error making process.
NASA Astrophysics Data System (ADS)
Ferreira, José C.; Fonseca, Carlos M.; Gaspar-Cunha, António
2007-04-01
Most of the real world optimization problems involve multiple, usually conflicting, optimization criteria. Generating Pareto optimal solutions plays an important role in multi-objective optimization, and the problem is considered to be solved when the Pareto optimal set is found, i.e., the set of non-dominated solutions. Multi-Objective Evolutionary Algorithms based on the principle of Pareto optimality are designed to produce the complete set of non-dominated solutions. However, this is not allays enough since the aim is not only to know the Pareto set but, also, to obtain one solution from this Pareto set. Thus, the definition of a methodology able to select a single solution from the set of non-dominated solutions (or a region of the Pareto frontier), and taking into account the preferences of a Decision Maker (DM), is necessary. A different method, based on a weighted stress function, is proposed. It is able to integrate the user's preferences in order to find the best region of the Pareto frontier accordingly with these preferences. This method was tested on some benchmark test problems, with two and three criteria, and on a polymer extrusion problem. This methodology is able to select efficiently the best Pareto-frontier region for the specified relative importance of the criteria.
Optimize Flue Gas Settings to Promote Microalgae Growth in Photobioreactors via Computer Simulations
He, Lian; Chen, Amelia B; Yu, Yi; Kucera, Leah; Tang, Yinjie
2013-01-01
Flue gas from power plants can promote algal cultivation and reduce greenhouse gas emissions1. Microalgae not only capture solar energy more efficiently than plants3, but also synthesize advanced biofuels2-4. Generally, atmospheric CO2 is not a sufficient source for supporting maximal algal growth5. On the other hand, the high concentrations of CO2 in industrial exhaust gases have adverse effects on algal physiology. Consequently, both cultivation conditions (such as nutrients and light) and the control of the flue gas flow into the photo-bioreactors are important to develop an efficient “flue gas to algae” system. Researchers have proposed different photobioreactor configurations4,6 and cultivation strategies7,8 with flue gas. Here, we present a protocol that demonstrates how to use models to predict the microalgal growth in response to flue gas settings. We perform both experimental illustration and model simulations to determine the favorable conditions for algal growth with flue gas. We develop a Monod-based model coupled with mass transfer and light intensity equations to simulate the microalgal growth in a homogenous photo-bioreactor. The model simulation compares algal growth and flue gas consumptions under different flue-gas settings. The model illustrates: 1) how algal growth is influenced by different volumetric mass transfer coefficients of CO2; 2) how we can find optimal CO2 concentration for algal growth via the dynamic optimization approach (DOA); 3) how we can design a rectangular on-off flue gas pulse to promote algal biomass growth and to reduce the usage of flue gas. On the experimental side, we present a protocol for growing Chlorella under the flue gas (generated by natural gas combustion). The experimental results qualitatively validate the model predictions that the high frequency flue gas pulses can significantly improve algal cultivation. PMID:24121788
Setting an Optimal α That Minimizes Errors in Null Hypothesis Significance Tests
Mudge, Joseph F.; Baker, Leanne F.; Edge, Christopher B.; Houlahan, Jeff E.
2012-01-01
Null hypothesis significance testing has been under attack in recent years, partly owing to the arbitrary nature of setting α (the decision-making threshold and probability of Type I error) at a constant value, usually 0.05. If the goal of null hypothesis testing is to present conclusions in which we have the highest possible confidence, then the only logical decision-making threshold is the value that minimizes the probability (or occasionally, cost) of making errors. Setting α to minimize the combination of Type I and Type II error at a critical effect size can easily be accomplished for traditional statistical tests by calculating the α associated with the minimum average of α and β at the critical effect size. This technique also has the flexibility to incorporate prior probabilities of null and alternate hypotheses and/or relative costs of Type I and Type II errors, if known. Using an optimal α results in stronger scientific inferences because it estimates and minimizes both Type I errors and relevant Type II errors for a test. It also results in greater transparency concerning assumptions about relevant effect size(s) and the relative costs of Type I and II errors. By contrast, the use of α = 0.05 results in arbitrary decisions about what effect sizes will likely be considered significant, if real, and results in arbitrary amounts of Type II error for meaningful potential effect sizes. We cannot identify a rationale for continuing to arbitrarily use α = 0.05 for null hypothesis significance tests in any field, when it is possible to determine an optimal α. PMID:22389720
Uncini, Antonino; Ippoliti, Luigi; Shahrizaila, Nortina; Sekiguchi, Yukari; Kuwabara, Satoshi
2017-07-01
To optimize the electrodiagnosis of Guillain-Barré syndrome (GBS) subtypes at first study. The reference electrodiagnosis was obtained in 53 demyelinating and 45 axonal GBS patients on the basis of two serial studies and results of anti-ganglioside antibodies assay. We retrospectively employed sparse linear discriminant analysis (LDA), two existing electrodiagnostic criteria sets (Hadden et al., 1998; Rajabally et al., 2015) and one we propose that additionally evaluates duration of motor responses, sural sparing pattern and defines reversible conduction failure (RCF) in motor and sensory nerves at second study. At first study the misclassification error rates, compared to reference diagnoses, were: 15.3% for sparse LDA, 30% for our criteria, 45% for Rajabally's and 48% for Hadden's. Sparse LDA identified seven most powerful electrophysiological variables differentiating demyelinating and axonal subtypes and assigned to each patient the diagnostic probability of belonging to either subtype. At second study 46.6% of axonal GBS patients showed RCF in two motor and 8.8% in two sensory nerves. Based on a single study, sparse LDA showed the highest diagnostic accuracy. RCF is present in a considerable percentage of axonal patients. Sparse LDA, a supervised statistical method of classification, should be introduced in the electrodiagnostic practice. Copyright © 2017. Published by Elsevier B.V.
NASA Astrophysics Data System (ADS)
Balabin, Roman M.
2008-10-01
In this paper, an extra error source for high-quality ab initio calculation of conformation equilibrium in normal alkanes—intramolecular basis set superposition error (BSSE)—is discussed. Normal butane (n-butane) and normal hexane (n-hexane) are used as representative examples. Single-point energy difference and BSSE values of trans and gauche conformations for n-butane (and trans-trans-trans and gauche-gauche-gauche conformations for n-hexane) were calculated using popular electron correlation methods: The second-order Moller-Plesset (MP2), the fourth-order Moller-Plesset (MP4), and coupled cluster with single and double substitutions with noniterative triple excitation [CCSD(T)] levels of theory. Extrapolation to the complete basis set is applied. The difference between BSSE-corrected and uncorrected relative energy values ranges from ˜100 cal/mol (in case of n-butane) to more than 1000 cal/mol (in case of n-hexane). The influence of basis set type (Pople or Dunning) and size [up to 6-311G(3df,3pd) and aug-cc-pVQZ] is discussed.
Cheng, Lan Stanton, John F.; Gauss, Jürgen
2015-06-14
A systematic relativistic coupled-cluster study is reported on the harmonic vibrational frequencies of the O{sub h}, C{sub 3v}, and C{sub 2v} conformers of XeF{sub 6}, with scalar-relativistic effects efficiently treated using the spin-free exact two-component theory in its one-electron variant (SFX2C-1e). Atomic natural orbital type basis sets recontracted for the SFX2C-1e scheme have been shown to provide rapid basis-set convergence for the vibrational frequencies. SFX2C-1e as well as complementary pseudopotential based computations consistently predicts that both O{sub h} and C{sub 3v} structures are local minima on the potential energy surface, while the C{sub 2v} structure is a transition state. Qualitative disagreement between the present results for the O{sub h} structure and those from CCSD(T)-F12b calculations [Peterson et al., J. Phys. Chem. A 116, 9777 (2012)], which yielded a triply degenerate imaginary frequency for the O{sub h} structure, is attributed here to the high sensitivity of the computed harmonic frequencies of the t{sub 1u} bending modes to the basis-set effects of triples contributions.
Tzeli, Demeter; Tsekouras, Athanassios A
2008-04-14
The electron affinity of GaN and Ga2N as well as the geometries and the dissociation energies of the ground states of gallium nitrides GaN, GaN(-), Ga2N, and Ga2N(-) were systematically studied by employing the coupled cluster method, RCCSD(T), in conjunction with a series of basis sets, (aug-)cc-pVxZ(-PP), x=D, T, Q, and 5 and cc-pwCVxZ(-PP), x=D, T, and Q. The calculated dissociation energy and the electron affinity of GaN are 2.12 and 1.84 eV, respectively, and those of Ga2N are 6.31 and 2.53 eV. The last value is in excellent agreement with a recent experimental value for the electron affinity of Ga2N of 2.506+/-0.008 eV. For such quality in the results to be achieved, the Ga 3d electrons had to be included in the correlation space. Moreover, when a basis set is used, which has not been developed for the number of the electrons which are correlated in a calculation, the quantities calculated need to be corrected for the basis set superposition error.
Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.
2012-01-01
We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587
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.
Chitwood, Daniel H.; Kumar, Ravi; Headland, Lauren R.; Ranjan, Aashish; Covington, Michael F.; Ichihashi, Yasunori; Fulop, Daniel; Jiménez-Gómez, José M.; Peng, Jie; Maloof, Julin N.; Sinha, Neelima R.
2013-01-01
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations. PMID:23872539
Optimal allocation of the limited oral cholera vaccine supply between endemic and epidemic settings
Moore, Sean M.; Lessler, Justin
2015-01-01
The World Health Organization (WHO) recently established a global stockpile of oral cholera vaccine (OCV) to be preferentially used in epidemic response (reactive campaigns) with any vaccine remaining after 1 year allocated to endemic settings. Hence, the number of cholera cases or deaths prevented in an endemic setting represents the minimum utility of these doses, and the optimal risk-averse response to any reactive vaccination request (i.e. the minimax strategy) is one that allocates the remaining doses between the requested epidemic response and endemic use in order to ensure that at least this minimum utility is achieved. Using mathematical models, we find that the best minimax strategy is to allocate the majority of doses to reactive campaigns, unless the request came late in the targeted epidemic. As vaccine supplies dwindle, the case for reactive use of the remaining doses grows stronger. Our analysis provides a lower bound for the amount of OCV to keep in reserve when responding to any request. These results provide a strategic context for the fulfilment of requests to the stockpile, and define allocation strategies that minimize the number of OCV doses that are allocated to suboptimal situations. PMID:26423441
Nonlocal games and optimal steering at the boundary of the quantum set
NASA Astrophysics Data System (ADS)
Zhen, Yi-Zheng; Goh, Koon Tong; Zheng, Yu-Lin; Cao, Wen-Fei; Wu, Xingyao; Chen, Kai; Scarani, Valerio
2016-08-01
The boundary between classical and quantum correlations is well characterized by linear constraints called Bell inequalities. It is much harder to characterize the boundary of the quantum set itself in the space of no-signaling correlations. For the points on the quantum boundary that violate maximally some Bell inequalities, J. Oppenheim and S. Wehner [Science 330, 1072 (2010), 10.1126/science.1192065] pointed out a complex property: Alice's optimal measurements steer Bob's local state to the eigenstate of an effective operator corresponding to its maximal eigenvalue. This effective operator is the linear combination of Bob's local operators induced by the coefficients of the Bell inequality, and it can be interpreted as defining a fine-grained uncertainty relation. It is natural to ask whether the same property holds for other points on the quantum boundary, using the Bell expression that defines the tangent hyperplane at each point. We prove that this is indeed the case for a large set of points, including some that were believed to provide counterexamples. The price to pay is to acknowledge that the Oppenheim-Wehner criterion does not respect equivalence under the no-signaling constraint: for each point, one has to look for specific forms of writing the Bell expressions.
Optimal allocation of the limited oral cholera vaccine supply between endemic and epidemic settings.
Moore, Sean M; Lessler, Justin
2015-10-06
The World Health Organization (WHO) recently established a global stockpile of oral cholera vaccine (OCV) to be preferentially used in epidemic response (reactive campaigns) with any vaccine remaining after 1 year allocated to endemic settings. Hence, the number of cholera cases or deaths prevented in an endemic setting represents the minimum utility of these doses, and the optimal risk-averse response to any reactive vaccination request (i.e. the minimax strategy) is one that allocates the remaining doses between the requested epidemic response and endemic use in order to ensure that at least this minimum utility is achieved. Using mathematical models, we find that the best minimax strategy is to allocate the majority of doses to reactive campaigns, unless the request came late in the targeted epidemic. As vaccine supplies dwindle, the case for reactive use of the remaining doses grows stronger. Our analysis provides a lower bound for the amount of OCV to keep in reserve when responding to any request. These results provide a strategic context for the fulfilment of requests to the stockpile, and define allocation strategies that minimize the number of OCV doses that are allocated to suboptimal situations.
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.
Legler, C R; Brown, N R; Dunbar, R A; Harness, M D; Nguyen, K; Oyewole, O; Collier, W B
2015-06-15
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. Copyright © 2015 Elsevier B.V. All rights reserved.
Zhang, Man; Zhao, Mengxi; Feng, Lijian; Luo, Xiao; Gao, Zhenting; Huang, Ying; Ardayfio, Ophelia; Zhang, Ji-Hu; Lin, Ying; Fan, Hong; Mi, Yuan; Li, Guobin; Liu, Lei; Feng, Leying; Luo, Fangjun; Teng, Lin; Qi, Wei; Ottl, Johannes; Lingel, Andreas; Bussiere, Dirksen E.; Yu, Zhengtian; Atadja, Peter; Lu, Chris; Li, En; Gu, Justin; Zhao, Kehao
2017-01-01
Polycomb repressive complex 2 (PRC2), a histone H3 lysine 27 methyltransferase, plays a key role in gene regulation and is a known epigenetics drug target for cancer therapy. The WD40 domain-containing protein EED is the regulatory subunit of PRC2. It binds to the tri-methylated lysine 27 of the histone H3 (H3K27me3), and through which stimulates the activity of PRC2 allosterically. Recently, we disclosed a novel PRC2 inhibitor EED226 which binds to the K27me3-pocket on EED and showed strong antitumor activity in xenograft mice model. Here, we further report the identification and validation of four other EED binders along with EED162, the parental compound of EED226. The crystal structures for all these five compounds in complex with EED revealed a common deep pocket induced by the binding of this diverse set of compounds. This pocket was created after significant conformational rearrangement of the aromatic cage residues (Y365, Y148 and F97) in the H3K27me3 binding pocket of EED, the width of which was delineated by the side chains of these rearranged residues. In addition, all five compounds interact with the Arg367 at the bottom of the pocket. Each compound also displays unique features in its interaction with EED, suggesting the dynamics of the H3K27me3 pocket in accommodating the binding of different compounds. Our results provide structural insights for rational design of novel EED binder for the inhibition of PRC2 complex activity. PMID:28072869
Hou, Bing-Bo; Yao, Yan; Wu, Ling-Min; Qiao, Yu; Zheng, Li-Hui; Ding, Li-Gang; Chen, Gang; Zhang, Shu
2015-05-05
Nonfluoroscopic three-dimensional electroanatomical system is widely used nowadays, but X-ray remains indispensable for complex electrophysiology procedures. This study aimed to evaluate the value of optimized parameter setting and different projection position to reduce X-ray radiation dose rates. From June 2013 to October 2013, 105 consecutive patients who underwent complex ablation were enrolled in the study. After the ablation, the radiation dose rates were measured by two different settings (default setting and optimized setting) with three projection positions (posteroanterior [PA] projection; left anterior oblique [LAO] 30° projection; and LAO 45° projection). The parameter of preset voltage, pulse width, critical voltage, peak voltage, noise reduction, edge enhancement, pulse rate, and dose per frame was modified in the optimized setting. The optimized setting reduced radiation dose rates by 87.5% (1.7 Gy/min vs. 13.6 Gy/min, P < 0.001) in PA, 87.3% (2.5 Gy/min vs. 19.7 Gy/min, P < 0.001) in LAO 30°, 85.9% (3.1 Gy/min vs. 22.1 Gy/min, P < 0.001) in LAO 45°. Increase the angle of projection position will increase the radiation dose rate. We can reduce X-ray radiation dose rates by adjusting the parameter setting of X-ray system. Avoiding oblique projection of large angle is another way to reduce X-ray radiation dose rates.
Use of an administrative data set to determine optimal scheduling of an alcohol intervention worker.
Peterson, Timothy A; Desmond, Jeffrey S; Cunningham, Rebecca
2012-06-01
Brief alcohol interventions are efficacious in reducing alcohol-related consequences among emergency department (ED) patients. Use of non-clinical staff may increase alcohol screening and intervention; however, optimal scheduling of an alcohol intervention worker (AIW) is unknown. Determine optimal scheduling of an AIW based on peak discharge time of alcohol-related ED visits. Discharge times for consecutive patients with an alcohol-related diagnosis were abstracted from an urban ED's administrative data set from September 2005 through August 2007. Queuing theory was used to identify optimal scheduling. Data for weekends and weekdays were analyzed separately. Stationary independent period-by-period analysis was performed for hourly periods. An M/M/s queuing model, for Markovian inter-arrival time/Markovian service time/and potentially more than one server, was developed for each hour assuming: 1) a single unlimited queue; 2) 75% of patients waited no longer than 30 min for intervention; 3) AIW spent an average 20 min/patient. Estimated average utilization/hour was calculated; if utilization/hour exceeded 25%, AIW staff was considered necessary. There were 2282 patient visits (mean age 38 years, range 11-84 years). Weekdays accounted for 45% of visits; weekends 55%. On weekdays, one AIW from 6:00 a.m.-9:00 a.m. (max utilization 42%/hour) would accommodate 28% of weekday alcohol-related patients. On weekends, 5:00 a.m.-11:00 a.m. (max utilization 50%), one AIW would cover 54% of all weekend alcohol-related visits. During other hours the utilization rate falls below 25%/hour. Evaluating 2 years of discharge data revealed that 30 h of dedicated AIW time--18 weekend hours (5:00 a.m.-11:00 a.m.), 12 weekday hours (6:00 a.m.-9:00 a.m.)--would allow maximal patient alcohol screening and intervention with minimal additional burden to clinical staff. Copyright © 2012 Elsevier Inc. All rights reserved.
Kashinski, D O; Chase, G M; Nelson, R G; Di Nallo, O E; Scales, A N; VanderLey, D L; Byrd, E F C
2017-03-23
We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.
Morita, Masato; Yabushita, Satoshi
2008-11-15
Within the framework of the complex basis function method, the photoionization cross sections of H(2)(+) and H(2) were calculated based on the variational principle for the frequency-dependent polarizabilities. In these calculations, complex orbital exponents of Gaussian-type basis functions for the final state continuum wavefunctions were fully optimized for each photon energy with the numerical Newton-Raphson method. In most cases, the use of only one or two complex Gaussian-type basis functions was enough to obtain excellent agreement with previous high precision calculations and available experimental results. However, there were a few cases, in which the use of complex basis functions having various angular momentum quantum numbers was crucial to obtain the accurate results. The behavior of the complex orbital exponents as a function of photon energy was discussed in relation to the scaling relation and the effective charge for photoelectron. The success of this method implies the effectiveness of the optimization of orbital exponents to reduce the number of basis functions and shows the possibility to calculate photoionization cross sections of general molecules using only Gaussian-type basis functions.
Defining the optimal animal model for translational research using gene set enrichment analysis.
Weidner, Christopher; Steinfath, Matthias; Opitz, Elisa; Oelgeschläger, Michael; Schönfelder, Gilbert
2016-08-01
The mouse is the main model organism used to study the functions of human genes because most biological processes in the mouse are highly conserved in humans. Recent reports that compared identical transcriptomic datasets of human inflammatory diseases with datasets from mouse models using traditional gene-to-gene comparison techniques resulted in contradictory conclusions regarding the relevance of animal models for translational research. To reduce susceptibility to biased interpretation, all genes of interest for the biological question under investigation should be considered. Thus, standardized approaches for systematic data analysis are needed. We analyzed the same datasets using gene set enrichment analysis focusing on pathways assigned to inflammatory processes in either humans or mice. The analyses revealed a moderate overlap between all human and mouse datasets, with average positive and negative predictive values of 48 and 57% significant correlations. Subgroups of the septic mouse models (i.e., Staphylococcus aureus injection) correlated very well with most human studies. These findings support the applicability of targeted strategies to identify the optimal animal model and protocol to improve the success of translational research. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.
Optimized settings for Nd:YAG laser treatments of leg telangiectasias.
Christiansen, Kaare; Drosner, Michael; Bjerring, Peter
2015-04-01
Telangiectasias of the lower extremities are very common. The objective of this study was to investigate whether the visual control of clinical signs for coagulation is needed to obtain an efficient treatment. A total of 28 pairs of close-to-identical telangiectasias located on their lower extremities of 14 Caucasian females were included in the study. One of the paired vessels was randomly treated with a theoretically optimized and clinically verified fixed fluence (FF). The fluence on the other vessel was manually adjusted to the lowest level that resulted in visual coagulation or obstruction of blood flow (judged fluence [JF]). One or two treatments were made. By the four-month follow-up the same high degree of clinically evaluated vessel clearance of 2.6 (0-4 scale) was obtained for both the FF- and JF-treated vessels (P > 0.95, power = 0.60). The JF-treated group showed a significant higher incidence of hyperpigmentation 39.3% versus 28.6% (P = 0.05). As the vessel clearance was equal in both groups, these results strongly indicate that the use of fixed, clinically proven standard device laser settings lead to fewer side effects and should be recommended as the most safe Nd:YAG laser treatment for leg telangiectasias.
Application of fuzzy sets to optimal reactive power planning with security constraints
Abdul-Rahman, K.H.; Shahidehpour, S.M. . Dept. of Electrical and Computer Engineering)
1994-05-01
This paper presents a mathematical formulation for the optimal reactive power planning taking into account the static security constraints and the non-probabilistic uncertainty in load values. The planning process is decomposed into investment and operation problems via the generalized Benders decomposition (GBD). Fixed and variable costs are considered in the investment problem. Linguistic declarations of load values in the operation problem are translated into possibility distribution functions. The operation problem is decomposed into 4 subproblems via Dantzig-Wolfe decomposition (DWD), and the modeling of multi-area power systems is considered by applying a second DWD to each subproblem, leading to a significant reduction in its dimensions for personal computer applications. Voltage constraints within each area are modeled as fuzzy sets for the static security analysis by biasing the final solution towards desired values of variables within their given ranges. The overall solution is a compromise between economics (lower investment and operation costs) and security (tighter feasible region). Numerical examples for the applicability of the proposed approach to multi-area power systems are discussed.
Sun, Guanchen; Nematollahi, Alireza; Nadvi, Naveed A; Kwan, Ann H; Jeffries, Cy M; Church, W Bret
2016-05-01
Kynurenine aminotransferase (KAT) is a pyridoxal-5'-phosphate (PLP) dependent enzyme that catalyses kynurenine (KYN) to kynurenic acid (KYNA), a neuroactive product in the tryptophan metabolic pathway. Evidence suggests that abnormal levels of KYNA are involved in many neurodegenerative diseases such as Parkinson's disease, Huntington's disease, Alzheimer's disease and schizophrenia. Reducing KYNA production through inhibiting kynurenine aminotransferase 2 (KAT2) would be a promising approach to understanding and treating the related neurological and mental disorders. In this study we used an optimized codon sequence to overexpress histidine-tagged human KAT2 (hKAT2) using an Escherichia coli expression system. After a single step of Ni-NTA based purification the purified protein (>95%) was confirmed to be active by an HPLC based activity assay and was crystallized using the hanging-drop vapour diffusion method. The crystal system represents a novel space group, and a complete X-ray diffraction data set was collected to 1.83 Å resolution, and higher resolution data than for any reported native human KAT2 structure. The optimised method of protein production provides a fast and reliable technique to generate large quantities of active human KAT2 suitable for future small-molecule lead compound screening and structural design work. Copyright © 2016 Elsevier Inc. All rights reserved.
Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review
NASA Astrophysics Data System (ADS)
Wu, Xing-Gang; Ma, Yang; Wang, Sheng-Quan; Fu, Hai-Bing; Ma, Hong-Hao; Brodsky, Stanley J.; Mojaza, Matin
2015-12-01
A valid prediction for a physical observable from quantum field theory should be independent of the choice of renormalization scheme—this is the primary requirement of renormalization group invariance (RGI). Satisfying scheme invariance is a challenging problem for perturbative QCD (pQCD), since a truncated perturbation series does not automatically satisfy the requirements of the renormalization group. In a previous review, we provided a general introduction to the various scale setting approaches suggested in the literature. As a step forward, in the present review, we present a discussion in depth of two well-established scale-setting methods based on RGI. One is the ‘principle of maximum conformality’ (PMC) in which the terms associated with the β-function are absorbed into the scale of the running coupling at each perturbative order; its predictions are scheme and scale independent at every finite order. The other approach is the ‘principle of minimum sensitivity’ (PMS), which is based on local RGI; the PMS approach determines the optimal renormalization scale by requiring the slope of the approximant of an observable to vanish. In this paper, we present a detailed comparison of the PMC and PMS procedures by analyzing two physical observables R e+e- and Γ(H\\to b\\bar{b}) up to four-loop order in pQCD. At the four-loop level, the PMC and PMS predictions for both observables agree within small errors with those of conventional scale setting assuming a physically-motivated scale, and each prediction shows small scale dependences. However, the convergence of the pQCD series at high orders, behaves quite differently: the PMC displays the best pQCD convergence since it eliminates divergent renormalon terms; in contrast, the convergence of the PMS prediction is questionable, often even worse than the conventional prediction based on an arbitrary guess for the renormalization scale. PMC predictions also have the property that any residual dependence on
Renormalization group invariance and optimal QCD renormalization scale-setting: a key issues review.
Wu, Xing-Gang; Ma, Yang; Wang, Sheng-Quan; Fu, Hai-Bing; Ma, Hong-Hao; Brodsky, Stanley J; Mojaza, Matin
2015-12-01
A valid prediction for a physical observable from quantum field theory should be independent of the choice of renormalization scheme--this is the primary requirement of renormalization group invariance (RGI). Satisfying scheme invariance is a challenging problem for perturbative QCD (pQCD), since a truncated perturbation series does not automatically satisfy the requirements of the renormalization group. In a previous review, we provided a general introduction to the various scale setting approaches suggested in the literature. As a step forward, in the present review, we present a discussion in depth of two well-established scale-setting methods based on RGI. One is the 'principle of maximum conformality' (PMC) in which the terms associated with the β-function are absorbed into the scale of the running coupling at each perturbative order; its predictions are scheme and scale independent at every finite order. The other approach is the 'principle of minimum sensitivity' (PMS), which is based on local RGI; the PMS approach determines the optimal renormalization scale by requiring the slope of the approximant of an observable to vanish. In this paper, we present a detailed comparison of the PMC and PMS procedures by analyzing two physical observables R(e+e-) and [Formula: see text] up to four-loop order in pQCD. At the four-loop level, the PMC and PMS predictions for both observables agree within small errors with those of conventional scale setting assuming a physically-motivated scale, and each prediction shows small scale dependences. However, the convergence of the pQCD series at high orders, behaves quite differently: the PMC displays the best pQCD convergence since it eliminates divergent renormalon terms; in contrast, the convergence of the PMS prediction is questionable, often even worse than the conventional prediction based on an arbitrary guess for the renormalization scale. PMC predictions also have the property that any residual dependence on the choice