Rational Density Functional Selection Using Game Theory.

PubMed

McAnanama-Brereton, Suzanne; Waller, Mark P

2018-01-22

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density functionals and basis sets. Traditionally, a particular density functional is chosen on the basis of the level of user expertise (i.e., subjective experiences). Herein we circumvent the user-centric selection procedure by describing a novel approach for objectively selecting a particular functional for a given application. We achieve this by employing game theory to identify optimal functional/basis set combinations. A three-player (accuracy, complexity, and similarity) game is devised, through which Nash equilibrium solutions can be obtained. This approach has the advantage that results can be systematically improved by enlarging the underlying knowledge base, and the deterministic selection procedure mathematically justifies the density functional and basis set selections.

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

NASA Astrophysics Data System (ADS)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Use of an auxiliary basis set to describe the polarization in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2014-03-01

We developed a dual basis approach within the fragment molecular orbital formalism enabling efficient and accurate use of large basis sets. The method was tested on water clusters and polypeptides and applied to perform geometry optimization of chignolin (PDB: 1UAO) in solution at the level of DFT/6-31++G∗∗, obtaining a structure in agreement with experiment (RMSD of 0.4526 Å). The polarization in polypeptides is discussed with a comparison of the α-helix and β-strand.

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

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

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

Proper Orthogonal Decomposition in Optimal Control of Fluids

NASA Technical Reports Server (NTRS)

Ravindran, S. S.

1999-01-01

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

A Novel Consensus-Based Particle Swarm Optimization-Assisted Trust-Tech Methodology for Large-Scale Global Optimization.

PubMed

Zhang, Yong-Feng; Chiang, Hsiao-Dong

2017-09-01

A novel three-stage methodology, termed the "consensus-based particle swarm optimization (PSO)-assisted Trust-Tech methodology," to find global optimal solutions for nonlinear optimization problems is presented. It is composed of Trust-Tech methods, consensus-based PSO, and local optimization methods that are integrated to compute a set of high-quality local optimal solutions that can contain the global optimal solution. The proposed methodology compares very favorably with several recently developed PSO algorithms based on a set of small-dimension benchmark optimization problems and 20 large-dimension test functions from the CEC 2010 competition. The analytical basis for the proposed methodology is also provided. Experimental results demonstrate that the proposed methodology can rapidly obtain high-quality optimal solutions that can contain the global optimal solution. The scalability of the proposed methodology is promising.

Employing general fit-bases for construction of potential energy surfaces with an adaptive density-guided approach

NASA Astrophysics Data System (ADS)

Klinting, Emil Lund; Thomsen, Bo; Godtliebsen, Ian Heide; Christiansen, Ove

2018-02-01

We present an approach to treat sets of general fit-basis functions in a single uniform framework, where the functional form is supplied on input, i.e., the use of different functions does not require new code to be written. The fit-basis functions can be used to carry out linear fits to the grid of single points, which are generated with an adaptive density-guided approach (ADGA). A non-linear conjugate gradient method is used to optimize non-linear parameters if such are present in the fit-basis functions. This means that a set of fit-basis functions with the same inherent shape as the potential cuts can be requested and no other choices with regards to the fit-basis functions need to be taken. The general fit-basis framework is explored in relation to anharmonic potentials for model systems, diatomic molecules, water, and imidazole. The behaviour and performance of Morse and double-well fit-basis functions are compared to that of polynomial fit-basis functions for unsymmetrical single-minimum and symmetrical double-well potentials. Furthermore, calculations for water and imidazole were carried out using both normal coordinates and hybrid optimized and localized coordinates (HOLCs). Our results suggest that choosing a suitable set of fit-basis functions can improve the stability of the fitting routine and the overall efficiency of potential construction by lowering the number of single point calculations required for the ADGA. It is possible to reduce the number of terms in the potential by choosing the Morse and double-well fit-basis functions. These effects are substantial for normal coordinates but become even more pronounced if HOLCs are used.

Correlation consistent valence basis sets for use with the Stuttgart-Dresden-Bonn relativistic effective core potentials: The atoms Ga-Kr and In-Xe

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Sundermann, Andreas

2001-02-01

We propose large-core correlation-consistent (cc) pseudopotential basis sets for the heavy p-block elements Ga-Kr and In-Xe. The basis sets are of cc-pVTZ and cc-pVQZ quality, and have been optimized for use with the large-core (valence-electrons only) Stuttgart-Dresden-Bonn (SDB) relativistic pseudopotentials. Validation calculations on a variety of third-row and fourth-row diatomics suggest them to be comparable in quality to the all-electron cc-pVTZ and cc-pVQZ basis sets for lighter elements. Especially the SDB-cc-pVQZ basis set in conjunction with a core polarization potential (CPP) yields excellent agreement with experiment for compounds of the later heavy p-block elements. For accurate calculations on Ga (and, to a lesser extent, Ge) compounds, explicit treatment of 13 valence electrons appears to be desirable, while it seems inevitable for In compounds. For Ga and Ge, we propose correlation consistent basis sets extended for (3d) correlation. For accurate calculations on organometallic complexes of interest to homogenous catalysis, we recommend a combination of the standard cc-pVTZ basis set for first- and second-row elements, the presently derived SDB-cc-pVTZ basis set for heavier p-block elements, and for transition metals, the small-core [6s5p3d] Stuttgart-Dresden basis set-relativistic effective core potential combination supplemented by (2f1g) functions with exponents given in the Appendix to the present paper.

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

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

PubMed

Hill, J Grant

2013-09-30

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

Some considerations about Gaussian basis sets for electric property calculations

NASA Astrophysics Data System (ADS)

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

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

Novel silicon-carbon fullerene-like nanostructures: an Ab initio study on the stability of Si54C6 and Si60C6 clusters.

PubMed

Srinivasan, Aravind; Ray, Asok K

2006-01-01

Silicon fullerene like nanostructures with six carbon atoms on the surface of Si60 cages by substitution, as well as inside the cage at various symmetry orientations have been studied within the generalized gradient approximation to density functional theory. Full geometry optimizations have been performed without any symmetry constraints using the Gaussian 03 suite of programs and the LANL2DZ basis set. Thus, for the silicon atom, the Hay-Wadt pseudopotential with the associated basis set are used for the core electrons and the valence electrons, respectively. For the carbon atom, the Dunning/Huzinaga double zeta basis set is employed. Electronic and geometric properties of the nanostructures are presented and discussed in detail. It was found that optimized silicon-carbon fullerene like nanostructures have increased stability compared to bare Si60 cage and the stability depends on the orientation of carbon atoms, as well as on the nature of bonding between silicon and carbon atoms and also on the carbon-carbon bonding.

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

PubMed

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

2013-09-01

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

An Algebraic Approach to the Study and Optimization of the Set of Rules of a Conditional Rewrite System

NASA Astrophysics Data System (ADS)

Makhortov, S. D.

2018-03-01

An algebraic system containing the semantics of a set of rules of the conditional equational theory (or the conditional term rewriting system) is introduced. The following basic questions are considered for the given model: existence of logical closure, structure of logical closure, possibility of equivalent transformations, and construction of logical reduction. The obtained results can be applied to the analysis and automatic optimization of the corresponding set of rules. The basis for the given research is the theory of lattices and binary relations.

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).

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

PubMed

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

2014-04-08

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

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

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

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

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

PubMed

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

2015-07-15

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

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

PubMed Central

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

2016-01-01

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

An optimized proportional-derivative controller for the human upper extremity with gravity.

PubMed

Jagodnik, Kathleen M; Blana, Dimitra; van den Bogert, Antonie J; Kirsch, Robert F

2015-10-15

When Functional Electrical Stimulation (FES) is used to restore movement in subjects with spinal cord injury (SCI), muscle stimulation patterns should be selected to generate accurate and efficient movements. Ideally, the controller for such a neuroprosthesis will have the simplest architecture possible, to facilitate translation into a clinical setting. In this study, we used the simulated annealing algorithm to optimize two proportional-derivative (PD) feedback controller gain sets for a 3-dimensional arm model that includes musculoskeletal dynamics and has 5 degrees of freedom and 22 muscles, performing goal-oriented reaching movements. Controller gains were optimized by minimizing a weighted sum of position errors, orientation errors, and muscle activations. After optimization, gain performance was evaluated on the basis of accuracy and efficiency of reaching movements, along with three other benchmark gain sets not optimized for our system, on a large set of dynamic reaching movements for which the controllers had not been optimized, to test ability to generalize. Robustness in the presence of weakened muscles was also tested. The two optimized gain sets were found to have very similar performance to each other on all metrics, and to exhibit significantly better accuracy, compared with the three standard gain sets. All gain sets investigated used physiologically acceptable amounts of muscular activation. It was concluded that optimization can yield significant improvements in controller performance while still maintaining muscular efficiency, and that optimization should be considered as a strategy for future neuroprosthesis controller design. Published by Elsevier Ltd.

Optimization of selected molecular orbitals in group basis sets.

PubMed

Ferenczy, György G; Adams, William H

2009-04-07

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

Model's sparse representation based on reduced mixed GMsFE basis methods

NASA Astrophysics Data System (ADS)

Jiang, Lijian; Li, Qiuqi

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a large number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.

Model's sparse representation based on reduced mixed GMsFE basis methods

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

Jiang, Lijian, E-mail: ljjiang@hnu.edu.cn; Li, Qiuqi, E-mail: qiuqili@hnu.edu.cn

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a largemore » number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.« less

[Application of simulated annealing method and neural network on optimizing soil sampling schemes based on road distribution].

PubMed

Han, Zong-wei; Huang, Wei; Luo, Yun; Zhang, Chun-di; Qi, Da-cheng

2015-03-01

Taking the soil organic matter in eastern Zhongxiang County, Hubei Province, as a research object, thirteen sample sets from different regions were arranged surrounding the road network, the spatial configuration of which was optimized by the simulated annealing approach. The topographic factors of these thirteen sample sets, including slope, plane curvature, profile curvature, topographic wetness index, stream power index and sediment transport index, were extracted by the terrain analysis. Based on the results of optimization, a multiple linear regression model with topographic factors as independent variables was built. At the same time, a multilayer perception model on the basis of neural network approach was implemented. The comparison between these two models was carried out then. The results revealed that the proposed approach was practicable in optimizing soil sampling scheme. The optimal configuration was capable of gaining soil-landscape knowledge exactly, and the accuracy of optimal configuration was better than that of original samples. This study designed a sampling configuration to study the soil attribute distribution by referring to the spatial layout of road network, historical samples, and digital elevation data, which provided an effective means as well as a theoretical basis for determining the sampling configuration and displaying spatial distribution of soil organic matter with low cost and high efficiency.

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

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

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

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

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

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

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

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

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

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

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

DOE PAGES

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

2017-01-27

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

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

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Tables Of Gaussian-Type Orbital Basis Functions

NASA Technical Reports Server (NTRS)

Partridge, Harry

1992-01-01

NASA technical memorandum contains tables of estimated Hartree-Fock wave functions for atoms lithium through neon and potassium through krypton. Sets contain optimized Gaussian-type orbital exponents and coefficients, and near Hartree-Fock quality. Orbital exponents optimized by minimizing restricted Hartree-Fock energy via scaled Newton-Raphson scheme in which Hessian evaluated numerically by use of analytically determined gradients.

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

PubMed

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

2008-06-21

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

The structure and energetics of Cr(CO)6 and Cr(CO)5

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Liu, Bowen; Lindh, Roland

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD, and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD, and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used. Calculations using larger basis sets reduce the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. In the largest basis set, the total CO binding energy of Cr(CO)6 is estimated to be 140 kcal/mol at the CCSD(T) level of theory, or about 86 percent of the experimental value. The remaining discrepancy between the experimental and theoretical value is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive set (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

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

PubMed Central

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

2017-01-01

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

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

PubMed Central

Kong, Wenwen; Zhang, Chu; Huang, Weihao

2018-01-01

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

How to calculate H3 better.

PubMed

Pavanello, Michele; Tung, Wei-Cheng; Adamowicz, Ludwik

2009-11-14

Efficient optimization of the basis set is key to achieving a very high accuracy in variational calculations of molecular systems employing basis functions that are explicitly dependent on the interelectron distances. In this work we present a method for a systematic enlargement of basis sets of explicitly correlated functions based on the iterative-complement-interaction approach developed by Nakatsuji [Phys. Rev. Lett. 93, 030403 (2004)]. We illustrate the performance of the method in the variational calculations of H(3) where we use explicitly correlated Gaussian functions with shifted centers. The total variational energy (-1.674 547 421 Hartree) and the binding energy (-15.74 cm(-1)) obtained in the calculation with 1000 Gaussians are the most accurate results to date.

Optimizing structure of complex technical system by heterogeneous vector criterion in interval form

NASA Astrophysics Data System (ADS)

Lysenko, A. V.; Kochegarov, I. I.; Yurkov, N. K.; Grishko, A. K.

2018-05-01

The article examines the methods of development and multi-criteria choice of the preferred structural variant of the complex technical system at the early stages of its life cycle in the absence of sufficient knowledge of parameters and variables for optimizing this structure. The suggested methods takes into consideration the various fuzzy input data connected with the heterogeneous quality criteria of the designed system and the parameters set by their variation range. The suggested approach is based on the complex use of methods of interval analysis, fuzzy sets theory, and the decision-making theory. As a result, the method for normalizing heterogeneous quality criteria has been developed on the basis of establishing preference relations in the interval form. The method of building preferential relations in the interval form on the basis of the vector of heterogeneous quality criteria suggest the use of membership functions instead of the coefficients considering the criteria value. The former show the degree of proximity of the realization of the designed system to the efficient or Pareto optimal variants. The study analyzes the example of choosing the optimal variant for the complex system using heterogeneous quality criteria.

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

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-09-01

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

Electronic Structure and Bonding in Transition Metal Inorganic and Organometallic Complexes: New Basis Sets, Linear Semibridging Carbonyls and Thiocarbonyls, and Oxidative Addition of Molecular Hydrogen to Square - Iridium Complexes.

NASA Astrophysics Data System (ADS)

Sargent, Andrew Landman

Approximate molecular orbital and ab initio quantum chemical techniques are used to investigate the electronic structure, bonding and reactivity of several transition metal inorganic and organometallic complexes. Modest-sized basis sets are developed for the second-row transition metal atoms and are designed for use in geometry optimizations of inorganic and organometallic complexes incorporating these atoms. The basis sets produce optimized equilibrium geometries which are slightly better than those produced with standard 3-21G basis sets, and which are significantly better than those produced with effective core potential basis sets. Linear semibridging carbonyl ligands in heterobimetallic complexes which contain a coordinatively unsaturated late transition metal center are found to accept electron density from, rather than donate electron density to, these centers. Only when the secondary metal center is a coordinatively unsaturated early transition metal center does the semibridging ligand donate electron density to this center. Large holes in the d shell around the metal center are more prominent and prevalent in early than in late transition metal centers, and the importance of filling in these holes outweighs the importance of mitigating the charge imbalance due to the dative metal-metal interaction. Semibridging thiocarbonyl ligands are more effective donors of electron density than the carbonyl ligands since the occupied donor orbitals of pi symmetry are higher in energy. The stereoselectivity of H_2 addition to d^8 square-planar transition metal complexes is controlled by the interactions between the ligands in the plane of addition and the concentrations of electronic charge around the metal center as the complex evolves from a four-coordinate to a six-coordinate species. Electron -withdrawing ligands help stabilize the five-coordinate species while strong electron donor ligands contribute only to the destabilizing repulsive interactions. The relative thermodynamic stabilities of the final complexes can be predicted based on the relative orientations of the strongest sigma-donor ligands.

Computational studies of metal-metal and metal-ligand interactions

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.

1992-01-01

The geometric structure of Cr(CO)6 is optimized at the modified coupled-pair functional (MCPF), single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory (including a perturbational estimate for connected triple excitations), and the force constants for the totally symmetric representation are determined. The geometry of Cr(CO)5 is partially optimized at the MCPF, CCSD and CCSD(T) levels of theory. Comparison with experimental data shows that the CCSD(T) method gives the best results for the structures and force constants, and that remaining errors are probably due to deficiencies in the one-particle basis sets used for CO. A detailed comparison of the properties of free CO is therefore given, at both the MCPF and CCSD/CCSD(T) levels of treatment, using a variety of basis sets. With very large one-particle basis sets, the SSCD(T) method gives excellent results for the bond distance, dipole moment and harmonic frequency of free CO. The total binding energies of Cr(CO)6 and Cr(CO)5 are also determined at the MCPF, CCSD and CCSD(T) levels of theory. The CCSD(T) method gives a much larger total binding energy than either the MCPF or CCSD methods. An analysis of the basis set superposition error (BSSE) at the MCPF level of treatment points out limitations in the one-particle basis used here and in a previous study. Calculations using larger basis sets reduced the BSSE, but the total binding energy of Cr(CO)6 is still significantly smaller than the experimental value, although the first CO bond dissociation energy of Cr(CO)6 is well described. An investigation of 3s3p correlation reveals only a small effect. The remaining discrepancy between the experimental and theoretical total binding energy of Cr(CO)6 is probably due to limitations in the one-particle basis, rather than limitations in the correlation treatment. In particular an additional d function and an f function on each C and O are needed to obtain quantitative results. This is underscored by the fact that even using a very large primitive se (1042 primitive functions contracted to 300 basis functions), the superposition error for the total binding energy of Cr(CO)6 is 22 kcal/mol at the MCPF level of treatment.

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

NASA Astrophysics Data System (ADS)

Lombardini, Richard; Nowara, Ewa; Johnson, Bruce

2015-03-01

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

Multiple crack detection in 3D using a stable XFEM and global optimization

NASA Astrophysics Data System (ADS)

Agathos, Konstantinos; Chatzi, Eleni; Bordas, Stéphane P. A.

2018-02-01

A numerical scheme is proposed for the detection of multiple cracks in three dimensional (3D) structures. The scheme is based on a variant of the extended finite element method (XFEM) and a hybrid optimizer solution. The proposed XFEM variant is particularly well-suited for the simulation of 3D fracture problems, and as such serves as an efficient solution to the so-called forward problem. A set of heuristic optimization algorithms are recombined into a multiscale optimization scheme. The introduced approach proves effective in tackling the complex inverse problem involved, where identification of multiple flaws is sought on the basis of sparse measurements collected near the structural boundary. The potential of the scheme is demonstrated through a set of numerical case studies of varying complexity.

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

PubMed

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

2017-02-15

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

Synthesis, characterization and theoretical studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole

NASA Astrophysics Data System (ADS)

Saglam, S.; Disli, A.; Erdogdu, Y.; Marchewka, M. K.; Kanagathara, N.; Bay, B.; Güllüoğlu, M. T.

2015-01-01

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, 1H NMR, 13C-APT and LC-MS spectroscopy techniques. The FT-IR, 1H NMR and 13C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G**, cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G** basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities.

Synthesis, characterization and theoretical studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole.

PubMed

Saglam, S; Disli, A; Erdogdu, Y; Marchewka, M K; Kanagathara, N; Bay, B; Güllüoğlu, M T

2015-01-25

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, (1)H NMR, (13)C-APT and LC-MS spectroscopy techniques. The FT-IR, (1)H NMR and (13)C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G(**), cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G(**) basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities. Copyright © 2014 Elsevier B.V. All rights reserved.

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes

NASA Astrophysics Data System (ADS)

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-01

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol-1. The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes.

PubMed

Maranzana, Andrea; Giordana, Anna; Indarto, Antonius; Tonachini, Glauco; Barone, Vincenzo; Causà, Mauro; Pavone, Michele

2013-12-28

Our purpose is to identify a computational level sufficiently dependable and affordable to assess trends in the interaction of a variety of radical or closed shell unsaturated hydro-carbons A adsorbed on soot platelet models B. These systems, of environmental interest, would unavoidably have rather large sizes, thus prompting to explore in this paper the performances of relatively low-level computational methods and compare them with higher-level reference results. To this end, the interaction of three complexes between non-polar species, vinyl radical, ethyne, or ethene (A) with benzene (B) is studied, since these species, involved themselves in growth processes of polycyclic aromatic hydrocarbons (PAHs) and soot particles, are small enough to allow high-level reference calculations of the interaction energy ΔEAB. Counterpoise-corrected interaction energies ΔEAB are used at all stages. (1) Density Functional Theory (DFT) unconstrained optimizations of the A-B complexes are carried out, using the B3LYP-D, ωB97X-D, and M06-2X functionals, with six basis sets: 6-31G(d), 6-311 (2d,p), and 6-311++G(3df,3pd); aug-cc-pVDZ and aug-cc-pVTZ; N07T. (2) Then, unconstrained optimizations by Møller-Plesset second order Perturbation Theory (MP2), with each basis set, allow subsequent single point Coupled Cluster Singles Doubles and perturbative estimate of the Triples energy computations with the same basis sets [CCSD(T)//MP2]. (3) Based on an additivity assumption of (i) the estimated MP2 energy at the complete basis set limit [EMP2/CBS] and (ii) the higher-order correlation energy effects in passing from MP2 to CCSD(T) at the aug-cc-pVTZ basis set, ΔECC-MP, a CCSD(T)/CBS estimate is obtained and taken as a computational energy reference. At DFT, variations in ΔEAB with basis set are not large for the title molecules, and the three functionals perform rather satisfactorily even with rather small basis sets [6-31G(d) and N07T], exhibiting deviation from the computational reference of less than 1 kcal mol(-1). The zero-point vibrational energy corrected estimates Δ(EAB+ZPE), obtained with the three functionals and the 6-31G(d) and N07T basis sets, are compared with experimental D0 measures, when available. In particular, this comparison is finally extended to the naphthalene and coronene dimers and to three π-π associations of different PAHs (R, made by 10, 16, or 24 C atoms) and P (80 C atoms).

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

PubMed

Zhu, Wuming; Trickey, S B

2017-12-28

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

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

NASA Astrophysics Data System (ADS)

Zhu, Wuming; Trickey, S. B.

2017-12-01

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

Evaluations of Some Scheduling Algorithms for Hard Real-Time Systems

DTIC Science & Technology

1990-06-01

construct because the mechanism is a dispatching procedure. Since all nonpreemptive schedules are contained in the set of all preemptive schedules, the...optimal value of Tmax in the preemptive case is at least a lower bound on the optimal Tmax for the nonpreemptive schedules. This principle is the basis...23 b. Nonpreemptable Version .............................................. 24 4. The Minimize Maximum Tardiness with Earliest Start

High-level ab initio studies of the complex formed between CO and O2

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2017-05-01

The explicitly correlated CCSD(T)-F12 method with VXZ-F12 basis sets was used to find the most stable structures of the van der Waals CO-O2 complexes. With geometry optimizations performed up to the quadruple-zeta level and basis set extrapolation, the calculated interaction energies for the triplet complexes are 123 cm-1 for the H complex in Cs symmetry (slipped near-parallel structure), 118 cm-1 for the X complex, also in Cs symmetry (perpendicular alignment) and 116 cm-1 for the CO-O2 T complex in C2v symmetry. The corresponding CCSD(T)-F12 results using the aug-cc-pVXZ basis sets are nearly the same. Similar calculations were performed for the CO-O2 singlet complexes, which are shown to have much higher stabilization energies, the highest being 206 cm-1 for the X complex.

Spectroscopic (FT-IR and UV-Vis) and theoretical (HF and DFT) investigation of 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline

NASA Astrophysics Data System (ADS)

Ceylan, Ümit; Tarı, Gonca Özdemir; Gökce, Halil; Ağar, Erbil

2016-04-01

Crystal structure of the title compound, 2-Ethyl-N-[(5-nitrothiophene-2-yl)methylidene]aniline, C13H12N2O2S, has been synthesized and characterized by FT-IR and UV-Vis spectrum. The compound crystallized in the monoclinic space group P 21/c with a = 11.3578 (4) Å, b = 7.4923 (2) Å, c = 14.9676 (6) Å and β = 99.589 (3)° and Z = 4 in the unit cell. The molecular geometry was also calculated using the Gaussian 03 software and structure was optimized using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set in ground state. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311++G(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. It was seen that the optimized structure was in excellent agreement with the X-ray crystal structure. The energetic behaviors of the title compound in solvent media were examined using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set applying the polarizable continuum model (PCM). In addition, the molecular orbitals (FMOs) analysis, molecular electrostatic potential (MEP), nonlinear optical and thermodynamic properties of the title compound were performed using the same methods with the 6-311++G(d,p) basis set.

Optimization of Turbine Blade Design for Reusable Launch Vehicles

NASA Technical Reports Server (NTRS)

Shyy, Wei

1998-01-01

To facilitate design optimization of turbine blade shape for reusable launching vehicles, appropriate techniques need to be developed to process and estimate the characteristics of the design variables and the response of the output with respect to the variations of the design variables. The purpose of this report is to offer insight into developing appropriate techniques for supporting such design and optimization needs. Neural network and polynomial-based techniques are applied to process aerodynamic data obtained from computational simulations for flows around a two-dimensional airfoil and a generic three- dimensional wing/blade. For the two-dimensional airfoil, a two-layered radial-basis network is designed and trained. The performances of two different design functions for radial-basis networks, one based on the accuracy requirement, whereas the other one based on the limit on the network size. While the number of neurons needed to satisfactorily reproduce the information depends on the size of the data, the neural network technique is shown to be more accurate for large data set (up to 765 simulations have been used) than the polynomial-based response surface method. For the three-dimensional wing/blade case, smaller aerodynamic data sets (between 9 to 25 simulations) are considered, and both the neural network and the polynomial-based response surface techniques improve their performance as the data size increases. It is found while the relative performance of two different network types, a radial-basis network and a back-propagation network, depends on the number of input data, the number of iterations required for radial-basis network is less than that for the back-propagation network.

Optimal resource states for local state discrimination

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Somshubhro; Halder, Saronath; Nathanson, Michael

2018-02-01

We study the problem of locally distinguishing pure quantum states using shared entanglement as a resource. For a given set of locally indistinguishable states, we define a resource state to be useful if it can enhance local distinguishability and optimal if it can distinguish the states as well as global measurements and is also minimal with respect to a partial ordering defined by entanglement and dimension. We present examples of useful resources and show that an entangled state need not be useful for distinguishing a given set of states. We obtain optimal resources with explicit local protocols to distinguish multipartite Greenberger-Horne-Zeilinger and graph states and also show that a maximally entangled state is an optimal resource under one-way local operations and classical communication to distinguish any bipartite orthonormal basis which contains at least one entangled state of full Schmidt rank.

An Optimization-Based Approach to Determine System Requirements Under Multiple-Domain Specific Uncertainties

DTIC Science & Technology

2016-04-30

determining the optimal design requirements of a new system, which will operate along with other existing systems to provide a set of overarching...passenger airline transportation (Mane et al., 2007; Govindaraju et al., 2015). Uncertainty in Fleet Operations The uncertainty associated with the...demand can provide the basis for a commercial passenger airline problem. The operations of the commercial air travel industry differ from military

Evolutionary optimization of radial basis function classifiers for data mining applications.

PubMed

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.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

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

PubMed

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

2013-12-23

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

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

PubMed

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

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

Feng, Rulin; Peterson, Kirk A.

2017-08-01

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

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

PubMed

Feng, Rulin; Peterson, Kirk A

2017-08-28

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

Pharmacodynamics of nicotine: implications for rational treatment of nicotine addiction.

PubMed

Benowitz, N L

1991-05-01

Rational treatment of the pharmacologic aspects of tobacco addiction includes nicotine substitution therapy. Understanding the pharmacodynamics of nicotine and its role in the addiction process provides a basis for rational therapeutic intervention. Pharmacodynamic considerations are discussed in relation to the elements of smoking cessation therapy: setting objectives, selecting appropriate medication and dosing form, selecting the optimal doses and dosage regimens, assessing therapeutic outcome, and adjusting therapy to optimize benefits and minimize risks.

Large-scale quantum transport calculations for electronic devices with over ten thousand atoms

NASA Astrophysics Data System (ADS)

Lu, Wenchang; Lu, Yan; Xiao, Zhongcan; Hodak, Miro; Briggs, Emil; Bernholc, Jerry

The non-equilibrium Green's function method (NEGF) has been implemented in our massively parallel DFT software, the real space multigrid (RMG) code suite. Our implementation employs multi-level parallelization strategies and fully utilizes both multi-core CPUs and GPU accelerators. Since the cost of the calculations increases dramatically with the number of orbitals, an optimal basis set is crucial for including a large number of atoms in the ``active device'' part of the simulations. In our implementation, the localized orbitals are separately optimized for each principal layer of the device region, in order to obtain an accurate and optimal basis set. As a large example, we calculated the transmission characteristics of a Si nanowire p-n junction. The nanowire is along (110) direction in order to minimize the number dangling bonds that are saturated by H atoms. Its diameter is 3 nm. The length of 24 nm is necessary because of the long-range screening length in Si. Our calculations clearly show the I-V characteristics of a diode, i.e., the current increases exponentially with forward bias and is near zero with backward bias. Other examples will also be presented, including three-terminal transistors and large sensor structures.

Spin Contamination Error in Optimized Geometry of Singlet Carbene (1A1) by Broken-Symmetry Method

NASA Astrophysics Data System (ADS)

Kitagawa, Yasutaka; Saito, Toru; Nakanishi, Yasuyuki; Kataoka, Yusuke; Matsui, Toru; Kawakami, Takashi; Okumura, Mitsutaka; Yamaguchi, Kizashi

2009-10-01

Spin contamination errors of a broken-symmetry (BS) method in optimized structural parameters of the singlet methylene (1A1) molecule are quantitatively estimated for the Hartree-Fock (HF) method, post-HF methods (CID, CCD, MP2, MP3, MP4(SDQ)), and a hybrid DFT (B3LYP) method. For the purpose, the optimized geometry by the BS method is compared with that of an approximate spin projection (AP) method. The difference between the BS and the AP methods is about 10-20° in the HCH angle. In order to examine the basis set dependency of the spin contamination error, calculated results by STO-3G, 6-31G*, and 6-311++G** are compared. The error depends on the basis sets, but the tendencies of each method are classified into two types. Calculated energy splitting values between the triplet and the singlet states (ST gap) indicate that the contamination of the stable triplet state makes the BS singlet solution stable and the ST gap becomes small. The energy order of the spin contamination error in the ST gap is estimated to be 10-1 eV.

A Grobner Basis Solution for Lightning Ground Flash Fraction Retrieval

NASA Technical Reports Server (NTRS)

Solakiewicz, Richard; Attele, Rohan; Koshak, William

2011-01-01

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

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

PubMed

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

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

NASA Astrophysics Data System (ADS)

Lee, Kyuho; Yu, Jaejun; Morikawa, Yoshitada

2007-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Computing single step operators of logic programming in radial basis function neural networks

NASA Astrophysics Data System (ADS)

Hamadneh, Nawaf; Sathasivam, Saratha; Choon, Ong Hong

2014-07-01

Logic programming is the process that leads from an original formulation of a computing problem to executable programs. A normal logic program consists of a finite set of clauses. A valuation I of logic programming is a mapping from ground atoms to false or true. The single step operator of any logic programming is defined as a function (Tp:I→I). Logic programming is well-suited to building the artificial intelligence systems. In this study, we established a new technique to compute the single step operators of logic programming in the radial basis function neural networks. To do that, we proposed a new technique to generate the training data sets of single step operators. The training data sets are used to build the neural networks. We used the recurrent radial basis function neural networks to get to the steady state (the fixed point of the operators). To improve the performance of the neural networks, we used the particle swarm optimization algorithm to train the networks.

Efficient evaluation of Coulomb integrals in a mixed Gaussian and plane-wave basis using the density fitting and Cholesky decomposition.

PubMed

Čársky, Petr; Čurík, Roman; Varga, Štefan

2012-03-21

The objective of this paper is to show that the density fitting (resolution of the identity approximation) can also be applied to Coulomb integrals of the type (k(1)(1)k(2)(1)|g(1)(2)g(2)(2)), where k and g symbols refer to plane-wave functions and gaussians, respectively. We have shown how to achieve the accuracy of these integrals that is needed in wave-function MO and density functional theory-type calculations using mixed Gaussian and plane-wave basis sets. The crucial issues for achieving such a high accuracy are application of constraints for conservation of the number electrons and components of the dipole moment, optimization of the auxiliary basis set, and elimination of round-off errors in the matrix inversion. © 2012 American Institute of Physics

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.

Optimization and analysis of large chemical kinetic mechanisms using the solution mapping method - Combustion of methane

NASA Technical Reports Server (NTRS)

Frenklach, Michael; Wang, Hai; Rabinowitz, Martin J.

1992-01-01

A method of systematic optimization, solution mapping, as applied to a large-scale dynamic model is presented. The basis of the technique is parameterization of model responses in terms of model parameters by simple algebraic expressions. These expressions are obtained by computer experiments arranged in a factorial design. The developed parameterized responses are then used in a joint multiparameter multidata-set optimization. A brief review of the mathematical background of the technique is given. The concept of active parameters is discussed. The technique is applied to determine an optimum set of parameters for a methane combustion mechanism. Five independent responses - comprising ignition delay times, pre-ignition methyl radical concentration profiles, and laminar premixed flame velocities - were optimized with respect to thirteen reaction rate parameters. The numerical predictions of the optimized model are compared to those computed with several recent literature mechanisms. The utility of the solution mapping technique in situations where the optimum is not unique is also demonstrated.

An unbiased Hessian representation for Monte Carlo PDFs.

PubMed

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

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

Criticism of generally accepted fundamentals and methodologies of traffic and transportation theory

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

Kerner, Boris S.

It is explained why the set of the fundamental empirical features of traffic breakdown (a transition from free flow to congested traffic) should be the empirical basis for any traffic and transportation theory that can be reliable used for control and optimization in traffic networks. It is shown that generally accepted fundamentals and methodologies of traffic and transportation theory are not consistent with the set of the fundamental empirical features of traffic breakdown at a highway bottleneck. To these fundamentals and methodologies of traffic and transportation theory belong (i) Lighthill-Whitham-Richards (LWR) theory, (ii) the General Motors (GM) model class (formore » example, Herman, Gazis et al. GM model, Gipps’s model, Payne’s model, Newell’s optimal velocity (OV) model, Wiedemann’s model, Bando et al. OV model, Treiber’s IDM, Krauß’s model), (iii) the understanding of highway capacity as a particular stochastic value, and (iv) principles for traffic and transportation network optimization and control (for example, Wardrop’s user equilibrium (UE) and system optimum (SO) principles). Alternatively to these generally accepted fundamentals and methodologies of traffic and transportation theory, we discuss three-phase traffic theory as the basis for traffic flow modeling as well as briefly consider the network breakdown minimization (BM) principle for the optimization of traffic and transportation networks with road bottlenecks.« less

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

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

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

Fourier spatial frequency analysis for image classification: training the training set

NASA Astrophysics Data System (ADS)

Johnson, Timothy H.; Lhamo, Yigah; Shi, Lingyan; Alfano, Robert R.; Russell, Stewart

2016-04-01

The Directional Fourier Spatial Frequencies (DFSF) of a 2D image can identify similarity in spatial patterns within groups of related images. A Support Vector Machine (SVM) can then be used to classify images if the inter-image variance of the FSF in the training set is bounded. However, if variation in FSF increases with training set size, accuracy may decrease as the size of the training set increases. This calls for a method to identify a set of training images from among the originals that can form a vector basis for the entire class. Applying the Cauchy product method we extract the DFSF spectrum from radiographs of osteoporotic bone, and use it as a matched filter set to eliminate noise and image specific frequencies, and demonstrate that selection of a subset of superclassifiers from within a set of training images improves SVM accuracy. Central to this challenge is that the size of the search space can become computationally prohibitive for all but the smallest training sets. We are investigating methods to reduce the search space to identify an optimal subset of basis training images.

Application of GA package in functional packaging

NASA Astrophysics Data System (ADS)

Belousova, D. A.; Noskova, E. E.; Kapulin, D. V.

2018-05-01

The approach to application program for the task of configuration of the elements of the commutation circuit for design of the radio-electronic equipment on the basis of the genetic algorithm is offered. The efficiency of the used approach for commutation circuits with different characteristics for computer-aided design on radio-electronic manufacturing is shown. The prototype of the computer-aided design subsystem on the basis of a package GA for R with a set of the general functions for optimization of multivariate models is programmed.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-09-28

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

Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

NASA Astrophysics Data System (ADS)

Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

DFT calculation and vibrational spectroscopic studies of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine

NASA Astrophysics Data System (ADS)

Premkumar, S.; Jawahar, A.; Mathavan, T.; Kumara Dhas, M.; Sathe, V. G.; Milton Franklin Benial, A.

2014-08-01

The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis.

The optimal design of UAV wing structure

NASA Astrophysics Data System (ADS)

Długosz, Adam; Klimek, Wiktor

2018-01-01

The paper presents an optimal design of UAV wing, made of composite materials. The aim of the optimization is to improve strength and stiffness together with reduction of the weight of the structure. Three different types of functionals, which depend on stress, stiffness and the total mass are defined. The paper presents an application of the in-house implementation of the evolutionary multi-objective algorithm in optimization of the UAV wing structure. Values of the functionals are calculated on the basis of results obtained from numerical simulations. Numerical FEM model, consisting of different composite materials is created. Adequacy of the numerical model is verified by results obtained from the experiment, performed on a tensile testing machine. Examples of multi-objective optimization by means of Pareto-optimal set of solutions are presented.

Protection coordination of the Kennedy Space Center electric distribution network

NASA Technical Reports Server (NTRS)

1976-01-01

A computer technique is described for visualizing the coordination and protection of any existing system of devices and settings by plotting the tripping characteristics of the involved devices on a common basis. The program determines the optimum settings of a given set of protective devices and configuration in the sense of the best expected coordinated operation of these devices. Subroutines are given for simulating time versus current characteristics of the different relays, circuit breakers, and fuses in the system; coordination index computation; protection checks; plotting; and coordination optimation.

A programmable optimization environment using the GAMESS-US and MERLIN/MCL packages. Applications on intermolecular interaction energies

NASA Astrophysics Data System (ADS)

Kalatzis, Fanis G.; Papageorgiou, Dimitrios G.; Demetropoulos, Ioannis N.

2006-09-01

The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of the molecular system, the size of the basis set and the method of electron correlation. Execution of the test run took approximately 5 min on a 2.8 GHz Intel Pentium CPU.

Swimming of a sphere in a viscous incompressible fluid with inertia

NASA Astrophysics Data System (ADS)

Felderhof, B. U.; Jones, R. B.

2017-08-01

The swimming of a sphere immersed in a viscous incompressible fluid with inertia is studied for surface modulations of small amplitude on the basis of the Navier-Stokes equations. The mean swimming velocity and the mean rate of dissipation are expressed as quadratic forms in term of the surface displacements. With a choice of a basis set of modes the quadratic forms correspond to two Hermitian matrices. Optimization of the mean swimming velocity for given rate of dissipation requires the solution of a generalized eigenvalue problem involving the two matrices. It is found for surface modulations of low multipole order that the optimal swimming efficiency depends in intricate fashion on a dimensionless scale number involving the radius of the sphere, the period of the cycle, and the kinematic viscosity of the fluid.

GAUSSIAN 76: An ab initio Molecular Orbital Program

DOE R&D Accomplishments Database

Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

1978-01-01

Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

NASA Astrophysics Data System (ADS)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.

On the origin independence of the Verdet tensor†

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

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

PubMed

Shukla, Manoj K; Poda, Aimee

2016-06-01

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

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

PubMed

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

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

The use of an integrated variable fuzzy sets in water resources management

NASA Astrophysics Data System (ADS)

Qiu, Qingtai; Liu, Jia; Li, Chuanzhe; Yu, Xinzhe; Wang, Yang

2018-06-01

Based on the evaluation of the present situation of water resources and the development of water conservancy projects and social economy, optimal allocation of regional water resources presents an increasing need in the water resources management. Meanwhile it is also the most effective way to promote the harmonic relationship between human and water. In view of the own limitations of the traditional evaluations of which always choose a single index model using in optimal allocation of regional water resources, on the basis of the theory of variable fuzzy sets (VFS) and system dynamics (SD), an integrated variable fuzzy sets model (IVFS) is proposed to address dynamically complex problems in regional water resources management in this paper. The model is applied to evaluate the level of the optimal allocation of regional water resources of Zoucheng in China. Results show that the level of allocation schemes of water resources ranging from 2.5 to 3.5, generally showing a trend of lower level. To achieve optimal regional management of water resources, this model conveys a certain degree of accessing water resources management, which prominently improve the authentic assessment of water resources management by using the eigenvector of level H.

An Efficient Radial Basis Function Mesh Deformation Scheme within an Adjoint-Based Aerodynamic Optimization Framework

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.

Recovery of sparse translation-invariant signals with continuous basis pursuit

PubMed Central

Ekanadham, Chaitanya; Tranchina, Daniel; Simoncelli, Eero

2013-01-01

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

Tractable Pareto Optimization of Temporal Preferences

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Network models for solving the problem of multicriterial adaptive optimization of investment projects control with several acceptable technologies

NASA Astrophysics Data System (ADS)

Shorikov, A. F.; Butsenko, E. V.

2017-10-01

This paper discusses the problem of multicriterial adaptive optimization the control of investment projects in the presence of several technologies. On the basis of network modeling proposed a new economic and mathematical model and a method for solving the problem of multicriterial adaptive optimization the control of investment projects in the presence of several technologies. Network economic and mathematical modeling allows you to determine the optimal time and calendar schedule for the implementation of the investment project and serves as an instrument to increase the economic potential and competitiveness of the enterprise. On a meaningful practical example, the processes of forming network models are shown, including the definition of the sequence of actions of a particular investment projecting process, the network-based work schedules are constructed. The calculation of the parameters of network models is carried out. Optimal (critical) paths have been formed and the optimal time for implementing the chosen technologies of the investment project has been calculated. It also shows the selection of the optimal technology from a set of possible technologies for project implementation, taking into account the time and cost of the work. The proposed model and method for solving the problem of managing investment projects can serve as a basis for the development, creation and application of appropriate computer information systems to support the adoption of managerial decisions by business people.

Doubly stochastic radial basis function methods

NASA Astrophysics Data System (ADS)

Yang, Fenglian; Yan, Liang; Ling, Leevan

2018-06-01

We propose a doubly stochastic radial basis function (DSRBF) method for function recoveries. Instead of a constant, we treat the RBF shape parameters as stochastic variables whose distribution were determined by a stochastic leave-one-out cross validation (LOOCV) estimation. A careful operation count is provided in order to determine the ranges of all the parameters in our methods. The overhead cost for setting up the proposed DSRBF method is O (n2) for function recovery problems with n basis. Numerical experiments confirm that the proposed method not only outperforms constant shape parameter formulation (in terms of accuracy with comparable computational cost) but also the optimal LOOCV formulation (in terms of both accuracy and computational cost).

Finite-dimensional compensators for infinite-dimensional systems via Galerkin-type approximation

NASA Technical Reports Server (NTRS)

Ito, Kazufumi

1990-01-01

In this paper existence and construction of stabilizing compensators for linear time-invariant systems defined on Hilbert spaces are discussed. An existence result is established using Galkerin-type approximations in which independent basis elements are used instead of the complete set of eigenvectors. A design procedure based on approximate solutions of the optimal regulator and optimal observer via Galerkin-type approximation is given and the Schumacher approach is used to reduce the dimension of compensators. A detailed discussion for parabolic and hereditary differential systems is included.

DFT calculation and vibrational spectroscopic studies of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine.

PubMed

Premkumar, S; Jawahar, A; Mathavan, T; Kumara Dhas, M; Sathe, V G; Milton Franklin Benial, A

2014-08-14

The molecular structure of 2-(tert-butoxycarbonyl (Boc) -amino)-5-bromopyridine (BABP) was optimized by the DFT/B3LYP method with 6-311G (d,p), 6-311++G (d,p) and cc-pVTZ basis sets using the Gaussian 09 program. The most stable optimized structure of the molecule was predicted by the DFT/B3LYP method with cc-pVTZ basis set. The vibrational frequencies, Mulliken atomic charge distribution, frontier molecular orbitals and thermodynamical parameters were calculated. These calculations were done at the ground state energy level of BABP without applying any constraint on the potential energy surface. The vibrational spectra were experimentally recorded using Fourier Transform-Infrared (FT-IR) and micro-Raman spectrometer. The computed vibrational frequencies were scaled by scale factors to yield a good agreement with observed experimental vibrational frequencies. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of Potential Energy Distribution (PED) calculation using the VEDA 4.0 program. The vibrational modes assignments were performed by using the animation option of GaussView 05 graphical interface for Gaussian program. The Mulliken atomic charge distribution was calculated for BABP molecule. The molecular reactivity and stability of BABP were also studied by frontier molecular orbitals (FMOs) analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Photobiomodulation therapy in the management of oral mucositis: search for the optimal clinical treatment parameters.

PubMed

Elad, Sharon; Arany, Praveen; Bensadoun, Rene-Jean; Epstein, Joel B; Barasch, Andrei; Raber-Durlacher, Judith

2018-05-22

This commentary attempts to clarify the setting of photobiomodulation (BPM) therapy in the management of oral mucositis. The suggested dose range balances efficacy data with our current understanding about PBM safety. The literature about the molecular basis of photobiomodulation and its controversial relationship to malignant transformation is briefly presented.

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Complete anatomy of {overline B_d} to {overline {text{K}}^{{*0}}} (→ Kπ) ℓ + ℓ - and its angular distribution

NASA Astrophysics Data System (ADS)

Matias, J.; Mescia, F.; Ramon, M.; Virto, J.

2012-04-01

We present a complete and optimal set of observables for the exclusive 4-body overline B meson decay {overline B_d} to {overline {text{K}}^{{*0}}} (→ Kπ) ℓ + ℓ -in the low dilepton mass region, that contains a maximal number of clean observables. This basis of observables is built in a systematic way. We show that all the previously defined observables and any observable that one can construct, can be expressed as a function of this basis. This set of observables contains all the information that can be extracted from the angular distribution in the cleanest possible way. We provide explicit expressions for the full and the uniangular distributions in terms of this basis. The conclusions presented here can be easily extended to the large- q 2 region. We study the sensitivity of the observables to right-handed currents and scalars. Finally, we present for the first time all the symmetries of the full distribution including massive terms and scalar contributions.

Structural, vibrational spectroscopic and quantum chemical studies on indole-3-carboxaldehyde

NASA Astrophysics Data System (ADS)

Premkumar, R.; Asath, R. Mohamed; Mathavan, T.; Benial, A. Milton Franklin

2017-05-01

The potential energy surface (PES) scan was performed for indole-3-carboxaldehyde (ICA) and the most stable optimized conformer was predicted using DFT/B3LYP method with 6-31G basis set. The vibrational frequencies of ICA were theoretically calculated by the DFT/B3LYP method with cc-pVTZ basis set using Gaussian 09 program. The vibrational spectra were experimentally recorded by Fourier transform-infrared (FT-IR) and Fourier transform-Raman spectrometer (FT-Raman). The computed vibrational frequencies were scaled by scaling factors to yield a good agreement with observed vibrational frequencies. The theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of potential energy distribution (PED) calculation using VEDA 4.0 program. The molecular interaction, stability and intramolecular charge transfer of ICA were studied using frontier molecular orbitals (FMOs) analysis and Mulliken atomic charge distribution shows the distribution of the atomic charges. The presence of intramolecular charge transfer was studied using natural bond orbital (NBO) analysis.

Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

NASA Astrophysics Data System (ADS)

Remko, Milan

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

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

PubMed

Plessow, Philipp N

2018-02-13

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

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Optimization of a Biometric System Based on Acoustic Images

PubMed Central

Izquierdo Fuente, Alberto; Del Val Puente, Lara; Villacorta Calvo, Juan J.; Raboso Mateos, Mariano

2014-01-01

On the basis of an acoustic biometric system that captures 16 acoustic images of a person for 4 frequencies and 4 positions, a study was carried out to improve the performance of the system. On a first stage, an analysis to determine which images provide more information to the system was carried out showing that a set of 12 images allows the system to obtain results that are equivalent to using all of the 16 images. Finally, optimization techniques were used to obtain the set of weights associated with each acoustic image that maximizes the performance of the biometric system. These results improve significantly the performance of the preliminary system, while reducing the time of acquisition and computational burden, since the number of acoustic images was reduced. PMID:24616643

Crystal structure, spectroscopic studies and quantum mechanical calculations of 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene.

PubMed

Özdemir Tarı, Gonca; Gümüş, Sümeyye; Ağar, Erbil

2015-04-15

The title compound, 2-[((3-iodo-4-methyl)phenylimino)methyl]-5-nitrothiophene, C12H9O2N2I1S1, was synthesized and characterized by IR, UV-Vis and single-crystal X-ray diffraction technique. The molecular structure was optimized at the B3LYP, B3PW91 and PBEPBE levels of the density functional method (DFT) with the 6-311G+(d,p) basis set. Using the TD-DFT method, the electronic absorption spectra of the title compound was computed in both the gas phase and ethanol solvent. The harmonic vibrational frequencies of the title compound were calculated using the same methods with the 6-311G+(d,p) basis set. The calculated results were compared with the experimental determination results of the compound. The energetic behavior such as the total energy, atomic charges, dipole moment of the title compound in solvent media were examined using the B3LYP, B3PW91 and PBEPBE methods with the 6-311G+(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The molecular orbitals (FMOs) analysis, the molecular electrostatic potential map (MEP) and the nonlinear optical properties (NLO) for the title compound were obtained with the same levels of theory. And then thermodynamic properties for the title compound were obtained using the same methods with the 6-311G(d,p) basis set. Copyright © 2015 Elsevier B.V. All rights reserved.

Unbiased nonorthogonal bases for tomographic reconstruction

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

Sainz, Isabel; Klimov, Andrei B.; Roa, Luis

2010-05-15

We have developed a general method for constructing a set of nonorthogonal bases with equal separations between all different basis states in prime dimensions. The results are that the corresponding biorthogonal counterparts are pairwise unbiased with the components of the original bases. Using these bases, we derive an explicit expression for the optimal tomography in nonorthogonal bases. A special two-dimensional case is analyzed separately.

European union standards for tuberculosis care.

PubMed

Migliori, G B; Zellweger, J P; Abubakar, I; Ibraim, E; Caminero, J A; De Vries, G; D'Ambrosio, L; Centis, R; Sotgiu, G; Menegale, O; Kliiman, K; Aksamit, T; Cirillo, D M; Danilovits, M; Dara, M; Dheda, K; Dinh-Xuan, A T; Kluge, H; Lange, C; Leimane, V; Loddenkemper, R; Nicod, L P; Raviglione, M C; Spanevello, A; Thomsen, V Ø; Villar, M; Wanlin, M; Wedzicha, J A; Zumla, A; Blasi, F; Huitric, E; Sandgren, A; Manissero, D

2012-04-01

The European Centre for Disease Prevention and Control (ECDC) and the European Respiratory Society (ERS) jointly developed European Union Standards for Tuberculosis Care (ESTC) aimed at providing European Union (EU)-tailored standards for the diagnosis, treatment and prevention of tuberculosis (TB). The International Standards for TB Care (ISTC) were developed in the global context and are not always adapted to the EU setting and practices. The majority of EU countries have the resources and capacity to implement higher standards to further secure quality TB diagnosis, treatment and prevention. On this basis, the ESTC were developed as standards specifically tailored to the EU setting. A panel of 30 international experts, led by a writing group and the ERS and ECDC, identified and developed the 21 ESTC in the areas of diagnosis, treatment, HIV and comorbid conditions, and public health and prevention. The ISTCs formed the basis for the 21 standards, upon which additional EU adaptations and supplements were developed. These patient-centred standards are targeted to clinicians and public health workers, providing an easy-to-use resource, guiding through all required activities to ensure optimal diagnosis, treatment and prevention of TB. These will support EU health programmes to identify and develop optimal procedures for TB care, control and elimination.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

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

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE PAGES

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.; ...

2017-07-21

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

The 6-31B(d) basis set and the BMC-QCISD and BMC-CCSD multicoefficient correlation methods.

PubMed

Lynch, Benjamin J; Zhao, Yan; Truhlar, Donald G

2005-03-03

Three new multicoefficient correlation methods (MCCMs) called BMC-QCISD, BMC-CCSD, and BMC-CCSD-C are optimized against 274 data that include atomization energies, electron affinities, ionization potentials, and reaction barrier heights. A new basis set called 6-31B(d) is developed and used as part of the new methods. BMC-QCISD has mean unsigned errors in calculating atomization energies per bond and barrier heights of 0.49 and 0.80 kcal/mol, respectively. BMC-CCSD has mean unsigned errors of 0.42 and 0.71 kcal/mol for the same two quantities. BMC-CCSD-C is an equally effective variant of BMC-CCSD that employs Cartesian rather than spherical harmonic basis sets. The mean unsigned error of BMC-CCSD or BMC-CCSD-C for atomization energies, barrier heights, ionization potentials, and electron affinities is 22% lower than G3SX(MP2) at an order of magnitude less cost for gradients for molecules with 9-13 atoms, and it scales better (N6 vs N,7 where N is the number of atoms) when the size of the molecule is increased.

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

NASA Astrophysics Data System (ADS)

Jiang, Hao; Lu, Jiangang

2018-05-01

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

Spectroscopic and DFT studies of bis-3-hydroxypyridinium and bis-3-hydroxymethylpyridinium dibromides with tetramethylene linker

NASA Astrophysics Data System (ADS)

Komasa, Anna

2018-01-01

Experimental and theoretical IR, Raman, UV-Vis, 1H and 13C NMR spectra of 1,4-di(3-hydroxypyridinium)butane dibromide and 1,4-di(3-hydroxymethylpyridinium)butane dibromide were obtained and analyzed. Optimized geometrical structures of the studied compounds were calculated by B3LYP method using 6-311++G(d,p) basis set and employed to determine the theoretical wavenumbers and intensities of IR and Raman spectra. The frequency assignments were supported by the potential energy distribution (PED) analysis. The significant role of the intermolecular interactions and the hydrogen bond was revealed on the basis of IR spectra. The calculated GIAO/B3LYP/6-311++G(d,p) isotropic magnetic shielding constants were used to predict the 1H and 13C chemical shifts for the optimized structures. Accuracy of the prediction of 1H and 13C chemical shifts was significantly improved by a simulation of the solvent in calculations. On the basis of UV-Vis spectra the acid-base equilibrium in the water solution of 1,4-di(3-hydroxypyridinium)butane dibromide was found.

Removal of BCG artifacts using a non-Kirchhoffian overcomplete representation.

PubMed

Dyrholm, Mads; Goldman, Robin; Sajda, Paul; Brown, Truman R

2009-02-01

We present a nonlinear unmixing approach for extracting the ballistocardiogram (BCG) from EEG recorded in an MR scanner during simultaneous acquisition of functional MRI (fMRI). First, an overcomplete basis is identified in the EEG based on a custom multipath EEG electrode cap. Next, the overcomplete basis is used to infer non-Kirchhoffian latent variables that are not consistent with a conservative electric field. Neural activity is strictly Kirchhoffian while the BCG artifact is not, and the representation can hence be used to remove the artifacts from the data in a way that does not attenuate the neural signals needed for optimal single-trial classification performance. We compare our method to more standard methods for BCG removal, namely independent component analysis and optimal basis sets, by looking at single-trial classification performance for an auditory oddball experiment. We show that our overcomplete representation method for removing BCG artifacts results in better single-trial classification performance compared to the conventional approaches, indicating that the derived neural activity in this representation retains the complex information in the trial-to-trial variability.

Low frequency vibrational spectra and the nature of metal-oxygen bond of alkaline earth metal acetylacetonates

NASA Astrophysics Data System (ADS)

Fakheri, Hamideh; Tayyari, Sayyed Faramarz; Heravi, Mohammad Momen; Morsali, Ali

2017-12-01

Theoretical quantum chemistry calculations were used to assign the observed vibrational band frequencies of Be, Mg, Ca, Sr, and Ba acetylacetonates complexes. Density functional theory (DFT) calculations have been carried out at the B3LYP level, using LanL2DZ, def2SVP, and mixed, GenECP, (def2SVP for metal ions and 6-311++G** for all other atoms) basis sets. The B3LYP level, with mixed basis sets, was utilized for calculations of vibrational frequencies, IR intensity, and Raman activity. Analysis of the vibrational spectra indicates that there are several bands which could almost be assigned mainly to the metal-oxygen vibrations. The strongest Raman band in this region could be used as a measure of the stability of the complex. The effects of central metal on the bond orders and charge distributions in alkaline earth metal acetylacetonates were studied by the Natural Bond Orbital (NBO) method for fully optimized compounds. Optimization were performed at the B3LYP/6-311++G** level for the lighter alkaline earth metal complexes (Be, Mg, and Ca acetylacetonates) while the B3LYP level, using LanL2DZ (extrabasis, d and f on oxygen and metal atoms), def2SVP and mixed (def2SVP on metal ions and 6-311++G** for all other atoms) basis sets for all understudy complexes. Calculations indicate that the covalence nature of metal-oxygen bonds considerably decreases from Be to Ba complexes. The nature of metal-oxygen bond was further studied by using Atoms In Molecules (AIM) analysis. The topological parameters, Wiberg bond orders, natural charges of O and metal ions, and also some vibrational band frequencies were correlated with the stability constants of understudy complexes.

Structural, physicochemical characterization, theoretical studies of carboxamides and their Cu(II), Zn(II) complexes having antibacterial activities against E. coli

NASA Astrophysics Data System (ADS)

Aktan, Ebru; Gündüzalp, Ayla Balaban; Özmen, Ümmühan Özdemir

2017-01-01

The carboxamides; N,N‧-bis(thiophene-2-carboxamido)-1,3-diaminopropanol (L1) and N,N‧-bis(furan-2-carboxamido)-1,3-diaminopropanol (L2) were synthesized and characterized using 1H NMR, 13C NMR, LC-MS and FT-IR spectrum. The molecular geometries of these molecules were optimized by DFT/B3LYP method with 6-311G(d,p) basis set in Gaussian 09 software. The geometrical parameters, frontier molecular orbitals (FMOs) and molecular electrostatic potential (MEP) mapped surfaces were calculated by the same basis set. Dinuclear Cu(II) and Zn(II) complexes having general formula as [MLCl]2Cl2.nH2O (in which M = Cu(II),Zn(II); n = 0,2) were also synthesized and characterized using LC-MS and FT-IR spectrum, thermogravimetric analysis (TGA/DTA curves), magnetic moments and molar conductivities. Coordination was found to be through carbonyl oxygen and two chlorine atoms as bridging in distorted tetrahedral geometry. The optimized structures, geometrical parameters, frontier molecular orbitals (FMOs) and dipole moments of metal complexes were also obtained by DFT/B3LYP method with LanL2DZ basis set. Antibacterial activities of the compounds were screened against E. coli using microdilution method (MIC's in μg/mL). The activity results show that the corresponding compounds exhibit good to moderate antibacterial effects when compared with sulfamethoxazole and sulfisoxazole antibiotics as positive controls. Also, metal complexes have remarkable increase in their activities than parent ligands against E. coli which is mostly effected by [Cu(L2)Cl]2Cl2 complex as potential antibacterial agent.

A comparative research of different ensemble surrogate models based on set pair analysis for the DNAPL-contaminated aquifer remediation strategy optimization.

PubMed

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. Copyright © 2017 Elsevier B.V. All rights reserved.

Analytic energy gradients for orbital-optimized MP3 and MP2.5 with the density-fitting approximation: An efficient implementation.

PubMed

Bozkaya, Uğur

2018-03-15

Efficient implementations of analytic gradients for the orbital-optimized MP3 and MP2.5 and their standard versions with the density-fitting approximation, which are denoted as DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5, are presented. The DF-MP3, DF-MP2.5, DF-OMP3, and DF-OMP2.5 methods are applied to a set of alkanes and noncovalent interaction complexes to compare the computational cost with the conventional MP3, MP2.5, OMP3, and OMP2.5. Our results demonstrate that density-fitted perturbation theory (DF-MP) methods considered substantially reduce the computational cost compared to conventional MP methods. The efficiency of our DF-MP methods arise from the reduced input/output (I/O) time and the acceleration of gradient related terms, such as computations of particle density and generalized Fock matrices (PDMs and GFM), solution of the Z-vector equation, back-transformations of PDMs and GFM, and evaluation of analytic gradients in the atomic orbital basis. Further, application results show that errors introduced by the DF approach are negligible. Mean absolute errors for bond lengths of a molecular set, with the cc-pCVQZ basis set, is 0.0001-0.0002 Å. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Adjoint Sensitivity Method to Determine Optimal Set of Stations for Tsunami Source Inversion

NASA Astrophysics Data System (ADS)

Gusman, A. R.; Hossen, M. J.; Cummins, P. R.; Satake, K.

2017-12-01

We applied the adjoint sensitivity technique in tsunami science for the first time to determine an optimal set of stations for a tsunami source inversion. The adjoint sensitivity (AS) method has been used in numerical weather prediction to find optimal locations for adaptive observations. We implemented this technique to Green's Function based Time Reverse Imaging (GFTRI), which is recently used in tsunami source inversion in order to reconstruct the initial sea surface displacement, known as tsunami source model. This method has the same source representation as the traditional least square (LSQ) source inversion method where a tsunami source is represented by dividing the source region into a regular grid of "point" sources. For each of these, Green's function (GF) is computed using a basis function for initial sea surface displacement whose amplitude is concentrated near the grid point. We applied the AS method to the 2009 Samoa earthquake tsunami that occurred on 29 September 2009 in the southwest Pacific, near the Tonga trench. Many studies show that this earthquake is a doublet associated with both normal faulting in the outer-rise region and thrust faulting in the subduction interface. To estimate the tsunami source model for this complex event, we initially considered 11 observations consisting of 5 tide gauges and 6 DART bouys. After implementing AS method, we found the optimal set of observations consisting with 8 stations. Inversion with this optimal set provides better result in terms of waveform fitting and source model that shows both sub-events associated with normal and thrust faulting.

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

Hamadneh, Nawaf; Sathasivam, Saratha; Choon, Ong Hong

Logic programming is the process that leads from an original formulation of a computing problem to executable programs. A normal logic program consists of a finite set of clauses. A valuation I of logic programming is a mapping from ground atoms to false or true. The single step operator of any logic programming is defined as a function (T{sub p}:I→I). Logic programming is well-suited to building the artificial intelligence systems. In this study, we established a new technique to compute the single step operators of logic programming in the radial basis function neural networks. To do that, we proposed amore » new technique to generate the training data sets of single step operators. The training data sets are used to build the neural networks. We used the recurrent radial basis function neural networks to get to the steady state (the fixed point of the operators). To improve the performance of the neural networks, we used the particle swarm optimization algorithm to train the networks.« less

PROBING THE EXPANSION HISTORY OF THE UNIVERSE BY MODEL-INDEPENDENT RECONSTRUCTION FROM SUPERNOVAE AND GAMMA-RAY BURST MEASUREMENTS

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

Feng, Chao-Jun; Li, Xin-Zhou, E-mail: fengcj@shnu.edu.cn, E-mail: kychz@shnu.edu.cn

To probe the late evolution history of the universe, we adopt two kinds of optimal basis systems. One of them is constructed by performing the principle component analysis, and the other is built by taking the multidimensional scaling approach. Cosmological observables such as the luminosity distance can be decomposed into these basis systems. These basis systems are optimized for different kinds of cosmological models that are based on different physical assumptions, even for a mixture model of them. Therefore, the so-called feature space that is projected from the basis systems is cosmological model independent, and it provides a parameterization for studying and reconstructing themore » Hubble expansion rate from the supernova luminosity distance and even gamma-ray burst (GRB) data with self-calibration. The circular problem when using GRBs as cosmological candles is naturally eliminated in this procedure. By using the Levenberg–Marquardt technique and the Markov Chain Monte Carlo method, we perform an observational constraint on this kind of parameterization. The data we used include the “joint light-curve analysis” data set that consists of 740 Type Ia supernovae and 109 long GRBs with the well-known Amati relation.« less

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

PubMed

Köhn, Andreas

2010-11-07

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

Galerkin Optimal Control

DTIC Science & Technology

2014-12-01

MATHEMATICS from the NAVAL POSTGRADUATE SCHOOL December 2014 Randy Boucher Approved By: Wei Kang Professor Chris L. Frenzen Professor Department of...also to the members of my committee: Dr. Frank Giraldo, Dr. Chris Frenzen, Dr. Mike Ross and Dr. Arthur Krener. Each of you planted great seeds of...Louis Lions, Universite Paris, Paris, France, Oct. 2005. [80] J. R. Higgins , Completeness and Basis Properties of Sets of Special Functions. Cam

Multilevel geometry optimization

NASA Astrophysics Data System (ADS)

Rodgers, Jocelyn M.; Fast, Patton L.; Truhlar, Donald G.

2000-02-01

Geometry optimization has been carried out for three test molecules using six multilevel electronic structure methods, in particular Gaussian-2, Gaussian-3, multicoefficient G2, multicoefficient G3, and two multicoefficient correlation methods based on correlation-consistent basis sets. In the Gaussian-2 and Gaussian-3 methods, various levels are added and subtracted with unit coefficients, whereas the multicoefficient Gaussian-x methods involve noninteger parameters as coefficients. The multilevel optimizations drop the average error in the geometry (averaged over the 18 cases) by a factor of about two when compared to the single most expensive component of a given multilevel calculation, and in all 18 cases the accuracy of the atomization energy for the three test molecules improves; with an average improvement of 16.7 kcal/mol.

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

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

NASA Astrophysics Data System (ADS)

Kruse, Holger; Grimme, Stefan

2012-04-01

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

Spectroscopic and chemical reactivity analysis of D-Myo-Inositol using quantum chemical approach and its experimental verification

NASA Astrophysics Data System (ADS)

Mishra, Devendra P.; Srivastava, Anchal; Shukla, R. K.

2017-07-01

This paper describes the spectroscopic (^1H and ^{13}C NMR, FT-IR and UV-Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with 6 {-}311{+}{+}G(d,p) basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6 {-}311{+}{+}G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO-LUMO states. The nature of the transitions in the observed UV-Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at B3LYP/ 6 {-}311{+}{+}G(d,p) level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase in temperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.

A structural study of fentanyl by DFT calculations, NMR and IR spectroscopy

NASA Astrophysics Data System (ADS)

Asadi, Zahra; Esrafili, Mehdi D.; Vessally, Esmail; Asnaashariisfahani, Manzarbanou; Yahyaei, Saeideh; Khani, Ali

2017-01-01

N-(1-(2-phenethyl)-4-piperidinyl-N-phenyl-propanamide (fentanyl) is synthesized and characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy and elemental analyses. The geometry optimization is performed using the B3LYP and M06 density functionals with 6-311 + G(d) and 6-311++G(d,p) basis sets. The complete assignments are performed on the basis of the potential energy distribution (PED) of the all vibrational modes. Almost a nice correlation is found between the calculated 13C chemical shifts and experimental data. The frontier molecular orbitals and molecular electrostatic potential of fentanyl are also obtained.

Two optimal working regimes of the ”long” Iguasu gas centrifuge

NASA Astrophysics Data System (ADS)

Borman, V. D.; Bogovalov, S. V.; Borisevich, V. D.; Tronin, I. V.; Tronin, V. N.

2016-09-01

We argue on the basis of the results of optimization calculations that the dependence of the optimal separative power of the Iguasu gas centrifuge with 2 m rotor has two local maxima,corresponding pressures of p max1 = 35 mmHg and p max2 = 350 mmHg. The optimal separative power values in these maxima differ by the value of 0.6%. Low pressure maximum is caused by the thermal drive, whereas high pressure maximum is caused by both thermal and mechanical drives. High pressure maximum is located on wide ’’plateau” from p 1 = 200 mmHg to p 2 = 500 mmHg, where the optimal separative power changes in the range of 0.7%. In this way, Iguasu gas centrifuge has two optimal working regimes with different sets of working parameters and close slightly different values of the separative power. Calculations show that high pressure regime is less sensitive to the parameters change than low pressure one.

Experimental and theoretical study on DPPH radical scavenging mechanism of some chalcone quinoline derivatives

NASA Astrophysics Data System (ADS)

Hamlaoui, Ikram; Bencheraiet, Reguia; Bensegueni, Rafik; Bencharif, Mustapha

2018-03-01

In this study, the antioxidant capacity of three chalcone derivatives was evaluated by DPPH free radical scavenging. Experimental data showed low antioxidant activity (IC50±SD) of these molecules in comparison with BHT. The mechanism of DPPH radical scavenging elucidated by means of density functional theory (DFT) calculations. The tested compounds and their corresponding radicals and anions were optimized using B3LYP functional with 6-31G (d,p) basis set in the gas phase. The C-PCM model was used to perform solvent medium calculations. On the basis of theoretical calculations, it was shown that HAT mechanism was predominant in the gas phase, whereas SET-PT and SPLET mechanisms were favored in the presence of the solvent. Moreover, the HOMO orbitals and spin density distribution was evaluated to predict the probable sites for free radical attack.

Analysis of vibrational, structural, and electronic properties of rivastigmine by density functional theory

NASA Astrophysics Data System (ADS)

Prasad, O.; Sinha, L.; Misra, N.; Narayan, V.; Kumar, N.; Kumar, A.

2010-09-01

The present work deals with the structural, electronic, and vibrational analysis of rivastigmine. Rivastigmine, an antidementia medicament, is credited with significant therapeutic effects on the cognitive, functional, and behavioural problems that are commonly associated with Alzheimer’s dementia. For rivastigmine, a number of minimum energy conformations are possible. The geometry of twelve possible conformers has been analyzed and the most stable conformer was further optimized at a higher basis set. The electronic properties and vibrational frequencies were then calculated using a density functional theory at the B3LYP level with the 6-311+G(d, p) basis set. The different molecular surfaces have also been drawn to understand the activity of the molecule. A narrower frontier orbital energy gap in rivastigmine makes it softer and more reactive than water and dimethylfuran. The calculated value of the dipole moment is 2.58 debye.

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

PubMed

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

2016-04-05

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

A principled approach to setting optimal diagnostic thresholds: where ROC and indifference curves meet.

PubMed

Irwin, R John; Irwin, Timothy C

2011-06-01

Making clinical decisions on the basis of diagnostic tests is an essential feature of medical practice and the choice of the decision threshold is therefore crucial. A test's optimal diagnostic threshold is the threshold that maximizes expected utility. It is given by the product of the prior odds of a disease and a measure of the importance of the diagnostic test's sensitivity relative to its specificity. Choosing this threshold is the same as choosing the point on the Receiver Operating Characteristic (ROC) curve whose slope equals this product. We contend that a test's likelihood ratio is the canonical decision variable and contrast diagnostic thresholds based on likelihood ratio with two popular rules of thumb for choosing a threshold. The two rules are appealing because they have clear graphical interpretations, but they yield optimal thresholds only in special cases. The optimal rule can be given similar appeal by presenting indifference curves, each of which shows a set of equally good combinations of sensitivity and specificity. The indifference curve is tangent to the ROC curve at the optimal threshold. Whereas ROC curves show what is feasible, indifference curves show what is desirable. Together they show what should be chosen. Copyright © 2010 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Optimization of camera exposure durations for multi-exposure speckle imaging of the microcirculation

PubMed Central

Kazmi, S. M. Shams; Balial, Satyajit; Dunn, Andrew K.

2014-01-01

Improved Laser Speckle Contrast Imaging (LSCI) blood flow analyses that incorporate inverse models of the underlying laser-tissue interaction have been used to develop more quantitative implementations of speckle flowmetry such as Multi-Exposure Speckle Imaging (MESI). In this paper, we determine the optimal camera exposure durations required for obtaining flow information with comparable accuracy with the prevailing MESI implementation utilized in recent in vivo rodent studies. A looping leave-one-out (LOO) algorithm was used to identify exposure subsets which were analyzed for accuracy against flows obtained from analysis with the original full exposure set over 9 animals comprising n = 314 regional flow measurements. From the 15 original exposures, 6 exposures were found using the LOO process to provide comparable accuracy, defined as being no more than 10% deviant, with the original flow measurements. The optimal subset of exposures provides a basis set of camera durations for speckle flowmetry studies of the microcirculation and confers a two-fold faster acquisition rate and a 28% reduction in processing time without sacrificing accuracy. Additionally, the optimization process can be used to identify further reductions in the exposure subsets for tailoring imaging over less expansive flow distributions to enable even faster imaging. PMID:25071956

Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

2013-09-01

Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

Determination of the mobility profile in GaAs-MESFETs. Thesis

NASA Technical Reports Server (NTRS)

Prost, W.

1985-01-01

A process for measuring charge carrier mobility for gallium-arsenide metal semiconductor field effect transistors is described in an attempt to optimize the relationship between this factor and production. The measuring procedure allows an actual determination of local mobility in the channel. The physical basis for the process and features of the measuring room are outlined. The measuring technique is described and recommendations are made for setting measuring parameters.

Inference of a Nonlinear Stochastic Model of the Cardiorespiratory Interaction

NASA Astrophysics Data System (ADS)

Smelyanskiy, V. N.; Luchinsky, D. G.; Stefanovska, A.; McClintock, P. V.

2005-03-01

We reconstruct a nonlinear stochastic model of the cardiorespiratory interaction in terms of a set of polynomial basis functions representing the nonlinear force governing system oscillations. The strength and direction of coupling and noise intensity are simultaneously inferred from a univariate blood pressure signal. Our new inference technique does not require extensive global optimization, and it is applicable to a wide range of complex dynamical systems subject to noise.

European Union Standards for Tuberculosis Care

PubMed Central

Migliori, G.B.; Zellweger, J.P.; Abubakar, I.; Ibraim, E.; Caminero, J.A.; De Vries, G.; D'Ambrosio, L.; Centis, R.; Sotgiu, G.; Menegale, O.; Kliiman, K.; Aksamit, T.; Cirillo, D.M.; Danilovits, M.; Dara, M.; Dheda, K.; Dinh-Xuan, A.T.; Kluge, H.; Lange, C.; Leimane, V.; Loddenkemper, R.; Nicod, L.P.; Raviglione, M.C.; Spanevello, A.; Thomsen, V.Ø.; Villar, M.; Wanlin, M.; Wedzicha, J.A.; Zumla, A.; Blasi, F.; Huitric, E.; Sandgren, A.; Manissero, D.

2012-01-01

The European Centre for Disease Prevention and Control (ECDC) and the European Respiratory Society (ERS) jointly developed European Union Standards for Tuberculosis Care (ESTC) aimed at providing European Union (EU)-tailored standards for the diagnosis, treatment and prevention of tuberculosis (TB). The International Standards for TB Care (ISTC) were developed in the global context and are not always adapted to the EU setting and practices. The majority of EU countries have the resources and capacity to implement higher standards to further secure quality TB diagnosis, treatment and prevention. On this basis, the ESTC were developed as standards specifically tailored to the EU setting. A panel of 30 international experts, led by a writing group and the ERS and ECDC, identified and developed the 21 ESTC in the areas of diagnosis, treatment, HIV and comorbid conditions, and public health and prevention. The ISTCs formed the basis for the 21 standards, upon which additional EU adaptations and supplements were developed. These patient-centred standards are targeted to clinicians and public health workers, providing an easy-to-use resource, guiding through all required activities to ensure optimal diagnosis, treatment and prevention of TB. These will support EU health programmes to identify and develop optimal procedures for TB care, control and elimination. PMID:22467723

Utilization of group theory in studies of molecular clusters

NASA Astrophysics Data System (ADS)

Ocak, Mahir E.

The structure of the molecular symmetry group of molecular clusters was analyzed and it is shown that the molecular symmetry group of a molecular cluster can be written as direct products and semidirect products of its subgroups. Symmetry adaptation of basis functions in direct product groups and semidirect product groups was considered in general and the sequential symmetry adaptation procedure which is already known for direct product groups was extended to the case of semidirect product groups. By using the sequential symmetry adaptation procedure a new method for calculating the VRT spectra of molecular clusters which is named as Monomer Basis Representation (MBR) method is developed. In the MBR method, calculations starts with a single monomer with the purpose of obtaining an optimized basis for that monomer as a linear combination of some primitive basis functions. Then, an optimized basis for each identical monomer is generated from the optimized basis of this monomer. By using the optimized bases of the monomers, a basis is generated generated for the solution of the full problem, and the VRT spectra of the cluster is obtained by using this basis. Since an optimized basis is used for each monomer which has a much smaller size than the primitive basis from which the optimized bases are generated, the MBR method leads to an exponential optimization in the size of the basis that is required for the calculations. Application of the MBR method has been illustrated by calculating the VRT spectra of water dimer by using the SAPT-5st potential surface of Groenenboom et al. The rest of the calculations are in good agreement with both the original calculations of Groenenboom et al. and also with the experimental results. Comparing the size of the optimized basis with the size of the primitive basis, it can be said that the method works efficiently. Because of its efficiency, the MBR method can be used for studies of clusters bigger than dimers. Thus, MBR method can be used for studying the many-body terms and for deriving accurate potential surfaces.

Model and Algorithm for Substantiating Solutions for Organization of High-Rise Construction Project

NASA Astrophysics Data System (ADS)

Anisimov, Vladimir; Anisimov, Evgeniy; Chernysh, Anatoliy

2018-03-01

In the paper the models and the algorithm for the optimal plan formation for the organization of the material and logistical processes of the high-rise construction project and their financial support are developed. The model is based on the representation of the optimization procedure in the form of a non-linear problem of discrete programming, which consists in minimizing the execution time of a set of interrelated works by a limited number of partially interchangeable performers while limiting the total cost of performing the work. The proposed model and algorithm are the basis for creating specific organization management methodologies for the high-rise construction project.

Accurate and Efficient Approximation to the Optimized Effective Potential for Exchange

NASA Astrophysics Data System (ADS)

Ryabinkin, Ilya G.; Kananenka, Alexei A.; Staroverov, Viktor N.

2013-07-01

We devise an efficient practical method for computing the Kohn-Sham exchange-correlation potential corresponding to a Hartree-Fock electron density. This potential is almost indistinguishable from the exact-exchange optimized effective potential (OEP) and, when used as an approximation to the OEP, is vastly better than all existing models. Using our method one can obtain unambiguous, nearly exact OEPs for any reasonable finite one-electron basis set at the same low cost as the Krieger-Li-Iafrate and Becke-Johnson potentials. For all practical purposes, this solves the long-standing problem of black-box construction of OEPs in exact-exchange calculations.

Intelligent Support System of Steel Technical Preparation in an Arc Furnace: Functional Scheme of Interactive Builder of the Multi Objective Optimization Problem

NASA Astrophysics Data System (ADS)

Logunova, O. S.; Sibileva, N. S.

2017-12-01

The purpose of the study is to increase the efficiency of the steelmaking process in large capacity arc furnace on the basis of implementation a new decision-making system about the composition of charge materials. The authors proposed an interactive builder for the formation of the optimization problem, taking into account the requirements of the customer, normative documents and stocks of charge materials in the warehouse. To implement the interactive builder, the sets of deterministic and stochastic model components are developed, as well as a list of preferences of criteria and constraints.

Evaluating structures, properties and vibrational and electronic spectra of the potassium 2-isonicotinoyltrifluoroborate salt

NASA Astrophysics Data System (ADS)

Iramain, Maximiliano A.; Davies, Lilian; Brandán, Silvia Antonia

2018-07-01

The potassium 2-isonicotinoyltrifluorborate salt has been characterized by using FT-IR, FT-Raman and UV-Visible spectroscopies while its structural properties were studied by using B3LYP/6-31G* and B3LYP/6-311++G** calculations in gas and aqueous solution phases. Four conformers with CS and C1 symmetries were found in the potential energy surfaces but only one of them presents the minimum energy. Two dimeric species of this salt were also optimized in accordance to the layered architectures suggested for trifluoroborate potassium salts in the solid phase. Here, the experimental Raman bands at 796, 748 and 676 cm-1 clearly support the presence of both dimers. On the other hand, the 2-isonicotinoyltrifluorborate anion was optimized because its presence is expected in solution. Reasonable correlations were observed between the predicted FTIR, Raman and UV-visible spectra with the corresponding experimental ones. The solvation energies for the salt in aqueous solution were predicted by using both methods. Here, it is observed that the change of furane by pyridine ring generates an increase in the solvation energies of the potassium 2-isonicotinoyltrifluorborate salt in relation to potassium 3-furoyltrifluoroborate salt. The study of the charges has revealed that there is an effect of the size of the basis set on the Mulliken charges while the AIM analyses suggest that the F⋯H and O⋯K interactions are also strongly dependent of the medium and the size of the basis sets. The bond orders for the F and K atoms evidence their higher ionic characteristics in solution with both basis sets. The NBO and AIM results clearly support the higher stability of this salt in both media. The studies by using the frontier orbitals indicate that the change of furane by pyridine ring decreases the reactivity of this salt by using 6-31G* basis set but increases when the other one is employed. Another effect of change of furane by pyridine ring is observed in the increase of the f(νCdbnd O) and f(νBF3) force constants. In addition, the force fields for the salt in both media were reported together to their complete vibrational assignments and force constants by using both levels of theory.

Advanced Interactive Display Formats for Terminal Area Traffic Control

NASA Technical Reports Server (NTRS)

Grunwald, Arthur J.; Shaviv, G. E.

1999-01-01

This research project deals with an on-line dynamic method for automated viewing parameter management in perspective displays. Perspective images are optimized such that a human observer will perceive relevant spatial geometrical features with minimal errors. In order to compute the errors at which observers reconstruct spatial features from perspective images, a visual spatial-perception model was formulated. The model was employed as the basis of an optimization scheme aimed at seeking the optimal projection parameter setting. These ideas are implemented in the context of an air traffic control (ATC) application. A concept, referred to as an active display system, was developed. This system uses heuristic rules to identify relevant geometrical features of the three-dimensional air traffic situation. Agile, on-line optimization was achieved by a specially developed and custom-tailored genetic algorithm (GA), which was to deal with the multi-modal characteristics of the objective function and exploit its time-evolving nature.

Optimal design of loudspeaker arrays for robust cross-talk cancellation using the Taguchi method and the genetic algorithm.

PubMed

Bai, Mingsian R; Tung, Chih-Wei; Lee, Chih-Chung

2005-05-01

An optimal design technique of loudspeaker arrays for cross-talk cancellation with application in three-dimensional audio is presented. An array focusing scheme is presented on the basis of the inverse propagation that relates the transducers to a set of chosen control points. Tikhonov regularization is employed in designing the inverse cancellation filters. An extensive analysis is conducted to explore the cancellation performance and robustness issues. To best compromise the performance and robustness of the cross-talk cancellation system, optimal configurations are obtained with the aid of the Taguchi method and the genetic algorithm (GA). The proposed systems are further justified by physical as well as subjective experiments. The results reveal that large number of loudspeakers, closely spaced configuration, and optimal control point design all contribute to the robustness of cross-talk cancellation systems (CCS) against head misalignment.

Structural, vibrational spectroscopic and nonlinear optical activity studies on 2-hydroxy- 3, 5-dinitropyridine: A DFT approach

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Premkumar, S.; Jawahar, A.; Mathavan, T.; Dhas, M. Kumara; Benial, A. Milton Franklin

2015-06-01

The conformational analysis was carried out for 2-Hydroxy- 3, 5-dinitropyridine molecule using potential energy surface scan and the most stable optimized conformer was predicted. The vibrational frequencies and Mulliken atomic charge distribution were calculated for the optimized geometry of the molecule using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intramolecular charge transfer studies and the calculation of ionization energy, electron affinity, global hardness, chemical potential, electrophilicity index and softness values of the title molecule were carried out. The nonlinear optical activity of the molecule was studied by means of first order hyperpolarizability, which was computed as 7.64 times greater than urea. The natural bond orbital analysis was performed to confirm the nonlinear optical activity of the molecule.

Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

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

Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed

2016-05-06

The molecular structure of fullerene (C{sub 60}) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electronmore » affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.« less

An introduction to optimal power flow: Theory, formulation, and examples

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

Frank, Stephen; Rebennack, Steffen

The set of optimization problems in electric power systems engineering known collectively as Optimal Power Flow (OPF) is one of the most practically important and well-researched subfields of constrained nonlinear optimization. OPF has enjoyed a rich history of research, innovation, and publication since its debut five decades ago. Nevertheless, entry into OPF research is a daunting task for the uninitiated--both due to the sheer volume of literature and because OPF's ubiquity within the electric power systems community has led authors to assume a great deal of prior knowledge that readers unfamiliar with electric power systems may not possess. This articlemore » provides an introduction to OPF from an operations research perspective; it describes a complete and concise basis of knowledge for beginning OPF research. The discussion is tailored for the operations researcher who has experience with nonlinear optimization but little knowledge of electrical engineering. Topics covered include power systems modeling, the power flow equations, typical OPF formulations, and common OPF extensions.« less

Density functional theory studies of etoricoxib

NASA Astrophysics Data System (ADS)

Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.

2016-05-01

Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Optimization of complex slater-type functions with analytic derivative methods for describing photoionization differential cross sections.

PubMed

Matsuzaki, Rei; Yabushita, Satoshi

2017-05-05

The complex basis function (CBF) method applied to various atomic and molecular photoionization problems can be interpreted as an L2 method to solve the driven-type (inhomogeneous) Schrödinger equation, whose driven term being dipole operator times the initial state wave function. However, efficient basis functions for representing the solution have not fully been studied. Moreover, the relation between their solution and that of the ordinary Schrödinger equation has been unclear. For these reasons, most previous applications have been limited to total cross sections. To examine the applicability of the CBF method to differential cross sections and asymmetry parameters, we show that the complex valued solution to the driven-type Schrödinger equation can be variationally obtained by optimizing the complex trial functions for the frequency dependent polarizability. In the test calculations made for the hydrogen photoionization problem with five or six complex Slater-type orbitals (cSTOs), their complex valued expansion coefficients and the orbital exponents have been optimized with the analytic derivative method. Both the real and imaginary parts of the solution have been obtained accurately in a wide region covering typical molecular regions. Their phase shifts and asymmetry parameters are successfully obtained by extrapolating the CBF solution from the inner matching region to the asymptotic region using WKB method. The distribution of the optimized orbital exponents in the complex plane is explained based on the close connection between the CBF method and the driven-type equation method. The obtained information is essential to constructing the appropriate basis sets in future molecular applications. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

Papajak, Ewa; Truhlar, Donald G.

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

Innovations in compact stellarator coil design

NASA Astrophysics Data System (ADS)

Pomphrey, N.; Berry, L.; Boozer, A.; Brooks, A.; Hatcher, R. E.; Hirshman, S. P.; Ku, L.-P.; Miner, W. H.; Mynick, H. E.; Reiersen, W.; Strickler, D. J.; Valanju, P. M.

2001-03-01

Experimental devices for the study of the physics of high beta (β gtrsim 4%), low aspect ratio (A lesssim 4.5) stellarator plasmas require coils that will produce plasmas satisfying a set of physics goals, provide experimental flexibility and be practical to construct. In the course of designing a flexible coil set for the National Compact Stellarator Experiment, several innovations have been made that may be useful in future stellarator design efforts. These include: the use of singular value decomposition methods for obtaining families of smooth current potentials on distant coil winding surfaces from which low current density solutions may be identified; the use of a control matrix method for identifying which few of the many detailed elements of a stellarator boundary must be targeted if a coil set is to provide fields to control the essential physics of the plasma; the use of a genetic algorithm for choosing an optimal set of discrete coils from a continuum of potential contours; the evaluation of alternate coil topologies for balancing the trade-off between physics objectives and engineering constraints; the development of a new coil optimization code for designing modular coils and the identification of a `natural' basis for describing current sheet distributions.

ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation

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

Mardirossian, Narbe; Head-Gordon, Martin

2016-06-07

A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation is presented in this paper. The final 12-parameter functional form is selected from approximately 10 × 10 9 candidate fits that are trained on a training set of 870 data points and tested on a primary test set of 2964 data points. The resulting density functional, ωB97M-V, is further tested for transferability on a secondary test set of 1152 data points. For comparison, ωB97M-V is benchmarked against 11 leading density functionals including M06-2X, ωB97X-D, M08-HX, M11, ωM05-D, ωB97X-V, and MN15. Encouragingly, the overall performance of ωB97M-V on nearlymore » 5000 data points clearly surpasses that of all of the tested density functionals. Finally, in order to facilitate the use of ωB97M-V, its basis set dependence and integration grid sensitivity are thoroughly assessed, and recommendations that take into account both efficiency and accuracy are provided.« less

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

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

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

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

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

NASA Astrophysics Data System (ADS)

Spackman, Peter R.; Karton, Amir

2015-05-01

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

Remote sensing imagery classification using multi-objective gravitational search algorithm

NASA Astrophysics Data System (ADS)

Zhang, Aizhu; Sun, Genyun; Wang, Zhenjie

2016-10-01

Simultaneous optimization of different validity measures can capture different data characteristics of remote sensing imagery (RSI) and thereby achieving high quality classification results. In this paper, two conflicting cluster validity indices, the Xie-Beni (XB) index and the fuzzy C-means (FCM) (Jm) measure, are integrated with a diversity-enhanced and memory-based multi-objective gravitational search algorithm (DMMOGSA) to present a novel multi-objective optimization based RSI classification method. In this method, the Gabor filter method is firstly implemented to extract texture features of RSI. Then, the texture features are syncretized with the spectral features to construct the spatial-spectral feature space/set of the RSI. Afterwards, cluster of the spectral-spatial feature set is carried out on the basis of the proposed method. To be specific, cluster centers are randomly generated initially. After that, the cluster centers are updated and optimized adaptively by employing the DMMOGSA. Accordingly, a set of non-dominated cluster centers are obtained. Therefore, numbers of image classification results of RSI are produced and users can pick up the most promising one according to their problem requirements. To quantitatively and qualitatively validate the effectiveness of the proposed method, the proposed classification method was applied to classifier two aerial high-resolution remote sensing imageries. The obtained classification results are compared with that produced by two single cluster validity index based and two state-of-the-art multi-objective optimization algorithms based classification results. Comparison results show that the proposed method can achieve more accurate RSI classification.

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

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

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

2015-06-21

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

An optimal control strategy for two-dimensional motion camouflage with non-holonimic constraints.

PubMed

Rañó, Iñaki

2012-07-01

Motion camouflage is a stealth behaviour observed both in hover-flies and in dragonflies. Existing controllers for mimicking motion camouflage generate this behaviour on an empirical basis or without considering the kinematic motion restrictions present in animal trajectories. This study summarises our formal contributions to solve the generation of motion camouflage as a non-linear optimal control problem. The dynamics of the system capture the kinematic restrictions to motion of the agents, while the performance index ensures camouflage trajectories. An extensive set of simulations support the technique, and a novel analysis of the obtained trajectories contributes to our understanding of possible mechanisms to obtain sensor based motion camouflage, for instance, in mobile robots.

A hybrid linear/nonlinear training algorithm for feedforward neural networks.

PubMed

McLoone, S; Brown, M D; Irwin, G; Lightbody, A

1998-01-01

This paper presents a new hybrid optimization strategy for training feedforward neural networks. The algorithm combines gradient-based optimization of nonlinear weights with singular value decomposition (SVD) computation of linear weights in one integrated routine. It is described for the multilayer perceptron (MLP) and radial basis function (RBF) networks and then extended to the local model network (LMN), a new feedforward structure in which a global nonlinear model is constructed from a set of locally valid submodels. Simulation results are presented demonstrating the superiority of the new hybrid training scheme compared to second-order gradient methods. It is particularly effective for the LMN architecture where the linear to nonlinear parameter ratio is large.

DFT simulations and vibrational spectra of 2-amino-2-methyl-1,3-propanediol

NASA Astrophysics Data System (ADS)

Renuga Devi, T. S.; Sharmi kumar, J.; Ramkumaar, G. R.

2014-12-01

The FTIR and FT-Raman spectra of 2-amino-2-methyl-1,3-propanediol were recorded in the regions 4000-400 cm-1 and 4000-50 cm-1 respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and density functional method (B3LYP) with the augmented-correlation consistent-polarized valence double zeta (aug-cc-pVDZ) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed on the basis of the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Mulliken charges were calculated using both Hartee-Fock and density functional method using the aug-cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-Independent Atomic Orbital (GIAO) method and were compared with experimental results.

Collaborative Emission Reduction Model Based on Multi-Objective Optimization for Greenhouse Gases and Air Pollutants.

PubMed

Meng, Qing-chun; Rong, Xiao-xia; Zhang, Yi-min; Wan, Xiao-le; Liu, Yuan-yuan; Wang, Yu-zhi

2016-01-01

CO2 emission influences not only global climate change but also international economic and political situations. Thus, reducing the emission of CO2, a major greenhouse gas, has become a major issue in China and around the world as regards preserving the environmental ecology. Energy consumption from coal, oil, and natural gas is primarily responsible for the production of greenhouse gases and air pollutants such as SO2 and NOX, which are the main air pollutants in China. In this study, a mathematical multi-objective optimization method was adopted to analyze the collaborative emission reduction of three kinds of gases on the basis of their common restraints in different ways of energy consumption to develop an economic, clean, and efficient scheme for energy distribution. The first part introduces the background research, the collaborative emission reduction for three kinds of gases, the multi-objective optimization, the main mathematical modeling, and the optimization method. The second part discusses the four mathematical tools utilized in this study, which include the Granger causality test to analyze the causality between air quality and pollutant emission, a function analysis to determine the quantitative relation between energy consumption and pollutant emission, a multi-objective optimization to set up the collaborative optimization model that considers energy consumption, and an optimality condition analysis for the multi-objective optimization model to design the optimal-pole algorithm and obtain an efficient collaborative reduction scheme. In the empirical analysis, the data of pollutant emission and final consumption of energies of Tianjin in 1996-2012 was employed to verify the effectiveness of the model and analyze the efficient solution and the corresponding dominant set. In the last part, several suggestions for collaborative reduction are recommended and the drawn conclusions are stated.

Collaborative Emission Reduction Model Based on Multi-Objective Optimization for Greenhouse Gases and Air Pollutants

PubMed Central

Zhang, Yi-min; Wan, Xiao-le; Liu, Yuan-yuan; Wang, Yu-zhi

2016-01-01

CO2 emission influences not only global climate change but also international economic and political situations. Thus, reducing the emission of CO2, a major greenhouse gas, has become a major issue in China and around the world as regards preserving the environmental ecology. Energy consumption from coal, oil, and natural gas is primarily responsible for the production of greenhouse gases and air pollutants such as SO2 and NOX, which are the main air pollutants in China. In this study, a mathematical multi-objective optimization method was adopted to analyze the collaborative emission reduction of three kinds of gases on the basis of their common restraints in different ways of energy consumption to develop an economic, clean, and efficient scheme for energy distribution. The first part introduces the background research, the collaborative emission reduction for three kinds of gases, the multi-objective optimization, the main mathematical modeling, and the optimization method. The second part discusses the four mathematical tools utilized in this study, which include the Granger causality test to analyze the causality between air quality and pollutant emission, a function analysis to determine the quantitative relation between energy consumption and pollutant emission, a multi-objective optimization to set up the collaborative optimization model that considers energy consumption, and an optimality condition analysis for the multi-objective optimization model to design the optimal-pole algorithm and obtain an efficient collaborative reduction scheme. In the empirical analysis, the data of pollutant emission and final consumption of energies of Tianjin in 1996–2012 was employed to verify the effectiveness of the model and analyze the efficient solution and the corresponding dominant set. In the last part, several suggestions for collaborative reduction are recommended and the drawn conclusions are stated. PMID:27010658

Diffusion Forecasting Model with Basis Functions from QR-Decomposition

NASA Astrophysics Data System (ADS)

Harlim, John; Yang, Haizhao

2018-06-01

The diffusion forecasting is a nonparametric approach that provably solves the Fokker-Planck PDE corresponding to Itô diffusion without knowing the underlying equation. The key idea of this method is to approximate the solution of the Fokker-Planck equation with a discrete representation of the shift (Koopman) operator on a set of basis functions generated via the diffusion maps algorithm. While the choice of these basis functions is provably optimal under appropriate conditions, computing these basis functions is quite expensive since it requires the eigendecomposition of an N× N diffusion matrix, where N denotes the data size and could be very large. For large-scale forecasting problems, only a few leading eigenvectors are computationally achievable. To overcome this computational bottleneck, a new set of basis functions constructed by orthonormalizing selected columns of the diffusion matrix and its leading eigenvectors is proposed. This computation can be carried out efficiently via the unpivoted Householder QR factorization. The efficiency and effectiveness of the proposed algorithm will be shown in both deterministically chaotic and stochastic dynamical systems; in the former case, the superiority of the proposed basis functions over purely eigenvectors is significant, while in the latter case forecasting accuracy is improved relative to using a purely small number of eigenvectors. Supporting arguments will be provided on three- and six-dimensional chaotic ODEs, a three-dimensional SDE that mimics turbulent systems, and also on the two spatial modes associated with the boreal winter Madden-Julian Oscillation obtained from applying the Nonlinear Laplacian Spectral Analysis on the measured Outgoing Longwave Radiation.

Diffusion Forecasting Model with Basis Functions from QR-Decomposition

NASA Astrophysics Data System (ADS)

Harlim, John; Yang, Haizhao

2017-12-01

The diffusion forecasting is a nonparametric approach that provably solves the Fokker-Planck PDE corresponding to Itô diffusion without knowing the underlying equation. The key idea of this method is to approximate the solution of the Fokker-Planck equation with a discrete representation of the shift (Koopman) operator on a set of basis functions generated via the diffusion maps algorithm. While the choice of these basis functions is provably optimal under appropriate conditions, computing these basis functions is quite expensive since it requires the eigendecomposition of an N× N diffusion matrix, where N denotes the data size and could be very large. For large-scale forecasting problems, only a few leading eigenvectors are computationally achievable. To overcome this computational bottleneck, a new set of basis functions constructed by orthonormalizing selected columns of the diffusion matrix and its leading eigenvectors is proposed. This computation can be carried out efficiently via the unpivoted Householder QR factorization. The efficiency and effectiveness of the proposed algorithm will be shown in both deterministically chaotic and stochastic dynamical systems; in the former case, the superiority of the proposed basis functions over purely eigenvectors is significant, while in the latter case forecasting accuracy is improved relative to using a purely small number of eigenvectors. Supporting arguments will be provided on three- and six-dimensional chaotic ODEs, a three-dimensional SDE that mimics turbulent systems, and also on the two spatial modes associated with the boreal winter Madden-Julian Oscillation obtained from applying the Nonlinear Laplacian Spectral Analysis on the measured Outgoing Longwave Radiation.

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

NASA Astrophysics Data System (ADS)

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

2005-06-01

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

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.

HM{sup +}–RG complexes (M = group 2 metal; RG = rare gas): Physical vs. chemical interactions

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

Harris, Joe P.; Dodson, Hannah; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk

2015-04-21

Previous work on the HM{sup +}–He complexes (M = Be–Ra) has been extended to the cases of the heavier rare gas atoms, HM{sup +}–RG (RG = Ne–Rn). Optimized geometries and harmonic vibrational frequencies have been calculated using MP2 theory and quadruple-ζ quality basis sets. Dissociation energies for the loss of the rare gas atom have been calculated at these optimized geometries using coupled cluster with single and double excitations and perturbative triples, CCSD(T)theory, extrapolating interaction energies to the basis set limit. Comparisons are made between the present data and the previously obtained helium results, as well as to those ofmore » the bare HM{sup +} molecules; furthermore, comparisons are made to the related M{sup +}–RG and M{sup 2+}–RG complexes. Partial atomic charge analyses have also been undertaken, and these used to test a simple charge-induced dipole model. Molecular orbital diagrams are presented together with contour plots of the natural orbitals from the quadratic configuration with single and double excitations (QCISD) density. The conclusion is that the majority of these complexes are physically bound, with very little sharing of electron density; however, for M = Be, and to a lesser extent M = Mg, some evidence for chemical effects is seen in HM{sup +}–RG complexes involving RG atoms with the higher atomic numbers.« less

Efficient parallel architecture for highly coupled real-time linear system applications

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Homaifar, Abdollah; Barua, Soumavo

1988-01-01

A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

Tests of the Grobner Basis Solution for Lightning Ground Flash Fraction Retrieval

NASA Technical Reports Server (NTRS)

Koshak, William; Solakiewicz, Richard; Attele, Rohan

2011-01-01

Satellite lightning imagers such as the NASA Tropical Rainfall Measuring Mission Lightning Imaging Sensor (TRMM/LIS) and the future GOES-R Geostationary Lightning Mapper (GLM) are designed to detect total lightning (ground flashes + cloud flashes). However, there is a desire to discriminate ground flashes from cloud flashes from the vantage point of space since this would enhance the overall information content of the satellite lightning data and likely improve its operational and scientific applications (e.g., in severe weather warning, lightning nitrogen oxides studies, and global electric circuit analyses). A Bayesian inversion method was previously introduced for retrieving the fraction of ground flashes in a set of flashes observed from a satellite lightning imager. The method employed a constrained mixed exponential distribution model to describe the lightning optical measurements. To obtain the optimum model parameters (one of which is the ground flash fraction), a scalar function was minimized by a numerical method. In order to improve this optimization, a Grobner basis solution was introduced to obtain analytic representations of the model parameters that serve as a refined initialization scheme to the numerical optimization. In this study, we test the efficacy of the Grobner basis initialization using actual lightning imager measurements and ground flash truth derived from the national lightning network.

Fast function-on-scalar regression with penalized basis expansions.

PubMed

Reiss, Philip T; Huang, Lei; Mennes, Maarten

2010-01-01

Regression models for functional responses and scalar predictors are often fitted by means of basis functions, with quadratic roughness penalties applied to avoid overfitting. The fitting approach described by Ramsay and Silverman in the 1990 s amounts to a penalized ordinary least squares (P-OLS) estimator of the coefficient functions. We recast this estimator as a generalized ridge regression estimator, and present a penalized generalized least squares (P-GLS) alternative. We describe algorithms by which both estimators can be implemented, with automatic selection of optimal smoothing parameters, in a more computationally efficient manner than has heretofore been available. We discuss pointwise confidence intervals for the coefficient functions, simultaneous inference by permutation tests, and model selection, including a novel notion of pointwise model selection. P-OLS and P-GLS are compared in a simulation study. Our methods are illustrated with an analysis of age effects in a functional magnetic resonance imaging data set, as well as a reanalysis of a now-classic Canadian weather data set. An R package implementing the methods is publicly available.

NDARC-NASA Design and Analysis of Rotorcraft Theoretical Basis and Architecture

NASA Technical Reports Server (NTRS)

Johnson, Wayne

2010-01-01

The theoretical basis and architecture of the conceptual design tool NDARC (NASA Design and Analysis of Rotorcraft) are described. The principal tasks of NDARC are to design (or size) a rotorcraft to satisfy specified design conditions and missions, and then analyze the performance of the aircraft for a set of off-design missions and point operating conditions. The aircraft consists of a set of components, including fuselage, rotors, wings, tails, and propulsion. For each component, attributes such as performance, drag, and weight can be calculated. The aircraft attributes are obtained from the sum of the component attributes. NDARC provides a capability to model general rotorcraft configurations, and estimate the performance and attributes of advanced rotor concepts. The software has been implemented with low-fidelity models, typical of the conceptual design environment. Incorporation of higher-fidelity models will be possible, as the architecture of the code accommodates configuration flexibility, a hierarchy of models, and ultimately multidisciplinary design, analysis and optimization.

Chopped random-basis quantum optimization

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

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.

Development of new business opportunities for minorities in nuclear energy. Final report

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

Spight, C.

1980-12-15

In Part I of this report the basis for the optimal development of new business opportunities for minorities in nuclear energy programs is defined within the successful completion of all contract tasks. The basis presented consists of an identification of a set of qualified minority-owned small businesses, a defined reservoir of highly trained minorities with applicable expertise, a policy context for the development of opportunities, and a proposed networking structure for information transfer/professional development. In Part II a contractor-focused analysis of the structure of the nuclear industry, a breakdown of the DOE nuclear program by region and functional area, andmore » a directory of minority-owned small businesses by region are presented.« less

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Correlation consistent basis sets for the atoms In–Xe

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

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

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

Optimal ordering quantities for substitutable deteriorating items under joint replenishment with cost of substitution

NASA Astrophysics Data System (ADS)

Mishra, Vinod Kumar

2017-09-01

In this paper we develop an inventory model, to determine the optimal ordering quantities, for a set of two substitutable deteriorating items. In this inventory model the inventory level of both items depleted due to demands and deterioration and when an item is out of stock, its demands are partially fulfilled by the other item and all unsatisfied demand is lost. Each substituted item incurs a cost of substitution and the demands and deterioration is considered to be deterministic and constant. Items are order jointly in each ordering cycle, to take the advantages of joint replenishment. The problem is formulated and a solution procedure is developed to determine the optimal ordering quantities that minimize the total inventory cost. We provide an extensive numerical and sensitivity analysis to illustrate the effect of different parameter on the model. The key observation on the basis of numerical analysis, there is substantial improvement in the optimal total cost of the inventory model with substitution over without substitution.

Prediction of chemical biodegradability using support vector classifier optimized with differential evolution.

PubMed

Cao, Qi; Leung, K M

2014-09-22

Reliable computer models for the prediction of chemical biodegradability from molecular descriptors and fingerprints are very important for making health and environmental decisions. Coupling of the differential evolution (DE) algorithm with the support vector classifier (SVC) in order to optimize the main parameters of the classifier resulted in an improved classifier called the DE-SVC, which is introduced in this paper for use in chemical biodegradability studies. The DE-SVC was applied to predict the biodegradation of chemicals on the basis of extensive sample data sets and known structural features of molecules. Our optimization experiments showed that DE can efficiently find the proper parameters of the SVC. The resulting classifier possesses strong robustness and reliability compared with grid search, genetic algorithm, and particle swarm optimization methods. The classification experiments conducted here showed that the DE-SVC exhibits better classification performance than models previously used for such studies. It is a more effective and efficient prediction model for chemical biodegradability.

Performance Analysis of the Automotive TEG with Respect to the Geometry of the Modules

NASA Astrophysics Data System (ADS)

Yu, C. G.; Zheng, S. J.; Deng, Y. D.; Su, C. Q.; Wang, Y. P.

2017-05-01

Recently there has been increasing interest in applying thermoelectric technology to recover waste heat in automotive exhaust gas. Due to the limited space in the vehicle, it's meaningful to improve the TEG (thermoelectric generator) performance by optimizing the module geometry. This paper analyzes the performance of bismuth telluride modules for two criteria (power density and power output per area), and researches the relationship between the performance and the geometry of the modules. A geometry factor is defined for the thermoelectric element to describe the module geometry, and a mathematical model is set up to study the effects of the module geometry on its performance. It has been found out that the optimal geometry factors for maximum output power, power density and power output per unit area are different, and the value of the optimal geometry factors will be affected by the volume of the thermoelectric material and the thermal input. The results can be referred to as the basis for optimizing the performance of the thermoelectric modules.

Sparse time-frequency decomposition based on dictionary adaptation.

PubMed

Hou, Thomas Y; Shi, Zuoqiang

2016-04-13

In this paper, we propose a time-frequency analysis method to obtain instantaneous frequencies and the corresponding decomposition by solving an optimization problem. In this optimization problem, the basis that is used to decompose the signal is not known a priori. Instead, it is adapted to the signal and is determined as part of the optimization problem. In this sense, this optimization problem can be seen as a dictionary adaptation problem, in which the dictionary is adaptive to one signal rather than a training set in dictionary learning. This dictionary adaptation problem is solved by using the augmented Lagrangian multiplier (ALM) method iteratively. We further accelerate the ALM method in each iteration by using the fast wavelet transform. We apply our method to decompose several signals, including signals with poor scale separation, signals with outliers and polluted by noise and a real signal. The results show that this method can give accurate recovery of both the instantaneous frequencies and the intrinsic mode functions. © 2016 The Author(s).

Proceedings of the 2016 Clinical Nutrition Week Research Workshop-The Optimal Dose of Protein Provided to Critically Ill Patients.

PubMed

Heyland, Daren K; Rooyakers, Olav; Mourtzakis, Marina; Stapleton, Renee D

2017-02-01

Recent literature has created considerable confusion about the optimal amount of protein/amino acids that should be provided to the critically ill patient. In fact, the evidentiary basis that directly tries to answer this question is relatively small. As a clinical nutrition research community, there is an urgent need to develop the optimal methods to assess the impact of exogenous protein/amino acid administration in the intensive care unit setting. That assessment can be conducted at various levels: (1) impact on stress response pathways, (2) impact on muscle synthesis and protein balance, (3) impact on muscle mass and function, and (4) impact on the patient's recovery. The objective of this research workshop was to review current literature relating to protein/amino acid administration for the critically ill patient and clinical outcomes and to discuss the key measurement and methodological features of future studies that should be done to inform the optimal protein/amino acid dose provided to critically ill patients.

Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311 ++G(d,2p) basis sets

NASA Astrophysics Data System (ADS)

Khajehzadeh, Mostafa; Moghadam, Majid

2017-06-01

Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ → σ ∗ and π → π ∗ and LP(1) → σ ∗ and LP(2) → σ ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H2O, CH3CN and C6H12. UV-Vis spectrum of the drug was taken using DFT/B3LYP and PBEPBE methods with 6-311 ++ G(d,2p) and LanL2DZ basis sets as well as solvents H2O, CH3CN and C6H12 and the associated transmissions were examined.

Vibrational spectroscopic, structural and nonlinear optical activity studies on 6-aminonicotinamide: A DFT approach

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

Asath, R. Mohamed; Premkumar, S.; Mathavan, T.

2016-05-23

The conformational analysis was carried out for 6-aminonicotinamide (ANA) using potential energy surface scan method and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the related molecular properties were calculated. The ultraviolet-visible spectrum was simulated for both in the gas phase andmore » liquid phase (ethanol) and the π to π* electronic transition was predicted. The nonlinear optical (NLO) activity was studied by means of the first order hyperpolarizability value, which was 8.61 times greater than the urea and the natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ANA molecule is a promising candidate for the NLO materials.« less

Coupling Network Computing Applications in Air-cooled Turbine Blades Optimization

NASA Astrophysics Data System (ADS)

Shi, Liang; Yan, Peigang; Xie, Ming; Han, Wanjin

2018-05-01

Through establishing control parameters from blade outside to inside, the parametric design of air-cooled turbine blade based on airfoil has been implemented. On the basis of fast updating structure features and generating solid model, a complex cooling system has been created. Different flow units are modeled into a complex network topology with parallel and serial connection. Applying one-dimensional flow theory, programs have been composed to get pipeline network physical quantities along flow path, including flow rate, pressure, temperature and other parameters. These inner units parameters set as inner boundary conditions for external flow field calculation program HIT-3D by interpolation, thus to achieve full field thermal coupling simulation. Referring the studies in literatures to verify the effectiveness of pipeline network program and coupling algorithm. After that, on the basis of a modified design, and with the help of iSIGHT-FD, an optimization platform had been established. Through MIGA mechanism, the target of enhancing cooling efficiency has been reached, and the thermal stress has been effectively reduced. Research work in this paper has significance for rapid deploying the cooling structure design.

Vibrational spectroscopic, structural and nonlinear optical activity studies on 2-amino-3-chloro-5-trifluoromethyl pyridine: A DFT approach

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

Asath, R. Mohamed; Premkumar, S.; Mathavan, T.

2016-05-23

The conformational analysis was carried out for 2-amino-3-chloro-5-trifluoromethylpyridine using potential energy surface (PES) scan and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program package. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the calculation of ionization energy, electron affinity, global hardness, chemical potential, electrophilicity index and softness of the moleculemore » were carried out. The nonlinear optical (NLO) activity was studied and the first order hyperpolarizability value was computed, which was 3.48 times greater than the urea. The natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ACTP molecule is a promising candidate for NLO materials.« less

DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

NASA Astrophysics Data System (ADS)

Sienkiewicz-Gromiuk, Justyna

2018-01-01

The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

Vibrational spectroscopic, structural and nonlinear optical activity studies on 6-aminonicotinamide: A DFT approach

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Premkumar, S.; Rekha, T. N.; Jawahar, A.; Mathavan, T.; Benial, A. Milton Franklin

2016-05-01

The conformational analysis was carried out for 6-aminonicotinamide (ANA) using potential energy surface scan method and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the related molecular properties were calculated. The ultraviolet-visible spectrum was simulated for both in the gas phase and liquid phase (ethanol) and the л to л* electronic transition was predicted. The nonlinear optical (NLO) activity was studied by means of the first order hyperpolarizability value, which was 8.61 times greater than the urea and the natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ANA molecule is a promising candidate for the NLO materials.

Vibrational spectroscopic, structural and nonlinear optical activity studies on 2-amino-3-chloro-5-trifluoromethyl pyridine: A DFT approach

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Premkumar, S.; Rekha, T. N.; Jawahar, A.; Mathavan, T.; Benial, A. Milton Franklin

2016-05-01

The conformational analysis was carried out for 2-amino-3-chloro-5-trifluoromethylpyridine using potential energy surface (PES) scan and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVQZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program package. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the calculation of ionization energy, electron affinity, global hardness, chemical potential, electrophilicity index and softness of the molecule were carried out. The nonlinear optical (NLO) activity was studied and the first order hyperpolarizability value was computed, which was 3.48 times greater than the urea. The natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the ACTP molecule is a promising candidate for NLO materials.

Conformational, vibrational spectroscopic and nonlinear optical activity studies on N,N-Di-Boc-2-amino pyridine : A DFT approach

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Premkumar, R.; Mathavan, T.; Benial, A. Milton Franklin

2017-05-01

The conformational analysis was carried out for N,N-Di-Boc-2-amino pyridine using potential energy surface (PES) scan and the most stable optimized conformer was predicted. The theoretical vibrational frequencies were calculated for the optimized geometry using DFT/B3LYP cc-pVTZ basis set by Gaussian 09 Program. The vibrational frequencies were assigned on the basis of potential energy distribution calculation using VEDA 4.0 program package. The Mulliken atomic charge values were calculated. In the Frontier molecular orbitals analysis, the molecular reactivity, kinetic stability, intermolecular charge transfer studies and the calculation of ionization energy, electron affinity, global hardness, chemical potential, electrophilicity index and softness of the molecule were carried out. The nonlinear optical (NLO) activity was examined and the first order hyperpolarizability value was computed, which was 2.27 times greater than the urea. The natural bond orbital analysis was also performed to confirm the NLO activity of the molecule. Hence, the DBAP molecule is a promising candidate for NLO materials.

Optimal diabetes care--can we afford it?: evidence-based diabetes care could be highly cost effective.

PubMed

Chowdhury, T A; Bennett-Richards, P

2013-11-01

Management of diabetes is expensive and set to get costlier. Managing the condition and it's devastating complications imposing a huge societal and economic toll on healthcare systems worldwide. While many interventions to reduce complications are available, a number of interventions do not have a strong basis in evidence, and lack cost effectiveness. In a time of economic austerity, and unprecedented pressure to reduce costs of health care in the UK, are there ways improving care, without driving up cost?

Efficient hybrid-symbolic methods for quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Scott, T. C.; Zhang, Wenxing

2015-06-01

We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

Optimal villi density for maximal oxygen uptake in the human placenta.

PubMed

Serov, A S; Salafia, C M; Brownbill, P; Grebenkov, D S; Filoche, M

2015-01-07

We present a stream-tube model of oxygen exchange inside a human placenta functional unit (a placentone). The effect of villi density on oxygen transfer efficiency is assessed by numerically solving the diffusion-convection equation in a 2D+1D geometry for a wide range of villi densities. For each set of physiological parameters, we observe the existence of an optimal villi density providing a maximal oxygen uptake as a trade-off between the incoming oxygen flow and the absorbing villus surface. The predicted optimal villi density 0.47±0.06 is compatible to previous experimental measurements. Several other ways to experimentally validate the model are also proposed. The proposed stream-tube model can serve as a basis for analyzing the efficiency of human placentas, detecting possible pathologies and diagnosing placental health risks for newborns by using routine histology sections collected after birth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Computing Finite-Time Lyapunov Exponents with Optimally Time Dependent Reduction

NASA Astrophysics Data System (ADS)

Babaee, Hessam; Farazmand, Mohammad; Sapsis, Themis; Haller, George

2016-11-01

We present a method to compute Finite-Time Lyapunov Exponents (FTLE) of a dynamical system using Optimally Time-Dependent (OTD) reduction recently introduced by H. Babaee and T. P. Sapsis. The OTD modes are a set of finite-dimensional, time-dependent, orthonormal basis {ui (x , t) } |i=1N that capture the directions associated with transient instabilities. The evolution equation of the OTD modes is derived from a minimization principle that optimally approximates the most unstable directions over finite times. To compute the FTLE, we evolve a single OTD mode along with the nonlinear dynamics. We approximate the FTLE from the reduced system obtained from projecting the instantaneous linearized dynamics onto the OTD mode. This results in a significant reduction in the computational cost compared to conventional methods for computing FTLE. We demonstrate the efficiency of our method for double Gyre and ABC flows. ARO project 66710-EG-YIP.

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

NASA Astrophysics Data System (ADS)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

The calculations of small molecular conformation energy differences by density functional method

NASA Astrophysics Data System (ADS)

Topol, I. A.; Burt, S. K.

1993-03-01

The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-02-01

In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid

NASA Astrophysics Data System (ADS)

Dikmen, Gökhan; Alver, Özgür

2015-11-01

Possible stable conformers and geometrical molecular structures of 6-Bromo-3-Pyridinyl Boronic acid (6B3PBA; C5H5BBrNO2) were studied experimentally and theoretically using FT-IR and Raman spectroscopic methods. FT-IR and Raman spectra were recorded in the region of 4000-400 cm-1 and 3700-400 cm-1, respectively. The structural properties were investigated further, using 1H, 13C, 1H coupled 13C, HETCOR, COSY and APT NMR techniques. The optimized geometric structures were searched by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. Vibrational wavenumbers of 6B3PBA were calculated whereby B3LYP density functional methods including 6-311++G(d, p), 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. The comparison of the experimentally and theoretically obtained results using mean absolute error and experimental versus calculated correlation coefficients for the vibrational wavenumbers indicates that B3LYP method with 6-311++G(d, p) gives more satisfactory results for predicting vibrational wavenumbers when compared to the 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. However, this method and none of the mentioned methods here seem suitable for the calculations of OH stretching modes, most likely because increasing unharmonicity in the high wave number region and possible intra and inter molecular interactions at OH edges lead some deviations between experimental and theoretical results. Moreover, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated using scaled quantum mechanical (SQM) method.

Toward a muon-specific electronic structure theory: effective electronic Hartree-Fock equations for muonic molecules.

PubMed

Rayka, Milad; Goli, Mohammad; Shahbazian, Shant

2018-02-07

An effective set of Hartree-Fock (HF) equations are derived for electrons of muonic systems, i.e., molecules containing a positively charged muon, conceiving the muon as a quantum oscillator, which are completely equivalent to the usual two-component HF equations used to derive stationary states of the muonic molecules. In these effective equations, a non-Coulombic potential is added to the orthodox coulomb and exchange potential energy terms, which describes the interaction of the muon and the electrons effectively and is optimized during the self-consistent field cycles. While in the two-component HF equations a muon is treated as a quantum particle, in the effective HF equations it is absorbed into the effective potential and practically transformed into an effective potential field experienced by electrons. The explicit form of the effective potential depends on the nature of muon's vibrations and is derivable from the basis set used to expand the muonic spatial orbital. The resulting effective Hartree-Fock equations are implemented computationally and used successfully, as a proof of concept, in a series of muonic molecules containing all atoms from the second and third rows of the Periodic Table. To solve the algebraic version of the equations muon-specific Gaussian basis sets are designed for both muon and surrounding electrons and it is demonstrated that the optimized exponents are quite distinct from those derived for the hydrogen isotopes. The developed effective HF theory is quite general and in principle can be used for any muonic system while it is the starting point for a general effective electronic structure theory that incorporates various types of quantum correlations into the muonic systems beyond the HF equations.

[Research on spectra recognition method for cabbages and weeds based on PCA and SIMCA].

PubMed

Zu, Qin; Deng, Wei; Wang, Xiu; Zhao, Chun-Jiang

2013-10-01

In order to improve the accuracy and efficiency of weed identification, the difference of spectral reflectance was employed to distinguish between crops and weeds. Firstly, the different combinations of Savitzky-Golay (SG) convolutional derivation and multiplicative scattering correction (MSC) method were applied to preprocess the raw spectral data. Then the clustering analysis of various types of plants was completed by using principal component analysis (PCA) method, and the feature wavelengths which were sensitive for classifying various types of plants were extracted according to the corresponding loading plots of the optimal principal components in PCA results. Finally, setting the feature wavelengths as the input variables, the soft independent modeling of class analogy (SIMCA) classification method was used to identify the various types of plants. The experimental results of classifying cabbages and weeds showed that on the basis of the optimal pretreatment by a synthetic application of MSC and SG convolutional derivation with SG's parameters set as 1rd order derivation, 3th degree polynomial and 51 smoothing points, 23 feature wavelengths were extracted in accordance with the top three principal components in PCA results. When SIMCA method was used for classification while the previously selected 23 feature wavelengths were set as the input variables, the classification rates of the modeling set and the prediction set were respectively up to 98.6% and 100%.

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

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

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

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

PubMed

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

2013-10-10

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

On the structure and spin states of Fe(III)-EDDHA complexes.

PubMed

Gómez-Gallego, Mar; Fernández, Israel; Pellico, Daniel; Gutiérrez, Angel; Sierra, Miguel A; Lucena, Juan J

2006-07-10

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.

The association between resting functional connectivity and dispositional optimism.

PubMed

Ran, Qian; Yang, Junyi; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Dong

2017-01-01

Dispositional optimism is an individual characteristic that plays an important role in human experience. Optimists are people who tend to hold positive expectations for their future. Previous studies have focused on the neural basis of optimism, such as task response neural activity and brain structure volume. However, the functional connectivity between brain regions of the dispositional optimists are poorly understood. Previous study suggested that the ventromedial prefrontal cortex (vmPFC) are associated with individual differences in dispositional optimism, but it is unclear whether there are other brain regions that combine with the vmPFC to contribute to dispositional optimism. Thus, the present study used the resting-state functional connectivity (RSFC) approach and set the vmPFC as the seed region to examine if differences in functional brain connectivity between the vmPFC and other brain regions would be associated with individual differences in dispositional optimism. The results found that dispositional optimism was significantly positively correlated with the strength of the RSFC between vmPFC and middle temporal gyrus (mTG) and negativly correlated with RSFC between vmPFC and inferior frontal gyrus (IFG). These findings may be suggested that mTG and IFG which associated with emotion processes and emotion regulation also play an important role in the dispositional optimism.

The association between resting functional connectivity and dispositional optimism

PubMed Central

Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Dong

2017-01-01

Dispositional optimism is an individual characteristic that plays an important role in human experience. Optimists are people who tend to hold positive expectations for their future. Previous studies have focused on the neural basis of optimism, such as task response neural activity and brain structure volume. However, the functional connectivity between brain regions of the dispositional optimists are poorly understood. Previous study suggested that the ventromedial prefrontal cortex (vmPFC) are associated with individual differences in dispositional optimism, but it is unclear whether there are other brain regions that combine with the vmPFC to contribute to dispositional optimism. Thus, the present study used the resting-state functional connectivity (RSFC) approach and set the vmPFC as the seed region to examine if differences in functional brain connectivity between the vmPFC and other brain regions would be associated with individual differences in dispositional optimism. The results found that dispositional optimism was significantly positively correlated with the strength of the RSFC between vmPFC and middle temporal gyrus (mTG) and negativly correlated with RSFC between vmPFC and inferior frontal gyrus (IFG). These findings may be suggested that mTG and IFG which associated with emotion processes and emotion regulation also play an important role in the dispositional optimism. PMID:28700613

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

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

Choi, Sunghwan; Hong, Kwangwoo; Kim, Jaewook

2015-03-07

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

Dire deadlines: coping with dysfunctional family dynamics in an end-of-life care setting.

PubMed

Holst, Lone; Lundgren, Maren; Olsen, Lutte; Ishøy, Torben

2009-01-01

Working in a hospice and being able to focus on individualized, specialized end-of-life care is a privilege for the hospice staff member. However, it also presents the hospice staff with unique challenges. This descriptive study is based upon two cases from an end-of-life care setting in Denmark, where dysfunctional family dynamics presented added challenges to the staff members in their efforts to provide optimal palliative care. The hospice triad--the patient, the staff member and the family member--forms the basis for communication and intervention in a hospice. Higher expectations and demands of younger, more well-informed patients and family members challenge hospice staff in terms of information and communication when planning for care. The inherent risk factors of working with patients in the terminal phase of life become a focal point in the prevention of the development of compassion fatigue among staff members. A series of coping strategies to more optimally manage dysfunctional families in a setting where time is of the essence are then presented in an effort to empower the hospice team, to prevent splitting among staff members, and to improve quality of care.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

A new optimized GA-RBF neural network algorithm.

PubMed

Jia, Weikuan; Zhao, Dean; Shen, Tian; Su, Chunyang; Hu, Chanli; Zhao, Yuyan

2014-01-01

When confronting the complex problems, radial basis function (RBF) neural network has the advantages of adaptive and self-learning ability, but it is difficult to determine the number of hidden layer neurons, and the weights learning ability from hidden layer to the output layer is low; these deficiencies easily lead to decreasing learning ability and recognition precision. Aiming at this problem, we propose a new optimized RBF neural network algorithm based on genetic algorithm (GA-RBF algorithm), which uses genetic algorithm to optimize the weights and structure of RBF neural network; it chooses new ways of hybrid encoding and optimizing simultaneously. Using the binary encoding encodes the number of the hidden layer's neurons and using real encoding encodes the connection weights. Hidden layer neurons number and connection weights are optimized simultaneously in the new algorithm. However, the connection weights optimization is not complete; we need to use least mean square (LMS) algorithm for further leaning, and finally get a new algorithm model. Using two UCI standard data sets to test the new algorithm, the results show that the new algorithm improves the operating efficiency in dealing with complex problems and also improves the recognition precision, which proves that the new algorithm is valid.

DFT simulations and vibrational spectra of 2-amino-2-methyl-1,3-propanediol.

PubMed

Renuga Devi, T S; Sharmi kumar, J; Ramkumaar, G R

2014-12-10

The FTIR and FT-Raman spectra of 2-amino-2-methyl-1,3-propanediol were recorded in the regions 4000-400cm(-1) and 4000-50cm(-1) respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and density functional method (B3LYP) with the augmented-correlation consistent-polarized valence double zeta (aug-cc-pVDZ) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed on the basis of the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Mulliken charges were calculated using both Hartee-Fock and density functional method using the aug-cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. (1)H and (13)C NMR chemical shifts of the molecule were calculated using Gauge-Independent Atomic Orbital (GIAO) method and were compared with experimental results. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2

NASA Astrophysics Data System (ADS)

Kalinić, Marko; Zloh, Mire; Erić, Slavica

2014-11-01

Enhancer of Zeste Homolog 2 (EZH2) is a SET domain protein lysine methyltransferase (PKMT) which has recently emerged as a chemically tractable and therapeutically promising epigenetic target, evidenced by the discovery and characterization of potent and highly selective EZH2 inhibitors. However, no experimental structures of the inhibitors co-crystallized to EZH2 have been resolved, and the structural basis for their activity and selectivity remains unknown. Considering the need to minimize cross-reactivity between prospective PKMT inhibitors, much can be learned from understanding the molecular basis for selective inhibition of EZH2. Thus, to elucidate the binding of small-molecule inhibitors to EZH2, we have developed a model of its fully-formed cofactor binding site and used it to carry out molecular dynamics simulations of protein-ligand complexes, followed by molecular mechanics/generalized born surface area calculations. The obtained results are in good agreement with biochemical inhibition data and reflect the structure-activity relationships of known ligands. Our findings suggest that the variable and flexible post-SET domain plays an important role in inhibitor binding, allowing possibly distinct binding modes of inhibitors with only small variations in their structure. Insights from this study present a good basis for design of novel and optimization of existing compounds targeting the cofactor binding site of EZH2.

On the efficiency of treating singularities in triatomic variational vibrational computations. The vibrational states of H(+)3 up to dissociation.

PubMed

Szidarovszky, Tamás; Császár, Attila G; Czakó, Gábor

2010-08-01

Several techniques of varying efficiency are investigated, which treat all singularities present in the triatomic vibrational kinetic energy operator given in orthogonal internal coordinates of the two distances-one angle type. The strategies are based on the use of a direct-product basis built from one-dimensional discrete variable representation (DVR) bases corresponding to the two distances and orthogonal Legendre polynomials, or the corresponding Legendre-DVR basis, corresponding to the angle. The use of Legendre functions ensures the efficient treatment of the angular singularity. Matrix elements of the singular radial operators are calculated employing DVRs using the quadrature approximation as well as special DVRs satisfying the boundary conditions and thus allowing for the use of exact DVR expressions. Potential optimized (PO) radial DVRs, based on one-dimensional Hamiltonians with potentials obtained by fixing or relaxing the two non-active coordinates, are also studied. The numerical calculations employed Hermite-DVR, spherical-oscillator-DVR, and Bessel-DVR bases as the primitive radial functions. A new analytical formula is given for the determination of the matrix elements of the singular radial operator using the Bessel-DVR basis. The usually claimed failure of the quadrature approximation in certain singular integrals is revisited in one and three dimensions. It is shown that as long as no potential optimization is carried out the quadrature approximation works almost as well as the exact DVR expressions. If wave functions with finite amplitude at the boundary are to be computed, the basis sets need to meet the required boundary conditions. The present numerical results also confirm that PO-DVRs should be constructed employing relaxed potentials and PO-DVRs can be useful for optimizing quadrature points for calculations applying large coordinate intervals and describing large-amplitude motions. The utility and efficiency of the different algorithms is demonstrated by the computation of converged near-dissociation vibrational energy levels for the H molecular ion.

Accurate Methods for Large Molecular Systems (Preprint)

DTIC Science & Technology

2009-01-06

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

An Alternative Mechanism for the Dimerization of Formic Acid

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

Brinkman, Nicole R.; Tschumper, Gregory; Yan, Ge

Gas-phase formic acid exists primarily as a cyclic dimer. The mechanism of dimerization has been traditionally considered to be a synchronous process; however, recent experimental findings suggest a possible alternative mechanism by which two formic acid monomers proceed through an acyclic dimer to the cyclic dimer in a stepwise process. To investigate this newly proposed process of dimerization in formic acid, density functional theory and second-order Moeller-Plesset perturbation theory (MP2) have been used to optimize cis and trans monomers of formic acid, the acyclic and cyclic dimers, and the acyclic and cyclic transition states between minima. Single-point energies of themore » trans monomer, dimer minima, and transition states at the MP2/TZ2P+diff optimized geometries were computed at the coupled-cluster level of theory including singles and doubles with perturbatively applied triple excitations [CCSD(T)] with an aug-cc-pVTZ basis set to obtain an accurate determination of energy barriers and dissociation energies. A counterpoise correction was performed to determine an estimate of the basis set superposition error in computing relative energies. The explicitly correlated MP2 method of Kutzelnigg and Klopper (MP2-R12) was used to provide an independent means for obtaining the MP2 one-particle limit. The cyclic minimum is predicted to be 6.3 kcal/mol more stable than the acyclic minimum, and the barrier to double proton transfer is 7.1 kcal/mol.« less

Structural and vibrational spectroscopic studies on charge transfer and ionic hydrogen bonding interactions of melaminium benzoate dihydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Gunasekaran, S.; Rajakumar, P. R.; Anbalagan, G.

2015-06-01

Single crystals of melaminium benzoate dihydrate (MBDH) have been grown from aqueous solution by the slow solvent evaporation method at room temperature. Crystalline nature of the grown crystal has been confirmed by X-ray powder diffraction studies. The optimized geometry, frequency and intensity of the vibrational bands of MBDH were obtained by the Hartree-Fock and density functional theory using B3LYP/cam-B3LYP with 6-311++G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with the experimental FT-IR and FT-Raman spectral values. The obtained vibrational wavenumbers and optimized geometric parameters are found to be in good agreement with the experimental data. UV-Visible spectrum was recorded in the region 200-400 nm and the electronic properties, HOMO-LUMO energies and other related electronic parameters are calculated. The isotropic chemical shifts computed by 1H and 13C NMR analysis also show good agreement with experimental observation. Natural bond orbital (NBO) analysis has been performed on MBDH compound to analyze the stability of the molecule arising from hyperconjugative interactions and charge delocalization. Molecular electrostatic potential surface (MEP) has also been performed by DFT/cam-B3LYP method with 6-311++G(d,p) basis set. Differential scanning calorimetric measurements performed on the powder sample indicate the phase transition point approximately at 368 and 358 K for heating and cooling, respectively.

Structural and vibrational spectroscopic studies on charge transfer and ionic hydrogen bonding interactions of melaminium benzoate dihydrate.

PubMed

Kanagathara, N; Marchewka, M K; Drozd, M; Gunasekaran, S; Rajakumar, P R; Anbalagan, G

2015-06-15

Single crystals of melaminium benzoate dihydrate (MBDH) have been grown from aqueous solution by the slow solvent evaporation method at room temperature. Crystalline nature of the grown crystal has been confirmed by X-ray powder diffraction studies. The optimized geometry, frequency and intensity of the vibrational bands of MBDH were obtained by the Hartree-Fock and density functional theory using B3LYP/cam-B3LYP with 6-311++G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with the experimental FT-IR and FT-Raman spectral values. The obtained vibrational wavenumbers and optimized geometric parameters are found to be in good agreement with the experimental data. UV-Visible spectrum was recorded in the region 200-400 nm and the electronic properties, HOMO-LUMO energies and other related electronic parameters are calculated. The isotropic chemical shifts computed by (1)H and (13)C NMR analysis also show good agreement with experimental observation. Natural bond orbital (NBO) analysis has been performed on MBDH compound to analyze the stability of the molecule arising from hyperconjugative interactions and charge delocalization. Molecular electrostatic potential surface (MEP) has also been performed by DFT/cam-B3LYP method with 6-311++G(d,p) basis set. Differential scanning calorimetric measurements performed on the powder sample indicate the phase transition point approximately at 368 and 358K for heating and cooling, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Study on the Rule of Super Strata Movement and Subsidence

NASA Astrophysics Data System (ADS)

Yao, Shunli; Yuan, Hongyong; Jiang, Fuxing; Chen, Tao; Wu, Peng

2018-01-01

The movement of key strata is related to the safety of the whole earth’s surface for coal mining under super strata. Based on the key strata theory, the paper comprehensively analyzes the characteristics of the subsidence before and after the instability of the super strata by studing through FLAC3D and microseismic dynamic monitoring of the surface rock movement observation. The stability of the super strata movement is analyzed according to the characteristic value of the subsidence. The subsidence law and quantitative indexes under the control of the super rock strata that provides basis for the prevention and control of surface risk, optimize mining area and face layout and reasonably set mining boundary around mining area. It provides basis for the even growth of mine safety production and regional public safety.

Structural and vibrational spectroscopy investigation of the 5-[(diphenyl) amino] isophthalic acid molecule

NASA Astrophysics Data System (ADS)

Kurt, M.; Şaş, E. Babur; Can, M.; Okur, S.; Icli, S.; Demic, S.

2014-10-01

The molecular structure and vibrations of 5-(diphenyl) amino] isophthalic acid (DPIFA) were investigated by different spectroscopic techniques (such as infrared and Raman). FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. HOMO-LUMO analyses were performed. The theoretical calculations for the molecular structure and spectroscopic studies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After optimizing the geometry of the molecule, vibration wavenumbers and fundamental vibrations wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

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

PubMed

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

2011-06-07

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

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

PubMed

Feller, David; Peterson, Kirk A

2013-08-28

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

Designing an artificial neural network using radial basis function to model exergetic efficiency of nanofluids in mini double pipe heat exchanger

NASA Astrophysics Data System (ADS)

Ghasemi, Nahid; Aghayari, Reza; Maddah, Heydar

2018-06-01

The present study aims at predicting and optimizing exergetic efficiency of TiO2-Al2O3/water nanofluid at different Reynolds numbers, volume fractions and twisted ratios using Artificial Neural Networks (ANN) and experimental data. Central Composite Design (CCD) and cascade Radial Basis Function (RBF) were used to display the significant levels of the analyzed factors on the exergetic efficiency. The size of TiO2-Al2O3/water nanocomposite was 20-70 nm. The parameters of ANN model were adapted by a training algorithm of radial basis function (RBF) with a wide range of experimental data set. Total mean square error and correlation coefficient were used to evaluate the results which the best result was obtained from double layer perceptron neural network with 30 neurons in which total Mean Square Error(MSE) and correlation coefficient (R2) were equal to 0.002 and 0.999, respectively. This indicated successful prediction of the network. Moreover, the proposed equation for predicting exergetic efficiency was extremely successful. According to the optimal curves, the optimum designing parameters of double pipe heat exchanger with inner twisted tape and nanofluid under the constrains of exergetic efficiency 0.937 are found to be Reynolds number 2500, twisted ratio 2.5 and volume fraction( v/v%) 0.05.

Mathematical Methods of System Analysis in Construction Materials

NASA Astrophysics Data System (ADS)

Garkina, Irina; Danilov, Alexander

2017-10-01

System attributes of construction materials are defined: complexity of an object, integrity of set of elements, existence of essential, stable relations between elements defining integrative properties of system, existence of structure, etc. On the basis of cognitive modelling (intensive and extensive properties; the operating parameters) materials (as difficult systems) and creation of the cognitive map the hierarchical modular structure of criteria of quality is under construction. It actually is a basis for preparation of the specification on development of material (the required organization and properties). Proceeding from a modern paradigm (model of statement of problems and their decisions) of development of materials, levels and modules are specified in structure of material. It when using the principles of the system analysis allows to considered technological process as the difficult system consisting of elements of the distinguished specification level: from atomic before separate process. Each element of system depending on an effective objective is considered as separate system with more detailed levels of decomposition. Among them, semantic and qualitative analyses of an object (are considered a research objective, decomposition levels, separate elements and communications between them come to light). Further formalization of the available knowledge in the form of mathematical models (structural identification) is carried out; communications between input and output parameters (parametrical identification) are defined. Hierarchical structures of criteria of quality are under construction for each allocated level. On her the relevant hierarchical structures of system (material) are under construction. Regularities of structurization and formation of properties, generally are considered at the levels from micro to a macrostructure. The mathematical model of material is represented as set of the models corresponding to private criteria by which separate modules and their levels (the mathematical description, a decision algorithm) are defined. Adequacy is established (compliance of results of modelling to experimental data; is defined by the level of knowledge of process and validity of the accepted assumptions). The global criterion of quality of material is considered as a set of private criteria (properties). Synthesis of material is carried out on the basis of one-criteria optimization on each of the chosen private criteria. Results of one-criteria optimization are used at multicriteria optimization. The methods of developing materials as single-purpose, multi-purpose, including contradictory, systems are indicated. The scheme of synthesis of composite materials as difficult systems is developed. The specified system approach effectively was used in case of synthesis of composite materials with special properties.

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

PubMed

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

2009-06-09

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

Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

PubMed

Kutateladze, Andrei G; Mukhina, Olga A

2014-09-05

Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

The electron affinities of C{sub 3}O and C{sub 4}O

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

Rienstra-Kiracofe, J.C.; Ellison, G.B.; Hoffman, B.C.

The authors predict the adiabatic electron affinities of C{sub 3}O and C{sub 4}O based on electronic structure calculations, using a large triple-{zeta} basis set with polarization and diffuse functions (TZ2Pf+diff) with the SCF, CCSD, and CCSD(T) methods as well as with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. The results imply electron affinities for C{sub 3}O and C{sub 4}O; EA(C{sub 3}O) = 0.93 eV {+-} 0.10 and EA(C{sub 4}O) = 2.99 {+-} 0.10. The EA(C{sub 3}O) is 0.41 eV lower than the experimental value of 1.34 {+-} 0.15 eV, while the EA(C{sub 4}O) is 0.94 eV higher than the experimental valuemore » of 2.05 {+-} 0.15 eV. Optimized geometries for all species at each level of theory are given, and harmonic vibrational frequencies are reported at the SCF/TZ2Pf+diff and CCSD/aug-cc-pVDZ levels.« less

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

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

Holden, Zachary C.; Richard, Ryan M.; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu

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 tomore » 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.« less

Experimental and DFT studies on the vibrational spectra of 1H-indene-2-boronic acid

NASA Astrophysics Data System (ADS)

Alver, Özgur; Kaya, Mehmet Fatih

2014-11-01

Stable conformers and geometrical molecular structures of 1H-indene-2-boronic acid (I-2B(OH)2) were studied experimentally and theoretically using FT-IR and FT-Raman spectroscopic methods. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm-1, and 3700-400 cm-1, respectively. The optimized geometric structures were searched by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d,p) basis set. Vibrational wavenumbers of I-2B(OH)2 were calculated using B3LYP density functional methods including 6-31++G(d,p) basis set. Experimental and theoretical results show that density functional B3LYP method gives satisfactory results for predicting vibrational wavenumbers except OH stretching modes which is probably due to increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges. To support the assigned vibrational wavenumbers, the potential energy distribution (PED) values were also calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

3-Iodobenzaldehyde: XRD, FT-IR, Raman and DFT studies.

PubMed

Kumar, Chandraju Sadolalu Chidan; Parlak, Cemal; Tursun, Mahir; Fun, Hoong-Kun; Rhyman, Lydia; Ramasami, Ponnadurai; Alswaidan, Ibrahim A; Keşan, Gürkan; Chandraju, Siddegowda; Quah, Ching Kheng

2015-06-15

The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X=F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed. Copyright © 2015 Elsevier B.V. All rights reserved.

Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

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

Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in

2016-03-14

A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H{sub 2}O){sub n} (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculationmore » MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%–65% saving of computational time. The methodology has a potential for application to molecular clusters containing ∼100 atoms.« less

Methodological basis for the optimization of a marine sea-urchin embryo test (SET) for the ecological assessment of coastal water quality.

PubMed

Saco-Alvarez, Liliana; Durán, Iria; Ignacio Lorenzo, J; Beiras, Ricardo

2010-05-01

The sea-urchin embryo test (SET) has been frequently used as a rapid, sensitive, and cost-effective biological tool for marine monitoring worldwide, but the selection of a sensitive, objective, and automatically readable endpoint, a stricter quality control to guarantee optimum handling and biological material, and the identification of confounding factors that interfere with the response have hampered its widespread routine use. Size increase in a minimum of n=30 individuals per replicate, either normal larvae or earlier developmental stages, was preferred to observer-dependent, discontinuous responses as test endpoint. Control size increase after 48 h incubation at 20 degrees C must meet an acceptability criterion of 218 microm. In order to avoid false positives minimums of 32 per thousand salinity, 7 pH and 2mg/L oxygen, and a maximum of 40 microg/L NH(3) (NOEC) are required in the incubation media. For in situ testing size increase rates must be corrected on a degree-day basis using 12 degrees C as the developmental threshold. Copyright 2010 Elsevier Inc. All rights reserved.

Exploring metabolic pathways in genome-scale networks via generating flux modes.

PubMed

Rezola, A; de Figueiredo, L F; Brock, M; Pey, J; Podhorski, A; Wittmann, C; Schuster, S; Bockmayr, A; Planes, F J

2011-02-15

The reconstruction of metabolic networks at the genome scale has allowed the analysis of metabolic pathways at an unprecedented level of complexity. Elementary flux modes (EFMs) are an appropriate concept for such analysis. However, their number grows in a combinatorial fashion as the size of the metabolic network increases, which renders the application of EFMs approach to large metabolic networks difficult. Novel methods are expected to deal with such complexity. In this article, we present a novel optimization-based method for determining a minimal generating set of EFMs, i.e. a convex basis. We show that a subset of elements of this convex basis can be effectively computed even in large metabolic networks. Our method was applied to examine the structure of pathways producing lysine in Escherichia coli. We obtained a more varied and informative set of pathways in comparison with existing methods. In addition, an alternative pathway to produce lysine was identified using a detour via propionyl-CoA, which shows the predictive power of our novel approach. The source code in C++ is available upon request.

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

NASA Astrophysics Data System (ADS)

Yu, Hua-Gen

2016-08-01

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using a multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH4 and H2CO are given, together with a comparison with previous results.

An exact variational method to calculate rovibrational spectra of polyatomic molecules with large amplitude motion

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

Yu, Hua-Gen, E-mail: hgy@bnl.gov

We report a new full-dimensional variational algorithm to calculate rovibrational spectra of polyatomic molecules using an exact quantum mechanical Hamiltonian. The rovibrational Hamiltonian of system is derived in a set of orthogonal polyspherical coordinates in the body-fixed frame. It is expressed in an explicitly Hermitian form. The Hamiltonian has a universal formulation regardless of the choice of orthogonal polyspherical coordinates and the number of atoms in molecule, which is suitable for developing a general program to study the spectra of many polyatomic systems. An efficient coupled-state approach is also proposed to solve the eigenvalue problem of the Hamiltonian using amore » multi-layer Lanczos iterative diagonalization approach via a set of direct product basis set in three coordinate groups: radial coordinates, angular variables, and overall rotational angles. A simple set of symmetric top rotational functions is used for the overall rotation whereas a potential-optimized discrete variable representation method is employed in radial coordinates. A set of contracted vibrationally diabatic basis functions is adopted in internal angular variables. Those diabatic functions are first computed using a neural network iterative diagonalization method based on a reduced-dimension Hamiltonian but only once. The final rovibrational energies are computed using a modified Lanczos method for a given total angular momentum J, which is usually fast. Two numerical applications to CH{sub 4} and H{sub 2}CO are given, together with a comparison with previous results.« less

Simulation of the transient processes of load rejection under different accident conditions in a hydroelectric generating set

NASA Astrophysics Data System (ADS)

Guo, W. C.; Yang, J. D.; Chen, J. P.; Peng, Z. Y.; Zhang, Y.; Chen, C. C.

2016-11-01

Load rejection test is one of the essential tests that carried out before the hydroelectric generating set is put into operation formally. The test aims at inspecting the rationality of the design of the water diversion and power generation system of hydropower station, reliability of the equipment of generating set and the dynamic characteristics of hydroturbine governing system. Proceeding from different accident conditions of hydroelectric generating set, this paper presents the transient processes of load rejection corresponding to different accident conditions, and elaborates the characteristics of different types of load rejection. Then the numerical simulation method of different types of load rejection is established. An engineering project is calculated to verify the validity of the method. Finally, based on the numerical simulation results, the relationship among the different types of load rejection and their functions on the design of hydropower station and the operation of load rejection test are pointed out. The results indicate that: The load rejection caused by the accident within the hydroelectric generating set is realized by emergency distributing valve, and it is the basis of the optimization for the closing law of guide vane and the calculation of regulation and guarantee. The load rejection caused by the accident outside the hydroelectric generating set is realized by the governor. It is the most efficient measure to inspect the dynamic characteristics of hydro-turbine governing system, and its closure rate of guide vane set in the governor depends on the optimization result in the former type load rejection.

Paving the COWpath: data-driven design of pediatric order sets

PubMed Central

Zhang, Yiye; Padman, Rema; Levin, James E

2014-01-01

Objective Evidence indicates that users incur significant physical and cognitive costs in the use of order sets, a core feature of computerized provider order entry systems. This paper develops data-driven approaches for automating the construction of order sets that match closely with user preferences and workflow while minimizing physical and cognitive workload. Materials and methods We developed and tested optimization-based models embedded with clustering techniques using physical and cognitive click cost criteria. By judiciously learning from users’ actual actions, our methods identify items for constituting order sets that are relevant according to historical ordering data and grouped on the basis of order similarity and ordering time. We evaluated performance of the methods using 47 099 orders from the year 2011 for asthma, appendectomy and pneumonia management in a pediatric inpatient setting. Results In comparison with existing order sets, those developed using the new approach significantly reduce the physical and cognitive workload associated with usage by 14–52%. This approach is also capable of accommodating variations in clinical conditions that affect order set usage and development. Discussion There is a critical need to investigate the cognitive complexity imposed on users by complex clinical information systems, and to design their features according to ‘human factors’ best practices. Optimizing order set generation using cognitive cost criteria introduces a new approach that can potentially improve ordering efficiency, reduce unintended variations in order placement, and enhance patient safety. Conclusions We demonstrate that data-driven methods offer a promising approach for designing order sets that are generalizable, data-driven, condition-based, and up to date with current best practices. PMID:24674844

The automated system for prevention of industrial-caused diseases

NASA Astrophysics Data System (ADS)

Varnavsky, A. N.

2017-01-01

The paper presents the automated system intended to prevent industrial-caused diseases of workers, the basis of which is represented by algorithms of preventing several negative functional conditions (stress, monotony). The emergence of such state shall be determined based on an analysis of bioelectric signals, in particular, skin-galvanic reactions. Proceeding from the dynamics of the functional state, the automated system offers to perform an optimized set of measures to restore the health of the worker. Implementation of an automated system is presented in Visual Programming system LabVIEW.

Orbital transfer vehicle concept definition and system analysis study. Volume 2: OTV concept definition and evaluation. Book 1: Mission and system requirements

NASA Technical Reports Server (NTRS)

Kofal, Allen E.

1987-01-01

The mission and system requirements for the concept definition and system analysis of the Orbital Transfer Vehicle (OTV) are established. The requirements set forth constitute the single authority for the selection, evaluation, and optimization of the technical performance and design of the OTV. This requirements document forms the basis for the Ground and Space Based OTV concept definition analyses and establishes the physical, functional, performance and design relationships to STS, Space Station, Orbital Maneuvering Vehicle (OMV), and payloads.

Tools for regulation of travel behaviour in small and medium towns

NASA Astrophysics Data System (ADS)

Carsky, J.; Gallia, J.

2018-04-01

The subject of this paper is to analyse traffic-sociological surveys focused on the attitudes of citizens living in small and medium-sized towns to solve selected traffic problems. The basis for the following research is the data obtained through questionnaire surveys carried out in selected Czech and Moravian towns. Applications are for example a tool for optimal setting of the price for parking in historic centres of towns as well as the suitability of closure of these centres for vehicles or the regulation of entry through its charging.

Optimal Design of Litz Wire Coils With Sandwich Structure Wirelessly Powering an Artificial Anal Sphincter System.

PubMed

Ke, Lei; Yan, Guozheng; Yan, Sheng; Wang, Zhiwu; Li, Xiaoyang

2015-07-01

Transcutaneous energy transfer system (TETS) is widely used to energize implantable biomedical devices. As a key part of the TETS, a pair of applicable coils with low losses, high unloaded Q factor, and strong coupling is required to realize an efficient TETS. This article presents an optimal design methodology of planar litz wire coils sandwiched between two ferrite substrates wirelessly powering a novel mechanical artificial anal sphincter system for treating severe fecal incontinence, with focus on the main parameters of the coils such as the wire diameter, number of turns, geometry, and the properties of the ferrite substrate. The theoretical basis of optimal power transfer efficiency in an inductive link was analyzed. A set of analytical expressions are outlined to calculate the winding resistance of a litz wire coil on ferrite substrate, taking into account eddy-current losses, including conduction losses and induction losses. Expressions that describe the geometrical dimension dependence of self- and mutual inductance are derived. The influence of ferrite substrate relative permeability and dimensions is also considered. We have used this foundation to devise an applicable coil design method that starts with a set of realistic constraints and ends with the optimal coil pair geometries. All theoretical predictions are verified with measurements using different types of fabricated coils. The results indicate that the analysis is useful for optimizing the geometry design of windings and the ferrite substrate in a sandwich structure as part of which, in addition to providing design insight, allows speeding up the system efficiency-optimizing design process. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Strong stabilization servo controller with optimization of performance criteria.

PubMed

Sarjaš, Andrej; Svečko, Rajko; Chowdhury, Amor

2011-07-01

Synthesis of a simple robust controller with a pole placement technique and a H(∞) metrics is the method used for control of a servo mechanism with BLDC and BDC electric motors. The method includes solving a polynomial equation on the basis of the chosen characteristic polynomial using the Manabe standard polynomial form and parametric solutions. Parametric solutions are introduced directly into the structure of the servo controller. On the basis of the chosen parametric solutions the robustness of a closed-loop system is assessed through uncertainty models and assessment of the norm ‖•‖(∞). The design procedure and the optimization are performed with a genetic algorithm differential evolution - DE. The DE optimization method determines a suboptimal solution throughout the optimization on the basis of a spectrally square polynomial and Šiljak's absolute stability test. The stability of the designed controller during the optimization is being checked with Lipatov's stability condition. Both utilized approaches: Šiljak's test and Lipatov's condition, check the robustness and stability characteristics on the basis of the polynomial's coefficients, and are very convenient for automated design of closed-loop control and for application in optimization algorithms such as DE. Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.

Theoretical Investigation Leading to Energy Storage in Atomic and Molecular Systems

DTIC Science & Technology

1990-12-01

can be calculated in a single run. 21 j) Non-gradient optimization of basis function exponents is possible. The source code can be modified to carry...basis. The 10s3p/5s3p basis consists of the 9s/4s contraction of Siegbahn and Liu (Reference 91) augmented by a diffuse s-type function ( exponent ...vibrational modes. Introduction of diffuse basis functions and optimization of the d-orbital exponents have a small but important effect on the

Optimization of wavelengths sets for multispectral reflectance imaging of rat olfactory bulb activation in vivo

NASA Astrophysics Data System (ADS)

Renaud, Rémi; Bendahmane, Mounir; Chery, Romain; Martin, Claire; Gurden, Hirac; Pain, Frederic

2012-06-01

Wide field multispectral imaging of light backscattered by brain tissues provides maps of hemodynamics changes (total blood volume and oxygenation) following activation. This technique relies on the fit of the reflectance images obtain at two or more wavelengths using a modified Beer-Lambert law1,2. It has been successfully applied to study the activation of several sensory cortices in the anesthetized rodent using visible light1-5. We have carried out recently the first multispectral imaging in the olfactory bulb6 (OB) of anesthetized rats. However, the optimization of wavelengths choice has not been discussed in terms of cross talk and uniqueness of the estimated parameters (blood volume and saturation maps) although this point was shown to be crucial for similar studies in Diffuse Optical Imaging in humans7-10. We have studied theoretically and experimentally the optimal sets of wavelength for multispectral imaging of rodent brain activation in the visible. Sets of optimal wavelengths have been identified and validated in vivo for multispectral imaging of the OB of rats following odor stimulus. We studied the influence of the wavelengths sets on the magnitude and time courses of the oxy- and deoxyhemoglobin concentration variations as well as on the spatial extent of activated brain areas following stimulation. Beyond the estimation of hemodynamic parameters from multispectral reflectance data, we observed repeatedly and for all wavelengths a decrease of light reflectance. For wavelengths longer than 590 nm, these observations differ from those observed in the somatosensory and barrel cortex and question the basis of the reflectance changes during activation in the OB. To solve this issue, Monte Carlo simulations (MCS) have been carried out to assess the relative contribution of absorption, scattering and anisotropy changes to the intrinsic optical imaging signals in somatosensory cortex (SsC) and OB model.

Optimizing spectral CT parameters for material classification tasks

NASA Astrophysics Data System (ADS)

Rigie, D. S.; La Rivière, P. J.

2016-06-01

In this work, we propose a framework for optimizing spectral CT imaging parameters and hardware design with regard to material classification tasks. Compared with conventional CT, many more parameters must be considered when designing spectral CT systems and protocols. These choices will impact material classification performance in a non-obvious, task-dependent way with direct implications for radiation dose reduction. In light of this, we adapt Hotelling Observer formalisms typically applied to signal detection tasks to the spectral CT, material-classification problem. The result is a rapidly computable metric that makes it possible to sweep out many system configurations, generating parameter optimization curves (POC’s) that can be used to select optimal settings. The proposed model avoids restrictive assumptions about the basis-material decomposition (e.g. linearity) and incorporates signal uncertainty with a stochastic object model. This technique is demonstrated on dual-kVp and photon-counting systems for two different, clinically motivated material classification tasks (kidney stone classification and plaque removal). We show that the POC’s predicted with the proposed analytic model agree well with those derived from computationally intensive numerical simulation studies.

Optimizing Spectral CT Parameters for Material Classification Tasks

PubMed Central

Rigie, D. S.; La Rivière, P. J.

2017-01-01

In this work, we propose a framework for optimizing spectral CT imaging parameters and hardware design with regard to material classification tasks. Compared with conventional CT, many more parameters must be considered when designing spectral CT systems and protocols. These choices will impact material classification performance in a non-obvious, task-dependent way with direct implications for radiation dose reduction. In light of this, we adapt Hotelling Observer formalisms typically applied to signal detection tasks to the spectral CT, material-classification problem. The result is a rapidly computable metric that makes it possible to sweep out many system configurations, generating parameter optimization curves (POC’s) that can be used to select optimal settings. The proposed model avoids restrictive assumptions about the basis-material decomposition (e.g. linearity) and incorporates signal uncertainty with a stochastic object model. This technique is demonstrated on dual-kVp and photon-counting systems for two different, clinically motivated material classification tasks (kidney stone classification and plaque removal). We show that the POC’s predicted with the proposed analytic model agree well with those derived from computationally intensive numerical simulation studies. PMID:27227430

XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations.

PubMed

Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A

2012-09-01

Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).

Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets.

PubMed

Khajehzadeh, Mostafa; Moghadam, Majid

2017-06-05

Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ→σ∗ and π→π∗ and LP(1)→σ∗ and LP(2)→σ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H 2 O, CH 3 CN and C 6 H 12 . UV-Vis spectrum of the drug was taken using DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets as well as solvents H 2 O, CH 3 CN and C 6 H 12 and the associated transmissions were examined. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Design of compactly supported wavelet to match singularities in medical images

NASA Astrophysics Data System (ADS)

Fung, Carrson C.; Shi, Pengcheng

2002-11-01

Analysis and understanding of medical images has important clinical values for patient diagnosis and treatment, as well as technical implications for computer vision and pattern recognition. One of the most fundamental issues is the detection of object boundaries or singularities, which is often the basis for further processes such as organ/tissue recognition, image registration, motion analysis, measurement of anatomical and physiological parameters, etc. The focus of this work involved taking a correlation based approach toward edge detection, by exploiting some of desirable properties of wavelet analysis. This leads to the possibility of constructing a bank of detectors, consisting of multiple wavelet basis functions of different scales which are optimal for specific types of edges, in order to optimally detect all the edges in an image. Our work involved developing a set of wavelet functions which matches the shape of the ramp and pulse edges. The matching algorithm used focuses on matching the edges in the frequency domain. It was proven that this technique could create matching wavelets applicable at all scales. Results have shown that matching wavelets can be obtained for the pulse edge while the ramp edge requires another matching algorithm.

Computational thermochemistry: Automated generation of scale factors for vibrational frequencies calculated by electronic structure model chemistries

NASA Astrophysics Data System (ADS)

Yu, Haoyu S.; Fiedler, Lucas J.; Alecu, I. M.; Truhlar, Donald G.

2017-01-01

We present a Python program, FREQ, for calculating the optimal scale factors for calculating harmonic vibrational frequencies, fundamental vibrational frequencies, and zero-point vibrational energies from electronic structure calculations. The program utilizes a previously published scale factor optimization model (Alecu et al., 2010) to efficiently obtain all three scale factors from a set of computed vibrational harmonic frequencies. In order to obtain the three scale factors, the user only needs to provide zero-point energies of 15 or 6 selected molecules. If the user has access to the Gaussian 09 or Gaussian 03 program, we provide the option for the user to run the program by entering the keywords for a certain method and basis set in the Gaussian 09 or Gaussian 03 program. Four other Python programs, input.py, input6, pbs.py, and pbs6.py, are also provided for generating Gaussian 09 or Gaussian 03 input and PBS files. The program can also be used with data from any other electronic structure package. A manual of how to use this program is included in the code package.

Developing a radiomics framework for classifying non-small cell lung carcinoma subtypes

NASA Astrophysics Data System (ADS)

Yu, Dongdong; Zang, Yali; Dong, Di; Zhou, Mu; Gevaert, Olivier; Fang, Mengjie; Shi, Jingyun; Tian, Jie

2017-03-01

Patient-targeted treatment of non-small cell lung carcinoma (NSCLC) has been well documented according to the histologic subtypes over the past decade. In parallel, recent development of quantitative image biomarkers has recently been highlighted as important diagnostic tools to facilitate histological subtype classification. In this study, we present a radiomics analysis that classifies the adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). We extract 52-dimensional, CT-based features (7 statistical features and 45 image texture features) to represent each nodule. We evaluate our approach on a clinical dataset including 324 ADCs and 110 SqCCs patients with CT image scans. Classification of these features is performed with four different machine-learning classifiers including Support Vector Machines with Radial Basis Function kernel (RBF-SVM), Random forest (RF), K-nearest neighbor (KNN), and RUSBoost algorithms. To improve the classifiers' performance, optimal feature subset is selected from the original feature set by using an iterative forward inclusion and backward eliminating algorithm. Extensive experimental results demonstrate that radiomics features achieve encouraging classification results on both complete feature set (AUC=0.89) and optimal feature subset (AUC=0.91).

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid

NASA Astrophysics Data System (ADS)

Renuga Devi, T. S.; Sharmi kumar, J.; Ramkumaar, G. R.

2015-02-01

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm-1 and 4000-50 cm-1 respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule.

Monomeric and dimeric structures, electronic properties and vibrational spectra of azelaic acid by HF and B3LYP methods

NASA Astrophysics Data System (ADS)

Kumar, Amarendra; Narayan, Vijay; Prasad, Onkar; Sinha, Leena

2012-08-01

Quantum chemical calculations of energies, dipole moment, polarizability, hyperpolarizability and vibrational wavenumbers of Azelaic acid (AZA) were carried out by using ab initio HF and B3LYP methods with 6-311++G(d,p) basis set. Hydrogen-bonded dimer of AZA, optimized by counterpoise correction, has also been studied by HF and B3LYP at the 6-311++G(d,p) level and the effects of molecular association through Osbnd H⋯O hydrogen bonding have been discussed. A complete vibrational analysis of AZA has been performed and assignments are made on the basis of potential energy distribution. The comparisons and assignments of the vibrational frequencies indicate that the experimental spectra also correspond acceptably with those of theoretically simulated spectra except the hydrogen-bonded coupled infrared vibrations.

Studies of The Durability of Belt Conveyor Idlers with Working Loads Taken into Account

NASA Astrophysics Data System (ADS)

Król, Robert

2017-12-01

The results of laboratory and operational studies conducted in the Machinery Systems Division of Wroclaw University of Technology in recent years have became the basis for selecting proper belt conveyor roller designs optimized for specific strength and operational criteria. The usefulness of the results for assessing the energy intensity of idlers, estimating their durability and determining modernization policies has been confirmed. Methods of estimating the durability of carrying idlers on the basis of the identified output stream distributions are presented. Results of studies carried out using an analytical method and a laboratory method are reported. It has been shown that the operational durability of a roller is determined by its design, the roller set parameters (the spacing and the angle of bevel) and the operating conditions having a bearing on the irregularity of the transported output stream.

Radial basis function network learns ceramic processing and predicts related strength and density

NASA Technical Reports Server (NTRS)

Cios, Krzysztof J.; Baaklini, George Y.; Vary, Alex; Tjia, Robert E.

1993-01-01

Radial basis function (RBF) neural networks were trained using the data from 273 Si3N4 modulus of rupture (MOR) bars which were tested at room temperature and 135 MOR bars which were tested at 1370 C. Milling time, sintering time, and sintering gas pressure were the processing parameters used as the input features. Flexural strength and density were the outputs by which the RBF networks were assessed. The 'nodes-at-data-points' method was used to set the hidden layer centers and output layer training used the gradient descent method. The RBF network predicted strength with an average error of less than 12 percent and density with an average error of less than 2 percent. Further, the RBF network demonstrated a potential for optimizing and accelerating the development and processing of ceramic materials.

An effective rumor-containing strategy

NASA Astrophysics Data System (ADS)

Pan, Cheng; Yang, Lu-Xing; Yang, Xiaofan; Wu, Yingbo; Tang, Yuan Yan

2018-06-01

False rumors can lead to huge economic losses or/and social instability. Hence, mitigating the impact of bogus rumors is of primary importance. This paper focuses on the problem of how to suppress a false rumor by use of the truth. Based on a set of rational hypotheses and a novel rumor-truth mixed spreading model, the effectiveness and cost of a rumor-containing strategy are quantified, respectively. On this basis, the original problem is modeled as a constrained optimization problem (the RC model), in which the independent variable and the objective function represent a rumor-containing strategy and the effectiveness of a rumor-containing strategy, respectively. The goal of the optimization problem is to find the most effective rumor-containing strategy subject to a limited rumor-containing budget. Some optimal rumor-containing strategies are given by solving their respective RC models. The influence of different factors on the highest cost effectiveness of a RC model is illuminated through computer experiments. The results obtained are instructive to develop effective rumor-containing strategies.

Environmental statistics and optimal regulation

NASA Astrophysics Data System (ADS)

Sivak, David; Thomson, Matt

2015-03-01

The precision with which an organism can detect its environment, and the timescale for and statistics of environmental change, will affect the suitability of different strategies for regulating protein levels in response to environmental inputs. We propose a general framework--here applied to the enzymatic regulation of metabolism in response to changing nutrient concentrations--to predict the optimal regulatory strategy given the statistics of fluctuations in the environment and measurement apparatus, and the costs associated with enzyme production. We find: (i) relative convexity of enzyme expression cost and benefit influences the fitness of thresholding or graded responses; (ii) intermediate levels of measurement uncertainty call for a sophisticated Bayesian decision rule; and (iii) in dynamic contexts, intermediate levels of uncertainty call for retaining memory of the past. Statistical properties of the environment, such as variability and correlation times, set optimal biochemical parameters, such as thresholds and decay rates in signaling pathways. Our framework provides a theoretical basis for interpreting molecular signal processing algorithms and a classification scheme that organizes known regulatory strategies and may help conceptualize heretofore unknown ones.

The design and implementation of a parallel unstructured Euler solver using software primitives

NASA Technical Reports Server (NTRS)

Das, R.; Mavriplis, D. J.; Saltz, J.; Gupta, S.; Ponnusamy, R.

1992-01-01

This paper is concerned with the implementation of a three-dimensional unstructured grid Euler-solver on massively parallel distributed-memory computer architectures. The goal is to minimize solution time by achieving high computational rates with a numerically efficient algorithm. An unstructured multigrid algorithm with an edge-based data structure has been adopted, and a number of optimizations have been devised and implemented in order to accelerate the parallel communication rates. The implementation is carried out by creating a set of software tools, which provide an interface between the parallelization issues and the sequential code, while providing a basis for future automatic run-time compilation support. Large practical unstructured grid problems are solved on the Intel iPSC/860 hypercube and Intel Touchstone Delta machine. The quantitative effect of the various optimizations are demonstrated, and we show that the combined effect of these optimizations leads to roughly a factor of three performance improvement. The overall solution efficiency is compared with that obtained on the CRAY-YMP vector supercomputer.

[Determination of process variable pH in solid-state fermentation by FT-NIR spectroscopy and extreme learning machine (ELM)].

PubMed

Liu, Guo-hai; Jiang, Hui; Xiao, Xia-hong; Zhang, Dong-juan; Mei, Cong-li; Ding, Yu-han

2012-04-01

Fourier transform near-infrared (FT-NIR) spectroscopy was attempted to determine pH, which is one of the key process parameters in solid-state fermentation of crop straws. First, near infrared spectra of 140 solid-state fermented product samples were obtained by near infrared spectroscopy system in the wavelength range of 10 000-4 000 cm(-1), and then the reference measurement results of pH were achieved by pH meter. Thereafter, the extreme learning machine (ELM) was employed to calibrate model. In the calibration model, the optimal number of PCs and the optimal number of hidden-layer nodes of ELM network were determined by the cross-validation. Experimental results showed that the optimal ELM model was achieved with 1040-1 topology construction as follows: R(p) = 0.961 8 and RMSEP = 0.104 4 in the prediction set. The research achievement could provide technological basis for the on-line measurement of the process parameters in solid-state fermentation.

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

PubMed

Saller, Maximilian A C; Habershon, Scott

2017-07-11

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

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

PubMed

Mitin, Alexander V

2013-09-05

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

Optimizing Quality of Care and Patient Safety in Malaysia: The Current Global Initiatives, Gaps and Suggested Solutions.

PubMed

Jarrar, Mu'taman; Abdul Rahman, Hamzah; Don, Mohammad Sobri

2015-10-20

Demand for health care service has significantly increased, while the quality of healthcare and patient safety has become national and international priorities. This paper aims to identify the gaps and the current initiatives for optimizing the quality of care and patient safety in Malaysia. Review of the current literature. Highly cited articles were used as the basis to retrieve and review the current initiatives for optimizing the quality of care and patient safety. The country health plan of Ministry of Health (MOH) Malaysia and the MOH Malaysia Annual Reports were reviewed. The MOH has set four strategies for optimizing quality and sustaining quality of life. The 10th Malaysia Health Plan promotes the theme "1 Care for 1 Malaysia" in order to sustain the quality of care. Despite of these efforts, the total number of complaints received by the medico-legal section of the MOH Malaysia is increasing. The current global initiatives indicted that quality performance generally belong to three main categories: patient; staffing; and working environment related factors. There is no single intervention for optimizing quality of care to maintain patient safety. Multidimensional efforts and interventions are recommended in order to optimize the quality of care and patient safety in Malaysia.

Optimizing Quality of Care and Patient Safety in Malaysia: The Current Global Initiatives, Gaps and Suggested Solutions

PubMed Central

Jarrar, Mu’taman; Rahman, Hamzah Abdul; Don, Mohammad Sobri

2016-01-01

Background and Objective: Demand for health care service has significantly increased, while the quality of healthcare and patient safety has become national and international priorities. This paper aims to identify the gaps and the current initiatives for optimizing the quality of care and patient safety in Malaysia. Design: Review of the current literature. Highly cited articles were used as the basis to retrieve and review the current initiatives for optimizing the quality of care and patient safety. The country health plan of Ministry of Health (MOH) Malaysia and the MOH Malaysia Annual Reports were reviewed. Results: The MOH has set four strategies for optimizing quality and sustaining quality of life. The 10th Malaysia Health Plan promotes the theme “1 Care for 1 Malaysia” in order to sustain the quality of care. Despite of these efforts, the total number of complaints received by the medico-legal section of the MOH Malaysia is increasing. The current global initiatives indicted that quality performance generally belong to three main categories: patient; staffing; and working environment related factors. Conclusions: There is no single intervention for optimizing quality of care to maintain patient safety. Multidimensional efforts and interventions are recommended in order to optimize the quality of care and patient safety in Malaysia. PMID:26755459

Towards automating the discovery of certain innovative design principles through a clustering-based optimization technique

NASA Astrophysics Data System (ADS)

Bandaru, Sunith; Deb, Kalyanmoy

2011-09-01

In this article, a methodology is proposed for automatically extracting innovative design principles which make a system or process (subject to conflicting objectives) optimal using its Pareto-optimal dataset. Such 'higher knowledge' would not only help designers to execute the system better, but also enable them to predict how changes in one variable would affect other variables if the system has to retain its optimal behaviour. This in turn would help solve other similar systems with different parameter settings easily without the need to perform a fresh optimization task. The proposed methodology uses a clustering-based optimization technique and is capable of discovering hidden functional relationships between the variables, objective and constraint functions and any other function that the designer wishes to include as a 'basis function'. A number of engineering design problems are considered for which the mathematical structure of these explicit relationships exists and has been revealed by a previous study. A comparison with the multivariate adaptive regression splines (MARS) approach reveals the practicality of the proposed approach due to its ability to find meaningful design principles. The success of this procedure for automated innovization is highly encouraging and indicates its suitability for further development in tackling more complex design scenarios.

Consensus Statement of the American Academy of Sleep Medicine on the Recommended Amount of Sleep for Healthy Children: Methodology and Discussion.

PubMed

Paruthi, Shalini; Brooks, Lee J; D'Ambrosio, Carolyn; Hall, Wendy A; Kotagal, Suresh; Lloyd, Robin M; Malow, Beth A; Maski, Kiran; Nichols, Cynthia; Quan, Stuart F; Rosen, Carol L; Troester, Matthew M; Wise, Merrill S

2016-11-15

Members of the American Academy of Sleep Medicine developed consensus recommendations for the amount of sleep needed to promote optimal health in children and adolescents using a modified RAND Appropriateness Method. After review of 864 published articles, the following sleep durations are recommended: Infants 4 months to 12 months should sleep 12 to 16 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 1 to 2 years of age should sleep 11 to 14 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 3 to 5 years of age should sleep 10 to 13 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 6 to 12 years of age should sleep 9 to 12 hours per 24 hours on a regular basis to promote optimal health. Teenagers 13 to 18 years of age should sleep 8 to 10 hours per 24 hours on a regular basis to promote optimal health. Sleeping the number of recommended hours on a regular basis is associated with better health outcomes including: improved attention, behavior, learning, memory, emotional regulation, quality of life, and mental and physical health. Regularly sleeping fewer than the number of recommended hours is associated with attention, behavior, and learning problems. Insufficient sleep also increases the risk of accidents, injuries, hypertension, obesity, diabetes, and depression. Insufficient sleep in teenagers is associated with increased risk of self-harm, suicidal thoughts, and suicide attempts. A commentary on this article apears in this issue on page 1439. © 2016 American Academy of Sleep Medicine

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

NASA Astrophysics Data System (ADS)

Saheb, Vahid; Maleki, Samira

2018-03-01

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

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

PubMed

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

2012-08-01

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

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

PubMed

Ferenczy, György G

2013-04-05

Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. Copyright © 2012 Wiley Periodicals, Inc.

Gas-phase Conformational Analysis of (R,R)-Tartaric Acid, its Diamide, N,N,N',N'- Tetramethyldiamide and Model Compounds

NASA Astrophysics Data System (ADS)

Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek

A review over most recent ab initio studies carried out at both RHF and MP2 levels on (R,R)-tartaric acid (TA), its diamide (DA), tetramethyldiamide (TMDA) and on three prototypic model systems (each of them constitutes a half of the respective parental molecule), i.e. 2-hydroxyacetic acid (HA), 2-hydroxyacetamide (HD) and 2-hydroxy-N,N-dimethylacetamide (HMD) is presented. (R,R)-tartaric acid and the derivatives have been completely optimized at RHF/6-31G* level and subsequently single-point energies of all conformers have been calculated with the use of second order perturbation theory according to the scheme: MP2/6-31G*//RHF/6-31G*. In the complete optimization of the model molecules at RHF level we have employed relatively large basis sets, augmented with polarisation and diffuse functions, namely 3-21G, 6-31G*, 6-31++G** and 6-311++G**. Electronic correlation has been included with the largest basis set used in this study, i.e. MP2/6-311++G**//RHF/6-311++G** single-point energy calculations have been performed. General confomational preferences of tartaric acid derivatives have been analysed as well as an attempt has been made to define main factors affecting the conformational behaviour of these molecules in the isolated state, in particular, the role and stability of intramolecular hydrogen bonding. In the case of the model compounds, our study principally concerned the conformational preferences and hydrogen bonding structure within the [alpha]-hydroxy-X moiety, where X=COOH, CONH2, CON(CH3)2.

Experimental and TD-DFT study of optical absorption of six explosive molecules: RDX, HMX, PETN, TNT, TATP, and HMTD.

PubMed

Cooper, Jason K; Grant, Christian D; Zhang, Jin Z

2013-07-25

Time dependent density function theory (TD-DFT) has been utilized to calculate the excitation energies and oscillator strengths of six common explosives: RDX (1,3,5-trinitroperhydro-1,3,5-triazine), β-HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), TATP (triacetone triperoxide), HMTD (hexamethylene triperoxide diamine), TNT (2,4,6-trinitrotoluene), and PETN (pentaerythritol tetranitrate). The results were compared to experimental UV-vis absorption spectra collected in acetonitrile. Four computational methods were tested including: B3LYP, CAM-B3LYP, ωB97XD, and PBE0. PBE0 outperforms the other methods tested. Basis set effects on the electronic energies and oscillator strengths were evaluated with 6-31G(d), 6-31+G(d), 6-31+G(d,p), and 6-311+G(d,p). The minimal basis set required was 6-31+G(d); however, additional calculations were performed with 6-311+G(d,p). For each molecule studied, the natural transition orbitals (NTOs) were reported for the most prominent singlet excitations. The TD-DFT results have been combined with the IPv calculated by CBS-QB3 to construct energy level diagrams for the six compounds. The results suggest optimization approaches for fluorescence based detection methods for these explosives by guiding materials selections for optimal band alignment between fluorescent probe and explosive analyte. Also, the role of the TNT Meisenheimer complex formation and the resulting electronic structure thereof on of the quenching mechanism of II-VI semiconductors is discussed.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

PubMed

Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

2018-06-27

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

NASA Astrophysics Data System (ADS)

Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

2018-06-01

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Extended polarization in 3rd order SCC-DFTB from chemical potential equilization

PubMed Central

Kaminski, Steve; Giese, Timothy J.; Gaus, Michael; York, Darrin M.; Elstner, Marcus

2012-01-01

In this work we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical potential equilization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for NDDO type methods by Giese and York, has been shown to emend minimal basis methods wrt response properties significantly, and has been applied to SCC-DFTB recently. CPE allows to overcome this inherent limitation of minimal basis methods by supplying an additional response density. The systematic underestimation is thereby corrected quantitatively without the need to extend the atomic orbital basis, i.e. without increasing the overall computational cost significantly. Especially the dependency of polarizability as a function of molecular charge state was significantly improved from the CPE extension of DFTB3. The empirical parameters introduced by the CPE approach were optimized for 172 organic molecules in order to match the results from density functional methods (DFT) methods using large basis sets. However, the first order derivatives of molecular polarizabilities, as e.g. required to compute Raman activities, are not improved by the current CPE implementation, i.e. Raman spectra are not improved. PMID:22894819

Discussion on runoff purification technology of highway bridge deck based on water quality safety

NASA Astrophysics Data System (ADS)

Tan, Sheng-guang; Liu, Xue-xin; Zou, Guo-ping; Xiong, Xin-zhu; Tao, Shuang-cheng

2018-06-01

Aiming at the actual problems existing, including a poor purification effect of highway bridge runoff collection and treatment system across sensitive water and necessary manual emergency operation, three kinds of technology, three pools system of bridge runoff purification, the integral pool of bridge runoff purification and ecological planting tank, are put forward by optimizing the structure of purification unit and system setting. At the same time, we come up with an emergency strategy for hazardous material leakage basing on automatic identification and remote control of traffic accidents. On the basis of combining these with the optimized pool structure, sensitive water safety can be guaranteed and water pollution, from directly discharging of bridge runoff, can be decreased. For making up for the shortages of green highway construction technology, the technique has important reference value.

A Case-Based Reasoning Method with Rank Aggregation

NASA Astrophysics Data System (ADS)

Sun, Jinhua; Du, Jiao; Hu, Jian

2018-03-01

In order to improve the accuracy of case-based reasoning (CBR), this paper addresses a new CBR framework with the basic principle of rank aggregation. First, the ranking methods are put forward in each attribute subspace of case. The ordering relation between cases on each attribute is got between cases. Then, a sorting matrix is got. Second, the similar case retrieval process from ranking matrix is transformed into a rank aggregation optimal problem, which uses the Kemeny optimal. On the basis, a rank aggregation case-based reasoning algorithm, named RA-CBR, is designed. The experiment result on UCI data sets shows that case retrieval accuracy of RA-CBR algorithm is higher than euclidean distance CBR and mahalanobis distance CBR testing.So we can get the conclusion that RA-CBR method can increase the performance and efficiency of CBR.

Shape design of internal cooling passages within a turbine blade

NASA Astrophysics Data System (ADS)

Nowak, Grzegorz; Nowak, Iwona

2012-04-01

The article concerns the optimization of the shape and location of non-circular passages cooling the blade of a gas turbine. To model the shape, four Bezier curves which form a closed profile of the passage were used. In order to match the shape of the passage to the blade profile, a technique was put forward to copy and scale the profile fragments into the component, and build the outline of the passage on the basis of them. For so-defined cooling passages, optimization calculations were carried out with a view to finding their optimal shape and location in terms of the assumed objectives. The task was solved as a multi-objective problem with the use of the Pareto method, for a cooling system composed of four and five passages. The tool employed for the optimization was the evolutionary algorithm. The article presents the impact of the population on the task convergence, and discusses the impact of different optimization objectives on the Pareto optimal solutions obtained. Due to the problem of different impacts of individual objectives on the position of the solution front which was noticed during the calculations, a two-step optimization procedure was introduced. Also, comparative optimization calculations for the scalar objective function were carried out and set up against the non-dominated solutions obtained in the Pareto approach. The optimization process resulted in a configuration of the cooling system that allows a significant reduction in the temperature of the blade and its thermal stress.

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

PubMed Central

Yim, Yung-Chang; Eyring, Henry

1981-01-01

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

Optimal wavelets for biomedical signal compression.

PubMed

Nielsen, Mogens; Kamavuako, Ernest Nlandu; Andersen, Michael Midtgaard; Lucas, Marie-Françoise; Farina, Dario

2006-07-01

Signal compression is gaining importance in biomedical engineering due to the potential applications in telemedicine. In this work, we propose a novel scheme of signal compression based on signal-dependent wavelets. To adapt the mother wavelet to the signal for the purpose of compression, it is necessary to define (1) a family of wavelets that depend on a set of parameters and (2) a quality criterion for wavelet selection (i.e., wavelet parameter optimization). We propose the use of an unconstrained parameterization of the wavelet for wavelet optimization. A natural performance criterion for compression is the minimization of the signal distortion rate given the desired compression rate. For coding the wavelet coefficients, we adopted the embedded zerotree wavelet coding algorithm, although any coding scheme may be used with the proposed wavelet optimization. As a representative example of application, the coding/encoding scheme was applied to surface electromyographic signals recorded from ten subjects. The distortion rate strongly depended on the mother wavelet (for example, for 50% compression rate, optimal wavelet, mean+/-SD, 5.46+/-1.01%; worst wavelet 12.76+/-2.73%). Thus, optimization significantly improved performance with respect to previous approaches based on classic wavelets. The algorithm can be applied to any signal type since the optimal wavelet is selected on a signal-by-signal basis. Examples of application to ECG and EEG signals are also reported.

Analysis of a Two-Dimensional Thermal Cloaking Problem on the Basis of Optimization

NASA Astrophysics Data System (ADS)

Alekseev, G. V.

2018-04-01

For a two-dimensional model of thermal scattering, inverse problems arising in the development of tools for cloaking material bodies on the basis of a mixed thermal cloaking strategy are considered. By applying the optimization approach, these problems are reduced to optimization ones in which the role of controls is played by variable parameters of the medium occupying the cloaking shell and by the heat flux through a boundary segment of the basic domain. The solvability of the direct and optimization problems is proved, and an optimality system is derived. Based on its analysis, sufficient conditions on the input data are established that ensure the uniqueness and stability of optimal solutions.

Identifying best-fitting inputs in health-economic model calibration: a Pareto frontier approach.

PubMed

Enns, Eva A; Cipriano, Lauren E; Simons, Cyrena T; Kong, Chung Yin

2015-02-01

To identify best-fitting input sets using model calibration, individual calibration target fits are often combined into a single goodness-of-fit (GOF) measure using a set of weights. Decisions in the calibration process, such as which weights to use, influence which sets of model inputs are identified as best-fitting, potentially leading to different health economic conclusions. We present an alternative approach to identifying best-fitting input sets based on the concept of Pareto-optimality. A set of model inputs is on the Pareto frontier if no other input set simultaneously fits all calibration targets as well or better. We demonstrate the Pareto frontier approach in the calibration of 2 models: a simple, illustrative Markov model and a previously published cost-effectiveness model of transcatheter aortic valve replacement (TAVR). For each model, we compare the input sets on the Pareto frontier to an equal number of best-fitting input sets according to 2 possible weighted-sum GOF scoring systems, and we compare the health economic conclusions arising from these different definitions of best-fitting. For the simple model, outcomes evaluated over the best-fitting input sets according to the 2 weighted-sum GOF schemes were virtually nonoverlapping on the cost-effectiveness plane and resulted in very different incremental cost-effectiveness ratios ($79,300 [95% CI 72,500-87,600] v. $139,700 [95% CI 79,900-182,800] per quality-adjusted life-year [QALY] gained). Input sets on the Pareto frontier spanned both regions ($79,000 [95% CI 64,900-156,200] per QALY gained). The TAVR model yielded similar results. Choices in generating a summary GOF score may result in different health economic conclusions. The Pareto frontier approach eliminates the need to make these choices by using an intuitive and transparent notion of optimality as the basis for identifying best-fitting input sets. © The Author(s) 2014.

Identifying best-fitting inputs in health-economic model calibration: a Pareto frontier approach

PubMed Central

Enns, Eva A.; Cipriano, Lauren E.; Simons, Cyrena T.; Kong, Chung Yin

2014-01-01

Background To identify best-fitting input sets using model calibration, individual calibration target fits are often combined into a single “goodness-of-fit” (GOF) measure using a set of weights. Decisions in the calibration process, such as which weights to use, influence which sets of model inputs are identified as best-fitting, potentially leading to different health economic conclusions. We present an alternative approach to identifying best-fitting input sets based on the concept of Pareto-optimality. A set of model inputs is on the Pareto frontier if no other input set simultaneously fits all calibration targets as well or better. Methods We demonstrate the Pareto frontier approach in the calibration of two models: a simple, illustrative Markov model and a previously-published cost-effectiveness model of transcatheter aortic valve replacement (TAVR). For each model, we compare the input sets on the Pareto frontier to an equal number of best-fitting input sets according to two possible weighted-sum GOF scoring systems, and compare the health economic conclusions arising from these different definitions of best-fitting. Results For the simple model, outcomes evaluated over the best-fitting input sets according to the two weighted-sum GOF schemes were virtually non-overlapping on the cost-effectiveness plane and resulted in very different incremental cost-effectiveness ratios ($79,300 [95%CI: 72,500 – 87,600] vs. $139,700 [95%CI: 79,900 - 182,800] per QALY gained). Input sets on the Pareto frontier spanned both regions ($79,000 [95%CI: 64,900 – 156,200] per QALY gained). The TAVR model yielded similar results. Conclusions Choices in generating a summary GOF score may result in different health economic conclusions. The Pareto frontier approach eliminates the need to make these choices by using an intuitive and transparent notion of optimality as the basis for identifying best-fitting input sets. PMID:24799456

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

PubMed

Mackie, Iain D; DiLabio, Gino A

2011-10-07

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

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

PubMed

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

2017-06-07

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

New more accurate calculations of the ground state potential energy surface of H(3) (+).

PubMed

Pavanello, Michele; Tung, Wei-Cheng; Leonarski, Filip; Adamowicz, Ludwik

2009-02-21

Explicitly correlated Gaussian functions with floating centers have been employed to recalculate the ground state potential energy surface (PES) of the H(3) (+) ion with much higher accuracy than it was done before. The nonlinear parameters of the Gaussians (i.e., the exponents and the centers) have been variationally optimized with a procedure employing the analytical gradient of the energy with respect to these parameters. The basis sets for calculating new PES points were guessed from the points already calculated. This allowed us to considerably speed up the calculations and achieve very high accuracy of the results.

Convex Regression with Interpretable Sharp Partitions

PubMed Central

Petersen, Ashley; Simon, Noah; Witten, Daniela

2016-01-01

We consider the problem of predicting an outcome variable on the basis of a small number of covariates, using an interpretable yet non-additive model. We propose convex regression with interpretable sharp partitions (CRISP) for this task. CRISP partitions the covariate space into blocks in a data-adaptive way, and fits a mean model within each block. Unlike other partitioning methods, CRISP is fit using a non-greedy approach by solving a convex optimization problem, resulting in low-variance fits. We explore the properties of CRISP, and evaluate its performance in a simulation study and on a housing price data set. PMID:27635120

The Calculation of Accurate Metal-Ligand Bond Energies

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

1997-01-01

The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

Synthesis, spectroscopic investigation and computational study of 3-(1-(((methoxycarbonyl)oxy)imino)ethyl)-2H-chromen-2-one

NASA Astrophysics Data System (ADS)

Gokula Krishnan, K.; Sivakumar, R.; Thanikachalam, V.; Saleem, H.; Arockia doss, M.

2015-06-01

The molecular structure and vibrational modes of 3-acetylcoumarin oxime carbonate (abbreviated as 3-ACOC) have been investigated by FT-IR, FT-Raman, NMR spectra and also by computational methods using HF and B3LYP with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths, bond angles and dihedral angles) were in good agreement with the corresponding experimental values of 3-ACOC. The calculated vibrational frequencies of normal modes from DFT method matched well with the experimental values. The complete assignments were made on the basis of the total energy distribution (TED) of the vibrational modes. NMR (1H and 13C) chemical shifts were calculated by GIAO method and the results were compared with the experimental values. The other parameters like dipole moment, polarizability, first order hyperpolarizability, zero-point vibrational energy, EHOMO, ELUMO, heat capacity and entropy have also been computed.

Vibrational spectroscopic and non-linear optical activity studies on nicotinanilide : A DFT approach

NASA Astrophysics Data System (ADS)

Premkumar, S.; Jawahar, A.; Mathavan, T.; Dhas, M. Kumara; Benial, A. Milton Franklin

2015-06-01

The molecular structure of nicotinanilide was optimized by the DFT/B3LYP method with cc-pVTZ basis set using Gaussian 09 program. The first order hyperpolarizability of the molecule was calculated, which exhibits the higher nonlinear optical activity. The natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction, which leads to the higher nonlinear optical activity of the molecule. The Frontier molecular orbitals analysis of the molecule shows that the delocalization of electron density occurs within the molecule. The lower energy gap indicates that the hydrogen bond formation between the charged species. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculation using the VEDA 4.0 program and the corresponding vibrational spectra were simulated. Hence, the nicotinanilide molecule can be a good candidate for second-order NLO material.

Conformational, vibrational spectroscopic and quantum chemical studies on 5-methoxyindole-3-carboxaldehyde: A DFT approach

NASA Astrophysics Data System (ADS)

Jeyaseelan, S. Christopher; Hussain, Shamima; Premkumar, R.; Rekha, T. N.; Benial, A. Milton Franklin

2018-04-01

Indole and its derivatives are considered as good ligands for various disease causing proteins in human because of presence of the single nitrogen atom. In the present study, the potential energy surface scan was performed for the most stable molecular structure of the 5-Methoxyindole-3-carboxaldehyde (MICA) molecule. The most stable molecular structure was optimized by DFT/B3LYP method with 6-311G++ (d, p) basis set using Gaussian 09 program package. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculations using VEDA 4.0 program. The Frontier molecular orbitals analysis was performed and related molecular propertieswere calculated. The possible electrophilic and nucleophilic reactive sites of the molecule were studied using molecular electrostatic potential analysis, which confirms the bioactivity of the molecule. The natural bond orbital analysis was also performed to confirm the bioactivity of the title molecule.

Molecular structure and spectroscopic investigation of sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl)benzoate: A DFT study

NASA Astrophysics Data System (ADS)

Shahab, Siyamak; Kumar, Rakesh; Darroudi, Mahdieh; Yousefzadeh Borzehandani, Mostafa

2015-03-01

Quantum-chemical calculations using the Density Functional Theory (DFT) approach for structural analysis of new azodye sodium(E)-2-hydroxy-5-((4-sulfonatophenyl)diazenyl) (trans isomer) is carried out using B3LYP methods with 6-31G∗ basis set. The comparison of measured UV-Vis data, IR and NMR spectra of the molecule with the experimental data were also described which allowed assignment of major spectral features of title molecule. The optimized geometrical parameters obtained by B3LYP methods show a good agreement with experimental data. On the basis of polyvinyl alcohol (PVA) and the dichroic synthesized dye polarizer absorbing in the UV region of the spectrum (λmax = 353 nm) with the effect of polarization in the absorption maximum 96% was developed. The spectral-polarization parameters of stretched PVA-films were calculated.

Basis for selecting optimum antibiotic regimens for secondary peritonitis.

PubMed

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

2016-01-01

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

Learning optimal features for visual pattern recognition

NASA Astrophysics Data System (ADS)

Labusch, Kai; Siewert, Udo; Martinetz, Thomas; Barth, Erhardt

2007-02-01

The optimal coding hypothesis proposes that the human visual system has adapted to the statistical properties of the environment by the use of relatively simple optimality criteria. We here (i) discuss how the properties of different models of image coding, i.e. sparseness, decorrelation, and statistical independence are related to each other (ii) propose to evaluate the different models by verifiable performance measures (iii) analyse the classification performance on images of handwritten digits (MNIST data base). We first employ the SPARSENET algorithm (Olshausen, 1998) to derive a local filter basis (on 13 × 13 pixels windows). We then filter the images in the database (28 × 28 pixels images of digits) and reduce the dimensionality of the resulting feature space by selecting the locally maximal filter responses. We then train a support vector machine on a training set to classify the digits and report results obtained on a separate test set. Currently, the best state-of-the-art result on the MNIST data base has an error rate of 0,4%. This result, however, has been obtained by using explicit knowledge that is specific to the data (elastic distortion model for digits). We here obtain an error rate of 0,55% which is second best but does not use explicit data specific knowledge. In particular it outperforms by far all methods that do not use data-specific knowledge.

Classification of EMG signals using PSO optimized SVM for diagnosis of neuromuscular disorders.

PubMed

Subasi, Abdulhamit

2013-06-01

Support vector machine (SVM) is an extensively used machine learning method with many biomedical signal classification applications. In this study, a novel PSO-SVM model has been proposed that hybridized the particle swarm optimization (PSO) and SVM to improve the EMG signal classification accuracy. This optimization mechanism involves kernel parameter setting in the SVM training procedure, which significantly influences the classification accuracy. The experiments were conducted on the basis of EMG signal to classify into normal, neurogenic or myopathic. In the proposed method the EMG signals were decomposed into the frequency sub-bands using discrete wavelet transform (DWT) and a set of statistical features were extracted from these sub-bands to represent the distribution of wavelet coefficients. The obtained results obviously validate the superiority of the SVM method compared to conventional machine learning methods, and suggest that further significant enhancements in terms of classification accuracy can be achieved by the proposed PSO-SVM classification system. The PSO-SVM yielded an overall accuracy of 97.41% on 1200 EMG signals selected from 27 subject records against 96.75%, 95.17% and 94.08% for the SVM, the k-NN and the RBF classifiers, respectively. PSO-SVM is developed as an efficient tool so that various SVMs can be used conveniently as the core of PSO-SVM for diagnosis of neuromuscular disorders. Copyright © 2013 Elsevier Ltd. All rights reserved.

Molecular structure, vibrational spectra, NLO and MEP analysis of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II)

NASA Astrophysics Data System (ADS)

Tanak, Hasan; Toy, Mehmet

2013-11-01

The molecular geometry and vibrational frequencies of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The energetic and atomic charge behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole (μ), linear polarizability (α) and first-order hyperpolarizability (β) were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-31+G(d) basis set. According to our calculations, the title compound exhibits nonzero (β) value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), frontier molecular orbitals, and thermodynamic properties were performed at B3LYP/6-311G(d,p) level of theory.

Neural network approach to quantum-chemistry data: accurate prediction of density functional theory energies.

PubMed

Balabin, Roman M; Lomakina, Ekaterina I

2009-08-21

Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6+/-0.2 kcal mol(-1). In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

NASA Astrophysics Data System (ADS)

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-07-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran ϕ and ψ and C = O…N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95** to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

PubMed Central

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J. J.

2012-01-01

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran ϕ and ψ and C = O…N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95** to aug-cc-pVTZ (which would not be possible with systems as large as the peptides). PMID:22852599

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.

PubMed

Marianski, Mateusz; Asensio, Amparo; Dannenberg, J J

2012-07-28

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

Theoretical study on the structure and stabilities of molecular clusters of oxalic acid with water.

PubMed

Weber, Kevin H; Morales, Francisco J; Tao, Fu-Ming

2012-11-29

The importance of aerosols to humankind is well-known, playing an integral role in determining Earth's climate and influencing human health. Despite this fact, much remains unknown about the initial events of nucleation. In this work, the molecular properties of common organic atmospheric pollutant oxalic acid and its gas phase interactions with water have been thoroughly examined. Local minima single-point energies for the monomer conformations were calculated at the B3LYP and MP2 level of theory with both 6-311++G(d,p) and aug-cc-pVDZ basis sets and are compared with previous works. Optimized geometries, relative energies, and free energy changes for the stable clusters of oxalic acid conformers with up to six waters were then obtained from B3LYP calculations with 6-31+G(d) and 6-311++G(d,p) basis sets. Initially, cooperative binding is predicted to be the most important factor in nucleation, but as the clusters grow, dipole cancellations are found to play a pivotal role. The clusters of oxalic acid hydrated purely with water tend to produce extremely stable and neutral core systems. Free energies of formation and atmospheric implications are discussed.

Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

NASA Astrophysics Data System (ADS)

Stoudenmire, Edwin Miles; White, Steven

We present a new approach for using DMRG for quantum chemistry that combines the advantages of a basis set with that of a grid approximation. Because DMRG scales linearly for quasi-one-dimensional systems, it is feasible to approximate the continuum with a fine grid in one direction while using a standard basis set approach for the transverse directions. Compared to standard basis set methods, we reach larger systems and achieve better scaling when approaching the basis set limit. The flexibility and reduced costs of our approach even make it feasible to incoporate advanced DMRG techniques such as simulating real-time dynamics. Supported by the Simons Collaboration on the Many-Electron Problem.

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid.

PubMed

Renuga Devi, T S; Sharmi kumar, J; Ramkumaar, G R

2015-02-25

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm(-1) and 4000-50 cm(-1) respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. (1)H and (13)C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study.

PubMed

Pitonák, M; Neogrády, P; Hobza, P

2010-02-14

Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.

CH(X2∏, a4∑-) ... OH2 and CH2(X˜3B1, ã1A1) ... OH2 interactions. A first principles investigation

NASA Astrophysics Data System (ADS)

Tzeli, Demeter; Mavridis, Aristides

We have investigated the interaction of the methylidene, CH(X2∏, a4∑-) and methylene, CH2(X˜3B1, ã1A1) with H2O, employing the (P)MPn (n = 2, 4) techniques in conjunction with the sequence of correlation consistent basis sets aug-cc-pVxZ, x = 2, 3, and 4. For the CH ... OH2 system, we have located four minima (m) and three transition states (ts) and for the CH2 ... OH2, five minima and four transition states. All our results have been corrected for zero-point energy (ZPE) and basis set superposition errors (BSSE), while for the most important m_ structures, we report complete basis set (CBS) interaction limits. We also report fully optimized geometries, harmonic frequencies, dipole moments, Mulliken charges, and potential energy curves. The highest CH(X2∏) ... OH2 (m1_2∏) and CH2(ã1A1) ... OH2 (m1_1A1) interactions are the result of electron transfer from the oxygen atom to the empty pπ orbitals of CH(X2∏) and CH2(ã1A1), respectively (ylide-like structures). At the (P)MP4/AQZ//MP2/ATZ level, including ZPE, BSSE, and CBS extrapolation, we obtain ΔE0(BSSE)+CBS = -9.36 kcal/mol at rC ... O = 1.752 Å, and -9.73 kcal/mol at rC ... O = 1.741 Å for the m1_2∏ and m1_1A1, respectively.

Effect of various binning methods and ROI sizes on the accuracy of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of texture features at HRCT

NASA Astrophysics Data System (ADS)

Kim, Namkug; Seo, Joon Beom; Sung, Yu Sub; Park, Bum-Woo; Lee, Youngjoo; Park, Seong Hoon; Lee, Young Kyung; Kang, Suk-Ho

2008-03-01

To find optimal binning, variable binning size linear binning (LB) and non-linear binning (NLB) methods were tested. In case of small binning size (Q <= 10), NLB shows significant better accuracy than the LB. K-means NLB (Q = 26) is statistically significant better than every LB. To find optimal binning method and ROI size of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of textural analysis at HRCT Six-hundred circular regions of interest (ROI) with 10, 20, and 30 pixel diameter, comprising of each 100 ROIs representing six regional disease patterns (normal, NL; ground-glass opacity, GGO; reticular opacity, RO; honeycombing, HC; emphysema, EMPH; and consolidation, CONS) were marked by an experienced radiologist from HRCT images. Histogram (mean) and co-occurrence matrix (mean and SD of angular second moment, contrast, correlation, entropy, and inverse difference momentum) features were employed to test binning and ROI effects. To find optimal binning, variable binning size LB (bin size Q: 4~30, 32, 64, 128, 144, 196, 256, 384) and NLB (Q: 4~30) methods (K-means, and Fuzzy C-means clustering) were tested. For automated classification, a SVM classifier was implemented. To assess cross-validation of the system, a five-folding method was used. Each test was repeatedly performed twenty times. Overall accuracies with every combination of variable ROIs, and binning sizes were statistically compared. In case of small binning size (Q <= 10), NLB shows significant better accuracy than the LB. K-means NLB (Q = 26) is statistically significant better than every LB. In case of 30x30 ROI size and most of binning size, the K-means method showed better than other NLB and LB methods. When optimal binning and other parameters were set, overall sensitivity of the classifier was 92.85%. The sensitivity and specificity of the system for each class were as follows: NL, 95%, 97.9%; GGO, 80%, 98.9%; RO 85%, 96.9%; HC, 94.7%, 97%; EMPH, 100%, 100%; and CONS, 100%, 100%, respectively. We determined the optimal binning method and ROI size of the automatic classification system for differentiation between diffuse infiltrative lung diseases on the basis of texture features at HRCT.

Application of artificial neural networks to chemostratigraphy

NASA Astrophysics Data System (ADS)

Malmgren, BjöRn A.; Nordlund, Ulf

1996-08-01

Artificial neural networks, a branch of artificial intelligence, are computer systems formed by a number of simple, highly interconnected processing units that have the ability to learn a set of target vectors from a set of associated input signals. Neural networks learn by self-adjusting a set of parameters, using some pertinent algorithm to minimize the error between the desired output and network output. We explore the potential of this approach in solving a problem involving classification of geochemical data. The data, taken from the literature, are derived from four late Quaternary zones of volcanic ash of basaltic and rhyolithic origin from the Norwegian Sea. These ash layers span the oxygen isotope zones 1, 5, 7, and 11, respectively (last 420,000 years). The data consist of nine geochemical variables (oxides) determined in each of 183 samples. We employed a three-layer back propagation neural network to assess its efficiency to optimally differentiate samples from the four ash zones on the basis of their geochemical composition. For comparison, three statistical pattern recognition techniques, linear discriminant analysis, the k-nearest neighbor (k-NN) technique, and SIMCA (soft independent modeling of class analogy), were applied to the same data. All of these showed considerably higher error rates than the artificial neural network, indicating that the back propagation network was indeed more powerful in correctly classifying the ash particles to the appropriate zone on the basis of their geochemical composition.

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

PubMed

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

2014-10-01

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

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

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

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters

PubMed Central

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme. PMID:27362762

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters.

PubMed

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme.

Recommendations for the optimal care of patients with recent‐onset psychosis in the Asia‐Pacific region

PubMed Central

Warden, Matthew; He, Yanling; Si, Tianmei; Kalyanasundaram, Seshadri; Thirunavukarasu, Manickam; Amir, Nurmiati; Hatim, Ahmad; Bautista, Tomas; Lee, Cheng; Emsley, Robin; Olivares, Jose; Yang, Yen Kuang; Kongsakon, Ronnachai; Castle, David

2016-01-01

Abstract Providing optimal care to patients with recent‐onset psychosis can improve outcomes and reduce relapse. However, there is a lack of consistency of the implementation of guidelines for such patients across the Asia‐Pacific region. We determined a pragmatic set of recommendations for use on a day‐to‐day basis to help provide optimal care at this crucial stage of illness. The recommendations were developed over a series of meetings by an international faculty of 15 experts from the Asia‐Pacific region, Europe, and South Africa. A structured search of the PubMed database was conducted. This was further developed based on the faculty's clinical experience and knowledge of the literature into 10 key aspects of optimal care for patients during the first five years of a diagnosis of a psychotic disorder, with particular relevance to the Asia‐Pacific region. Several common principles emerged: adherence to antipsychotic medications is crucial; substance abuse, psychiatric and medical comorbidities should be addressed; psychosocial interventions play a pivotal role; and family members can play a vital role in overall patient care. By following these recommendations, clinicians may improve outcomes for patients with recent‐onset psychosis. PMID:27062665

Interactive K-Means Clustering Method Based on User Behavior for Different Analysis Target in Medicine.

PubMed

Lei, Yang; Yu, Dai; Bin, Zhang; Yang, Yang

2017-01-01

Clustering algorithm as a basis of data analysis is widely used in analysis systems. However, as for the high dimensions of the data, the clustering algorithm may overlook the business relation between these dimensions especially in the medical fields. As a result, usually the clustering result may not meet the business goals of the users. Then, in the clustering process, if it can combine the knowledge of the users, that is, the doctor's knowledge or the analysis intent, the clustering result can be more satisfied. In this paper, we propose an interactive K -means clustering method to improve the user's satisfactions towards the result. The core of this method is to get the user's feedback of the clustering result, to optimize the clustering result. Then, a particle swarm optimization algorithm is used in the method to optimize the parameters, especially the weight settings in the clustering algorithm to make it reflect the user's business preference as possible. After that, based on the parameter optimization and adjustment, the clustering result can be closer to the user's requirement. Finally, we take an example in the breast cancer, to testify our method. The experiments show the better performance of our algorithm.

Quantum chemical calculation (electronic and topologic) and experimental (FT-IR, FT-Raman and UV) analysis of isonicotinic acid N-oxide

NASA Astrophysics Data System (ADS)

Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

2015-04-01

In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.

Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.

PubMed

Suresh, S; Gunasekaran, S; Srinivasan, S

2014-11-11

The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Published by Elsevier B.V.

Problem of quantifying quantum correlations with non-commutative discord

NASA Astrophysics Data System (ADS)

Majtey, A. P.; Bussandri, D. G.; Osán, T. M.; Lamberti, P. W.; Valdés-Hernández, A.

2017-09-01

In this work we analyze a non-commutativity measure of quantum correlations recently proposed by Guo (Sci Rep 6:25241, 2016). By resorting to a systematic survey of a two-qubit system, we detected an undesirable behavior of such a measure related to its representation-dependence. In the case of pure states, this dependence manifests as a non-satisfactory entanglement measure whenever a representation other than the Schmidt's is used. In order to avoid this basis-dependence feature, we argue that a minimization procedure over the set of all possible representations of the quantum state is required. In the case of pure states, this minimization can be analytically performed and the optimal basis turns out to be that of Schmidt's. In addition, the resulting measure inherits the main properties of Guo's measure and, unlike the latter, it reduces to a legitimate entanglement measure in the case of pure states. Some examples involving general mixed states are also analyzed considering such an optimization. The results show that, in most cases of interest, the use of Guo's measure can result in an overestimation of quantum correlations. However, since Guo's measure has the advantage of being easily computable, it might be used as a qualitative estimator of the presence of quantum correlations.

Localized basis sets for unbound electrons in nanoelectronics.

PubMed

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

2008-02-21

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

Multivariate optimization of headspace trap for furan and furfural simultaneous determination in sponge cake.

PubMed

Cepeda-Vázquez, Mayela; Blumenthal, David; Camel, Valérie; Rega, Barbara

2017-03-01

Furan, a possibly carcinogenic compound to humans, and furfural, a naturally occurring volatile contributing to aroma, can be both found in thermally treated foods. These process-induced compounds, formed by close reaction pathways, play an important role as markers of food safety and quality. A method capable of simultaneously quantifying both molecules is thus highly relevant for developing mitigation strategies and preserving the sensory properties of food at the same time. We have developed a unique reliable and sensitive headspace trap (HS trap) extraction method coupled to GC-MS for the simultaneous quantification of furan and furfural in a solid processed food (sponge cake). HS Trap extraction has been optimized using an optimal design of experiments (O-DOE) approach, considering four instrumental and two sample preparation variables, as well as a blocking factor identified during preliminary assays. Multicriteria and multiple response optimization was performed based on a desirability function, yielding the following conditions: thermostatting temperature, 65°C; thermostatting time, 15min; number of pressurization cycles, 4; dry purge time, 0.9min; water / sample amount ratio (dry basis), 16; and total amount (water + sample amount, dry basis), 10g. The performances of the optimized method were also assessed: repeatability (RSD: ≤3.3% for furan and ≤2.6% for furfural), intermediate precision (RSD: 4.0% for furan and 4.3% for furfural), linearity (R 2 : 0.9957 for furan and 0.9996 for furfural), LOD (0.50ng furan g sample dry basis -1 and 10.2ng furfural g sample dry basis -1 ), LOQ (0.99ng furan g sample dry basis -1 and 41.1ng furfural g sample dry basis -1 ). Matrix effect was observed mainly for furan. Finally, the optimized method was applied to other sponge cakes with different matrix characteristics and levels of analytes. Copyright © 2016. Published by Elsevier B.V.

Consensus Statement of the American Academy of Sleep Medicine on the Recommended Amount of Sleep for Healthy Children: Methodology and Discussion

PubMed Central

Paruthi, Shalini; Brooks, Lee J.; D'Ambrosio, Carolyn; Hall, Wendy A.; Kotagal, Suresh; Lloyd, Robin M.; Malow, Beth A.; Maski, Kiran; Nichols, Cynthia; Quan, Stuart F.; Rosen, Carol L.; Troester, Matthew M.; Wise, Merrill S.

2016-01-01

Members of the American Academy of Sleep Medicine developed consensus recommendations for the amount of sleep needed to promote optimal health in children and adolescents using a modified RAND Appropriateness Method. After review of 864 published articles, the following sleep durations are recommended: Infants 4 months to 12 months should sleep 12 to 16 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 1 to 2 years of age should sleep 11 to 14 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 3 to 5 years of age should sleep 10 to 13 hours per 24 hours (including naps) on a regular basis to promote optimal health. Children 6 to 12 years of age should sleep 9 to 12 hours per 24 hours on a regular basis to promote optimal health. Teenagers 13 to 18 years of age should sleep 8 to 10 hours per 24 hours on a regular basis to promote optimal health. Sleeping the number of recommended hours on a regular basis is associated with better health outcomes including: improved attention, behavior, learning, memory, emotional regulation, quality of life, and mental and physical health. Regularly sleeping fewer than the number of recommended hours is associated with attention, behavior, and learning problems. Insufficient sleep also increases the risk of accidents, injuries, hypertension, obesity, diabetes, and depression. Insufficient sleep in teenagers is associated with increased risk of self-harm, suicidal thoughts, and suicide attempts. Commentary: A commentary on this article apears in this issue on page 1439. Citation: Paruthi S, Brooks LJ, D'Ambrosio C, Hall WA, Kotagal S, Lloyd RM, Malow BA, Maski K, Nichols C, Quan SF, Rosen CL, Troester MM, Wise MS. Consensus statement of the American Academy of Sleep Medicine on the recommended amount of sleep for healthy children: methodology and discussion. J Clin Sleep Med 2016;12(11):1549–1561. PMID:27707447

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization

PubMed Central

Li, Zukui; Ding, Ran; Floudas, Christodoulos A.

2011-01-01

Robust counterpart optimization techniques for linear optimization and mixed integer linear optimization problems are studied in this paper. Different uncertainty sets, including those studied in literature (i.e., interval set; combined interval and ellipsoidal set; combined interval and polyhedral set) and new ones (i.e., adjustable box; pure ellipsoidal; pure polyhedral; combined interval, ellipsoidal, and polyhedral set) are studied in this work and their geometric relationship is discussed. For uncertainty in the left hand side, right hand side, and objective function of the optimization problems, robust counterpart optimization formulations induced by those different uncertainty sets are derived. Numerical studies are performed to compare the solutions of the robust counterpart optimization models and applications in refinery production planning and batch process scheduling problem are presented. PMID:21935263

Study on Temperature and Synthetic Compensation of Piezo-Resistive Differential Pressure Sensors by Coupled Simulated Annealing and Simplex Optimized Kernel Extreme Learning Machine

PubMed Central

Li, Ji; Hu, Guoqing; Zhou, Yonghong; Zou, Chong; Peng, Wei; Alam SM, Jahangir

2017-01-01

As a high performance-cost ratio solution for differential pressure measurement, piezo-resistive differential pressure sensors are widely used in engineering processes. However, their performance is severely affected by the environmental temperature and the static pressure applied to them. In order to modify the non-linear measuring characteristics of the piezo-resistive differential pressure sensor, compensation actions should synthetically consider these two aspects. Advantages such as nonlinear approximation capability, highly desirable generalization ability and computational efficiency make the kernel extreme learning machine (KELM) a practical approach for this critical task. Since the KELM model is intrinsically sensitive to the regularization parameter and the kernel parameter, a searching scheme combining the coupled simulated annealing (CSA) algorithm and the Nelder-Mead simplex algorithm is adopted to find an optimal KLEM parameter set. A calibration experiment at different working pressure levels was conducted within the temperature range to assess the proposed method. In comparison with other compensation models such as the back-propagation neural network (BP), radius basis neural network (RBF), particle swarm optimization optimized support vector machine (PSO-SVM), particle swarm optimization optimized least squares support vector machine (PSO-LSSVM) and extreme learning machine (ELM), the compensation results show that the presented compensation algorithm exhibits a more satisfactory performance with respect to temperature compensation and synthetic compensation problems. PMID:28422080

Study on Temperature and Synthetic Compensation of Piezo-Resistive Differential Pressure Sensors by Coupled Simulated Annealing and Simplex Optimized Kernel Extreme Learning Machine.

PubMed

Li, Ji; Hu, Guoqing; Zhou, Yonghong; Zou, Chong; Peng, Wei; Alam Sm, Jahangir

2017-04-19

As a high performance-cost ratio solution for differential pressure measurement, piezo-resistive differential pressure sensors are widely used in engineering processes. However, their performance is severely affected by the environmental temperature and the static pressure applied to them. In order to modify the non-linear measuring characteristics of the piezo-resistive differential pressure sensor, compensation actions should synthetically consider these two aspects. Advantages such as nonlinear approximation capability, highly desirable generalization ability and computational efficiency make the kernel extreme learning machine (KELM) a practical approach for this critical task. Since the KELM model is intrinsically sensitive to the regularization parameter and the kernel parameter, a searching scheme combining the coupled simulated annealing (CSA) algorithm and the Nelder-Mead simplex algorithm is adopted to find an optimal KLEM parameter set. A calibration experiment at different working pressure levels was conducted within the temperature range to assess the proposed method. In comparison with other compensation models such as the back-propagation neural network (BP), radius basis neural network (RBF), particle swarm optimization optimized support vector machine (PSO-SVM), particle swarm optimization optimized least squares support vector machine (PSO-LSSVM) and extreme learning machine (ELM), the compensation results show that the presented compensation algorithm exhibits a more satisfactory performance with respect to temperature compensation and synthetic compensation problems.

The vibrational spectroscopic studies and molecular property analysis of Estradiol, Tamoxifen and their interaction by density functional theory

NASA Astrophysics Data System (ADS)

Borah, Mukunda Madhab; Gomti Devi, Th.

2018-07-01

In the present work Tamoxifen, Estradiol and their interaction are studied using the experimental and theoretical methodologies. The spectral characterization was made by using Raman, FTIR, DFT and VEDA calculation. The optimization of the molecules have been studied using basis set B3LYP/6-31 G(d,p). Complete vibrational assignment of Tamoxifen, Estradiol and Estradiol + Tamoxifen have been attempted and the potential energy distribution and normal mode analysis had also been carried out to determine the contributions of bond oscillators in each normal mode. We have optimized several binding modes of Estradiol and Tamoxifen and taken the lowest energy conformer in our interest. The molecular geometry, HOMO-LUMO energy gap, molecular hardness (η), ionization energy (IE), electron affinity (EA), total energy and dipole moment were analyzed. The observed experimental and the scaled theoretical results were found in good agreement.

Manifold Learning by Preserving Distance Orders.

PubMed

Ataer-Cansizoglu, Esra; Akcakaya, Murat; Orhan, Umut; Erdogmus, Deniz

2014-03-01

Nonlinear dimensionality reduction is essential for the analysis and the interpretation of high dimensional data sets. In this manuscript, we propose a distance order preserving manifold learning algorithm that extends the basic mean-squared error cost function used mainly in multidimensional scaling (MDS)-based methods. We develop a constrained optimization problem by assuming explicit constraints on the order of distances in the low-dimensional space. In this optimization problem, as a generalization of MDS, instead of forcing a linear relationship between the distances in the high-dimensional original and low-dimensional projection space, we learn a non-decreasing relation approximated by radial basis functions. We compare the proposed method with existing manifold learning algorithms using synthetic datasets based on the commonly used residual variance and proposed percentage of violated distance orders metrics. We also perform experiments on a retinal image dataset used in Retinopathy of Prematurity (ROP) diagnosis.

Nonlinear programming for classification problems in machine learning

NASA Astrophysics Data System (ADS)

Astorino, Annabella; Fuduli, Antonio; Gaudioso, Manlio

2016-10-01

We survey some nonlinear models for classification problems arising in machine learning. In the last years this field has become more and more relevant due to a lot of practical applications, such as text and web classification, object recognition in machine vision, gene expression profile analysis, DNA and protein analysis, medical diagnosis, customer profiling etc. Classification deals with separation of sets by means of appropriate separation surfaces, which is generally obtained by solving a numerical optimization model. While linear separability is the basis of the most popular approach to classification, the Support Vector Machine (SVM), in the recent years using nonlinear separating surfaces has received some attention. The objective of this work is to recall some of such proposals, mainly in terms of the numerical optimization models. In particular we tackle the polyhedral, ellipsoidal, spherical and conical separation approaches and, for some of them, we also consider the semisupervised versions.

Vibrational, spectroscopic, molecular docking and density functional theory studies on N-(5-aminopyridin-2-yl)acetamide

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin

2016-12-01

Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

NASA Astrophysics Data System (ADS)

Saravanan, R. R.; Seshadri, S.; Gunasekaran, S.; Mendoza-Meroño, R.; Garcia-Granda, S.

2015-03-01

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

Synthesis, crystal structure, biological activity and theoretical calculations of novel isoxazole derivatives

NASA Astrophysics Data System (ADS)

Jin, R. Y.; Sun, X. H.; Liu, Y. F.; Long, W.; Chen, B.; Shen, S. Q.; Ma, H. X.

2016-01-01

Series of isoxazole derivatives were synthesized by substituted chalcones and 2-chloro-6-fluorobenzene formaldehyde oxime with 1,3-dipolar cycloaddition. The target compounds were determined by melting point, IR, 1H NMR, elemental analyses and HRMS. The crystal structure of compound 3a was detected by X-ray diffraction and it crystallizes in the triclinic space group p2(1)/c with z = 4. The molecular geometry of compound 3a was optimized using density functional theory (DFT/B3LYP) method with the 6-31G+(d,p) basis set in the ground state. From the optimized geometry of the molecule, FT-IR, FT-Raman, HOMO-LUMO and natural bond orbital (NBO) were calculated at B3LYP/6-31G+(d,p) level. Finally, the antifungal activity of the synthetic compounds were evaluated against Pythium solani, Gibberella nicotiancola, Fusarium oxysporium f.sp. niveum and Gibberella saubinetii.

Optimally robust redundancy relations for failure detection in uncertain systems

NASA Technical Reports Server (NTRS)

Lou, X.-C.; Willsky, A. S.; Verghese, G. C.

1986-01-01

All failure detection methods are based, either explicitly or implicitly, on the use of redundancy, i.e. on (possibly dynamic) relations among the measured variables. The robustness of the failure detection process consequently depends to a great degree on the reliability of the redundancy relations, which in turn is affected by the inevitable presence of model uncertainties. In this paper the problem of determining redundancy relations that are optimally robust is addressed in a sense that includes several major issues of importance in practical failure detection and that provides a significant amount of intuition concerning the geometry of robust failure detection. A procedure is given involving the construction of a single matrix and its singular value decomposition for the determination of a complete sequence of redundancy relations, ordered in terms of their level of robustness. This procedure also provides the basis for comparing levels of robustness in redundancy provided by different sets of sensors.

Quantum chemical investigation of levofloxacin-boron complexes: A computational approach

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran

2018-04-01

Quantum chemical calculations are performed over some boron complexes with levofloxacin. Boron complex with fluorine atoms are optimized at three different methods (HF, B3LYP and M062X) with 6-31 + G(d) basis set. The best level is determined as M062X/6-31 + G(d) by comparison of experimental and calculated results of complex (1). The other complexes are optimized by using the best level. Structural properties, IR and NMR spectrum are examined in detail. Biological activities of mentioned complexes are investigated by some quantum chemical descriptors and molecular docking analyses. As a result, biological activities of complex (2) and (4) are close to each other and higher than those of other complexes. Additionally, NLO properties of mentioned complexes are investigated by some quantum chemical parameters. It is found that complex (3) is the best candidate for NLO applications.

Mono and binuclear ruthenium(II) complexes containing 5-chlorothiophene-2-carboxylic acid ligands: Spectroscopic analysis and computational studies

NASA Astrophysics Data System (ADS)

Swarnalatha, Kalaiyar; Kamalesu, Subramaniam; Subramanian, Ramasamy

2016-11-01

New Ruthenium complexes I, II and III were synthesized using 5-chlorothiophene-2-carboxylic acid (5TPC), as ligand and the complexes were characterized by elemental analysis, FT-IR, 1H, 13C NMR, and mass spectroscopic techniques. Photophysical and electrochemical studies were carried out and the structures of the synthesized complex were optimized using density functional theory (DFT). The molecular geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies and Mulliken atomic charges of the molecules are determined at the B3LYP method and standard 6-311++G (d,p) basis set starting from optimized geometry. They possess excellent stabilities and their thermal decomposition temperatures are 185 °C, 180 °C and 200 °C respectively, indicating that the metal complexes are suitable for the fabrication processes of optoelectronic devices.

A Fast Gradient Method for Nonnegative Sparse Regression With Self-Dictionary

NASA Astrophysics Data System (ADS)

Gillis, Nicolas; Luce, Robert

2018-01-01

A nonnegative matrix factorization (NMF) can be computed efficiently under the separability assumption, which asserts that all the columns of the given input data matrix belong to the cone generated by a (small) subset of them. The provably most robust methods to identify these conic basis columns are based on nonnegative sparse regression and self dictionaries, and require the solution of large-scale convex optimization problems. In this paper we study a particular nonnegative sparse regression model with self dictionary. As opposed to previously proposed models, this model yields a smooth optimization problem where the sparsity is enforced through linear constraints. We show that the Euclidean projection on the polyhedron defined by these constraints can be computed efficiently, and propose a fast gradient method to solve our model. We compare our algorithm with several state-of-the-art methods on synthetic data sets and real-world hyperspectral images.

CONORBIT: constrained optimization by radial basis function interpolation in trust regions

DOE PAGES

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

Nursing workload, patient safety incidents and mortality: an observational study from Finland

PubMed Central

Kinnunen, Marina; Saarela, Jan

2018-01-01

Objective To investigate whether the daily workload per nurse (Oulu Patient Classification (OPCq)/nurse) as measured by the RAFAELA system correlates with different types of patient safety incidents and with patient mortality, and to compare the results with regressions based on the standard patients/nurse measure. Setting We obtained data from 36 units from four Finnish hospitals. One was a tertiary acute care hospital, and the three others were secondary acute care hospitals. Participants Patients’ nursing intensity (249 123 classifications), nursing resources, patient safety incidents and patient mortality were collected on a daily basis during 1 year, corresponding to 12 475 data points. Associations between OPC/nurse and patient safety incidents or mortality were estimated using unadjusted logistic regression models, and models that adjusted for ward-specific effects, and effects of day of the week, holiday and season. Primary and secondary outcome measures Main outcome measures were patient safety incidents and death of a patient. Results When OPC/nurse was above the assumed optimal level, the adjusted odds for a patient safety incident were 1.24 (95% CI 1.08 to 1.42) that of the assumed optimal level, and 0.79 (95% CI 0.67 to 0.93) if it was below the assumed optimal level. Corresponding estimates for patient mortality were 1.43 (95% CI 1.18 to 1.73) and 0.78 (95% CI 0.60 to 1.00), respectively. As compared with the patients/nurse classification, models estimated on basis of the RAFAELA classification system generally provided larger effect sizes, greater statistical power and better model fit, although the difference was not very large. Net benefits as calculated on the basis of decision analysis did not provide any clear evidence on which measure to prefer. Conclusions We have demonstrated an association between daily workload per nurse and patient safety incidents and mortality. Current findings need to be replicated by future studies. PMID:29691240

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

PubMed

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

2017-03-14

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

Combination of large and small basis sets in electronic structure calculations on large systems

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

Synthesis, spectroscopic and TD-DFT quantum mechanical study of azo-azomethine dyes. A laser induced trans-cis-trans photoisomerization cycle

NASA Astrophysics Data System (ADS)

Georgiev, Anton; Kostadinov, Anton; Ivanov, Deyan; Dimov, Deyan; Stoyanov, Simeon; Nedelchev, Lian; Nazarova, Dimana; Yancheva, Denitsa

2018-03-01

This paper describes the synthesis, spectroscopic characterization and quantum mechanical calculations of three azo-azomethine dyes. The dyes were synthesized via condensation reaction between 4-(dimethylamino)benzaldehyde and three different 4-aminobenzene azo dyes. Quantum chemical calculations on the optimized molecular geometry and electron densities of the trans (E) and cis (Z) isomers and their vibrational frequencies have been computed by using DFT/B3LYP density-functional theory with 6-311 ++G(d,p) basis set in vacuo. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis,ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. After molecular geometry optimization the electronic spectra have been obtained by TD-DFT calculations at same basis set and correlated with the spectra of vapour deposited nanosized films of the dyes. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. Solvatochromism was investigated by UV-VIS spectroscopy in five different organic solvents with increasing polarity. The dynamic photoisomerization experiments have been performed in DMF by pump lasers λ = 355 nm (mostly E → Z) and λ = 491 nm (mostly Z → E) in spectral region 300 nm - 800 nm at equal concentrations and times of illumination in order to investigate the photodynamical trans-cis-trans properties of the sbnd CHdbnd Nsbnd and sbnd Ndbnd Nsbnd chromophore groups of the dyes.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal?

PubMed

Wolański, Łukasz; Grabarek, Dawid; Andruniów, Tadeusz

2018-04-10

To account for systematic error of CASPT2 method empirical modification of the zeroth-order Hamiltonian with Ionization Potential-Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S-IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S-IPEA, is whether the introduction of the modified zeroth-order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0-0.35 a.u., on vertical excitation energies to low-lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S-IPEA significantly overestimates both S 0 →S 1 and S 0 →S 2 energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth-order Hamiltonian or small value of the IPEA shift in a range of 0.05-0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Hyperfine coupling constants of the nitrogen and phosphorus atoms: A challenge for exact-exchange density-functional and post-Hartree-Fock methods

NASA Astrophysics Data System (ADS)

Kaupp, Martin; Arbuznikov, Alexei V.; Heßelmann, Andreas; Görling, Andreas

2010-05-01

The isotropic hyperfine coupling constants of the free N(S4) and P(S4) atoms have been evaluated with high-level post-Hartree-Fock and density-functional methods. The phosphorus hyperfine coupling presents a significant challenge to both types of methods. With large basis sets, MP2 and coupled-cluster singles and doubles calculations give much too small values for the phosphorus atom. Triple excitations are needed in coupled-cluster calculations to achieve reasonable agreement with experiment. None of the standard density functionals reproduce even the correct sign of this hyperfine coupling. Similarly, the computed hyperfine couplings depend crucially on the self-consistent treatment in exact-exchange density-functional theory within the optimized effective potential (OEP) method. Well-balanced auxiliary and orbital basis sets are needed for basis-expansion exact-exchange-only OEP approaches to come close to Hartree-Fock or numerical OEP data. Results from the localized Hartree-Fock and Krieger-Li-Iafrate approximations deviate notably from exact OEP data in spite of very similar total energies. Of the functionals tested, only full exact-exchange methods augmented by a correlation functional gave at least the correct sign of the P(S4) hyperfine coupling but with too low absolute values. The subtle interplay between the spin-polarization contributions of the different core shells has been analyzed, and the influence of even very small changes in the exchange-correlation potential could be identified.

Promoting Resilience in New Perioperative Nurses.

PubMed

Stephens, Teresa M; Smith, Pamela; Cherry, Caitlin

2017-03-01

New nursing graduates experience many challenges when transitioning from the academic environment to the practice setting. For many, the period of transition from student to employee is less than optimal, with many still experiencing reality shock, cognitive dissonance, and theory-practice gaps. The Stephens Model of Nursing Student Resilience addresses the unique issues faced by new graduate nurses to assist them in developing healthy coping strategies and to promote resilience. This model forms the basis of the RN Personal Resilience Enhancement Plan, a supplemental onboarding program created to assist new nurses in confidently facing challenges encountered during orientation and successfully moving forward as nursing professionals. This article describes the concept of resilience and explains how to link the RN Personal Resilience Enhancement Plan to the onboarding process in the perioperative setting. Copyright © 2017 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Convolutional neural network approach for enhanced capture of breast parenchymal complexity patterns associated with breast cancer risk

NASA Astrophysics Data System (ADS)

Oustimov, Andrew; Gastounioti, Aimilia; Hsieh, Meng-Kang; Pantalone, Lauren; Conant, Emily F.; Kontos, Despina

2017-03-01

We assess the feasibility of a parenchymal texture feature fusion approach, utilizing a convolutional neural network (ConvNet) architecture, to benefit breast cancer risk assessment. Hypothesizing that by capturing sparse, subtle interactions between localized motifs present in two-dimensional texture feature maps derived from mammographic images, a multitude of texture feature descriptors can be optimally reduced to five meta-features capable of serving as a basis on which a linear classifier, such as logistic regression, can efficiently assess breast cancer risk. We combine this methodology with our previously validated lattice-based strategy for parenchymal texture analysis and we evaluate the feasibility of this approach in a case-control study with 424 digital mammograms. In a randomized split-sample setting, we optimize our framework in training/validation sets (N=300) and evaluate its descriminatory performance in an independent test set (N=124). The discriminatory capacity is assessed in terms of the the area under the curve (AUC) of the receiver operator characteristic (ROC). The resulting meta-features exhibited strong classification capability in the test dataset (AUC = 0.90), outperforming conventional, non-fused, texture analysis which previously resulted in an AUC=0.85 on the same case-control dataset. Our results suggest that informative interactions between localized motifs exist and can be extracted and summarized via a fairly simple ConvNet architecture.

The application of the Luus-Jaakola direct search method to the optimization of a hybrid renewable energy system

NASA Astrophysics Data System (ADS)

Jatzeck, Bernhard Michael

2000-10-01

The application of the Luus-Jaakola direct search method to the optimization of stand-alone hybrid energy systems consisting of wind turbine generators (WTG's), photovoltaic (PV) modules, batteries, and an auxiliary generator was examined. The loads for these systems were for agricultural applications, with the optimization conducted on the basis of minimum capital, operating, and maintenance costs. Five systems were considered: two near Edmonton, Alberta, and one each near Lethbridge, Alberta, Victoria, British Columbia, and Delta, British Columbia. The optimization algorithm used hourly data for the load demand, WTG output power/area, and PV module output power. These hourly data were in two sets: seasonal (summer and winter values separated) and total (summer and winter values combined). The costs for the WTG's, PV modules, batteries, and auxiliary generator fuel were full market values. To examine the effects of price discounts or tax incentives, these values were lowered to 25% of the full costs for the energy sources and two-thirds of the full cost for agricultural fuel. Annual costs for a renewable energy system depended upon the load, location, component costs, and which data set (seasonal or total) was used. For one Edmonton load, the cost for a renewable energy system consisting of 27.01 m2 of WTG area, 14 PV modules, and 18 batteries (full price, total data set) was 6873/year. For Lethbridge, a system with 22.85 m2 of WTG area, 47 PV modules, and 5 batteries (reduced prices, seasonal data set) cost 2913/year. The performance of renewable energy systems based on the obtained results was tested in a simulation using load and weather data for selected days. Test results for one Edmonton load showed that the simulations for most of the systems examined ran for at least 17 hours per day before failing due to either an excessive load on the auxiliary generator or a battery constraint being violated. Additional testing indicated that increasing the generator capacity and reducing the maximum allowed battery charge current during the time of the day at which these failures occurred allowed the simulation to successfully operate.

[Reconstruction of Vehicle-human Crash Accident and Injury Analysis Based on 3D Laser Scanning, Multi-rigid-body Reconstruction and Optimized Genetic Algorithm].

PubMed

Sun, J; Wang, T; Li, Z D; Shao, Y; Zhang, Z Y; Feng, H; Zou, D H; Chen, Y J

2017-12-01

To reconstruct a vehicle-bicycle-cyclist crash accident and analyse the injuries using 3D laser scanning technology, multi-rigid-body dynamics and optimized genetic algorithm, and to provide biomechanical basis for the forensic identification of death cause. The vehicle was measured by 3D laser scanning technology. The multi-rigid-body models of cyclist, bicycle and vehicle were developed based on the measurements. The value range of optimal variables was set. A multi-objective genetic algorithm and the nondominated sorting genetic algorithm were used to find the optimal solutions, which were compared to the record of the surveillance video around the accident scene. The reconstruction result of laser scanning on vehicle was satisfactory. In the optimal solutions found by optimization method of genetic algorithm, the dynamical behaviours of dummy, bicycle and vehicle corresponded to that recorded by the surveillance video. The injury parameters of dummy were consistent with the situation and position of the real injuries on the cyclist in accident. The motion status before accident, damage process by crash and mechanical analysis on the injury of the victim can be reconstructed using 3D laser scanning technology, multi-rigid-body dynamics and optimized genetic algorithm, which have application value in the identification of injury manner and analysis of death cause in traffic accidents. Copyright© by the Editorial Department of Journal of Forensic Medicine

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Gunasekaran, S.; Anbalagan, G.

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

[Integrated health information system based on Resident Assessment Instruments].

PubMed

Frijters, D; Achterberg, W; Hirdes, J P; Fries, B E; Morris, J N; Steel, K

2001-02-01

The paper explores the meaning of Resident Assessment Instruments. It gives a summary of existing RAI instruments and derived applications. It argues how all of these form the basis for an integrated health information system for "chain care" (home care, home for the elderly care, nursing home care, mental health care and acute care). The primary application of RAI systems is the assessment of client care needs, followed by an analysis of the required and administered care with the objective to make an optimal individual care plan. On the basis of RAI, however, applications have been derived for reimbursement systems, quality improvement programs, accreditation, benchmarking, best practice comparison and care eligibility systems. These applications have become possible by the development on the basis of the Minimum Data Set of RAI of outcome measures (item scores, scales and indices), case-mix classifications and quality indicators. To illustrate the possibilities of outcome measures of RAI we present a table and a figure with data of six Dutch nursing homes which shows how social engagement is related to ADL and cognition. We argue that RAI/MDS assessment instruments comprise an integrated health information system because they have consistent terminology, common core items, and a common conceptual basis in a clinical approach that emphasizes the identification of functional problems.

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

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

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

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

Orbital-optimized MP2.5 and its analytic gradients: Approaching CCSD(T) quality for noncovalent interactions

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

Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr; Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332; Sherrill, C. David

2014-11-28

Orbital-optimized MP2.5 [or simply “optimized MP2.5,” OMP2.5, for short] and its analytic energy gradients are presented. The cost of the presented method is as much as that of coupled-cluster singles and doubles (CCSD) [O(N{sup 6}) scaling] for energy computations. However, for analytic gradient computations the OMP2.5 method is only half as expensive as CCSD because there is no need to solve λ{sub 2}-amplitude equations for OMP2.5. The performance of the OMP2.5 method is compared with that of the standard second-order Møller–Plesset perturbation theory (MP2), MP2.5, CCSD, and coupled-cluster singles and doubles with perturbative triples (CCSD(T)) methods for equilibrium geometries, hydrogenmore » transfer reactions between radicals, and noncovalent interactions. For bond lengths of both closed and open-shell molecules, the OMP2.5 method improves upon MP2.5 and CCSD by 38%–43% and 31%–28%, respectively, with Dunning's cc-pCVQZ basis set. For complete basis set (CBS) predictions of hydrogen transfer reaction energies, the OMP2.5 method exhibits a substantially better performance than MP2.5, providing a mean absolute error of 1.1 kcal mol{sup −1}, which is more than 10 times lower than that of MP2.5 (11.8 kcal mol{sup −1}), and comparing to MP2 (14.6 kcal mol{sup −1}) there is a more than 12-fold reduction in errors. For noncovalent interaction energies (at CBS limits), the OMP2.5 method maintains the very good performance of MP2.5 for closed-shell systems, and for open-shell systems it significantly outperforms MP2.5 and CCSD, and approaches CCSD(T) quality. The MP2.5 errors decrease by a factor of 5 when the optimized orbitals are used for open-shell noncovalent interactions, and comparing to CCSD there is a more than 3-fold reduction in errors. Overall, the present application results indicate that the OMP2.5 method is very promising for open-shell noncovalent interactions and other chemical systems with difficult electronic structures.« less

Electron correlation within the relativistic no-pair approximation

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

Almoukhalalati, Adel; Saue, Trond, E-mail: trond.saue@irsamc.ups-tlse.fr; Knecht, Stefan

This paper addresses the definition of correlation energy within 4-component relativistic atomic and molecular calculations. In the nonrelativistic domain the correlation energy is defined as the difference between the exact eigenvalue of the electronic Hamiltonian and the Hartree-Fock energy. In practice, what is reported is the basis set correlation energy, where the “exact” value is provided by a full Configuration Interaction (CI) calculation with some specified one-particle basis. The extension of this definition to the relativistic domain is not straightforward since the corresponding electronic Hamiltonian, the Dirac-Coulomb Hamiltonian, has no bound solutions. Present-day relativistic calculations are carried out within themore » no-pair approximation, where the Dirac-Coulomb Hamiltonian is embedded by projectors eliminating the troublesome negative-energy solutions. Hartree-Fock calculations are carried out with the implicit use of such projectors and only positive-energy orbitals are retained at the correlated level, meaning that the Hartree-Fock projectors are frozen at the correlated level. We argue that the projection operators should be optimized also at the correlated level and that this is possible by full Multiconfigurational Self-Consistent Field (MCSCF) calculations, that is, MCSCF calculations using a no-pair full CI expansion, but including orbital relaxation from the negative-energy orbitals. We show by variational perturbation theory that the MCSCF correlation energy is a pure MP2-like correlation expression, whereas the corresponding CI correlation energy contains an additional relaxation term. We explore numerically our theoretical analysis by carrying out variational and perturbative calculations on the two-electron rare gas atoms with specially tailored basis sets. In particular, we show that the correlation energy obtained by the suggested MCSCF procedure is smaller than the no-pair full CI correlation energy, in accordance with the underlying minmax principle and our theoretical analysis. We also show that the relativistic correlation energy, obtained from no-pair full MCSCF calculations, scales at worst as X{sup −2} with respect to the cardinal number X of our correlation-consistent basis sets optimized for the two-electron atoms. This is better than the X{sup −1} scaling suggested by previous studies, but worse than the X{sup −3} scaling observed in the nonrelativistic domain. The well-known 1/Z- expansion in nonrelativistic atomic theory follows from coordinate scaling. We point out that coordinate scaling for consistency should be accompanied by velocity scaling. In the nonrelativistic domain this comes about automatically, whereas in the relativistic domain an explicit scaling of the speed of light is required. This in turn explains why the relativistic correlation energy to the lowest order is not independent of nuclear charge, in contrast to nonrelativistic theory.« less

Jig-Shape Optimization of a Low-Boom Supersonic Aircraft

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi

2018-01-01

A simple approach for optimizing the jig-shape is proposed in this study. This simple approach is based on an unconstrained optimization problem and applied to a low-boom supersonic aircraft. In this study, the jig-shape optimization is performed using the two-step approach. First, starting design variables are computed using the least-squares surface fitting technique. Next, the jig-shape is further tuned using a numerical optimization procedure based on an in-house object-oriented optimization tool. During the numerical optimization procedure, a design jig-shape is determined by the baseline jig-shape and basis functions. A total of 12 symmetric mode shapes of the cruise-weight configuration, rigid pitch shape, rigid left and right stabilator rotation shapes, and a residual shape are selected as sixteen basis functions. After three optimization runs, the trim shape error distribution is improved, and the maximum trim shape error of 0.9844 inches of the starting configuration becomes 0.00367 inch by the end of the third optimization run.

Performance assessment of density functional methods with Gaussian and Slater basis sets using 7σ orbital momentum distributions of N2O

NASA Astrophysics Data System (ADS)

Wang, Feng; Pang, Wenning; Duffy, Patrick

2012-12-01

Performance of a number of commonly used density functional methods in chemistry (B3LYP, Bhandh, BP86, PW91, VWN, LB94, PBe0, SAOP and X3LYP and the Hartree-Fock (HF) method) has been assessed using orbital momentum distributions of the 7σ orbital of nitrous oxide (NNO), which models electron behaviour in a chemically significant region. The density functional methods are combined with a number of Gaussian basis sets (Pople's 6-31G*, 6-311G**, DGauss TZVP and Dunning's aug-cc-pVTZ as well as even-tempered Slater basis sets, namely, et-DZPp, et-QZ3P, et-QZ+5P and et-pVQZ). Orbital momentum distributions of the 7σ orbital in the ground electronic state of NNO, which are obtained from a Fourier transform into momentum space from single point electronic calculations employing the above models, are compared with experimental measurement of the same orbital from electron momentum spectroscopy (EMS). The present study reveals information on performance of (a) the density functional methods, (b) Gaussian and Slater basis sets, (c) combinations of the density functional methods and basis sets, that is, the models, (d) orbital momentum distributions, rather than a group of specific molecular properties and (e) the entire region of chemical significance of the orbital. It is found that discrepancies of this orbital between the measured and the calculated occur in the small momentum region (i.e. large r region). In general, Slater basis sets achieve better overall performance than the Gaussian basis sets. Performance of the Gaussian basis sets varies noticeably when combining with different Vxc functionals, but Dunning's augcc-pVTZ basis set achieves the best performance for the momentum distributions of this orbital. The overall performance of the B3LYP and BP86 models is similar to newer models such as X3LYP and SAOP. The present study also demonstrates that the combinations of the density functional methods and the basis sets indeed make a difference in the quality of the calculated orbitals.

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

NASA Astrophysics Data System (ADS)

Miliordos, Evangelos; Xantheas, Sotiris S.

2015-03-01

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

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

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

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

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.

Atomization Energies of SO and SO2; Basis Set Extrapolation Revisted

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

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

ERIC Educational Resources Information Center

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

2007-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Theoretical study of optical activity of 1:1 hydrogen bond complexes of water with S-warfarin

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Abdolmaleki, Ahmad; Zabardasti, Abedin

2016-11-01

The molecular interaction between S-warfarin (SW) and a single water molecule was investigated using the B3LYP method at 6-311 ++G(d,p) basis set. The vibrational spectra of the optimized complexes have been investigated for stabilization checking. Quantum theories of atoms in molecules, natural bond orbitals, molecular electrostatic potentials and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. The intermolecular charge transfer in the most stable complex is in the opposite direction from those in the other complexes. The optical spectra and the hyperpolarizabilities of SW-water hydrogen bond complexes have been computed.

Methanol in its own gravy. A PCM study for simulation of vibrational spectra.

PubMed

Billes, Ferenc; Mohammed-Ziegler, Ildikó; Mikosch, Hans

2011-05-07

For studying both hydrogen bond and dipole-dipole interactions between methanol molecules (self-association) the geometry of clusters of increasing numbers of methanol molecules (n = 1,2,3) were optimized and also their vibrational frequencies were calculated with quantum chemical methods. Beside these B3LYP/6-311G** calculations, PCM calculations were also done for all systems with PCM at the same quantum chemical method and basis set, for considering the effect of the liquid continuum on the cluster properties. Comparing the results, the measured and calculated infrared spectra are in good accordance. This journal is © the Owner Societies 2011

Genetic algorithm based adaptive neural network ensemble and its application in predicting carbon flux

USGS Publications Warehouse

Xue, Y.; Liu, S.; Hu, Y.; Yang, J.; Chen, Q.

2007-01-01

To improve the accuracy in prediction, Genetic Algorithm based Adaptive Neural Network Ensemble (GA-ANNE) is presented. Intersections are allowed between different training sets based on the fuzzy clustering analysis, which ensures the diversity as well as the accuracy of individual Neural Networks (NNs). Moreover, to improve the accuracy of the adaptive weights of individual NNs, GA is used to optimize the cluster centers. Empirical results in predicting carbon flux of Duke Forest reveal that GA-ANNE can predict the carbon flux more accurately than Radial Basis Function Neural Network (RBFNN), Bagging NN ensemble, and ANNE. ?? 2007 IEEE.

2018 update to the HIV-TRePS system: the development of new computational models to predict HIV treatment outcomes, with or without a genotype, with enhanced usability for low-income settings.

PubMed

Revell, Andrew D; Wang, Dechao; Perez-Elias, Maria-Jesus; Wood, Robin; Cogill, Dolphina; Tempelman, Hugo; Hamers, Raph L; Reiss, Peter; van Sighem, Ard I; Rehm, Catherine A; Pozniak, Anton; Montaner, Julio S G; Lane, H Clifford; Larder, Brendan A

2018-06-08

Optimizing antiretroviral drug combination on an individual basis can be challenging, particularly in settings with limited access to drugs and genotypic resistance testing. Here we describe our latest computational models to predict treatment responses, with or without a genotype, and compare their predictive accuracy with that of genotyping. Random forest models were trained to predict the probability of virological response to a new therapy introduced following virological failure using up to 50 000 treatment change episodes (TCEs) without a genotype and 18 000 TCEs including genotypes. Independent data sets were used to evaluate the models. This study tested the effects on model accuracy of relaxing the baseline data timing windows, the use of a new filter to exclude probable non-adherent cases and the addition of maraviroc, tipranavir and elvitegravir to the system. The no-genotype models achieved area under the receiver operator characteristic curve (AUC) values of 0.82 and 0.81 using the standard and relaxed baseline data windows, respectively. The genotype models achieved AUC values of 0.86 with the new non-adherence filter and 0.84 without. Both sets of models were significantly more accurate than genotyping with rules-based interpretation, which achieved AUC values of only 0.55-0.63, and were marginally more accurate than previous models. The models were able to identify alternative regimens that were predicted to be effective for the vast majority of cases in which the new regimen prescribed in the clinic failed. These latest global models predict treatment responses accurately even without a genotype and have the potential to help optimize therapy, particularly in resource-limited settings.

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

PubMed

Corcoran, Timothy C

2018-03-01

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

The effect of diffuse basis functions on valence bond structural weights

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

Forensic SNP genotyping with SNaPshot: Technical considerations for the development and optimization of multiplexed SNP assays.

PubMed

Fondevila, M; Børsting, C; Phillips, C; de la Puente, M; Consortium, Euroforen-NoE; Carracedo, A; Morling, N; Lareu, M V

2017-01-01

This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides an advantage. In order to provide the basis for developing such expertise, we cover in this paper the most challenging aspects of the SNaPshot technology, focusing on the steps taken to design primer sets, optimize the PCR and single-base extension chemistries, and the important features of the peak patterns observed in typical forensic SNP profiles using SNaPshot. With that purpose in mind, we provide guidelines and troubleshooting for multiplex-SNaPshot-oriented primer design and the resulting capillary electrophoresis (CE) profile interpretation (covering the most commonly observed artifacts and expected departures from the ideal conditions). Copyright © 2017 Central Police University.

The anesthetic action of some polyhalogenated ethers-Monte Carlo method based QSAR study.

PubMed

Golubović, Mlađan; Lazarević, Milan; Zlatanović, Dragan; Krtinić, Dane; Stoičkov, Viktor; Mladenović, Bojan; Milić, Dragan J; Sokolović, Dušan; Veselinović, Aleksandar M

2018-04-13

Up to this date, there has been an ongoing debate about the mode of action of general anesthetics, which have postulated many biological sites as targets for their action. However, postoperative nausea and vomiting are common problems in which inhalational agents may have a role in their development. When a mode of action is unknown, QSAR modelling is essential in drug development. To investigate the aspects of their anesthetic, QSAR models based on the Monte Carlo method were developed for a set of polyhalogenated ethers. Until now, their anesthetic action has not been completely defined, although some hypotheses have been suggested. Therefore, a QSAR model should be developed on molecular fragments that contribute to anesthetic action. QSAR models were built on the basis of optimal molecular descriptors based on the SMILES notation and local graph invariants, whereas the Monte Carlo optimization method with three random splits into the training and test set was applied for model development. Different methods, including novel Index of ideality correlation, were applied for the determination of the robustness of the model and its predictive potential. The Monte Carlo optimization process was capable of being an efficient in silico tool for building up a robust model of good statistical quality. Molecular fragments which have both positive and negative influence on anesthetic action were determined. The presented study can be useful in the search for novel anesthetics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Thermal management in closed incubators: New software for assessing the impact of humidity on the optimal incubator air temperature.

PubMed

Delanaud, Stéphane; Decima, Pauline; Pelletier, Amandine; Libert, Jean-Pierre; Durand, Estelle; Stephan-Blanchard, Erwan; Bach, Véronique; Tourneux, Pierre

2017-08-01

Low-birth-weight (LBW) neonates are nursed in closed incubators to prevent transcutaneous water loss. The RH's impact on the optimal incubator air temperature setting has not been studied. On the basis of a clinical cohort study, we modelled all the ambient parameters influencing body heat losses and gains. The algorithm quantifies the change in RH on the air temperature, to maintain optimal thermal conditions in the incubator. Twenty-three neonates (gestational age (GA): 30.0 [28.9-31.6] weeks) were included. A 20% increase and a 20% decrease in the RH induced a change in air temperature of between -1.51 and +1.85°C for a simulated 650g neonate (GA: 26 weeks), between -1.66 and +1.87°C for a 1000g neonate (GA: 31 weeks), and between -1.77 and +1.97°C for a 2000g neonate (GA: 33 weeks) (p<0.001). According to regression analyses, the optimal incubator air temperature=a+b relative humidity +c age +d weight (p<0.001). We have developed new mathematical equations for calculating the optimal temperature for the incubator air as a function of the latter's relative humidity. The software constitutes a decision support tool for improving patient care in routine clinical practice. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

The optimized effective potential and the self-interaction correction in density functional theory: Application to molecules

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

Garza, Jorge; Nichols, Jeffrey A.; Dixon, David A.

2000-05-08

The Krieger, Li, and Iafrate approximation to the optimized effective potential including the self-interaction correction for density functional theory has been implemented in a molecular code, NWChem, that uses Gaussian functions to represent the Kohn and Sham spin-orbitals. The differences between the implementation of the self-interaction correction in codes where planewaves are used with an optimized effective potential are discussed. The importance of the localization of the spin-orbitals to maximize the exchange-correlation of the self-interaction correction is discussed. We carried out exchange-only calculations to compare the results obtained with these approximations, and those obtained with the local spin density approximation,more » the generalized gradient approximation and Hartree-Fock theory. Interesting results for the energy difference (GAP) between the highest occupied molecular orbital, HOMO, and the lowest unoccupied molecular orbital, LUMO, (spin-orbital energies of closed shell atoms and molecules) using the optimized effective potential and the self-interaction correction have been obtained. The effect of the diffuse character of the basis set on the HOMO and LUMO eigenvalues at the various levels is discussed. Total energies obtained with the optimized effective potential and the self-interaction correction show that the exchange energy with these approximations is overestimated and this will be an important topic for future work. (c) 2000 American Institute of Physics.« less

Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

PubMed Central

Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

2015-01-01

In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

First example of a high-level correlated calculation of the indirect spin-spin coupling constants involving tellurium: tellurophene and divinyl telluride.

PubMed

Rusakov, Yury Yu; Krivdin, Leonid B; Østerstrøm, Freja F; Sauer, Stephan P A; Potapov, Vladimir A; Amosova, Svetlana V

2013-08-21

This paper documents the very first example of a high-level correlated calculation of spin-spin coupling constants involving tellurium taking into account relativistic effects, vibrational corrections and solvent effects for medium sized organotellurium molecules. The (125)Te-(1)H spin-spin coupling constants of tellurophene and divinyl telluride were calculated at the SOPPA and DFT levels, in good agreement with experimental data. A new full-electron basis set, av3z-J, for tellurium derived from the "relativistic" Dyall's basis set, dyall.av3z, and specifically optimized for the correlated calculations of spin-spin coupling constants involving tellurium was developed. The SOPPA method shows a much better performance compared to DFT, if relativistic effects calculated within the ZORA scheme are taken into account. Vibrational and solvent corrections are next to negligible, while conformational averaging is of prime importance in the calculation of (125)Te-(1)H spin-spin couplings. Based on the performed calculations at the SOPPA(CCSD) level, a marked stereospecificity of geminal and vicinal (125)Te-(1)H spin-spin coupling constants originating in the orientational lone pair effect of tellurium has been established, which opens a new guideline in organotellurium stereochemistry.

Principles of Antipsychotic Prescribing for Policy Makers, Circa 2008. Translating Knowledge to Promote Individualized Treatment

PubMed Central

Parks, Joseph; Radke, Alan; Parker, George; Foti, May-Ellen; Eilers, Robert; Diamond, Mary; Svendsen, Dale; Tandon, Rajiv

2009-01-01

Findings from 2 pivotal government-funded studies of comparative antipsychotic effectiveness undermine assumptions about the marked superiority of the more expensive second-generation “atypical” medications in comparison to the less expensive first-generation “typical” drugs. Because this assumption was the basis for the almost universal recommendation that these newer antipsychotics be used preferentially resulting in a 10-fold increase in state governmental expenditures on this class of medications over the past decade, a reassessment of policy is called for. To address the issue, the Medical Directors Council of the National Association of State Mental Health Program Directors critically reviewed findings of these studies in the context of other data and considered policy implications in the light of the obligations of state government to make available best possible and individually optimized treatment that is cost-effective. The Medical Directors Council unanimously adopted a set of recommendations to promote appropriate access, efficient utilization, and best practice use. We present our policy statement, in which we provide a succinct background, articulate general principles, and describe a set of 4 broad recommendations. We then summarize our understanding of the current state of knowledge about comparative antipsychotic effectiveness, best antipsychotic practice, and considerations for state policy that represent the basis of our position statement. PMID:18385207

Spectroscopic and DFT studies of flurbiprofen as dimer and its Cu(II) and Hg(II) complexes

NASA Astrophysics Data System (ADS)

Sagdinc, Seda; Pir, Hacer

2009-07-01

The vibrational study in the solid state of flurbiprofen and its Cu(II) and Hg(II) complexes was performed by IR and Raman spectroscopy. The changes observed between the IR and Raman spectra of the ligand and of the complexes allowed us to establish the coordination mode of the metal in both complexes. The comparative vibrational analysis of the free ligand and its complexes gave evidence that flurbiprofen binds metal (II) through the carboxylate oxygen. The fully optimized equilibrium structure of flurbiprofen and its metal complexes was obtained by density functional B3LYP method by using LanL2DZ and 6-31 G(d,p) basis sets. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of flurbiprofen were calculated by density functional B3LYP methods by using 6-31G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The electronic properties of the free molecule and its complexes were also performed at B3LYP/6-31G(d,p) level of theory. Detailed interpretations of the infrared and Raman spectra of flurbiprofen are reported. The UV-vis spectra of flurbiprofen and its metal complexes were also investigated in organic solvents.

A Phase-Space Approach to Collisionless Stellar Systems Using a Particle Method

NASA Astrophysics Data System (ADS)

Hozumi, Shunsuke

1997-10-01

A particle method for reproducing the phase space of collisionless stellar systems is described. The key idea originates in Liouville's theorem, which states that the distribution function (DF) at time t can be derived from tracing necessary orbits back to t = 0. To make this procedure feasible, a self-consistent field (SCF) method for solving Poisson's equation is adopted to compute the orbits of arbitrary stars. As an example, for the violent relaxation of a uniform density sphere, the phase-space evolution generated by the current method is compared to that obtained with a phase-space method for integrating the collisionless Boltzmann equation, on the assumption of spherical symmetry. Excellent agreement is found between the two methods if an optimal basis set for the SCF technique is chosen. Since this reproduction method requires only the functional form of initial DFs and does not require any assumptions to be made about the symmetry of the system, success in reproducing the phase-space evolution implies that there would be no need of directly solving the collisionless Boltzmann equation in order to access phase space even for systems without any special symmetries. The effects of basis sets used in SCF simulations on the reproduced phase space are also discussed.

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

PubMed

Lemke, Kono H

2017-06-21

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

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

NASA Astrophysics Data System (ADS)

Lemke, Kono H.

2017-06-01

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

Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation

PubMed Central

2014-01-01

Introduction Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory or degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Methods Three multi-center genome-wide transcriptomic data sets (Affymetrix HG-U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule-based classifiers to discriminate the disease groups. The rules were ranked with respect to Kiendl’s statistical relevance index, and the resulting rule set was optimized by pruning. The rule sets were inferred separately from data of one of three centers and applied to the two remaining centers for validation. All rules from the optimized rule sets of all centers were used to analyze their biological relevance applying the software Pathway Studio. Results The optimized rule sets for the three centers contained a total of 29, 20, and 8 rules (including 10, 8, and 4 rules for ‘RA’), respectively. The mean sensitivity for the prediction of RA based on six center-to-center tests was 96% (range 90% to 100%), that for OA 86% (range 40% to 100%). The mean specificity for RA prediction was 94% (range 80% to 100%), that for OA 96% (range 83.3% to 100%). The average overall accuracy of the three different rule-based classifiers was 91% (range 80% to 100%). Unbiased analyses by Pathway Studio of the gene sets obtained by discrimination of RA from OA and CG with rule-based classifiers resulted in the identification of the pathogenetically and/or therapeutically relevant interferon-gamma and GM-CSF pathways. Conclusion First-time application of rule-based classifiers for the discrimination of RA resulted in high performance, with means for all assessment parameters close to or higher than 90%. In addition, this unbiased, new approach resulted in the identification not only of pathways known to be critical to RA, but also of novel molecules such as serine/threonine kinase 10. PMID:24690414

[Rapid identification of hogwash oil by using synchronous fluorescence spectroscopy].

PubMed

Sun, Yan-Hui; An, Hai-Yang; Jia, Xiao-Li; Wang, Juan

2012-10-01

To identify hogwash oil quickly, the characteristic delta lambda of hogwash oil was analyzed by three dimensional fluorescence spectroscopy with parallel factor analysis, and the model was built up by using synchronous fluorescence spectroscopy with support vector machines (SVM). The results showed that the characteristic delta lambda of hogwash oil was 60 nm. Collecting original spectrum of different samples under the condition of characteristic delta lambda 60 nm, the best model was established while 5 principal components were selected from original spectrum and the radial basis function (RBF) was used as the kernel function, and the optimal penalty factor C and kernel function g were 512 and 0.5 respectively obtained by the grid searching and 6-fold cross validation. The discrimination rate of the model was 100% for both training sets and prediction sets. Thus, it is quick and accurate to apply synchronous fluorescence spectroscopy to identification of hogwash oil.

Model-Free Primitive-Based Iterative Learning Control Approach to Trajectory Tracking of MIMO Systems With Experimental Validation.

PubMed

Radac, Mircea-Bogdan; Precup, Radu-Emil; Petriu, Emil M

2015-11-01

This paper proposes a novel model-free trajectory tracking of multiple-input multiple-output (MIMO) systems by the combination of iterative learning control (ILC) and primitives. The optimal trajectory tracking solution is obtained in terms of previously learned solutions to simple tasks called primitives. The library of primitives that are stored in memory consists of pairs of reference input/controlled output signals. The reference input primitives are optimized in a model-free ILC framework without using knowledge of the controlled process. The guaranteed convergence of the learning scheme is built upon a model-free virtual reference feedback tuning design of the feedback decoupling controller. Each new complex trajectory to be tracked is decomposed into the output primitives regarded as basis functions. The optimal reference input for the control system to track the desired trajectory is next recomposed from the reference input primitives. This is advantageous because the optimal reference input is computed straightforward without the need to learn from repeated executions of the tracking task. In addition, the optimization problem specific to trajectory tracking of square MIMO systems is decomposed in a set of optimization problems assigned to each separate single-input single-output control channel that ensures a convenient model-free decoupling. The new model-free primitive-based ILC approach is capable of planning, reasoning, and learning. A case study dealing with the model-free control tuning for a nonlinear aerodynamic system is included to validate the new approach. The experimental results are given.

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

NASA Astrophysics Data System (ADS)

Choi, Chu Hwan

2002-09-01

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

[Preparation of curcumin-EC sustained-release composite particles by supercritical CO2 anti-solvent technology].

PubMed

Bai, Wei-li; Yan, Ting-yuan; Wang, Zhi-xiang; Huang, De-chun; Yan, Ting-xuan; Li, Ping

2015-01-01

Curcumin-ethyl-cellulose (EC) sustained-release composite particles were prepared by using supercritical CO2 anti-solvent technology. With drug loading and yield of inclusion complex as evaluation indexes, on the basis of single factor tests, orthogonal experimental design was used to optimize the preparation process of curcumin-EC sustained-release composite particles. The experiments such as drug loading, yield, particle size distribution, electron microscope analysis (SEM) , infrared spectrum (IR), differential scanning calorimetry (DSC) and in vitro dissolution were used to analyze the optimal process combination. The orthogonal experimental optimization process conditions were set as follows: crystallization temperature 45 degrees C, crystallization pressure 10 MPa, curcumin concentration 8 g x L(-1), solvent flow rate 0.9 mL x min(-1), and CO2 velocity 4 L x min(-1). Under the optimal conditions, the average drug loading and yield of curcumin-EC sustained-release composite particles were 33.01% and 83.97%, and the average particle size of the particles was 20.632 μm. IR and DSC analysis showed that curcumin might complex with EC. The experiments of in vitro dissolution showed that curcumin-EC composite particles had good sustained-release effect. Curcumin-EC sustained-release composite particles can be prepared by supercritical CO2 anti-solvent technology.

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

PubMed

Ferenczy, György G

2013-04-05

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

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

NASA Astrophysics Data System (ADS)

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

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

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Ab Initio and Analytic Intermolecular Potentials for Ar-CF₄

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

Vayner, Grigoriy; Alexeev, Yuri; Wang, Jiangping

2006-03-09

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

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

NASA Technical Reports Server (NTRS)

Martin, J. M. L.

1992-01-01

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

Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform.

PubMed

Nagy, Péter R; Kállay, Mihály

2017-06-07

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can always be performed if the preceding CCSD iterations are feasible, and the new scheme enables the computation of LNO-CCSD(T) correlation energies with at least triple-zeta quality basis sets for realistic three-dimensional molecules with more than 600 atoms and 12 000 basis functions in a matter of days on a single processor.

Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform

PubMed Central

2017-01-01

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can always be performed if the preceding CCSD iterations are feasible, and the new scheme enables the computation of LNO-CCSD(T) correlation energies with at least triple-zeta quality basis sets for realistic three-dimensional molecules with more than 600 atoms and 12 000 basis functions in a matter of days on a single processor. PMID:28576082

Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations

NASA Astrophysics Data System (ADS)

Nagabalasubramanian, P. B.; Periandy, S.; Karabacak, Mehmet; Govindarajan, M.

2015-06-01

The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100 cm-1. The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.

Synthesis, spectroscopic investigation and theoretical studies of 2-((E)-(2-(2-cyanoacetyl)hydrazono)methyl)-4-((E)-phenyldiazenyl)phenyl methyl carbonate

NASA Astrophysics Data System (ADS)

Arokiasamy, A.; Manikandan, G.; Thanikachalam, V.; Gokula Krishnan, K.

2017-04-01

Synthesis and computational optimization studies have been carried out by Hartree-Fock (HF) and Density Functional Theory (DFT-B3LYP) methods with 6-31+G(d, p) basis set for 2-((E)-(2-(2-cyanoacetyl)hydrazono)methyl)-4-((E)-phenyldiazenyl)phenyl methyl carbonate (CHPMC). The stable configuration of CHPMC was confirmed theoretically by potential energy surface scan analysis. The complete vibrational assignments were performed on the basis of total energy distribution (TED) analysis. The vibrational properties studied by IR and Raman spectroscopic data complemented by quantum chemical calculations support the formation of intramolecular hydrogen bond. Furthermore, the UV-Vis spectra are interpreted in terms of TD-DFT quantum chemical calculations. The shapes of the simulated absorption spectra are in good agreement with the experimental data. The comparison between the experimental and theoretical values of FT-IR, FT-Raman vibrational spectra, NMR (1H and 13C) and UV-Vis spectra have also been discussed.

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

NASA Astrophysics Data System (ADS)

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

2011-05-01

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

An experimental and theoretical study of molecular structure and vibrational spectra of 2-methylphenyl boronic acid by density functional theory calculations

NASA Astrophysics Data System (ADS)

Hiremath, Sudhir M.; Hiremath, C. S.; Khemalapure, S. S.; Patil, N. R.

2018-05-01

This paper reports the experimental and theoretical study on the structure and vibrations of 2-Methylphenyl boronic acid (2MPBA). The different spectroscopic techniques such as FT-IR (4000-400 cm-1) and FT-Raman (4000-50 cm-1) of the title molecule in the solid phase were recorded. The geometry of the molecule was fully optimized using density functional theory (DFT) (B3LYP) with 6-311++G(d, p) basis set calculations. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. Vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the potential energy distribution (PED) of the vibrational modes obtained from VEDA 4 program. The calculated wavenumbers showed the best agreement with the experimental results. Whereas, it is observed that, the theoretical frequencies are more than the experimental one for O-H stretching vibration modes of the title molecule.

Data analytics approach to create waste generation profiles for waste management and collection.

PubMed

Niska, Harri; Serkkola, Ari

2018-04-30

Extensive monitoring data on waste generation is increasingly collected in order to implement cost-efficient and sustainable waste management operations. In addition, geospatial data from different registries of the society are opening for free usage. Novel data analytics approaches can be built on the top of the data to produce more detailed, and in-time waste generation information for the basis of waste management and collection. In this paper, a data-based approach based on the self-organizing map (SOM) and the k-means algorithm is developed for creating a set of waste generation type profiles. The approach is demonstrated using the extensive container-level waste weighting data collected in the metropolitan area of Helsinki, Finland. The results obtained highlight the potential of advanced data analytic approaches in producing more detailed waste generation information e.g. for the basis of tailored feedback services for waste producers and the planning and optimization of waste collection and recycling. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

2015-01-01

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

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

PubMed

Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet

2015-01-25

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

Finite basis representations with nondirect product basis functions having structure similar to that of spherical harmonics.

PubMed

Czakó, Gábor; Szalay, Viktor; Császár, Attila G

2006-01-07

The currently most efficient finite basis representation (FBR) method [Corey et al., in Numerical Grid Methods and Their Applications to Schrodinger Equation, NATO ASI Series C, edited by C. Cerjan (Kluwer Academic, New York, 1993), Vol. 412, p. 1; Bramley et al., J. Chem. Phys. 100, 6175 (1994)] designed specifically to deal with nondirect product bases of structures phi(n) (l)(s)f(l)(u), chi(m) (l)(t)phi(n) (l)(s)f(l)(u), etc., employs very special l-independent grids and results in a symmetric FBR. While highly efficient, this method is not general enough. For instance, it cannot deal with nondirect product bases of the above structure efficiently if the functions phi(n) (l)(s) [and/or chi(m) (l)(t)] are discrete variable representation (DVR) functions of the infinite type. The optimal-generalized FBR(DVR) method [V. Szalay, J. Chem. Phys. 105, 6940 (1996)] is designed to deal with general, i.e., direct and/or nondirect product, bases and grids. This robust method, however, is too general, and its direct application can result in inefficient computer codes [Czako et al., J. Chem. Phys. 122, 024101 (2005)]. It is shown here how the optimal-generalized FBR method can be simplified in the case of nondirect product bases of structures phi(n) (l)(s)f(l)(u), chi(m) (l)(t)phi(n) (l)(s)f(l)(u), etc. As a result the commonly used symmetric FBR is recovered and simplified nonsymmetric FBRs utilizing very special l-dependent grids are obtained. The nonsymmetric FBRs are more general than the symmetric FBR in that they can be employed efficiently even when the functions phi(n) (l)(s) [and/or chi(m) (l)(t)] are DVR functions of the infinite type. Arithmetic operation counts and a simple numerical example presented show unambiguously that setting up the Hamiltonian matrix requires significantly less computer time when using one of the proposed nonsymmetric FBRs than that in the symmetric FBR. Therefore, application of this nonsymmetric FBR is more efficient than that of the symmetric FBR when one wants to diagonalize the Hamiltonian matrix either by a direct or via a basis-set contraction method. Enormous decrease of computer time can be achieved, with respect to a direct application of the optimal-generalized FBR, by employing one of the simplified nonsymmetric FBRs as is demonstrated in noniterative calculations of the low-lying vibrational energy levels of the H3+ molecular ion. The arithmetic operation counts of the Hamiltonian matrix vector products and the properties of a recently developed diagonalization method [Andreozzi et al., J. Phys. A Math. Gen. 35, L61 (2002)] suggest that the nonsymmetric FBR applied along with this particular diagonalization method is suitable to large scale iterative calculations. Whether or not the nonsymmetric FBR is competitive with the symmetric FBR in large-scale iterative calculations still has to be investigated numerically.

Optimization of global model composed of radial basis functions using the term-ranking approach

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

Cai, Peng; Tao, Chao, E-mail: taochao@nju.edu.cn; 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.

Maximizing the probability of satisfying the clinical goals in radiation therapy treatment planning under setup uncertainty

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

Fredriksson, Albin, E-mail: albin.fredriksson@raysearchlabs.com; Hårdemark, Björn; Forsgren, Anders

2015-07-15

Purpose: This paper introduces a method that maximizes the probability of satisfying the clinical goals in intensity-modulated radiation therapy treatments subject to setup uncertainty. Methods: The authors perform robust optimization in which the clinical goals are constrained to be satisfied whenever the setup error falls within an uncertainty set. The shape of the uncertainty set is included as a variable in the optimization. The goal of the optimization is to modify the shape of the uncertainty set in order to maximize the probability that the setup error will fall within the modified set. Because the constraints enforce the clinical goalsmore » to be satisfied under all setup errors within the uncertainty set, this is equivalent to maximizing the probability of satisfying the clinical goals. This type of robust optimization is studied with respect to photon and proton therapy applied to a prostate case and compared to robust optimization using an a priori defined uncertainty set. Results: Slight reductions of the uncertainty sets resulted in plans that satisfied a larger number of clinical goals than optimization with respect to a priori defined uncertainty sets, both within the reduced uncertainty sets and within the a priori, nonreduced, uncertainty sets. For the prostate case, the plans taking reduced uncertainty sets into account satisfied 1.4 (photons) and 1.5 (protons) times as many clinical goals over the scenarios as the method taking a priori uncertainty sets into account. Conclusions: Reducing the uncertainty sets enabled the optimization to find better solutions with respect to the errors within the reduced as well as the nonreduced uncertainty sets and thereby achieve higher probability of satisfying the clinical goals. This shows that asking for a little less in the optimization sometimes leads to better overall plan quality.« less

A Mine of Information: Can Sports Analytics Provide Wisdom From Your Data?

PubMed

Passfield, Louis; Hopker, James G

2017-08-01

This paper explores the notion that the availability and analysis of large data sets have the capacity to improve practice and change the nature of science in the sport and exercise setting. The increasing use of data and information technology in sport is giving rise to this change. Web sites hold large data repositories, and the development of wearable technology, mobile phone applications, and related instruments for monitoring physical activity, training, and competition provide large data sets of extensive and detailed measurements. Innovative approaches conceived to more fully exploit these large data sets could provide a basis for more objective evaluation of coaching strategies and new approaches to how science is conducted. An emerging discipline, sports analytics, could help overcome some of the challenges involved in obtaining knowledge and wisdom from these large data sets. Examples of where large data sets have been analyzed, to evaluate the career development of elite cyclists and to characterize and optimize the training load of well-trained runners, are discussed. Careful verification of large data sets is time consuming and imperative before useful conclusions can be drawn. Consequently, it is recommended that prospective studies be preferred over retrospective analyses of data. It is concluded that rigorous analysis of large data sets could enhance our knowledge in the sport and exercise sciences, inform competitive strategies, and allow innovative new research and findings.

Cell wall-bound silicon optimizes ammonium uptake and metabolism in rice cells.

PubMed

Sheng, Huachun; Ma, Jie; Pu, Junbao; Wang, Lijun

2018-05-16

Turgor-driven plant cell growth depends on cell wall structure and mechanics. Strengthening of cell walls on the basis of an association and interaction with silicon (Si) could lead to improved nutrient uptake and optimized growth and metabolism in rice (Oryza sativa). However, the structural basis and physiological mechanisms of nutrient uptake and metabolism optimization under Si assistance remain obscure. Single-cell level biophysical measurements, including in situ non-invasive micro-testing (NMT) of NH4+ ion fluxes, atomic force microscopy (AFM) of cell walls, and electrolyte leakage and membrane potential, as well as whole-cell proteomics using isobaric tags for relative and absolute quantification (iTRAQ), were performed. The altered cell wall structure increases the uptake rate of the main nutrient NH4+ in Si-accumulating cells, whereas the rate is only half in Si-deprived counterparts. Rigid cell walls enhanced by a wall-bound form of Si as the structural basis stabilize cell membranes. This, in turn, optimizes nutrient uptake of the cells in the same growth phase without any requirement for up-regulation of transmembrane ammonium transporters. Optimization of cellular nutrient acquisition strategies can substantially improve performance in terms of growth, metabolism and stress resistance.

Tuning to optimize SVM approach for assisting ovarian cancer diagnosis with photoacoustic imaging.

PubMed

Wang, Rui; Li, Rui; Lei, Yanyan; Zhu, Quing

2015-01-01

Support vector machine (SVM) is one of the most effective classification methods for cancer detection. The efficiency and quality of a SVM classifier depends strongly on several important features and a set of proper parameters. Here, a series of classification analyses, with one set of photoacoustic data from ovarian tissues ex vivo and a widely used breast cancer dataset- the Wisconsin Diagnostic Breast Cancer (WDBC), revealed the different accuracy of a SVM classification in terms of the number of features used and the parameters selected. A pattern recognition system is proposed by means of SVM-Recursive Feature Elimination (RFE) with the Radial Basis Function (RBF) kernel. To improve the effectiveness and robustness of the system, an optimized tuning ensemble algorithm called as SVM-RFE(C) with correlation filter was implemented to quantify feature and parameter information based on cross validation. The proposed algorithm is first demonstrated outperforming SVM-RFE on WDBC. Then the best accuracy of 94.643% and sensitivity of 94.595% were achieved when using SVM-RFE(C) to test 57 new PAT data from 19 patients. The experiment results show that the classifier constructed with SVM-RFE(C) algorithm is able to learn additional information from new data and has significant potential in ovarian cancer diagnosis.

A Computationally Inexpensive Optimal Guidance via Radial-Basis-Function Neural Network for Autonomous Soft Landing on Asteroids

PubMed Central

Zhang, Peng; Liu, Keping; Zhao, Bo; Li, Yuanchun

2015-01-01

Optimal guidance is essential for the soft landing task. However, due to its high computational complexities, it is hardly applied to the autonomous guidance. In this paper, a computationally inexpensive optimal guidance algorithm based on the radial basis function neural network (RBFNN) is proposed. The optimization problem of the trajectory for soft landing on asteroids is formulated and transformed into a two-point boundary value problem (TPBVP). Combining the database of initial states with the relative initial co-states, an RBFNN is trained offline. The optimal trajectory of the soft landing is determined rapidly by applying the trained network in the online guidance. The Monte Carlo simulations of soft landing on the Eros433 are performed to demonstrate the effectiveness of the proposed guidance algorithm. PMID:26367382

Visualization and Nowcasting for Aviation using online verified ensemble weather radar extrapolation.

NASA Astrophysics Data System (ADS)

Kaltenboeck, Rudolf; Kerschbaum, Markus; Hennermann, Karin; Mayer, Stefan

2013-04-01

Nowcasting of precipitation events, especially thunderstorm events or winter storms, has high impact on flight safety and efficiency for air traffic management. Future strategic planning by air traffic control will result in circumnavigation of potential hazardous areas, reduction of load around efficiency hot spots by offering alternatives, increase of handling capacity, anticipation of avoidance manoeuvres and increase of awareness before dangerous areas are entered by aircraft. To facilitate this rapid update forecasts of location, intensity, size, movement and development of local storms are necessary. Weather radar data deliver precipitation analysis of high temporal and spatial resolution close to real time by using clever scanning strategies. These data are the basis to generate rapid update forecasts in a time frame up to 2 hours and more for applications in aviation meteorological service provision, such as optimizing safety and economic impact in the context of sub-scale phenomena. On the basis of tracking radar echoes by correlation the movement vectors of successive weather radar images are calculated. For every new successive radar image a set of ensemble precipitation fields is collected by using different parameter sets like pattern match size, different time steps, filter methods and an implementation of history of tracking vectors and plausibility checks. This method considers the uncertainty in rain field displacement and different scales in time and space. By validating manually a set of case studies, the best verification method and skill score is defined and implemented into an online-verification scheme which calculates the optimized forecasts for different time steps and different areas by using different extrapolation ensemble members. To get information about the quality and reliability of the extrapolation process additional information of data quality (e.g. shielding in Alpine areas) is extrapolated and combined with an extrapolation-quality-index. Subsequently the probability and quality information of the forecast ensemble is available and flexible blending to numerical prediction model for each subarea is possible. Simultaneously with automatic processing the ensemble nowcasting product is visualized in a new innovative way which combines the intensity, probability and quality information for different subareas in one forecast image.

Potential impact on cardiovascular public health of over-the-counter statin availability.

PubMed

Brass, Eric P; Allen, Shannon E; Melin, Jeffrey M

2006-03-15

Over-the-counter (OTC) statin availability has been hypothesized to represent a strategy for treating consumers at moderate risk of coronary heart disease (CHD) who are currently not receiving drug therapy. The viability of this strategy has been questioned, particularly with respect to the public health benefit that can be obtained in an unsupervised treatment environment. The previously reported Consumer Use Study of Over-the-Counter Lovastatin (CUSTOM) examined consumer behavior in a simulated OTC setting in which 20 mg lovastatin could be purchased. Framingham CHD risk scores were calculated for 981 self-selected consumers who used OTC lovastatin in CUSTOM. Overall, this group had a median 10-year CHD risk of 10%, but with significant numbers of consumers with estimated risks of <5% and >20%. According to the risk profile of CUSTOM consumers, the use of 20 mg lovastatin for 10 years would be expected to prevent approximately 33,100 CHD events per 1 million users. This represents a 10-year number needed to treat of 30 consumers. This optimal benefit may be reduced because some higher risk consumers in CUSTOM used lovastatin rather than appropriate, more aggressive supervised care. On the basis of the frequencies of diversion from optimal care observed in CUSTOM, the number of events prevented might be reduced to 23,000 (number needed to treat 43 consumers). Sensitivity analyses have demonstrated that these estimates are robust and that the predicted public health benefit likely falls in the range of 23,000 to 33,000 CHD events prevented per 1 million treated for 10 years. In conclusion, on a population basis, OTC statin availability is likely to result in clinically meaningful reductions in CHD morbidity and mortality. The analyses also identified opportunities for optimizing the use of OTC statins in the marketplace.

Computer-Aided Classification of Visual Ventilation Patterns in Patients with Chronic Obstructive Pulmonary Disease at Two-Phase Xenon-Enhanced CT

PubMed Central

Yoon, Soon Ho; Jung, Julip; Hong, Helen; Park, Eun Ah; Lee, Chang Hyun; Lee, Youkyung; Jin, Kwang Nam; Choo, Ji Yung; Lee, Nyoung Keun

2014-01-01

Objective To evaluate the technical feasibility, performance, and interobserver agreement of a computer-aided classification (CAC) system for regional ventilation at two-phase xenon-enhanced CT in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods Thirty-eight patients with COPD underwent two-phase xenon ventilation CT with resulting wash-in (WI) and wash-out (WO) xenon images. The regional ventilation in structural abnormalities was visually categorized into four patterns by consensus of two experienced radiologists who compared the xenon attenuation of structural abnormalities with that of adjacent normal parenchyma in the WI and WO images, and it served as the reference. Two series of image datasets of structural abnormalities were randomly extracted for optimization and validation. The proportion of agreement on a per-lesion basis and receiver operating characteristics on a per-pixel basis between CAC and reference were analyzed for optimization. Thereafter, six readers independently categorized the regional ventilation in structural abnormalities in the validation set without and with a CAC map. Interobserver agreement was also compared between assessments without and with CAC maps using multirater κ statistics. Results Computer-aided classification maps were successfully generated in 31 patients (81.5%). The proportion of agreement and the average area under the curve of optimized CAC maps were 94% (75/80) and 0.994, respectively. Multirater κ value was improved from moderate (κ = 0.59; 95% confidence interval [CI], 0.56-0.62) at the initial assessment to excellent (κ = 0.82; 95% CI, 0.79-0.85) with the CAC map. Conclusion Our proposed CAC system demonstrated the potential for regional ventilation pattern analysis and enhanced interobserver agreement on visual classification of regional ventilation. PMID:24843245

Computer-aided classification of visual ventilation patterns in patients with chronic obstructive pulmonary disease at two-phase xenon-enhanced CT.

PubMed

Yoon, Soon Ho; Goo, Jin Mo; Jung, Julip; Hong, Helen; Park, Eun Ah; Lee, Chang Hyun; Lee, Youkyung; Jin, Kwang Nam; Choo, Ji Yung; Lee, Nyoung Keun

2014-01-01

To evaluate the technical feasibility, performance, and interobserver agreement of a computer-aided classification (CAC) system for regional ventilation at two-phase xenon-enhanced CT in patients with chronic obstructive pulmonary disease (COPD). Thirty-eight patients with COPD underwent two-phase xenon ventilation CT with resulting wash-in (WI) and wash-out (WO) xenon images. The regional ventilation in structural abnormalities was visually categorized into four patterns by consensus of two experienced radiologists who compared the xenon attenuation of structural abnormalities with that of adjacent normal parenchyma in the WI and WO images, and it served as the reference. Two series of image datasets of structural abnormalities were randomly extracted for optimization and validation. The proportion of agreement on a per-lesion basis and receiver operating characteristics on a per-pixel basis between CAC and reference were analyzed for optimization. Thereafter, six readers independently categorized the regional ventilation in structural abnormalities in the validation set without and with a CAC map. Interobserver agreement was also compared between assessments without and with CAC maps using multirater κ statistics. Computer-aided classification maps were successfully generated in 31 patients (81.5%). The proportion of agreement and the average area under the curve of optimized CAC maps were 94% (75/80) and 0.994, respectively. Multirater κ value was improved from moderate (κ = 0.59; 95% confidence interval [CI], 0.56-0.62) at the initial assessment to excellent (κ = 0.82; 95% CI, 0.79-0.85) with the CAC map. Our proposed CAC system demonstrated the potential for regional ventilation pattern analysis and enhanced interobserver agreement on visual classification of regional ventilation.

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

Code of Federal Regulations, 2010 CFR

2010-10-01

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

An intertwined method for making low-rank, sum-of-product basis functions that makes it possible to compute vibrational spectra of molecules with more than 10 atoms

PubMed Central

Thomas, Phillip S.

2017-01-01

We propose a method for solving the vibrational Schrödinger equation with which one can compute spectra for molecules with more than ten atoms. It uses sum-of-product (SOP) basis functions stored in a canonical polyadic tensor format and generated by evaluating matrix-vector products. By doing a sequence of partial optimizations, in each of which the factors in a SOP basis function for a single coordinate are optimized, the rank of the basis functions is reduced as matrix-vector products are computed. This is better than using an alternating least squares method to reduce the rank, as is done in the reduced-rank block power method. Partial optimization is better because it speeds up the calculation by about an order of magnitude and allows one to significantly reduce the memory cost. We demonstrate the effectiveness of the new method by computing vibrational spectra of two molecules, ethylene oxide (C2H4O) and cyclopentadiene (C5H6), with 7 and 11 atoms, respectively. PMID:28571348

An intertwined method for making low-rank, sum-of-product basis functions that makes it possible to compute vibrational spectra of molecules with more than 10 atoms.

PubMed

Thomas, Phillip S; Carrington, Tucker

2017-05-28

We propose a method for solving the vibrational Schrödinger equation with which one can compute spectra for molecules with more than ten atoms. It uses sum-of-product (SOP) basis functions stored in a canonical polyadic tensor format and generated by evaluating matrix-vector products. By doing a sequence of partial optimizations, in each of which the factors in a SOP basis function for a single coordinate are optimized, the rank of the basis functions is reduced as matrix-vector products are computed. This is better than using an alternating least squares method to reduce the rank, as is done in the reduced-rank block power method. Partial optimization is better because it speeds up the calculation by about an order of magnitude and allows one to significantly reduce the memory cost. We demonstrate the effectiveness of the new method by computing vibrational spectra of two molecules, ethylene oxide (C 2 H 4 O) and cyclopentadiene (C 5 H 6 ), with 7 and 11 atoms, respectively.

Separation and reconstruction of BCG and EEG signals during continuous EEG and fMRI recordings

PubMed Central

Xia, Hongjing; Ruan, Dan; Cohen, Mark S.

2014-01-01

Despite considerable effort to remove it, the ballistocardiogram (BCG) remains a major artifact in electroencephalographic data (EEG) acquired inside magnetic resonance imaging (MRI) scanners, particularly in continuous (as opposed to event-related) recordings. In this study, we have developed a new Direct Recording Prior Encoding (DRPE) method to extract and separate the BCG and EEG components from contaminated signals, and have demonstrated its performance by comparing it quantitatively to the popular Optimal Basis Set (OBS) method. Our modified recording configuration allows us to obtain representative bases of the BCG- and EEG-only signals. Further, we have developed an optimization-based reconstruction approach to maximally incorporate prior knowledge of the BCG/EEG subspaces, and of the signal characteristics within them. Both OBS and DRPE methods were tested with experimental data, and compared quantitatively using cross-validation. In the challenging continuous EEG studies, DRPE outperforms the OBS method by nearly sevenfold in separating the continuous BCG and EEG signals. PMID:25002836

Wind turbine power tracking using an improved multimodel quadratic approach.

PubMed

Khezami, Nadhira; Benhadj Braiek, Naceur; Guillaud, Xavier

2010-07-01

In this paper, an improved multimodel optimal quadratic control structure for variable speed, pitch regulated wind turbines (operating at high wind speeds) is proposed in order to integrate high levels of wind power to actively provide a primary reserve for frequency control. On the basis of the nonlinear model of the studied plant, and taking into account the wind speed fluctuations, and the electrical power variation, a multimodel linear description is derived for the wind turbine, and is used for the synthesis of an optimal control law involving a state feedback, an integral action and an output reference model. This new control structure allows a rapid transition of the wind turbine generated power between different desired set values. This electrical power tracking is ensured with a high-performance behavior for all other state variables: turbine and generator rotational speeds and mechanical shaft torque; and smooth and adequate evolution of the control variables. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Self-Determination and Personal Identity in University Students: The Mediating Role of Future Orientation.

PubMed

Zhou, Mingming; Kam, Chester Chun Seng

2018-05-17

In this study, we sought to extend the research on self-determination, future orientation, and personal identity construction by integrating the theories on self-determination and future orientation to provide a conceptual framework for understanding the relations between personal identity and the following individual characteristics: Hope, optimism, awareness of self, and perceived choice. 191 university students in China responded surveys in hardcopies on an individual basis. Our SEM results revealed that proximal future orientation influenced the mechanisms through which distal psychological traits affected identity construction. Specifically, hope mediated the effects of self-awareness on the participants' personal identity ratings (b = .45, p < .05). Although optimism was related to both awareness of self and perceived choice, it was not significantly related to personal identity. This study suggested an extended framework through which we could understand how the interaction between future orientation and self-determination can predict personal identity. The findings have significant implications for interventions in educational settings.

AUCTION MECHANISMS FOR IMPLEMENTING TRADABLE NETWORK PERMIT MARKETS

NASA Astrophysics Data System (ADS)

Wada, Kentaro; Akamatsu, Takashi

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

Experimental and theoretical study on the structure and vibrational spectra of β-2-aminopyridinium dihydrogenphosphate

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Demir, Selçuk; Ucun, Fatih; Çubuk, Osman

2011-08-01

Experimental and theoretical vibrational spectra of β-2-aminopyridinium dihydrogenphosphate (β-2APDP) have been investigated. The FT-IR spectrum of β-2APDP was recorded in the region 4000-400 cm -1. The optimized molecular structure and theoretical vibrational frequencies of β-2APDP have been investigated using ab initio Hartree-Fock (HF) and density functional B3LYP method with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths and bond angles) and theoretical frequencies have been compared with the corresponding experimental data and it is found that they agree well with each other. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Furthermore, the used scale factors were obtained from the ratio of the frequency values of the strongest peaks in the experimental and theoretical IR spectra. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies.

Statistical process control using optimized neural networks: a case study.

PubMed

Addeh, Jalil; Ebrahimzadeh, Ata; Azarbad, Milad; Ranaee, Vahid

2014-09-01

The most common statistical process control (SPC) tools employed for monitoring process changes are control charts. A control chart demonstrates that the process has altered by generating an out-of-control signal. This study investigates the design of an accurate system for the control chart patterns (CCPs) recognition in two aspects. First, an efficient system is introduced that includes two main modules: feature extraction module and classifier module. In the feature extraction module, a proper set of shape features and statistical feature are proposed as the efficient characteristics of the patterns. In the classifier module, several neural networks, such as multilayer perceptron, probabilistic neural network and radial basis function are investigated. Based on an experimental study, the best classifier is chosen in order to recognize the CCPs. Second, a hybrid heuristic recognition system is introduced based on cuckoo optimization algorithm (COA) algorithm to improve the generalization performance of the classifier. The simulation results show that the proposed algorithm has high recognition accuracy. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Quantum chemical investigations on the molecular structure, FTIR, UV-Vis and HOMO-LUMO analysis of 15-16-epoxy-7b, 9a dihydroxylabdane 13(16), 14-dien-6-one

NASA Astrophysics Data System (ADS)

Uppal, Anshul; Pathania, Kamni; Khajuria, Yugal

2018-05-01

The structural, spectroscopic (Fourier Transform Infrared (FT-IR), Ultra-Violet Visible (UV-VIS)) and thermodynamic properties of 15, 16-epoxy-7b, 9a dihydroxylabdane-13(16), 14-dien-6-one were studied by using both experimental techniques and theoretical methods. The FTIR spectrum of the title compound was recorded in the spectral range 4000-400 cm-1. The UV-VIS spectrum was measured in the spectral range 190-800 nm. The quantum chemistry calculations have been performed to compute optimized geometry, molecular parameters, vibrational frequencies along with intensities using Hartree Fock (HF) theory and Density Functional Theory (DFT) with 6-31G basis set. The calculated HOMO-LUMO energies show that the charge transfer occurs within the molecule. The temperature dependence of the thermodynamic properties like heat capacity, entropy and enthalpy of the optimized structure were obtained. Finally, a comparison between the experimental data and the calculated results presented a good agreement.

Spectroscopic investigation, HOMO-LUMO and NLO studies on L-histidinium maleate based on DFT approach

NASA Astrophysics Data System (ADS)

Dhanavel, S.; Stephen, A.; Asirvatham, P. Samuel

2017-05-01

The molecular structure of the title compound L-Histidinium Maleate (LHM) was constructed and optimized based on Density Functional Theory method (DFT-B3LYP) with the 6-31G (d,p) basis set. The fundamental vibrational spectral assignment was analyzed with the aid of optimized structure of LHM. The study on electronic properties such as, HOMO-LUMO energies and absorption wavelength were performed using Time dependent DFT (TD-DFT) approach which reveals that energy transfer occur within the molecule. 13C NMR chemical shift values were measured using Gauge independent atomic orbital method (GIAO) and the obtained values are in good agreement with the reported experimental values. Hardness, ionization potential and electrophilicity index also calculated. The electric dipole moment (μtot) and hyperpolarizability (βtot) values of the investigated molecules were computed. The calculated value (β) was 3.7 times higher than that of urea, which confirms the LHM molecule is a potential candidate for NLO applications.

Projected Hybrid Orbitals: A General QM/MM Method

PubMed Central

2015-01-01

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

SU-F-R-10: Selecting the Optimal Solution for Multi-Objective Radiomics Model

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

Zhou, Z; Folkert, M; Wang, J

2016-06-15

Purpose: To develop an evidential reasoning approach for selecting the optimal solution from a Pareto solution set obtained by a multi-objective radiomics model for predicting distant failure in lung SBRT. Methods: In the multi-objective radiomics model, both sensitivity and specificity are considered as the objective functions simultaneously. A Pareto solution set with many feasible solutions will be resulted from the multi-objective optimization. In this work, an optimal solution Selection methodology for Multi-Objective radiomics Learning model using the Evidential Reasoning approach (SMOLER) was proposed to select the optimal solution from the Pareto solution set. The proposed SMOLER method used the evidentialmore » reasoning approach to calculate the utility of each solution based on pre-set optimal solution selection rules. The solution with the highest utility was chosen as the optimal solution. In SMOLER, an optimal learning model coupled with clonal selection algorithm was used to optimize model parameters. In this study, PET, CT image features and clinical parameters were utilized for predicting distant failure in lung SBRT. Results: Total 126 solution sets were generated by adjusting predictive model parameters. Each Pareto set contains 100 feasible solutions. The solution selected by SMOLER within each Pareto set was compared to the manually selected optimal solution. Five-cross-validation was used to evaluate the optimal solution selection accuracy of SMOLER. The selection accuracies for five folds were 80.00%, 69.23%, 84.00%, 84.00%, 80.00%, respectively. Conclusion: An optimal solution selection methodology for multi-objective radiomics learning model using the evidential reasoning approach (SMOLER) was proposed. Experimental results show that the optimal solution can be found in approximately 80% cases.« less

Optimization design and dynamic analysis on the drive mechanisms of flapping-wing air vehicles based on flapping trajectories

NASA Astrophysics Data System (ADS)

Xie, Lingwang; Zhang, Xingwei; Luo, Pan; Huang, Panpan

2017-10-01

The optimization designs and dynamic analysis on the driving mechanism of flapping-wing air vehicles on base of flapping trajectory patterns is carried out in this study. Three different driving mechanisms which are spatial double crank-rocker, plane five-bar and gear-double slider, are systematically optimized and analysed by using the Mat lab and Adams software. After a series debugging on the parameter, the comparatively ideal flapping trajectories are obtained by the simulation of Adams. Present results indicate that different drive mechanisms output different flapping trajectories and have their unique characteristic. The spatial double crank-rocker mechanism can only output the arc flapping trajectory and it has the advantages of small volume, high flexibility and efficient space utilization. Both planar five-bar mechanism and gear-double slider mechanism can output the oval, figure of eight and double eight flapping trajectories. Nevertheless, the gear-double slider mechanism has the advantage of convenient parameter setting and better performance in output double eight flapping trajectory. This study can provide theoretical basis and helpful reference for the design of the drive mechanisms of flapping-wing air vehicles with different output flapping trajectories.

Removing ballistocardiogram (BCG) artifact from full-scalp EEG acquired inside the MR scanner with Orthogonal Matching Pursuit (OMP)

PubMed Central

Xia, Hongjing; Ruan, Dan; Cohen, Mark S.

2014-01-01

Ballistocardiogram (BCG) artifact remains a major challenge that renders electroencephalographic (EEG) signals hard to interpret in simultaneous EEG and functional MRI (fMRI) data acquisition. Here, we propose an integrated learning and inference approach that takes advantage of a commercial high-density EEG cap, to estimate the BCG contribution in noisy EEG recordings from inside the MR scanner. To estimate reliably the full-scalp BCG artifacts, a near-optimal subset (20 out of 256) of channels first was identified using a modified recording setup. In subsequent recordings inside the MR scanner, BCG-only signal from this subset of channels was used to generate continuous estimates of the full-scalp BCG artifacts via inference, from which the intended EEG signal was recovered. The reconstruction of the EEG was performed with both a direct subtraction and an optimization scheme. We evaluated the performance on both synthetic and real contaminated recordings, and compared it to the benchmark Optimal Basis Set (OBS) method. In the challenging non-event-related-potential (non-ERP) EEG studies, our reconstruction can yield more than fourteen-fold improvement in reducing the normalized RMS error of EEG signals, compared to OBS. PMID:25120421

Particle swarm optimization algorithm for optimizing assignment of blood in blood banking system.

PubMed

Olusanya, Micheal O; Arasomwan, Martins A; Adewumi, Aderemi O

2015-01-01

This paper reports the performance of particle swarm optimization (PSO) for the assignment of blood to meet patients' blood transfusion requests for blood transfusion. While the drive for blood donation lingers, there is need for effective and efficient management of available blood in blood banking systems. Moreover, inherent danger of transfusing wrong blood types to patients, unnecessary importation of blood units from external sources, and wastage of blood products due to nonusage necessitate the development of mathematical models and techniques for effective handling of blood distribution among available blood types in order to minimize wastages and importation from external sources. This gives rise to the blood assignment problem (BAP) introduced recently in literature. We propose a queue and multiple knapsack models with PSO-based solution to address this challenge. Simulation is based on sets of randomly generated data that mimic real-world population distribution of blood types. Results obtained show the efficiency of the proposed algorithm for BAP with no blood units wasted and very low importation, where necessary, from outside the blood bank. The result therefore can serve as a benchmark and basis for decision support tools for real-life deployment.

Dynamic Obstacle Avoidance for Unmanned Underwater Vehicles Based on an Improved Velocity Obstacle Method

PubMed Central

Zhang, Wei; Wei, Shilin; Teng, Yanbin; Zhang, Jianku; Wang, Xiufang; Yan, Zheping

2017-01-01

In view of a dynamic obstacle environment with motion uncertainty, we present a dynamic collision avoidance method based on the collision risk assessment and improved velocity obstacle method. First, through the fusion optimization of forward-looking sonar data, the redundancy of the data is reduced and the position, size and velocity information of the obstacles are obtained, which can provide an accurate decision-making basis for next-step collision avoidance. Second, according to minimum meeting time and the minimum distance between the obstacle and unmanned underwater vehicle (UUV), this paper establishes the collision risk assessment model, and screens key obstacles to avoid collision. Finally, the optimization objective function is established based on the improved velocity obstacle method, and a UUV motion characteristic is used to calculate the reachable velocity sets. The optimal collision speed of UUV is searched in velocity space. The corresponding heading and speed commands are calculated, and outputted to the motion control module. The above is the complete dynamic obstacle avoidance process. The simulation results show that the proposed method can obtain a better collision avoidance effect in the dynamic environment, and has good adaptability to the unknown dynamic environment. PMID:29186878

Choosing the optimal wind turbine variant using the ”ELECTRE” method

NASA Astrophysics Data System (ADS)

Ţişcă, I. A.; Anuşca, D.; Dumitrescu, C. D.

2017-08-01

This paper presents a method of choosing the “optimal” alternative, both under certainty and under uncertainty, based on relevant analysis criteria. Taking into account that a product can be assimilated to a system and that the reliability of the system depends on the reliability of its components, the choice of product (the appropriate system decision) can be done using the “ELECTRE” method and depending on the level of reliability of each product. In the paper, the “ELECTRE” method is used in choosing the optimal version of a wind turbine required to equip a wind farm in western Romania. The problems to be solved are related to the current situation of wind turbines that involves reliability problems. A set of criteria has been proposed to compare two or more products from a range of available products: Operating conditions, Environmental conditions during operation, Time requirements. Using the ELECTRE hierarchical mathematical method it was established that on the basis of the obtained coefficients of concordance the optimal variant of the wind turbine and the order of preference of the variants are determined, the values chosen as limits being arbitrary.

Design and implementation of an automated compound management system in support of lead optimization.

PubMed

Quintero, Catherine; Kariv, Ilona

2009-06-01

To meet the needs of the increasingly rapid and parallelized lead optimization process, a fully integrated local compound storage and liquid handling system was designed and implemented to automate the generation of assay-ready plates directly from newly submitted and cherry-picked compounds. A key feature of the system is the ability to create project- or assay-specific compound-handling methods, which provide flexibility for any combination of plate types, layouts, and plate bar-codes. Project-specific workflows can be created by linking methods for processing new and cherry-picked compounds and control additions to produce a complete compound set for both biological testing and local storage in one uninterrupted workflow. A flexible cherry-pick approach allows for multiple, user-defined strategies to select the most appropriate replicate of a compound for retesting. Examples of custom selection parameters include available volume, compound batch, and number of freeze/thaw cycles. This adaptable and integrated combination of software and hardware provides a basis for reducing cycle time, fully automating compound processing, and ultimately increasing the rate at which accurate, biologically relevant results can be produced for compounds of interest in the lead optimization process.

Assimilation of seasonal chlorophyll and nutrient data into an adjoint three-dimensional ocean carbon cycle model: Sensitivity analysis and ecosystem parameter optimization

NASA Astrophysics Data System (ADS)

Tjiputra, Jerry F.; Polzin, Dierk; Winguth, Arne M. E.

2007-03-01

An adjoint method is applied to a three-dimensional global ocean biogeochemical cycle model to optimize the ecosystem parameters on the basis of SeaWiFS surface chlorophyll observation. We showed with identical twin experiments that the model simulated chlorophyll concentration is sensitive to perturbation of phytoplankton and zooplankton exudation, herbivore egestion as fecal pellets, zooplankton grazing, and the assimilation efficiency parameters. The assimilation of SeaWiFS chlorophyll data significantly improved the prediction of chlorophyll concentration, especially in the high-latitude regions. Experiments that considered regional variations of parameters yielded a high seasonal variance of ecosystem parameters in the high latitudes, but a low variance in the tropical regions. These experiments indicate that the adjoint model is, despite the many uncertainties, generally capable to optimize sensitive parameters and carbon fluxes in the euphotic zone. The best fit regional parameters predict a global net primary production of 36 Pg C yr-1, which lies within the range suggested by Antoine et al. (1996). Additional constraints of nutrient data from the World Ocean Atlas showed further reduction in the model-data misfit and that assimilation with extensive data sets is necessary.

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations.

PubMed

Sangeetha, V; Govindarajan, M; Kanagathara, N; Marchewka, M K; Gunasekaran, S; Anbalagan, G

2014-05-05

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted. Copyright © 2014 Elsevier B.V. All rights reserved.

Complexes and saddle point structures, vibrational frequencies and relative energies of intermediates for CH2Br + HBr «-» CH3Br + Br

NASA Astrophysics Data System (ADS)

Espinosa-Garcia, J.

Ab initio molecular orbital theory was used to study parts of the reaction between the CH2Br radical and the HBr molecule, and two possibilities were analysed: attack on the hydrogen and attack on the bromine of the HBr molecule. Optimized geometries and harmonic vibrational frequencies were calculated at the second-order Moller-Plesset perturbation theory levels, and comparison with available experimental data was favourable. Then single-point calculations were performed at several higher levels of calculation. In the attack on the hydrogen of HBr, two stationary points were located on the direct hydrogen abstraction reaction path: a very weak hydrogen bonded complex of reactants, C···HBr, close to the reactants, followed by the saddle point (SP). The effects of level of calculation (method + basis set), spin projection, zeropoint energy, thermal corrections (298K), spin-orbit coupling and basis set superposition error (BSSE) on the energy changes were analysed. Taking the reaction enthalpy (298K) as reference, agreement with experiment was obtained only when high correlation energy and large basis sets were used. It was concluded that at room temperature (i.e., with zero-point energy and thermal corrections), when the BSSE was included, the complex disappears and the activation enthalpy (298K) ranges from 0.8kcal mol-1 to 1.4kcal mol-1 above the reactants, depending on the level of calculation. It was concluded also that this result is the balance of a complicated interplay of many factors, which are affected by uncertainties in the theoretical calculations. Finally, another possible complex (X complex), which involves the alkyl radical being attracted to the halogen end of HBr (C···BrH), was explored also. It was concluded that this X complex does not exist at room temperature.

Mechanistic and kinetic study of the CH3CO + O2 reaction.

PubMed

Hou, Hua; Li, Aixiao; Hu, Hongyi; Li, Yuzhen; Li, Hui; Wang, Baoshan

2005-06-08

Potential-energy surface of the CH3CO + O2 reaction has been calculated by ab initio quantum chemistry methods. The geometries were optimized using the second-order Moller-Plesset theory (MP2) with the 6-311G(d,p) basis set and the coupled-cluster theory with single and double excitations (CCSD) with the correlation consistent polarized valence double zeta (cc-pVDZ) basis set. The relative energies were calculated using the Gaussian-3 second-order Moller-Plesset theory with the CCSD/cc-pVDZ geometries. Multireference self-consistent-field and MP2 methods were also employed using the 6-311G(d,p) and 6-311++G(3df,2p) basis sets. Both addition/elimination and direct abstraction mechanisms have been investigated. It was revealed that acetylperoxy radical [CH3C(O)OO] is the initial adduct and the formation of OH and alpha-lactone [CH2CO2(1A')] is the only energetically accessible decomposition channel. The other channels, e.g., abstraction, HO2 + CH2CO, O + CH3CO2, CO + CH3O2, and CO2 + CH3O, are negligible. Multichannel Rice-Ramsperger-Kassel-Marcus theory and transition state theory (E-resolved) were employed to calculate the overall and individual rate coefficients and the temperature and pressure dependences. Fairly good agreement between theory and experiments has been obtained without any adjustable parameters. It was concluded that at pressures below 3 Torr, OH and CH2CO2(1A') are the major nascent products of the oxidation of acetyl radicals, although CH2CO2(1A') might either undergo unimolecular decomposition to form the final products of CH2O + CO or react with OH and Cl to generate H2O and HCl. The acetylperoxy radicals formed by collisional stabilization are the major products at the elevated pressures. In atmosphere, the yield of acetylperoxy is nearly unity and the contribution of OH is only marginal.

The Anharmonic Force Field of Ethylene, C2H4, by Means of Accurate Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Martin, Jan M. L.; Lee, Timothy J.; Taylor, Peter R.; Francois, Jean-Pierre; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The quartic force field of ethylene, C2H4, has been calculated ab initio using augmented coupled cluster, CCSD(T), methods and correlation consistent basis sets of spdf quality. For the C-12 isotopomers C2H4, C2H3D, H2CCD2, cis-C2H2D2, trans-C2H2D2, C2HD3, and C2D4, all fundamentals could be reproduced to better than 10 per centimeter, except for three cases of severe Fermi type 1 resonance. The problem with these three bands is identified as a systematic overestimate of the Kiij Fermi resonance constants by a factor of two or more; if this is corrected for, the predicted fundamentals come into excellent agreement with experiment. No such systematic overestimate is seen for Fermi type 2 resonances. Our computed harmonic frequencies suggest a thorough revision of the accepted experimentally derived values. Our computed and empirically corrected re geometry differs substantially from experimentally derived values: both the predicted rz geometry and the ground-state rotational constants are, however, in excellent agreement with experiment, suggesting revision of the older values. Anharmonicity constants agree well with experiment for stretches, but differ substantially for stretch-bend interaction constants, due to equality constraints in the experimental analysis that do not hold. Improved criteria for detecting Fermi and Coriolis resonances are proposed and found to work well, contrary to the established method based on harmonic frequency differences that fails to detect several important resonances for C2H4 and its isotopomers. Surprisingly good results are obtained with a small spd basis at the CCSD(T) level. The well-documented strong basis set effect on the v8 out-of-plane motion is present to a much lesser extent when correlation-optimized polarization functions are used. Complete sets of anharmonic, rovibrational coupling, and centrifugal distortion constants for the isotopomers are available as supplementary material to the paper.

Conformational Analysis of Free and Bound Retinoic Acid

PubMed Central

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

2012-01-01

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

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

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

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 definablemore » 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.« less

C2 Fragmentation Energy of C60 Revisited: Theory Disagrees with Most Experiments

NASA Technical Reports Server (NTRS)

Boese, A. Daniel; Scuseria, Gustavo E.

1998-01-01

Following our earlier work on the subject, we have carried out density functional theory (DFT) and second-order Moller-Plesset perturbation theory (MP2) calculations of the dissociation energy of the reaction C60 yields C58 + C2 using polarized basis sets and geometries optimized with DFT methods. The present theoretical results support an electronic fragmentation energy D(sub e) around 10-11 eV in disagreement with most experimental results that place the dissociation energy D(sub o) (including zero point energy) around 7-8 eV. The plausible errors remaining in the theoretical calculations are unlikely to account for this big difference (2-4 eV).

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

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

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

A chromophoric study of 2-ethylhexyl p-methoxycinnamate

NASA Astrophysics Data System (ADS)

Alves, Leonardo F.; Gargano, Ricardo; Alcanfor, Silvia K. B.; Romeiro, Luiz A. S.; Martins, João B. L.

2011-11-01

Ultraviolet absorption spectra of 2-ethylhexyl p-methoxycinnamate have been recorded in different solvents and calculated using the time dependent density functional theory. The calculations were performed with the aid of B3LYP, PBE1PBE, M06, and PBEPBE functionals and 6-31+G(2d) basis set. The geometries were initially optimized using PM5 semiempirical method for the conformational search. The calculations of excited states were carried out using the time dependent with IEF-PCM solvent reaction field method. The experimental data were obtained in the wavelength range from 200 to 400 nm using 10 different solvents. The TD-PBE1PBE method shows the best agreement to the experimental results.

A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

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

Rastogi, Rupali, E-mail: rastogirupali@ymail.com; Tarannum, Nazia; Butcher, R. J.

2016-03-15

5-Bromosalicylalcohol was prepared by the interaction of NaBH{sub 4} and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, {sup 1}H NMR, {sup 13}C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

Noble gas cluster ions

NASA Astrophysics Data System (ADS)

Kaya, Yunus; Kalkan, Yalçin; Veenhof, Rob

2018-02-01

In this work, a reaction mechanism of formation of noble gas (Ng) cluster ions has been theoretically investigated in detail. The kinetic studies of formation of Xe+Xe cluster in Xe, Ar+Ar cluster ions in Ar, and Ne+Ne cluster ions in Ne have been made as theoretically. The optimized structures in the ground state were calculated using the density functional theory (DFT) by the B3LYP method combined with the Stuttgart/Dresden effective core potential basis set (SDD). In addition, we calculated the rate constants of all cluster formations. The results are 1.15 × 10-31, 3.58 × 10-31, 0.23 × 10-31cm6/s, respectively for Neon, Argon, Xenon cluster ions.

Computer-Assisted Traffic Engineering Using Assignment, Optimal Signal Setting, and Modal Split

DOT National Transportation Integrated Search

1978-05-01

Methods of traffic assignment, traffic signal setting, and modal split analysis are combined in a set of computer-assisted traffic engineering programs. The system optimization and user optimization traffic assignments are described. Travel time func...

Identifying Attributes of CO2 Leakage Zones in Shallow Aquifers Using a Parametric Level Set Method

NASA Astrophysics Data System (ADS)

Sun, A. Y.; Islam, A.; Wheeler, M.

2016-12-01

Leakage through abandoned wells and geologic faults poses the greatest risk to CO2 storage permanence. For shallow aquifers, secondary CO2 plumes emanating from the leak zones may go undetected for a sustained period of time and has the greatest potential to cause large-scale and long-term environmental impacts. Identification of the attributes of leak zones, including their shape, location, and strength, is required for proper environmental risk assessment. This study applies a parametric level set (PaLS) method to characterize the leakage zone. Level set methods are appealing for tracking topological changes and recovering unknown shapes of objects. However, level set evolution using the conventional level set methods is challenging. In PaLS, the level set function is approximated using a weighted sum of basis functions and the level set evolution problem is replaced by an optimization problem. The efficacy of PaLS is demonstrated through recovering the source zone created by CO2 leakage into a carbonate aquifer. Our results show that PaLS is a robust source identification method that can recover the approximate source locations in the presence of measurement errors, model parameter uncertainty, and inaccurate initial guesses of source flux strengths. The PaLS inversion framework introduced in this work is generic and can be adapted for any reactive transport model by switching the pre- and post-processing routines.

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

PubMed

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

2017-07-11

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

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

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity.

PubMed

Chiang, Yi-Kun; Kuo, Ching-Chuan; Wu, Yu-Shan; Chen, Chung-Tong; Coumar, Mohane Selvaraj; Wu, Jian-Sung; Hsieh, Hsing-Pang; Chang, Chi-Yen; Jseng, Huan-Yi; Wu, Ming-Hsine; Leou, Jiun-Shyang; Song, Jen-Shin; Chang, Jang-Yang; Lyu, Ping-Chiang; Chao, Yu-Sheng; Wu, Su-Ying

2009-07-23

A pharmacophore model, Hypo1, was built on the basis of 21 training-set indole compounds with varying levels of antiproliferative activity. Hypo1 possessed important chemical features required for the inhibitors and demonstrated good predictive ability for biological activity, with high correlation coefficients of 0.96 and 0.89 for the training-set and test-set compounds, respectively. Further utilization of the Hypo1 pharmacophore model to screen chemical database in silico led to the identification of four compounds with antiproliferative activity. Among these four compounds, 43 showed potent antiproliferative activity against various cancer cell lines with the strongest inhibition on the proliferation of KB cells (IC(50) = 187 nM). Further biological characterization revealed that 43 effectively inhibited tubulin polymerization and significantly induced cell cycle arrest in G(2)-M phase. In addition, 43 also showed the in vivo-like anticancer effects. To our knowledge, 43 is the most potent antiproliferative compound with antitubulin activity discovered by computer-aided drug design. The chemical novelty of 43 and its anticancer activities make this compound worthy of further lead optimization.

Adaptive density trajectory cluster based on time and space distance

NASA Astrophysics Data System (ADS)

Liu, Fagui; Zhang, Zhijie

2017-10-01

There are some hotspot problems remaining in trajectory cluster for discovering mobile behavior regularity, such as the computation of distance between sub trajectories, the setting of parameter values in cluster algorithm and the uncertainty/boundary problem of data set. As a result, based on the time and space, this paper tries to define the calculation method of distance between sub trajectories. The significance of distance calculation for sub trajectories is to clearly reveal the differences in moving trajectories and to promote the accuracy of cluster algorithm. Besides, a novel adaptive density trajectory cluster algorithm is proposed, in which cluster radius is computed through using the density of data distribution. In addition, cluster centers and number are selected by a certain strategy automatically, and uncertainty/boundary problem of data set is solved by designed weighted rough c-means. Experimental results demonstrate that the proposed algorithm can perform the fuzzy trajectory cluster effectively on the basis of the time and space distance, and obtain the optimal cluster centers and rich cluster results information adaptably for excavating the features of mobile behavior in mobile and sociology network.

Carboxydothermus islandicus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic bacterium isolated from a hot spring.

PubMed

Novikov, Andrey A; Sokolova, Tatyana G; Lebedinsky, Alexander V; Kolganova, Tatyana V; Bonch-Osmolovskaya, Elizaveta A

2011-10-01

An anaerobic, thermophilic bacterium, strain SET IS-9(T), was isolated from an Icelandic hot spring. Cells of strain SET IS-9(T) are short, slightly curved, motile rods. The strain grows chemolithotrophically on CO, producing equimolar quantities of H(2) and CO(2). It also grows fermentatively on lactate or pyruvate in the presence of yeast extract (0.2 g l(-1)). Products of pyruvate fermentation are acetate, CO(2) and H(2). Growth occurs at 50-70 °C, with an optimum at 65 °C, and at pH 5.0-8.0, with an optimum at pH 5.5-6.0. The generation time during chemolithotrophic growth on CO under optimal conditions is 2.0 h. 16S rRNA gene sequence analysis suggested that the organism belongs to the genus Carboxydothermus. On the basis of phenotypic features and phylogenetic analysis, Carboxydothermus islandicus sp. nov. is proposed, with the type strain SET IS-9(T) ( = DSM 21830(T)  = VKM B-2561(T)). An emended description of the genus Carboxydothermus is also given.

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

Quantum chemical modeling of enzymatic reactions: the case of histone lysine methyltransferase.

PubMed

Georgieva, Polina; Himo, Fahmi

2010-06-01

Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods. Copyright 2010 Wiley Periodicals, Inc.

The effect of shower/bath frequency on the health and operational effectiveness of soldiers in a field setting

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

Hall, L.C.; Daniels, J.I.

1991-01-31

Dermal disease can be a significant cause of morbidity among soldiers in a combat setting. For example, among American combat troops in Vietnam, disability from skin disease was one of the single most important medical causes of man-days lost from combat. Currently, the US Army makes shower or bath facilities available to soldiers in the field on a weekly basis. US Army after-action reports and anecdotal descriptions from the field indicate that this may not be an optimal regimen for the maintenance of personal hygiene, especially with respect to diseases of the skin. Determination of the optimal frequency of showeringmore » or bathing for soldiers in an combat setting is complicated by the fact that soldiers in the US Army may be involved in field exercises or combat in many different areas of the world with a variety of climatic conditions. Although certain aspects of the role of environmental factors in the incidence and severity of dermal disease have been documented, the role of hygiene in the potential mitigation of these effects has not been evaluated. The present project entails a comprehensive review and analysis of available literature in order to determine the health impact of shower/bath frequency for soldiers in a combat setting. An integral component of this work is an evaluation of the impact of climate, and microclimate produced by clothing, on the type, frequency, and severity of skin disease. A separate but related area of interest involves evaluating whether the use of antimicrobial soaps or similar products minimize the incidence of skin infections by decreasing populations of disease-causing microorganisms on the skin. 13 refs., 2 figs., 2 tabs.« less

efficient association study design via power-optimized tag SNP selection

PubMed Central

HAN, BUHM; KANG, HYUN MIN; SEO, MYEONG SEONG; ZAITLEN, NOAH; ESKIN, ELEAZAR

2008-01-01

Discovering statistical correlation between causal genetic variation and clinical traits through association studies is an important method for identifying the genetic basis of human diseases. Since fully resequencing a cohort is prohibitively costly, genetic association studies take advantage of local correlation structure (or linkage disequilibrium) between single nucleotide polymorphisms (SNPs) by selecting a subset of SNPs to be genotyped (tag SNPs). While many current association studies are performed using commercially available high-throughput genotyping products that define a set of tag SNPs, choosing tag SNPs remains an important problem for both custom follow-up studies as well as designing the high-throughput genotyping products themselves. The most widely used tag SNP selection method optimizes over the correlation between SNPs (r2). However, tag SNPs chosen based on an r2 criterion do not necessarily maximize the statistical power of an association study. We propose a study design framework that chooses SNPs to maximize power and efficiently measures the power through empirical simulation. Empirical results based on the HapMap data show that our method gains considerable power over a widely used r2-based method, or equivalently reduces the number of tag SNPs required to attain the desired power of a study. Our power-optimized 100k whole genome tag set provides equivalent power to the Affymetrix 500k chip for the CEU population. For the design of custom follow-up studies, our method provides up to twice the power increase using the same number of tag SNPs as r2-based methods. Our method is publicly available via web server at http://design.cs.ucla.edu. PMID:18702637

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

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

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

ωB97X-V: A 10-parameter, range-separated hybrid, generalized gradient approximation density functional with nonlocal correlation, designed by a survival-of-the-fittest strategy

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

Mardirossian, Narbe; Head-Gordon, Martin

2013-12-18

A 10-parameter, range-separated hybrid (RSH), generalized gradient approximation (GGA) density functional with nonlocal correlation (VV10) is presented in this paper. Instead of truncating the B97-type power series inhomogeneity correction factors (ICF) for the exchange, same-spin correlation, and opposite-spin correlation functionals uniformly, all 16 383 combinations of the linear parameters up to fourth order (m = 4) are considered. These functionals are individually fit to a training set and the resulting parameters are validated on a primary test set in order to identify the 3 optimal ICF expansions. Through this procedure, it is discovered that the functional that performs best onmore » the training and primary test sets has 7 linear parameters, with 3 additional nonlinear parameters from range-separation and nonlocal correlation. The resulting density functional, ωB97X-V, is further assessed on a secondary test set, the parallel-displaced coronene dimer, as well as several geometry datasets. Finally and furthermore, the basis set dependence and integration grid sensitivity of ωB97X-V are analyzed and documented in order to facilitate the use of the functional.« less

Semi-Supervised Learning of Lift Optimization of Multi-Element Three-Segment Variable Camber Airfoil

NASA Technical Reports Server (NTRS)

Kaul, Upender K.; Nguyen, Nhan T.

2017-01-01

This chapter describes a new intelligent platform for learning optimal designs of morphing wings based on Variable Camber Continuous Trailing Edge Flaps (VCCTEF) in conjunction with a leading edge flap called the Variable Camber Krueger (VCK). The new platform consists of a Computational Fluid Dynamics (CFD) methodology coupled with a semi-supervised learning methodology. The CFD component of the intelligent platform comprises of a full Navier-Stokes solution capability (NASA OVERFLOW solver with Spalart-Allmaras turbulence model) that computes flow over a tri-element inboard NASA Generic Transport Model (GTM) wing section. Various VCCTEF/VCK settings and configurations were considered to explore optimal design for high-lift flight during take-off and landing. To determine globally optimal design of such a system, an extremely large set of CFD simulations is needed. This is not feasible to achieve in practice. To alleviate this problem, a recourse was taken to a semi-supervised learning (SSL) methodology, which is based on manifold regularization techniques. A reasonable space of CFD solutions was populated and then the SSL methodology was used to fit this manifold in its entirety, including the gaps in the manifold where there were no CFD solutions available. The SSL methodology in conjunction with an elastodynamic solver (FiDDLE) was demonstrated in an earlier study involving structural health monitoring. These CFD-SSL methodologies define the new intelligent platform that forms the basis for our search for optimal design of wings. Although the present platform can be used in various other design and operational problems in engineering, this chapter focuses on the high-lift study of the VCK-VCCTEF system. Top few candidate design configurations were identified by solving the CFD problem in a small subset of the design space. The SSL component was trained on the design space, and was then used in a predictive mode to populate a selected set of test points outside of the given design space. The new design test space thus populated was evaluated by using the CFD component by determining the error between the SSL predictions and the true (CFD) solutions, which was found to be small. This demonstrates the proposed CFD-SSL methodologies for isolating the best design of the VCK-VCCTEF system, and it holds promise for quantitatively identifying best designs of flight systems, in general.

COMPARATIVE ASSESSMENT OF THE COMPOSITION AND CHARGE STATE OF NITROGENASE FeMo-COFACTOR

PubMed Central

Harris, Travis V.; Szilagyi, Robert K.

2011-01-01

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed the exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional and basis set. Overall, we found that a more oxidized [MoIV-2FeII-5FeIII-9S2−-C4−] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria, and is thus favored over the currently preferred composition of [MoIV-4FeII-3FeIII-9S2−-N3−] from the literature. PMID:21545160

Bayesian image reconstruction - The pixon and optimal image modeling

NASA Technical Reports Server (NTRS)

Pina, R. K.; Puetter, R. C.

1993-01-01

In this paper we describe the optimal image model, maximum residual likelihood method (OptMRL) for image reconstruction. OptMRL is a Bayesian image reconstruction technique for removing point-spread function blurring. OptMRL uses both a goodness-of-fit criterion (GOF) and an 'image prior', i.e., a function which quantifies the a priori probability of the image. Unlike standard maximum entropy methods, which typically reconstruct the image on the data pixel grid, OptMRL varies the image model in order to find the optimal functional basis with which to represent the image. We show how an optimal basis for image representation can be selected and in doing so, develop the concept of the 'pixon' which is a generalized image cell from which this basis is constructed. By allowing both the image and the image representation to be variable, the OptMRL method greatly increases the volume of solution space over which the image is optimized. Hence the likelihood of the final reconstructed image is greatly increased. For the goodness-of-fit criterion, OptMRL uses the maximum residual likelihood probability distribution introduced previously by Pina and Puetter (1992). This GOF probability distribution, which is based on the spatial autocorrelation of the residuals, has the advantage that it ensures spatially uncorrelated image reconstruction residuals.

Optimal fold symmetry of LH2 rings on a photosynthetic membrane

PubMed Central

Cleary, Liam; Chen, Hang; Chuang, Chern; Silbey, Robert J.; Cao, Jianshu

2013-01-01

An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a hexagonal lattice and establish two related mechanisms for the promotion of maximum excitation energy transfer (EET). (i) For certain fold numbers, there exist optimal basis cells with rotational symmetry, extendable to the entire lattice for the global optimization of the EET network. (ii) The type of basis cell can reduce or remove the frustration of EET rates across the photosynthetic network. We find that the existence of a basis cell and its type are directly related to the number of matching points S between the fold symmetry and the hexagonal lattice. The two complementary mechanisms provide selection criteria for the fold number and identify groups of consecutive numbers. Remarkably, one such group consists of the naturally occurring 8-, 9-, and 10-fold rings. By considering the inter-ring distance and EET rate, we demonstrate that this group can achieve minimal rotational sensitivity in addition to an optimal packing density, achieving robust and efficient EET. This corroborates our findings i and ii and, through their direct relation to S, suggests the design principle of matching the internal symmetry with the lattice order. PMID:23650366

Optimal fold symmetry of LH2 rings on a photosynthetic membrane.

PubMed

Cleary, Liam; Chen, Hang; Chuang, Chern; Silbey, Robert J; Cao, Jianshu

2013-05-21

An intriguing observation of photosynthetic light-harvesting systems is the N-fold symmetry of light-harvesting complex 2 (LH2) of purple bacteria. We calculate the optimal rotational configuration of N-fold rings on a hexagonal lattice and establish two related mechanisms for the promotion of maximum excitation energy transfer (EET). (i) For certain fold numbers, there exist optimal basis cells with rotational symmetry, extendable to the entire lattice for the global optimization of the EET network. (ii) The type of basis cell can reduce or remove the frustration of EET rates across the photosynthetic network. We find that the existence of a basis cell and its type are directly related to the number of matching points S between the fold symmetry and the hexagonal lattice. The two complementary mechanisms provide selection criteria for the fold number and identify groups of consecutive numbers. Remarkably, one such group consists of the naturally occurring 8-, 9-, and 10-fold rings. By considering the inter-ring distance and EET rate, we demonstrate that this group can achieve minimal rotational sensitivity in addition to an optimal packing density, achieving robust and efficient EET. This corroborates our findings i and ii and, through their direct relation to S, suggests the design principle of matching the internal symmetry with the lattice order.

Optimal inverse functions created via population-based optimization.

PubMed

Jennings, Alan L; Ordóñez, Raúl

2014-06-01

Finding optimal inputs for a multiple-input, single-output system is taxing for a system operator. Population-based optimization is used to create sets of functions that produce a locally optimal input based on a desired output. An operator or higher level planner could use one of the functions in real time. For the optimization, each agent in the population uses the cost and output gradients to take steps lowering the cost while maintaining their current output. When an agent reaches an optimal input for its current output, additional agents are generated in the output gradient directions. The new agents then settle to the local optima for the new output values. The set of associated optimal points forms an inverse function, via spline interpolation, from a desired output to an optimal input. In this manner, multiple locally optimal functions can be created. These functions are naturally clustered in input and output spaces allowing for a continuous inverse function. The operator selects the best cluster over the anticipated range of desired outputs and adjusts the set point (desired output) while maintaining optimality. This reduces the demand from controlling multiple inputs, to controlling a single set point with no loss in performance. Results are demonstrated on a sample set of functions and on a robot control problem.

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

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Principle component analysis to separate deformation signals from multiple sources during a 2015 intrusive sequence at Kīlauea Volcano

NASA Astrophysics Data System (ADS)

Johanson, I. A.; Miklius, A.; Poland, M. P.

2016-12-01

A sequence of magmatic events in April-May 2015 at Kīlauea Volcano produced a complex deformation pattern that can be described by multiple deforming sources, active simultaneously. The 2015 intrusive sequence began with inflation in the volcano's summit caldera near Halema`uma`u (HMM) Crater, which continued over a few weeks, followed by rapid deflation of the HMM source and inflation of a source in the south caldera region during the next few days. In Kīlauea Volcano's summit area, multiple deformation centers are active at varying times, and all contribute to the overall pattern observed with GPS, tiltmeters, and InSAR. Isolating the contribution of different signals related to each source is a challenge and complicates the determination of optimal source geometry for the underlying magma bodies. We used principle component analysis of continuous GPS time series from the 2015 intrusion sequence to determine three basis vectors which together account for 83% of the variance in the data set. The three basis vectors are non-orthogonal and not strictly the principle components of the data set. In addition to separating deformation sources in the continuous GPS data, the basis vectors provide a means to scale the contribution of each source in a given interferogram. This provides an additional constraint in a joint model of GPS and InSAR data (COSMO-SkyMed and Sentinel-1A) to determine source geometry. The first basis vector corresponds with inflation in the south caldera region, an area long recognized as the location of a long-term storage reservoir. The second vector represents deformation of the HMM source, which is in the same location as a previously modeled shallow reservoir, however InSAR data suggest a more complicated source. Preliminary modeling of the deformation attributed to the third basis vector shows that it is consistent with inflation of a steeply dipping ellipsoid centered below Keanakāko`i crater, southeast of HMM. Keanakāko`i crater is the locus of a known, intermittently active deformation source, which was not previously recognized to have been active during the 2015 event.

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

NASA Astrophysics Data System (ADS)

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

1997-12-01

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

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

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

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

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

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

2016-01-01

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

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

PubMed

Womack, James C; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-28

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Antiferromagnetic vs. non-magnetic ε phase of solid oxygen. Periodic density functional theory studies using a localized atomic basis set and the role of exact exchange.

PubMed

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 ε 1 phase and a higher pressure NM ε 0 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 O 2 molecules in the (O 2 ) 4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O 2 ) 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 (O 2 ) 4 unit cell for the low-pressure regime of the ε phase.

Heteroleptic complexes of Zn(II) based on 1-(5-bromo-2-hydroxybenzylidene)-4-phenylthiosemicarbazide: Synthesis, structural characterization, theoretical studies and antibacterial activity

NASA Astrophysics Data System (ADS)

Azarkish, Mohammad; Akbari, Alireza; Sedaghat, Tahereh; Simpson, Jim

2017-04-01

Four new ternary complexes, [ZnL (2,2‧-bipy)] (1), Zn2L2(4,4‧-bipy)] (2), [ZnL(Imd)]·H2O (3) and [ZnL3(MeImd)] (4), have been synthesized from the reaction of Zn(II) acetate with 1-(5-bromo-2-hydroxybenzylidene)-4-phenylthiosemicarbazide (H2L) in the presence of a heterocyclic base, 2,2‧-bipyridine, 4,4‧-bipyridine, imidazole or 2-methylimidazole, as an auxiliary ligand. The complexes have been investigated by elemental analysis and FT-IR, UV-Vis and 1HNMR spectroscopy. These data show that the thiosemicarbazone acts as a tridentate dianionic ligand and coordinates via the thiol group, imine nitrogen, and phenolic oxygen. The coordination sphere was completed by the nitrogen atom(s) of the secondary ligand. The structure of 1 was also confirmed by X-ray crystallography and shown to be a five coordinate complex with coordination geometry between the square-pyramidal and trigonal-bipyramidal. Density functional theory (DFT) calculations including geometry optimization, vibrational frequencies and electronic absorptions have been performed for 1 with the B3LYP functional at the TZP(6-311G*) basis set using the Gaussian 03 or ADF 2009 packages. The optimization calculation showed that the crystallographically determined geometry parameters can be reproduced with that basis set. Experimental IR frequencies and calculated vibration frequencies also support each other. The in vitro antibacterial activities of the ligand and complexes have been evaluated against Gram-positive (B. subtilis and S. aureus) and Gram-negative (P. aeruginosa) bacteria and compared with the standard antibacterial drugs. The results reveal that all of the complexes show much better activity in comparison to the individual thiosemoicarbazone ligand (H2L), against all bacterial strains used, with complex 3 showing the most promising results.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

NASA Astrophysics Data System (ADS)

Womack, James C.; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-01

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Analytic Energy Gradients for Variational Two-Electron Reduced-Density-Matrix-Driven Complete Active Space Self-Consistent Field Theory.

PubMed

Maradzike, Elvis; Gidofalvi, Gergely; Turney, Justin M; Schaefer, Henry F; DePrince, A Eugene

2017-09-12

Analytic energy gradients are presented for a variational two-electron reduced-density-matrix (2-RDM)-driven complete active space self-consistent field (CASSCF) method. The active-space 2-RDM is determined using a semidefinite programing (SDP) algorithm built upon an augmented Lagrangian formalism. Expressions for analytic gradients are simplified by the fact that the Lagrangian is stationary with respect to variations in both the primal and the dual solutions to the SDP problem. Orbital response contributions to the gradient are identical to those that arise in conventional CASSCF methods in which the electronic structure of the active space is described by a full configuration interaction (CI) wave function. We explore the relative performance of variational 2-RDM (v2RDM)- and CI-driven CASSCF for the equilibrium geometries of 20 small molecules. When enforcing two-particle N-representability conditions, full-valence v2RDM-CASSCF-optimized bond lengths display a mean unsigned error of 0.0060 Å and a maximum unsigned error of 0.0265 Å, relative to those obtained from full-valence CI-CASSCF. When enforcing partial three-particle N-representability conditions, the mean and maximum unsigned errors are reduced to only 0.0006 and 0.0054 Å, respectively. For these same molecules, full-valence v2RDM-CASSCF bond lengths computed in the cc-pVQZ basis set deviate from experimentally determined ones on average by 0.017 and 0.011 Å when enforcing two- and three-particle conditions, respectively, whereas CI-CASSCF displays an average deviation of 0.010 Å. The v2RDM-CASSCF approach with two-particle conditions is also applied to the equilibrium geometry of pentacene; optimized bond lengths deviate from those derived from experiment, on average, by 0.015 Å when using a cc-pVDZ basis set and a (22e,22o) active space.

Structures, Bonding, and Energetics of Potential Triatomic Circumstellar Molecules Containing Group 15 and 16 Elements.

PubMed

Turner, Walter E; Agarwal, Jay; Schaefer, Henry F

2015-12-03

The recent discovery of PN in the oxygen-rich shell of the supergiant star VY Canis Majoris points to the formation of several triatomic molecules involving oxygen, nitrogen, and phosphorus; these are also intriguing targets for main-group synthetic inorganic chemistry. In this research, high-level ab initio electronic structure computations were conducted on the potential circumstellar molecule OPN and several of its heavier group 15 and 16 congeners (SPN, SePN, TePN, OPP, OPAs, and OPSb). For each congener, four isomers were examined. Optimized geometries were obtained with coupled cluster theory [CCSD(T)] using large Dunning basis sets [aug-cc-pVQZ, aug-cc-pV(Q+d)Z, and aug-cc-pVQZ-PP], and relative energies were determined at the complete basis set limit of CCSDT(Q) from focal point analyses. The linear phosphorus-centered molecules were consistently the lowest in energy of the group 15 congeners by at least 6 kcal mol(-1), resulting from double-triple and single-double bond resonances within the molecule. The linear nitrogen-centered molecules were consistently the lowest in energy of the group 16 congeners by at least 5 kcal mol(-1), due to the electronegative central nitrogen atom encouraging electron delocalization throughout the molecule. For OPN, OPP, and SPN, anharmonic vibrational frequencies and vibrationally corrected rotational constants are predicted; good agreement with available experimental data is observed.

How widely applicable is river basin management? An analysis of wastewater management in an arid transboundary case.

PubMed

Dombrowsky, Ines; Almog, Ram; Becker, Nir; Feitelson, Eran; Klawitter, Simone; Lindemann, Stefan; Mutlak, Natalie

2010-05-01

The basin scale has been promoted universally as the optimal management unit that allows for the internalization of all external effects caused by multiple water uses. However, the basin scale has been put forward largely on the basis of experience in temperate zones. Hence whether the basin scale is the best scale for management in other settings remains questionable. To address these questions this paper analyzes the economic viability and the political feasibility of alternative management options in the Kidron/Wadi Nar region. The Kidron/Wadi Nar is a small basin in which wastewater from eastern Jerusalem flows through the desert to the Dead Sea. Various options for managing these wastewater flows were analyzed ex ante on the basis of both a cost benefit and a multi-criteria analysis. The paper finds that due to economies of scale, a pure basin approach is not desirable from a physical and economic perspective. Furthermore, in terms of political feasibility, it seems that the option which prompts the fewest objections from influential stakeholder groups in the two entities under the current asymmetrical political setting is not a basin solution either, but a two plant solution based on an outsourcing arrangement. These findings imply that the river basin management approach can not be considered the best management approach for the arid transboundary case at hand, and hence is not unequivocally universally applicable.

How Widely Applicable is River Basin Management? An Analysis of Wastewater Management in an Arid Transboundary Case

NASA Astrophysics Data System (ADS)

Dombrowsky, Ines; Almog, Ram; Becker, Nir; Feitelson, Eran; Klawitter, Simone; Lindemann, Stefan; Mutlak, Natalie

2010-05-01

The basin scale has been promoted universally as the optimal management unit that allows for the internalization of all external effects caused by multiple water uses. However, the basin scale has been put forward largely on the basis of experience in temperate zones. Hence whether the basin scale is the best scale for management in other settings remains questionable. To address these questions this paper analyzes the economic viability and the political feasibility of alternative management options in the Kidron/Wadi Nar region. The Kidron/Wadi Nar is a small basin in which wastewater from eastern Jerusalem flows through the desert to the Dead Sea. Various options for managing these wastewater flows were analyzed ex ante on the basis of both a cost benefit and a multi-criteria analysis. The paper finds that due to economies of scale, a pure basin approach is not desirable from a physical and economic perspective. Furthermore, in terms of political feasibility, it seems that the option which prompts the fewest objections from influential stakeholder groups in the two entities under the current asymmetrical political setting is not a basin solution either, but a two plant solution based on an outsourcing arrangement. These findings imply that the river basin management approach can not be considered the best management approach for the arid transboundary case at hand, and hence is not unequivocally universally applicable.

Computational and spectral studies of 6-phenylazo-3-(p-tolyl)-2H-chromen-2-one

NASA Astrophysics Data System (ADS)

Manimekalai, A.; Vijayalakshmi, N.

2015-02-01

6-Phenylazo-3-(p-tolyl)-2H-chromen-2-one 4 was prepared and characterized by IR, 1H, and 13C NMR spectral studies. The optimized structure of the chromen-2-one 4 was investigated by the Gaussian 03 B3LYP density functional method calculations at 6-31G(d,p) basis set. The gauge-independent atomic orbital (GIAO) 13C and 1H chemical shift calculations for the synthesized chromen-2-one in CDCl3 were also made by the same method. The computed IR frequencies of the chromen-2-one and the corresponding vibrational assignments were analyzed by means of potential energy distribution (PED%) calculation using vibrational energy distribution analysis (VEDA) program. The first order hyperpolarizability (βtot), polarizability (α) and dipole moment (μ) were calculated using 6-311G(d,p) basis set and the nonlinear optical (NLO) properties are also addressed theoretically. Stability of the chromen-2-one 4 molecule has been analyzed by calculating the intramolecular charge transfer using natural bond order (NBO) analysis. The molecular electrostatic potentials, HOMO-LUMO energy gap and geometrical parameters were also computed. Topological properties of the electronic charge density in chromen-2-one 4 were analyzed employing the Bader's Atoms in Molecule (AIM) theory which indicated the presence of intramolecular hydrogen bond in the molecule.

Computational and spectral studies of 6-phenylazo-3-(p-tolyl)-2H-chromen-2-one.

PubMed

Manimekalai, A; Vijayalakshmi, N

2015-02-05

6-Phenylazo-3-(p-tolyl)-2H-chromen-2-one 4 was prepared and characterized by IR, (1)H, and (13)C NMR spectral studies. The optimized structure of the chromen-2-one 4 was investigated by the Gaussian 03 B3LYP density functional method calculations at 6-31G(d,p) basis set. The gauge-independent atomic orbital (GIAO) (13)C and (1)H chemical shift calculations for the synthesized chromen-2-one in CDCl3 were also made by the same method. The computed IR frequencies of the chromen-2-one and the corresponding vibrational assignments were analyzed by means of potential energy distribution (PED%) calculation using vibrational energy distribution analysis (VEDA) program. The first order hyperpolarizability (βtot), polarizability (α) and dipole moment (μ) were calculated using 6-311G(d,p) basis set and the nonlinear optical (NLO) properties are also addressed theoretically. Stability of the chromen-2-one 4 molecule has been analyzed by calculating the intramolecular charge transfer using natural bond order (NBO) analysis. The molecular electrostatic potentials, HOMO-LUMO energy gap and geometrical parameters were also computed. Topological properties of the electronic charge density in chromen-2-one 4 were analyzed employing the Bader's Atoms in Molecule (AIM) theory which indicated the presence of intramolecular hydrogen bond in the molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics

NASA Astrophysics Data System (ADS)

Ünal, Aslı; Bozkaya, Uǧur

2018-03-01

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

PubMed

Ünal, Aslı; Bozkaya, Uğur

2018-03-28

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol -1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol -1 . Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol -1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Synthesis, X-ray diffraction method, spectroscopic characterization (FT-IR, 1H and 13C NMR), antimicrobial activity, Hirshfeld surface analysis and DFT computations of novel sulfonamide derivatives

NASA Astrophysics Data System (ADS)

Demircioğlu, Zeynep; Özdemir, Fethi Ahmet; Dayan, Osman; Şerbetçi, Zafer; Özdemir, Namık

2018-06-01

Synthesized compounds of N-(2-aminophenyl)benzenesulfonamide 1 and (Z)-N-(2-((2-nitrobenzylidene)amino)phenyl)benzenesulfonamide 2 were characterized by antimicrobial activity, FT-IR, 1H and 13C NMR. Two new Schiff base ligands containing aromatic sulfonamide fragment of (Z)-N-(2-((3-nitrobenzylidene)amino)phenyl)benzenesulfonamide 3 and (Z)-N-(2-((4-nitrobenzylidene)amino)phenyl)benzenesulfonamide 4 were synthesized and investigated by spectroscopic techniques including 1H and 13C NMR, FT-IR, single crystal X-ray diffraction, Hirshfeld surface, theoretical method analyses and by antimicrobial activity. The molecular geometry obtained from the X-ray structure determination was optimized Density Functional Theory (DFT/B3LYP) method with the 6-311++G(d,p) basis set in ground state. From the optimized geometry of the molecules of 3 and 4, the geometric parameters, vibrational wavenumbers and chemical shifts were computed. The optimized geometry results, which were well represented the X-ray data, were shown that the chosen of DFT/B3LYP 6-311G++(d,p) was a successful choice. After a successful optimization, frontier molecular orbitals, chemical activity, non-linear optical properties (NLO), molecular electrostatic mep (MEP), Mulliken population method, natural population analysis (NPA) and natural bond orbital analysis (NBO), which cannot be obtained experimentally, were calculated and investigated.

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

NASA Astrophysics Data System (ADS)

van Hoeve, Miriam D.; Klobukowski, Mariusz

2018-03-01

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

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

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

Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization.

PubMed

Libbrecht, Maxwell W; Bilmes, Jeffrey A; Noble, William Stafford

2018-04-01

Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from metagenomics data. Previous methods for this task, such as CD-HIT, PISCES, and UCLUST, apply a heuristic threshold-based algorithm that has no theoretical guarantees. We propose a new approach based on submodular optimization. Submodular optimization, a discrete analogue to continuous convex optimization, has been used with great success for other representative set selection problems. We demonstrate that the submodular optimization approach results in representative protein sequence subsets with greater structural diversity than sets chosen by existing methods, using as a gold standard the SCOPe library of protein domain structures. In this setting, submodular optimization consistently yields protein sequence subsets that include more SCOPe domain families than sets of the same size selected by competing approaches. We also show how the optimization framework allows us to design a mixture objective function that performs well for both large and small representative sets. The framework we describe is the best possible in polynomial time (under some assumptions), and it is flexible and intuitive because it applies a suite of generic methods to optimize one of a variety of objective functions. © 2018 Wiley Periodicals, Inc.

An externally validated model for predicting long-term survival after exercise treadmill testing in patients with suspected coronary artery disease and a normal electrocardiogram.

PubMed

Lauer, Michael S; Pothier, Claire E; Magid, David J; Smith, S Scott; Kattan, Michael W

2007-12-18

The exercise treadmill test is recommended for risk stratification among patients with intermediate to high pretest probability of coronary artery disease. Posttest risk stratification is based on the Duke treadmill score, which includes only functional capacity and measures of ischemia. To develop and externally validate a post-treadmill test, multivariable mortality prediction rule for adults with suspected coronary artery disease and normal electrocardiograms. Prospective cohort study conducted from September 1990 to May 2004. Exercise treadmill laboratories in a major medical center (derivation set) and a separate HMO (validation set). 33,268 patients in the derivation set and 5821 in the validation set. All patients had normal electrocardiograms and were referred for evaluation of suspected coronary artery disease. The derivation set patients were followed for a median of 6.2 years. A nomogram-illustrated model was derived on the basis of variables easily obtained in the stress laboratory, including age; sex; history of smoking, hypertension, diabetes, or typical angina; and exercise findings of functional capacity, ST-segment changes, symptoms, heart rate recovery, and frequent ventricular ectopy in recovery. The derivation data set included 1619 deaths. Although both the Duke treadmill score and our nomogram-illustrated model were significantly associated with death (P < 0.001), the nomogram was better at discrimination (concordance index for right-censored data, 0.83 vs. 0.73) and calibration. We reclassified many patients with intermediate- to high-risk Duke treadmill scores as low risk on the basis of the nomogram. The model also predicted 3-year mortality rates well in the validation set: Based on an optimal cut-point for a negative predictive value of 0.97, derivation and validation rates were, respectively, 1.7% and 2.5% below the cut-point and 25% and 29% above the cut-point. Blood test-based measures or left ventricular ejection fraction were not included. The nomogram can be applied only to patients with a normal electrocardiogram. Clinical utility remains to be tested. A simple nomogram based on easily obtained pretest and exercise test variables predicted all-cause mortality in adults with suspected coronary artery disease and normal electrocardiograms.