Kananenka, Alexei A; Zgid, Dominika
2017-11-14
We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.
Multi-configuration time-dependent density-functional theory based on range separation
DEFF Research Database (Denmark)
Fromager, E.; Knecht, S.; Jensen, Hans Jørgen Aagaard
2013-01-01
Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration- Self-Consistent Field (MCSCF) treatment with an adiabatic short......-range density-functional (DFT) description, is then considered. The resulting time-dependent multi-configuration short-range DFT (TD-MC-srDFT) model is applied to the calculation of singlet excitation energies in H, Be, and ferrocene, considering both short-range local density (srLDA) and generalized gradient...
DEFF Research Database (Denmark)
Cornaton, Y.; Stoyanova, A.; Jensen, Hans Jørgen Aagaard
2013-01-01
An alternative separation of short-range exchange and correlation energies is used in the framework of second-order range-separated density-functional perturbation theory. This alternative separation was initially proposed by Toulouse and relies on a long-range-interacting wave function instead...... of the noninteracting Kohn-Sham one. When second-order corrections to the density are neglected, the energy expression reduces to a range-separated double-hybrid (RSDH) type of functional, RSDHf, where "f" stands for "full-range integrals" as the regular full-range interaction appears explicitly in the energy...... on the potential energy curves in the equilibrium region, improving the accuracy of binding energies and equilibrium bond distances when second-order perturbation theory is appropriate....
Multi-configuration time-dependent density-functional theory based on range separation
Fromager, Emmanuel; Jensen, Hans Jørgen Aa
2012-01-01
Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration-Self-Consistent Field (MCSCF) treatment with an adiabatic short-range density-functional (DFT) description, is then considered. The resulting time-dependent multi-configuration short-range DFT (TD-MC-srDFT) model is applied to the calculation of singlet excitation energies in H2, Be and ferrocene, considering both short-range local density (srLDA) and generalized gradient (srGGA) approximations. In contrast to regular TD-DFT, TD-MC-srDFT can describe double excitations. As expected, when modeling long-range interactions with the MCSCF model instead of the adiabatic Buijse-Baerends density-matrix functional as recently proposed by Pernal [K. Pernal, J. Chem. Phys. 136, 184105 (2012)], the description of both the 1^1D doubly-excited state in Be and the 1^1\\Sigma^+_u state in the stretch...
Self-consistent many-body perturbation theory in range-separated density-functional theory
DEFF Research Database (Denmark)
Fromager, Emmanuel; Jensen, Hans Jørgen Aagaard
2008-01-01
In many cases, density-functional theory (DFT) with current standard approximate functionals offers a relatively accurate and computationally cheap description of the short-range dynamic electron correlation effects. However, in general, standard DFT does not treat the dispersion interaction...... effects adequately which, on the other hand, can be described by many-body perturbation theory MBPT. It is therefore of interest to develop a hybrid model which combines the best of both the MBPT and DFT approaches. This can be achieved by splitting the two-electron interaction into long-range and short...
Aberrant long-range functional connectivity density in generalized tonic-clonic seizures.
Zhu, Ling; Li, Yibo; Wang, Yifeng; Li, Rong; Zhang, Zhiqiang; Lu, Guangming; Chen, Huafu
2016-06-01
Studies in generalized tonic-clonic seizures (GTCS) have reported both structural and functional alterations in the brain. However, changes in spontaneous neuronal functional organization in GTCS remain largely unknown.In this study, 70 patients with idiopathic generalized epilepsy characterized by tonic-clonic seizures and 70 age- and sex-matched healthy controls were recruited. Here, functional connectivity density (FCD) mapping, an ultrafast data-driven method based on functional magnetic resonance imaging (fMRI), was applied for the first time to investigate the changes of spontaneous functional brain activity caused by epilepsy.The results showed significantly decreased long-range FCD in the middle and inferior temporal, prefrontal, and inferior parietal cortices as well as increased long-range FCD in the cerebellum anterior lobe and sensorimotor areas. Negative correlation between duration of disease and reduced long-range FCD was found. In addition, most regions with reduced long-range FCD showed decreased resting-state functional connectivity (rsFC) within default mode network.Negative correlation between duration of disease and long-range FCD may reflect an adverse consequence eventually from original. Furthermore, the observed FCD and rsFC alterations have been speculated to be associated with the social-cognitive impairments as well as motor control. Our study provided novel evidences to look into neuro-pathophysiological mechanisms underlying GTCS.
DEFF Research Database (Denmark)
Hubert, Mickaël; Hedegård, Erik D.; Jensen, Hans Jørgen Aa
2016-01-01
-srDFT for a selected benchmark set of electronic excitations of organic molecules, covering the most common types of organic chromophores. This investigation confirms the expectation that the MC-srDFT method is accurate for a broad range of excitations and comparable to accurate wave function methods such as CASPT2......Computational methods that can accurately and effectively predict all types of electronic excitations for any molecular system are missing in the toolbox of the computational chemist. Although various Kohn-Sham density-functional methods (KS-DFT) fulfill this aim in some cases, they become...... and double excitations have been promising, it is nevertheless important that the accuracy of MC-srDFT is at least comparable to the best KS-DFT methods also for organic molecules that are typically of single-reference character. In this paper we therefore systematically investigate the performance of MC...
Energy Technology Data Exchange (ETDEWEB)
Lutsker, V.; Niehaus, T. A., E-mail: thomas.niehaus@physik.uni-regensburg.de [Department of Theoretical Physics, University of Regensburg, 93040 Regensburg (Germany); Aradi, B. [BCCMS, University of Bremen, 28359 Bremen (Germany)
2015-11-14
Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.
DEFF Research Database (Denmark)
Fromager, Emmanuel; Toulouse, Julien; Jensen, Hans Jørgen Aagaard
2007-01-01
) adequately which, on the other hand, can be described in wave-function theory (WFT), for example, with a multiconfigurational self-consistent field (MCSCF) model. It is therefore of high interest to develop a hybrid model which combines the best of both WFT and DFT approaches. The merge of WFT and DFT can......In many cases, the dynamic correlation can be calculated quite accurately and at a fairly low computational cost in Kohn-Sham density-functional theory (KS-DFT), using current standard approximate functionals. However, in general, KS-DFT does not treat static correlation effects (near degeneracy...
DEFF Research Database (Denmark)
Hedegård, Erik Donovan
2017-01-01
considered the large collection of organic molecules whose excited states were investigated with a range of electronic structure methods by Thiel et al. As a by-product of our calculations of oscillator strengths, we also obtain electronic excitation energies, which enable us to compare the performance......We have in a series of recent papers investigated electronic excited states with a hybrid between a complete active space self-consistent field (CASSCF) wave function and density functional theory (DFT). This method has been dubbed the CAS short-range DFT method (CAS–srDFT). The previous papers...
A finite range pairing force for density functional theory in superfluid nuclei
Tian, Y.; Ma, Z. Y.; Ring, P.
2009-06-01
The problem of pairing in the S10 channel of finite nuclei is revisited. In nuclear matter forces of separable form can be adjusted to the bare nuclear force, to any phenomenological pairing interaction such as the Gogny force or to exact solutions of the gap equation. In finite nuclei, because of translational invariance, such forces are no longer separable. Using well-known techniques of Talmi and Moshinsky we expand the matrix elements in a series of separable terms, which converges quickly preserving translational invariance and finite range. In this way the complicated problem of a cut-off at large momenta or energies inherent in other separable or zero range pairing forces is avoided. Applications in the framework of the relativistic Hartree-Bogoliubov approach show that the pairing properties are depicted on almost the same footing as by the original pairing interaction not only in nuclear matter, but also in finite nuclei. This simple separable force can be easily applied for the investigation of pairing properties in nuclei far from stability as well as for further investigations going beyond mean field theory.
DEFF Research Database (Denmark)
Fromager, Emmanuel; Jensen, Hans Jørgen Aagaard
2011-01-01
-cluster theories, self-consistency effects are introduced in the density functional part, which for an exact solution requires iterations. They are generally assumed to be small but no detailed study has been performed so far. Here, the authors analyze self-consistency when using Møller-Plesset-type (MP......Range-separated density-functional theory combines wave function theory for the long-range part of the two-electron interaction with density-functional theory for the short-range part. When describing the long-range interaction with non-variational methods, such as perturbation or coupled......) perturbation theory for the long range interaction. The lowest-order self-consistency corrections to the wave function and the energy, that enter the perturbation expansions at the second and fourth order, respectively, are both expressed in terms of the one-electron reduced density matrix. The computational...
DEFF Research Database (Denmark)
Senjean, Bruno; Knecht, Stefan; Jensen, Hans Jørgen Aa
2015-01-01
Gross-Oliveira-Kohn density-functional theory (GOK-DFT) for ensembles is, in principle, very attractive but has been hard to use in practice. A practical model based on GOK-DFT for the calculation of electronic excitation energies is discussed. The model relies on two modifications of GOK-DFT: us...
DEFF Research Database (Denmark)
Hedegård, Erik D.; Jensen, Hans Jørgen Aagaard; Knecht, Stefan
2013-01-01
Charge transfer excitations can be described within Time-Dependent Density Functional Theory (TD-DFT), not only by means of the Coulomb Attenuated Method (CAM) but also with a combination of wave function theory and TD-DFT based on range separation. The latter approach enables a rigorous formulat......Charge transfer excitations can be described within Time-Dependent Density Functional Theory (TD-DFT), not only by means of the Coulomb Attenuated Method (CAM) but also with a combination of wave function theory and TD-DFT based on range separation. The latter approach enables a rigorous...... formulation of multi-determinantal TD-DFT schemes where excitation classes, which are absent in conventional TD-DFT spectra (like for example double excitations), can be addressed. This paper investigates the combination of both the long-range Multi-Configuration Self-Consistent Field (MCSCF) and Second Order...... Polarization Propagator Approximation (SOPPA) ansätze with a short-range DFT (srDFT) description. We find that the combinations of SOPPA or MCSCF with TD-DFT yield better results than could be expected from the pure wave function schemes. For the Time-Dependent MCSCF short-range DFT ansatz (TD...
Otero-de-la-Roza, A; Johnson, Erin R
2013-05-28
The exchange-hole dipole-moment model (XDM) for dispersion is combined with a collection of semilocal, hybrid, and range-separated hybrid functionals. The resulting XDM-corrected functionals are tested against standard benchmarks for non-covalent interactions at and away from equilibrium, conformer ranking in water clusters, thermochemistry, and kinetics. We show that functionals with the correct -1∕r tail of the exchange potential yield superior accuracy for weak interactions. Thus, balancing long-range exchange with dispersion interactions in XDM is essential in the correct description of dimers with significant non-dispersion contributions to binding. With the exception of the noble gases, the performance of PW86PBE-XDM is improved upon at the semilocal (BLYP), hybrid (B3LYP), and range-separated hybrid (LC-ωPBE) levels. Based on its excellent performance, we propose LC-ωPBE-XDM as an accurate functional for hard and soft matter.
Rebolini, Elisa
2015-01-01
We present a range-separated linear-response time-dependent density-functional theory (TDDFT) which combines a density-functional approximation for the short-range response kernel and a frequency-dependent second-order Bethe-Salpeter approximation for the long-range response kernel. This approach goes beyond the adiabatic approximation usually used in linear-response TDDFT and aims at improving the accuracy of calculations of electronic excitation energies of molecular systems. A detailed derivation of the frequency-dependent second-order Bethe-Salpeter correlation kernel is given using many-body Green-function theory. Preliminary tests of this range-separated TDDFT method are presented for the calculation of excitation energies of four small molecules: N2, CO2, H2CO, and C2H4. The results suggest that the addition of the long-range second-order Bethe-Salpeter correlation kernel overall slightly improves the excitation energies.
Long-Range van der Waals Correction to a Semilocal Density Functional: The Tail Need Not Wag the Dog
Perdew, John P.
The SCAN (strongly constrained and appropriately normed) meta-generalized gradient approximation satisfies all 17 exact constraints that a semilocal functional can. Without being fitted to any bonded system, it correctly describes most kinds of bonding, including intermediate-range van der Waals (vdW) interaction. It can be supplemented [3.4] with a long-range vdW correction such as D3 or rVV10, which have the flexibility to exclude any intermediate-range contribution. Accurate results are found for free molecules, for molecules weakly bound to metal surfaces, and for interlayer binding energies of layered materials. Despite being a pair-interaction model, the rVV10 correction to SCAN also gives a random-phase-approximation-like long-range contribution to the binding energy curve for graphene on a nickel surface. Supported by DOE BES and NSF DMR.
Laboratory Density Functionals
Giraud, B. G.
2007-01-01
We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals.
Song, Jong-Won; Hirao, Kimihiko
2015-10-14
Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory.
Energy Technology Data Exchange (ETDEWEB)
Goll, Erich [Institut fuer Theoretische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, D-70550 Stuttgart (Germany)], E-mail: goll@theochem.uni-stuttgart.de; Werner, Hans-Joachim [Institut fuer Theoretische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, D-70550 Stuttgart (Germany); Stoll, Hermann [Institut fuer Theoretische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, D-70550 Stuttgart (Germany); Leininger, Thierry [Laboratoire de Physique Quantique, UMR 5626 du CNRS, Universite Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse Cedex 04 (France); Gori-Giorgi, Paola [Laboratoire de Chimie Theorique, CNRS UMR7616, Universite Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris (France); Savin, Andreas [Laboratoire de Chimie Theorique, CNRS UMR7616, Universite Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris (France)
2006-10-26
We extend our recently published short-range gradient-corrected density functional from the closed-shell to Open-shell case, combine it with long-range coupled-cluster methods (CCSD, CCSD(T)), and apply it to the weakly bound alkali-metal rare-gas dimers AmRg (Am = Li-Cs; Rg = Ne-Xe). The results are shown to be superior, with medium-size basis sets, to pure DFT and pure coupled-cluster calculations.
Quantal density functional theory
Sahni, Viraht
2016-01-01
This book deals with quantal density functional theory (QDFT) which is a time-dependent local effective potential theory of the electronic structure of matter. The treated time-independent QDFT constitutes a special case. In the 2nd edition, the theory is extended to include the presence of external magnetostatic fields. The theory is a description of matter based on the ‘quantal Newtonian’ first and second laws which is in terms of “classical” fields that pervade all space, and their quantal sources. The fields, which are explicitly defined, are separately representative of electron correlations due to the Pauli exclusion principle, Coulomb repulsion, correlation-kinetic, correlation-current-density, and correlation-magnetic effects. The book further describes Schrödinger theory from the new physical perspective of fields and quantal sources. It also describes traditional Hohenberg-Kohn-Sham DFT, and explains via QDFT the physics underlying the various energy functionals and functional derivatives o...
Fuks, Johanna I
2014-01-01
We explore an asymmetric two-fermion Hubbard dimer to test the accuracy of the adiabatic approximation of time-dependent density functional theory in modelling time-resolved charge transfer. We show that the model shares essential features of a ground state long-range molecule in real-space, and by applying a resonant field we show that the model also reproduces essential traits of the CT dynamics. The simplicity of the model allows us to propagate with an "adiabatically-exact" approximation, i.e. one that uses the exact ground-state exchange-correlation functional, and compare with the exact propagation. This allows us to study the impact of the time-dependent charge-transfer step feature in the exact correlation potential of real molecules on the resulting dynamics. Tuning the parameters of the dimer allows a study both of charge-transfer between open-shell fragments and between closed-shell fragments. We find that the adiabatically-exact functional is unable to properly transfer charge, even in situations ...
DEFF Research Database (Denmark)
Fromager, Emmanuel; Cimiraglia, Renzo; Jensen, Hans Jørgen Aagaard
2010-01-01
A rigorous combination of multireference perturbation theory and density functional theory (DFT) is proposed. Based on a range separation of the regular two-electron Coulomb interaction, it combines a short-range density functional with second-order strongly contracted n-electron valence state pe...... zero. The method yields very promising results for the van der Waals systems Be2, Mg2, and Ca2; including the multireference system Be2....
Density functional theory: Foundations reviewed
Energy Technology Data Exchange (ETDEWEB)
Kryachko, Eugene S., E-mail: eugene.kryachko@ulg.ac.be [Bogolyubov Institute for Theoretical Physics, Kiev, 03680 (Ukraine); Ludeña, Eduardo V., E-mail: popluabe@yahoo.es [Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Apartado 21827, Caracas 1020-A (Venezuela, Bolivarian Republic of); Prometheus Program, Senescyt (Ecuador); Grupo Ecuatoriano para el Estudio Experimental y Teórico de Nanosistemas, GETNano, USFQ, N104-E, Quito (Ecuador); Escuela Politécnica Superior del Litoral, ESPOL, Guayaquil (Ecuador)
2014-11-10
Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg–Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb’s comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn–Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn–Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn–Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem
Pandey, Laxman
2012-01-01
Polymers with low optical gaps are of importance to the organic photovoltaics community due to their potential for harnessing a large portion of the solar energy spectrum. The combination along their backbones of electron-rich and electron-deficient fragments contributes to the presence of low-lying excited states that are expected to display significant charge-transfer character. While conventional hybrid functionals are known to provide unsatisfactory results for charge-transfer excitations at the time-dependent DFT level, long-range corrected (LRC) functionals have been reported to give improved descriptions in a number of systems. Here, we use such LRC functionals, considering both tuned and default range-separation parameters, to characterize the absorption spectra of low-optical-gap systems of interest. Our results indicate that tuned LRC functionals lead to simulated optical-absorption properties in good agreement with experimental data. Importantly, the lowest-lying excited states (excitons) are shown to present a much more localized nature than initially anticipated. © 2012 the Owner Societies.
DEFF Research Database (Denmark)
Fromager, Emmanuel; Réal, Florent; Wåhlin, Pernilla
2009-01-01
the universality of this value by considering "extreme" study cases, namely, neutral and charged isoelectronic f0 actinide compounds (ThO2, PaO2+, UO22+, UN2, CUO, and NpO23+). We find for these compounds that μ(opt)=0.3 a.u. but show that 0.4 a.u. is still acceptable. This is a promising result...... in the investigation of a universal range separation. The accuracy of the currently best MC-srDFT (μ=0.3 a.u.) approach has also been tested for equilibrium geometries. Though it performs as well as wave function theory and DFT for static-correlation-free systems, it fails in describing the neptunyl (VII) ion NpO23......+ where static correlation is significant; bending is preferred at the MC-srDFT (μ=0.3 a.u.) level, whereas the molecule is known to be linear. This clearly shows the need for better short-range functionals, especially for the description of the short-range exchange. It also suggests that the bending...
Sun, Haitao
2016-05-16
We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a non-empirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal-phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials.
SYNTHESIS, CHARACTERIZATION AND DENSITY FUNCTIONAL ...
African Journals Online (AJOL)
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ABSTRACT. We synthesized a number of aniline derivatives containing acyl groups to compare their barriers of rotation around the N-CO groups. Geometry optimization for all the rotamers have been performed using density functional theory (DFT) at the B3LYP/6-31G** level of theory. For each stationary point we carried ...
Density functionals from deep learning
McMahon, Jeffrey
Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional (DF) are necessary. Machine learning has recently been proposed as a novel approach to discover such a DF (or components of it). Conventional machine learning algorithms, however, are limited in their ability to process data in their raw form, leading to invariance and/or sensitivity issues. In this presentation, an alternative approach based on deep learning will be demonstrated. Deep learning allows computational models that are capable of discovering intricate structure in large and/or high-dimensional data sets with multiple levels of abstraction, and do not suffer from the aforementioned issues. Results from the application of this approach to the prediction of the kinetic-energy DF of noninteracting electrons will be presented. Using theoretical results from computer science, a connection between the underlying model and the theorems of Hohenberg and Kohn will also be suggested.
Evolution of density-dependent movement during experimental range expansions.
Fronhofer, E A; Gut, S; Altermatt, F
2017-12-01
Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.
Epidemiological reference ranges for low-density lipoprotein ...
African Journals Online (AJOL)
Although there is widespread acceptance that total cholesterol (TC) value reference ranges should be based on epidemiological rather than statistical considerations, the epidemiological action limits for Iow-density lipoprotein cholesterol (LDL-C) are still incomplete and only statistical reference ranges for apolipoprotein B ...
Density Functional Theory Models for Radiation Damage
Dudarev, S. L.
2013-07-01
Density functional theory models developed over the past decade provide unique information about the structure of nanoscale defects produced by irradiation and about the nature of short-range interaction between radiation defects, clustering of defects, and their migration pathways. These ab initio models, involving no experimental input parameters, appear to be as quantitatively accurate and informative as the most advanced experimental techniques developed for the observation of radiation damage phenomena. Density functional theory models have effectively created a new paradigm for the scientific investigation and assessment of radiation damage effects, offering new insight into the origin of temperature- and dose-dependent response of materials to irradiation, a problem of pivotal significance for applications.
Density functional theory a practical introduction
Sholl, David
2009-01-01
Demonstrates how anyone in math, science, and engineering can master DFT calculations Density functional theory (DFT) is one of the most frequently used computational tools for studying and predicting the properties of isolated molecules, bulk solids, and material interfaces, including surfaces. Although the theoretical underpinnings of DFT are quite complicated, this book demonstrates that the basic concepts underlying the calculations are simple enough to be understood by anyone with a background in chemistry, physics, engineering, or mathematics. The authors show how the widespread availability of powerful DFT codes makes it possible for students and researchers to apply this important computational technique to a broad range of fundamental and applied problems. Density Functional Theory: A Practical Introduction offers a concise, easy-to-follow introduction to the key concepts and practical applications of DFT, focusing on plane-wave DFT. The authors have many years of experience introducing DFT to studen...
Generalized density-functional theory: Conquering the ...
Indian Academy of Sciences (India)
Home; Journals; Journal of Chemical Sciences; Volume 117; Issue 5. Generalized density-functional theory: Conquering the -representability problem with exact functionals for the electron pair density and the second-order reduced density matrix. Paul W Ayers Mel Levy. Volume 117 Issue 5 September 2005 pp 507-514 ...
A Density Functional Theory Study
Lim, XiaoZhi
2011-12-11
Complexes with pincer ligand moieties have garnered much attention in the past few decades. They have been shown to be highly active catalysts in several known transition metal-catalyzed organic reactions as well as some unprecedented organic transformations. At the same time, the use of computational organometallic chemistry to aid in the understanding of the mechanisms in organometallic catalysis for the development of improved catalysts is on the rise. While it was common in earlier studies to reduce computational cost by truncating donor group substituents on complexes such as tertbutyl or isopropyl groups to hydrogen or methyl groups, recent advancements in the processing capabilities of computer clusters and codes have streamlined the time required for calculations. As the full modeling of complexes become increasingly popular, a commonly overlooked aspect, especially in the case of complexes bearing isopropyl substituents, is the conformational analysis of complexes. Isopropyl groups generate a different conformer with each 120 ° rotation (rotamer), and it has been found that each rotamer typically resides in its own potential energy well in density functional theory studies. As a result, it can be challenging to select the most appropriate structure for a theoretical study, as the adjustment of isopropyl substituents from a higher-energy rotamer to the lowest-energy rotamer usually does not occur during structure optimization. In this report, the influence of the arrangement of isopropyl substituents in pincer complexes on calculated complex structure energies as well as a case study on the mechanism of the isomerization of an iPrPCP-Fe complex is covered. It was found that as many as 324 rotamers can be generated for a single complex, as in the case of an iPrPCP-Ni formato complex, with the energy difference between the global minimum and the highest local minimum being as large as 16.5 kcalmol-1. In the isomerization of a iPrPCP-Fe complex, it was found
A Safari Through Density Functional Theory
Dreizler, Reiner M.; Lüdde, Cora S.
Density functional theory is widely used to treat quantum many body problems in many areas of physics and related fields. A brief survey of this method covering foundations, functionals and applications is presented here.
Density functional theory in quantum chemistry
Tsuneda, Takao
2014-01-01
This book examines density functional theory based on the foundation of quantum chemistry. Unconventional in approach, it reviews basic concepts, then describes the physical meanings of state-of-the-art exchange-correlation functionals and their corrections.
A multiconfigurational hybrid density-functional theory
DEFF Research Database (Denmark)
Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...
Joint product numerical range and geometry of reduced density matrices
Chen, Jianxin; Guo, Cheng; Ji, Zhengfeng; Poon, Yiu-Tung; Yu, Nengkun; Zeng, Bei; Zhou, Jie
2017-02-01
The reduced density matrices of a many-body quantum system form a convex set, whose three-dimensional projection Θ is convex in R3. The boundary ∂Θ of Θ may exhibit nontrivial geometry, in particular ruled surfaces. Two physical mechanisms are known for the origins of ruled surfaces: symmetry breaking and gapless. In this work, we study the emergence of ruled surfaces for systems with local Hamiltonians in infinite spatial dimension, where the reduced density matrices are known to be separable as a consequence of the quantum de Finetti's theorem. This allows us to identify the reduced density matrix geometry with joint product numerical range Π of the Hamiltonian interaction terms. We focus on the case where the interaction terms have certain structures, such that a ruled surface emerges naturally when taking a convex hull of Π. We show that, a ruled surface on ∂Θ sitting in Π has a gapless origin, otherwise it has a symmetry breaking origin. As an example, we demonstrate that a famous ruled surface, known as the oloid, is a possible shape of Θ, with two boundary pieces of symmetry breaking origin separated by two gapless lines.
Magnetic fields and density functional theory
Energy Technology Data Exchange (ETDEWEB)
Salsbury Jr., Freddie [Univ. of California, Berkeley, CA (United States)
1999-02-01
A major focus of this dissertation is the development of functionals for the magnetic susceptibility and the chemical shielding within the context of magnetic field density functional theory (BDFT). These functionals depend on the electron density in the absence of the field, which is unlike any other treatment of these responses. There have been several advances made within this theory. The first of which is the development of local density functionals for chemical shieldings and magnetic susceptibilities. There are the first such functionals ever proposed. These parameters have been studied by constructing functionals for the current density and then using the Biot-Savart equations to obtain the responses. In order to examine the advantages and disadvantages of the local functionals, they were tested numerically on some small molecules.
SYNTHESIS, CHARACTERIZATION AND DENSITY FUNCTIONAL ...
African Journals Online (AJOL)
B. S. Chandravanshi
functional theory (DFT) calculation of relative energies, relative enthalpies and free energies shows that E isomers ... The basic design of today's high performance dye sensitized solar cells (DSSC) was developed in the early ... theoretical investigations of the physical properties of dye sensitizers are very important in order.
Multicomponent density functional theory embedding formulation.
Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon
2016-07-28
Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.
Density functional theory and multiscale materials modeling*
Indian Academy of Sciences (India)
Unknown
wide class of problems involving nanomaterials, interfacial science and soft condensed matter has been addressed using the density based ... Keywords. Density functional theory; soft condensed matter; materials modeling. 1. Introduction ... the basic laws of quantum mechanics, their prediction through a direct ab initio ...
Relativistic density functional for nuclear structure
2016-01-01
This book aims to provide a detailed introduction to the state-of-the-art covariant density functional theory, which follows the Lorentz invariance from the very beginning and is able to describe nuclear many-body quantum systems microscopically and self-consistently. Covariant density functional theory was introduced in nuclear physics in the 1970s and has since been developed and used to describe the diversity of nuclear properties and phenomena with great success. In order to provide an advanced and updated textbook of covariant density functional theory for graduate students and nuclear physics researchers, this book summarizes the enormous amount of material that has accumulated in the field of covariant density functional theory over the last few decades as well as the latest developments in this area. Moreover, the book contains enough details for readers to follow the formalism and theoretical results, and provides exhaustive references to explore the research literature.
A multiconfigurational hybrid density-functional theory
Sharkas, Kamal; Jensen, Hans Jørgen Aa; Toulouse, Julien; 10.1063/1.4733672
2012-01-01
We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension of the usual hybrid approximations by essentially adding a fraction \\lambda of exact static correlation in addition to the fraction \\lambda of exact exchange. Test calculations on the cycloaddition reactions of ozone with ethylene or acetylene and the dissociation of diatomic molecules with the Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) density functionals show that a good value of \\lambda is 0.25, as in the usual hybrid approximations. The results suggest that the proposed multiconfigurational hybrid approximations can improve over usual density-functional calculations for situations with strong static correlation effects.
Gender Differences in Brain Functional Connectivity Density
Tomasi, Dardo; Volkow, Nora D.
2011-01-01
The neural bases of gender differences in emotional, cognitive, and socials behaviors are largely unknown. Here, magnetic resonance imaging data from 336 women and 225 men revealed a gender dimorphism in the functional organization of the brain. Consistently across five research sites, women had 14% higher local functional connectivity density (lFCD) and up to 5% higher gray matter density than men in cortical and subcortical regions. The negative power scaling of the lFCD was steeper for men...
Versatile Density Functionals for Computational Surface Science
DEFF Research Database (Denmark)
Wellendorff, Jess
Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy-to-computational c......Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy...... resampling techniques, thereby systematically avoiding problems with overfitting. The first ever density functional presenting both reliable accuracy and convincing error estimation is generated. The methodology is general enough to be applied to more complex functional forms with higher-dimensional fitting...
A molecular density functional theory to study solvation in water
Jeanmairet, Guillaume
2014-01-01
A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...
Choosing a density functional for static molecular polarizabilities
Wu, Taozhe; Thakkar, Ajit J
2015-01-01
Coupled-cluster calculations of static electronic dipole polarizabilities for 145 organic molecules are performed to create a reference data set. The molecules are composed from carbon, hydrogen, nitrogen, oxygen, fluorine, sulfur, chlorine, and bromine atoms. They range in size from triatomics to 14 atoms. The Hartree-Fock and 2nd-order M{\\o}ller-Plesset methods and 34 density functionals, including local functionals, global hybrid functionals, and range-separated functionals of the long-range-corrected and screened-exchange varieties, are tested against this data set. On the basis of the test results, detailed recommendations are made for selecting density functionals for polarizability computations on relatively small organic molecules.
Noncovalent Interactions in Density-Functional Theory
DiLabio, Gino A
2014-01-01
Non-covalent interactions are essential in the description of soft matter, including materials of technological importance and biological molecules. In density-functional theory, common approaches fail to describe dispersion forces, an essential component in noncovalent binding interactions. In the last decade, great progress has been made in the development of accurate and computationally-efficient methods to describe noncovalently bound systems within the framework of density-functional theory. In this review, we give an account of the field from a chemical and didactic perspective, describing different approaches to the calculation of dispersion energies and comparing their accuracy, complexity, popularity, and general availability. This review should be useful to the newcomer who wants to learn more about noncovalent interactions and the different methods available at present to describe them using density-functional theory.
Nucleon localization within nuclear density functional theory
Zhang, Chunli; Schuetrumpf, Bastian; Nazarewicz, Witold
2016-09-01
Recently, a nucleon localization measure based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic density, the nucleon localization function (NLF) has been shown to be an excellent indicator of cluster correlations. To investigate the cluster structures in light nuclei and study the development of fission fragments in heavy nuclei, we analyse NLFs in deformed nuclei. We use both the deformed harmonic oscillator model and self-consistent nuclear density functional theory (DFT) with energy density functionals UNEDF1 and UNEDF1-HFB, which were optimized for fission studies. In this contribution, we will discuss particle densities and spatial localization functions for deformed configurations of 8Be and 20Ne and along fission pathways of 232Th and 240Pu. We illustrate the usefulness of the NLF by showing how the third hyperdeformed minimum of 232Th can be understood in terms of the ground states of 132Sn and 100Zr. This material is based upon work supported by the U.S. Department of Energy, Office of Science under Award Numbers DOE-DE-NA0002847, DE-SC0013365 (Michigan State University), and DE-SC0008511 (NUCLEI SciDAC-3 collaboration).
Density functional study of the electric double layer formed by a high density electrolyte.
Henderson, Douglas; Lamperski, Stanisław; Jin, Zhehui; Wu, Jianzhong
2011-11-10
We use a classical density functional theory (DFT) to study the electric double layer formed by charged hard spheres near a planar charged surface. The DFT predictions are found to be in good agreement with recent computer simulation results. We study the capacitance of the charged hard-sphere system at a range of densities and surface charges and find that the capacitance exhibits a local minimum at low ionic densities and small electrode charge. Although this charging behavior is typical for an aqueous electrolyte solution, the local minimum gradually turns into a maximum as the density of the hard spheres increases. Charged hard spheres at high density provide a reasonable first approximation for ionic liquids. In agreement with experiment, the capacitance of this model ionic liquid double layer has a maximum at small electrode charge density.
Dynamical density functional theory for microswimmers
Menzel, Andreas M.; Saha, Arnab; Hoell, Christian; Löwen, Hartmut
2016-01-01
Dynamical density functional theory (DDFT) has been successfully derived and applied to describe on one hand passive colloidal suspensions, including hydrodynamic interactions between individual particles. On the other hand, active "dry" crowds of self-propelled particles have been characterized using DDFT. Here, we go one essential step further and combine these two approaches. We establish a DDFT for active microswimmer suspensions. For this purpose, simple minimal model microswimmers are introduced. These microswimmers self-propel by setting the surrounding fluid into motion. They hydrodynamically interact with each other through their actively self-induced fluid flows and via the common "passive" hydrodynamic interactions. An effective soft steric repulsion is also taken into account. We derive the DDFT starting from common statistical approaches. Our DDFT is then tested and applied by characterizing a suspension of microswimmers, the motion of which is restricted to a plane within a three-dimensional bulk fluid. Moreover, the swimmers are confined by a radially symmetric trapping potential. In certain parameter ranges, we find rotational symmetry breaking in combination with the formation of a "hydrodynamic pumping state," which has previously been observed in the literature as a result of particle-based simulations. An additional instability of this pumping state is revealed.
Kohn-Sham density functional inspired approach to nuclear binding
Energy Technology Data Exchange (ETDEWEB)
Baldo, M. [Instituto Nazionale di Fisica Nucleare, Sezione di Catania Via Santa Sofia 64, I-95123 Catania (Italy); Schuck, P. [Institut de Physique Nucleaire, CNRS, UMR8608, Orsay F-91406 (France); Universite Paris-Sud, Orsay F-91505 (France); Vinas, X. [Departament d' Estructura i Constituents de la Materia, Universitat de Barcelona, Av. Diagonal 647, E-08028 Barcelona (Spain)], E-mail: xavier@ecm.ub.es
2008-06-05
A non-relativistic nuclear density functional theory is constructed, not as done most of the time, from an effective density dependent nucleon-nucleon force but directly introducing in the functional results from microscopic nuclear and neutron matter Bruckner G-matrix calculations at various densities. A purely phenomenological finite range part to account for surface properties is added. The striking result is that only four to five adjustable parameters, spin-orbit included, suffice to reproduce nuclear binding energies and radii with the same quality as obtained with the most performant effective forces. In this pilot work, for the pairing correlations, simply a density dependent zero range force is adopted from the literature. Possible future extensions of this approach are pointed out.
Communication: Embedded fragment stochastic density functional theory
Energy Technology Data Exchange (ETDEWEB)
Neuhauser, Daniel, E-mail: dxn@chem.ucla.edu [Department of Chemistry, University of California at Los Angeles, Los Angeles, California 90095 (United States); Baer, Roi, E-mail: roi.baer@huji.ac.il [Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Rabani, Eran, E-mail: eran.rabani@gmail.com [School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)
2014-07-28
We develop a method in which the electronic densities of small fragments determined by Kohn-Sham density functional theory (DFT) are embedded using stochastic DFT to form the exact density of the full system. The new method preserves the scaling and the simplicity of the stochastic DFT but cures the slow convergence that occurs when weakly coupled subsystems are treated. It overcomes the spurious charge fluctuations that impair the applications of the original stochastic DFT approach. We demonstrate the new approach on a fullerene dimer and on clusters of water molecules and show that the density of states and the total energy can be accurately described with a relatively small number of stochastic orbitals.
Radiative Strength Functions and Level Densities
Energy Technology Data Exchange (ETDEWEB)
Schiller, A; Becker, J A; Bernstein, L A; Voinov, A; Guttormsen, M; Hjorth-Jensen, M; Rekstad, J; Siem, S; Mitchell, G E; Tavukcu, E
2002-08-28
Radiative strength functions and level densities have been extracted from primary {gamma}-ray spectra for {sup 27,28}Si, {sup 56,57}Fe, {sup 96,97}Mo, and several rare earth nuclei. An unexpectedly strong ({approx} 1 mb MeV) resonance at 3 MeV in the radiative strength function has been observed for well-deformed rare earth nuclei. The physical origin of this resonance and its connection to the scissors mode is discussed.
Synthesis, Crystal Structure, Density Function Theory, Molecular ...
African Journals Online (AJOL)
Conclusion: The test compound has a moderate antimicrobial activity and the optimized molecular structure of the studied compound using B3LYP/6-31G (d,p) method showed good agreement with the reported x-ray structure. Keywords: Isoindoline-1, 3-dione, X-ray analysis, Density function theory, Antimicrobial, Molecular ...
Chemical hardness and density functional theory
Indian Academy of Sciences (India)
Keywords. Hardness; softness; hard & soft acids bases (HSAB); principle of maximum hardness (PMH) density functional theory (DFT). Abstract. The concept of chemical hardness is reviewed from a personal point of view. Author Affiliations. Ralph G Pearson1. Chemistry Department, University of California, Santa Barbara, ...
Density Functional Simulation of a Breaking Nanowire
DEFF Research Database (Denmark)
Nakamura, A.; Brandbyge, Mads; Hansen, Lars Bruno
1999-01-01
We study the deformation and breaking of an atomic-sized sodium wire using density functional simulations. The wire deforms through sudden atomic rearrangements and smoother atomic displacements. The conductance of the wire exhibits plateaus at integer values in units of 2e(2)/h corresponding...
A DENSITY FUNCTIONAL THEORY STUDY OF SUBSTITUTED ...
African Journals Online (AJOL)
Preferred Customer
Key words/phrases: Bridged oligothiophenes, density functional theory, low band gap oligomers, ... theoretical viewpoint, polythiophene has become subject of ..... Solar Ener.Mater. Solar Cells. 84:315–328. 31. Onoda, M., Kato, Y., Shonaka, H. and Tada, K. (2004). Artificial muscle using conducting polymers. Elect. Engin.
Density functional and neural network analysis
DEFF Research Database (Denmark)
Jalkanen, K. J.; Suhai, S.; Bohr, Henrik
1997-01-01
Density functional theory (DFT) calculations have been carried out for hydrated L-alanine, L-alanyl-L-alanine and N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA) and vibrational circular...
Synthesis, characterization and density functional theory ...
African Journals Online (AJOL)
We synthesized a number of aniline derivatives containing acyl groups to compare their barriers of rotation around the N-CO groups. Geometry optimization for all the rotamers have been performed using density functional theory (DFT) at the B3LYP/6-31G** level of theory. For each stationary point we carried out vibrational ...
Energy Technology Data Exchange (ETDEWEB)
Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)
2012-02-15
The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Reproducibility in density functional theory calculations of solids
DEFF Research Database (Denmark)
Lejaeghere, Kurt; Bihlmayer, Gustav; Björkman, Torbjörn
2016-01-01
The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We...
Buckled graphene: A model study based on density functional theory
Khan, M. A.; Mukaddam, M. A.; Schwingenschlögl, U.
2010-09-01
We make use of ab initio calculations within density functional theory to investigate the influence of buckling on the electronic structure of single layer graphene. Our systematic study addresses a wide range of bond length and bond angle variations in order to obtain insights into the energy scale associated with the formation of ripples in a graphene sheet.
Reproducibility in density functional theory calculations of solids
DEFF Research Database (Denmark)
Lejaeghere, Kurt; Bihlmayer, Gustav; Björkman, Torbjörn
2016-01-01
The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We r...
Joint product numerical range and geometry of reduced density matrices
Chen, Jianxin; Guo, Cheng; Ji, Zhengfeng; Poon, Yiu-Tung; Yu, Nengkun; Zeng, Bei; Zhou, Jie
2016-01-01
The reduced density matrices of a many-body quantum system form a convex set, whose three-dimensional projection $\\Theta$ is convex in $\\mathbb{R}^3$. The boundary $\\partial\\Theta$ of $\\Theta$ may exhibit nontrivial geometry, in particular ruled surfaces. Two physical mechanisms are known for the origins of ruled surfaces: symmetry breaking and gapless. In this work, we study the emergence of ruled surfaces for systems with local Hamiltonians in infinite spatial dimension, where the reduced d...
Electronic Structure of Matter Wave Functions and Density Functionals.
Kohn, W
1999-01-01
Since the 1920's Schroedinger wave functions have been the principal theoretical concept for understanding and computing the electronic structure of matter. More recently, Density Functional Theory (DFT), couched in terms of the electronic density distribution, n(r), has provided a new perspective and new computational possibilities, especially for systems consisting of very many (up to ~1000) atoms. In this talk some fundamental limitations of wave function methods for very-many-atom-systems will be discussed. The DFT approach will be explained together with some physical/chemical applications and a discussion of its strenghts and weaknesses.
Safarov, M. M.; Abdukhamidova, Z.
1995-09-01
We present the results from an experimental investigation of the density of the sunflower oil system as a function of the mass concentration of n-hexane in the ranges of temperatures T=290 520 K and pressures P=0.101 98.1 MPa. A method of hydrostatic weighing was used to measure the density of the solutions under study.
Extended screened exchange functional derived from transcorrelated density functional theory
Umezawa, Naoto
2017-09-01
We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, HTC, is introduced by a similarity transformation of a many-body Hamiltonian, H , with respect to a complex function F: HTC=1/F H F . It is proved that an expectation value of HTC for a normalized single Slater determinant, Dn, corresponds to the total energy: E [n ] = ⟨Ψn|H |Ψn ⟩ /⟨Ψn|Ψn ⟩ = ⟨Dn|HTC|Dn ⟩ under the two assumptions: (1) The electron density n (r ) associated with a trial wave function Ψn = DnF is v -representable and (2) Ψn and Dn give rise to the same electron density n (r ). This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H- ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.
A density functional for liquid [sup 3]He
Energy Technology Data Exchange (ETDEWEB)
Barranco, M. (Dept. de Estructura y Constituyentes de la Materia, Barcelona Univ. (Spain)); Jezek, D.M. (Dept. de Estructura y Constituyentes de la Materia, Barcelona Univ. (Spain)); Hernandez, E.S. (Dept. de Fisica, Univ. de Buenos Aires (Argentina)); Navarro, J. (Dept. de Fisica Atomica, Molecular y Nuclear, Valencia Univ. (Spain)); Serra, Ll. (Dipt. di Fisica, Milan Univ. (Italy))
1993-11-01
We present a density functional for the description of liquid [sup 3]He properties at zero temperture in a mean field approximation. Its basic ingredients are a zero-range, particle- and spin-density dependent effective interaction of Skyrme type, and a long-range effective interaction of Lennard-Jones type supplemented with a weighted density approximation similar to the one used in the study of classical fluids, to phenomenologically account for short range correlations. After fixing the value of its parameters, the functional yields a good desription of the equation of state and Landau parameters (spin symmetric and spin antisymmetric as well) from saturation to solidification densities. The zero sound propagation at finite momentum transfer is quantitatively reproduced up to the Fermi momentum, and qualitatively above it. The surface tension is in agreement with experiment, which makes the functional well suited for [sup 3]He drop calculations. We describe the structure of drops made of up to 516 atoms. As a novel application, we discuss the possible appearance of triplet pairing in a nl-shell of a drop applying the formalism to the 1j-shell holding up to 30 atoms from N=169 to 198. (orig.)
Covariant density functional theory for nuclear matter
Energy Technology Data Exchange (ETDEWEB)
Badarch, U.
2007-07-01
The present thesis is organized as follows. In Chapter 2 we study the Nucleon-Nucleon (NN) interaction in Dirac-Brueckner (DB) approach. We start by considering the NN interaction in free-space in terms of the Bethe-Salpeter (BS) equation to the meson exchange potential model. Then we present the DB approach for nuclear matter by extending the BS equation for the in-medium NN interaction. From the solution of the three-dimensional in-medium BS equation, we derive the DB self-energies and total binding energy which are the main results of the DB approach, which we later incorporate in the field theoretical calculation of the nuclear equation of state. In Chapter 3, we introduce the basic concepts of density functional theory in the context of Quantum Hadrodynamics (QHD-I). We reach the main point of this work in Chapter 4 where we introduce the DDRH approach. In the DDRH theory, the medium dependence of the meson-nucleon vertices is expressed as functionals of the baryon field operators. Because of the complexities of the operator-valued functionals we decide to use the mean-field approximation. In Chapter 5, we contrast microscopic and phenomenological approaches to extracting density dependent meson-baryon vertices. Chapter 6 gives the results of our studies of the EOS of infinite nuclear matter in detail. Using formulas derived in Chapters 4 and 5 we calculate the properties of symmetric and asymmetric nuclear matter and pure neutron matter. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Mattsson, Ann Elisabet; Modine, Normand Arthur; Desjarlais, Michael Paul; Muller, Richard Partain; Sears, Mark P.; Wright, Alan Francis
2006-11-01
A finite temperature version of 'exact-exchange' density functional theory (EXX) has been implemented in Sandia's Socorro code. The method uses the optimized effective potential (OEP) formalism and an efficient gradient-based iterative minimization of the energy. The derivation of the gradient is based on the density matrix, simplifying the extension to finite temperatures. A stand-alone all-electron exact-exchange capability has been developed for testing exact exchange and compatible correlation functionals on small systems. Calculations of eigenvalues for the helium atom, beryllium atom, and the hydrogen molecule are reported, showing excellent agreement with highly converged quantumMonte Carlo calculations. Several approaches to the generation of pseudopotentials for use in EXX calculations have been examined and are discussed. The difficult problem of finding a correlation functional compatible with EXX has been studied and some initial findings are reported.
Modulation Based on Probability Density Functions
Williams, Glenn L.
2009-01-01
A proposed method of modulating a sinusoidal carrier signal to convey digital information involves the use of histograms representing probability density functions (PDFs) that characterize samples of the signal waveform. The method is based partly on the observation that when a waveform is sampled (whether by analog or digital means) over a time interval at least as long as one half cycle of the waveform, the samples can be sorted by frequency of occurrence, thereby constructing a histogram representing a PDF of the waveform during that time interval.
Symmetry energy in nuclear density functional theory
Energy Technology Data Exchange (ETDEWEB)
Nazarewicz, W. [University of Tennessee Knoxville, Department of Physics and Astronomy, Knoxville, Tennessee (United States); Oak Ridge National Laboratory, Oak Ridge, Tennessee (United States); University of Warsaw, Faculty of Physics, Warsaw (Poland); Reinhard, P.G. [Universitaet Erlangen/Nuernberg, Institut fuer Theoretische Physik, Erlangen (Germany); Satula, W. [University of Warsaw, Faculty of Physics, Warsaw (Poland); Vretenar, D. [University of Zagreb, Physics Department, Faculty of Science, Zagreb (Croatia)
2014-02-15
The nuclear symmetry energy represents a response to the neutron-proton asymmetry. In this paper we discuss various aspects of symmetry energy in the framework of nuclear density functional theory, considering both non-relativistic and relativistic self-consistent mean-field realizations side by side. Key observables pertaining to bulk nucleonic matter and finite nuclei are reviewed. Constraints on the symmetry energy and correlations between observables and symmetry energy parameters, using statistical covariance analysis, are investigated. Perspectives for future work are outlined in the context of ongoing experimental efforts. (orig.)
Campbell, D L M; Hinch, G N; Dyall, T R; Warin, L; Little, B A; Lee, C
2017-01-01
The number and size of free-range laying hen (Gallus gallus domesticus) production systems are increasing within Australia in response to consumer demand for perceived improvement in hen welfare. However, variation in outdoor stocking density has generated consumer dissatisfaction leading to the development of a national information standard on free-range egg labelling by the Australian Consumer Affairs Ministers. The current Australian Model Code of Practice for Domestic Poultry states a guideline of 1500 hens/ha, but no maximum density is set. Radio-frequency identification (RFID) tracking technology was used to measure daily range usage by individual ISA Brown hens housed in six small flocks (150 hens/flock - 50% of hens tagged), each with access to one of three outdoor stocking density treatments (two replicates per treatment: 2000, 10 000, 20 000 hens/ha), from 22 to 26, 27 to 31 and 32 to 36 weeks of age. There was some variation in range usage across the sampling periods and by weeks 32 to 36 individual hens from the lowest stocking density on average used the range for longer each day (Paccessed the range with 2% of tagged hens in each treatment never venturing outdoors and a large proportion that accessed the range daily (2000 hens/ha: 80.5%; 10 000 hens/ha: 66.5%; 20 000 hens/ha: 71.4%). On average, 38% to 48% of hens were seen on the range simultaneously and used all available areas of all ranges. These results of experimental-sized flocks have implications for determining optimal outdoor stocking densities for commercial free-range laying hens but further research would be needed to determine the effects of increased range usage on hen welfare.
Buckled graphene: A model study based on density functional theory
Khan, Yasser
2010-09-01
We make use of ab initio calculations within density functional theory to investigate the influence of buckling on the electronic structure of single layer graphene. Our systematic study addresses a wide range of bond length and bond angle variations in order to obtain insights into the energy scale associated with the formation of ripples in a graphene sheet. © 2010 Elsevier B.V. All rights reserved.
Renormalization group approach to density functional theory
Energy Technology Data Exchange (ETDEWEB)
Kemler, Sandra; Braun, Jens [Institut fuer Kernphysik, TU Darmstadt (Germany)
2015-07-01
We study a two-point particle irreducible (2PPI) approach to many-body physics which relies on a renormalization group (RG) flow equation for the associated effective action. This approach relates to Density Functional Theory and can in principle be used to study ground-state properties of non-relativistic many-body systems from microscopic interactions, such as (heavy) nuclei. We apply our formalism to a 0+1-dimensional model, namely the quantum anharmonic oscillator and use the well-known exact solution to benchmark our approximations of the full RG flow. Moreover, we present flow equations for specific types of 1+1-dimensional field theories which allow us study the ground-state properties of self-bound systems of spinless fermions which can also be viewed as toy models of nuclei.
Low larval densities in northern populations reinforce range expansion by a Mediterranean damselfly
DEFF Research Database (Denmark)
Therry, Lieven; Swaegers, Janne; Dinh, Khuong Van
2016-01-01
towards the very edge of the expansion front has been neglected. Density effects may, however, have a profound direct impact on traits involved in range expansion and influence range dynamics. 2. In this study, we contrast the effects of high conspecific larval density typical for established populations...... and low larval density typical for newly founded populations at the edge of the expansion front on a set of larval traits that may affect the range dynamics in the poleward moving damselfly Coenagrion scitulum. We therefore ran an outdoor mesocosm experiment with a low- and high-density treatment close...... in voltinism) at low conspecific density will translate in increased population growth rates. Furthermore, nutritional advantages at low conspecific density may increase investment in dispersal ability. Together, these direct and delayed density-dependent effects that gradually increase towards the expansion...
Building a Universal Nuclear Energy Density Functional
Energy Technology Data Exchange (ETDEWEB)
Carlson, Joe A. [Michigan State Univ., East Lansing, MI (United States); Furnstahl, Dick; Horoi, Mihai; Lust, Rusty; Nazaewicc, Witek; Ng, Esmond; Thompson, Ian; Vary, James
2012-12-30
During the period of Dec. 1 2006 – Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Orbital functionals in density-matrix- and current-density-functional theory
Energy Technology Data Exchange (ETDEWEB)
Helbig, N.
2006-05-15
Density-Functional Theory (DFT), although widely used and very successful in the calculation of several observables, fails to correctly describe strongly correlated materials. In the first part of this work we, therefore, introduce reduced-densitymatrix- functional theory (RDMFT) which is one possible way to treat electron correlation beyond DFT. Within this theory the one-body reduced density matrix (1- RDM) is used as the basic variable. Our main interest is the calculation of the fundamental gap which proves very problematic within DFT. In order to calculate the fundamental gap we generalize RDMFT to fractional particle numbers M by describing the system as an ensemble of an N and an N+1 particle system (with N{<=}M{<=}N+1). For each fixed particle number, M, the total energy is minimized with respect to the natural orbitals and their occupation numbers. This leads to the total energy as a function of M. The derivative of this function with respect to the particle number has a discontinuity at integer particle number which is identical to the gap. In addition, we investigate the necessary and sufficient conditions for the 1- RDM of a system with fractional particle number to be N-representable. Numerical results are presented for alkali atoms, small molecules, and periodic systems. Another problem within DFT is the description of non-relativistic many-electron systems in the presence of magnetic fields. It requires the paramagnetic current density and the spin magnetization to be used as basic variables besides the electron density. However, electron-gas-based functionals of current-spin-density-functional Theory (CSDFT) exhibit derivative discontinuities as a function of the magnetic field whenever a new Landau level is occupied, which makes them difficult to use in practice. Since the appearance of Landau levels is, intrinsically, an orbital effect it is appealing to use orbital-dependent functionals. We have developed a CSDFT version of the optimized
Outdoor stocking density in free-range laying hens: effects on behaviour and welfare.
Campbell, D L M; Hinch, G N; Downing, J A; Lee, C
2017-06-01
Free-range laying hen systems are increasing within Australia and research is needed to determine optimal outdoor stocking densities. Six small (n=150 hens) experimental flocks of ISA Brown laying hens were housed with access to ranges simulating one of three outdoor stocking densities with two pen replicates per density: 2000 hens/ha, 10 000 hens/ha or 20 000 hens/ha. Birds were provided daily range access from 21 to 36 weeks of age and the range usage of 50% of hens was tracked using radio-frequency identification technology. Throughout the study, basic external health assessments following a modified version of the Welfare Quality® protocol showed most birds were in visibly good condition (although keel damage was increasingly present with age) with few differences between stocking densities. Toenail length at 36 weeks of age was negatively correlated with hours spent ranging for all pens of birds (all r⩾-0.23, P⩽0.04). At 23 weeks of age, there were no differences between outdoor stocking densities in albumen corticosterone concentrations (P=0.44). At 35 weeks of age, density effects were significant (Pdensity showed the highest albumen corticosterone concentrations, although eggs from hens in the 10 000 hens/ha density showed the lowest concentrations (Pdensities showed the least foraging on the range but the most resting outdoors, with hens from the 20 000 hens/ha densities showing the least amount of resting outdoors (all Pdensities (P=0.08). For each of the health and behavioural measures there were differences between pen replicates within stocking densities. These data show outdoor stocking density has some effects on hen welfare, and it appears that consideration of both individual and group-level behaviour is necessary when developing optimal stocking density guidelines and free-range system management practices.
Density of wild prey modulates lynx kill rates on free-ranging domestic sheep.
Directory of Open Access Journals (Sweden)
John Odden
Full Text Available Understanding the factors shaping the dynamics of carnivore-livestock conflicts is vital to facilitate large carnivore conservation in multi-use landscapes. We investigated how the density of their main wild prey, roe deer Capreolus capreolus, modulates individual Eurasian lynx Lynx lynx kill rates on free-ranging domestic sheep Ovis aries across a range of sheep and roe deer densities. Lynx kill rates on free-ranging domestic sheep were collected in south-eastern Norway from 1995 to 2011 along a gradient of different livestock and wild prey densities using VHF and GPS telemetry. We used zero-inflated negative binomial (ZINB models including lynx sex, sheep density and an index of roe deer density as explanatory variables to model observed kill rates on sheep, and ranked the models based on their AICc values. The model including the effects of lynx sex and sheep density in the zero-inflation model and the effect of lynx sex and roe deer density in the negative binomial part received most support. Irrespective of sheep density and sex, we found the lowest sheep kill rates in areas with high densities of roe deer. As roe deer density decreased, males killed sheep at higher rates, and this pattern held for both high and low sheep densities. Similarly, females killed sheep at higher rates in areas with high densities of sheep and low densities of roe deer. However, when sheep densities were low females rarely killed sheep irrespective of roe deer density. Our quantification of depredation rates can be the first step towards establishing fairer compensation systems based on more accurate and area specific estimation of losses. This study demonstrates how we can use ecological theory to predict where losses of sheep will be greatest, and can be used to identify areas where mitigation measures are most likely to be needed.
Density of wild prey modulates lynx kill rates on free-ranging domestic sheep.
Odden, John; Nilsen, Erlend B; Linnell, John D C
2013-01-01
Understanding the factors shaping the dynamics of carnivore-livestock conflicts is vital to facilitate large carnivore conservation in multi-use landscapes. We investigated how the density of their main wild prey, roe deer Capreolus capreolus, modulates individual Eurasian lynx Lynx lynx kill rates on free-ranging domestic sheep Ovis aries across a range of sheep and roe deer densities. Lynx kill rates on free-ranging domestic sheep were collected in south-eastern Norway from 1995 to 2011 along a gradient of different livestock and wild prey densities using VHF and GPS telemetry. We used zero-inflated negative binomial (ZINB) models including lynx sex, sheep density and an index of roe deer density as explanatory variables to model observed kill rates on sheep, and ranked the models based on their AICc values. The model including the effects of lynx sex and sheep density in the zero-inflation model and the effect of lynx sex and roe deer density in the negative binomial part received most support. Irrespective of sheep density and sex, we found the lowest sheep kill rates in areas with high densities of roe deer. As roe deer density decreased, males killed sheep at higher rates, and this pattern held for both high and low sheep densities. Similarly, females killed sheep at higher rates in areas with high densities of sheep and low densities of roe deer. However, when sheep densities were low females rarely killed sheep irrespective of roe deer density. Our quantification of depredation rates can be the first step towards establishing fairer compensation systems based on more accurate and area specific estimation of losses. This study demonstrates how we can use ecological theory to predict where losses of sheep will be greatest, and can be used to identify areas where mitigation measures are most likely to be needed.
Bone mineral density, adiposity and cognitive functions
Directory of Open Access Journals (Sweden)
Hamid R Sohrabi
2015-02-01
Full Text Available Cognitive decline and dementia due to Alzheimer’s disease have been associated with genetic, lifestyle, and environmental factors. A number of potentially modifiable risk factors should be taken into account when preventive or ameliorative interventions targeting dementia and its preclinical stages are investigated. Bone mineral density (BMD and body composition are two such potentially modifiable risk factors, and their association with cognitive decline was investigated in this study. 164 participants, aged 34 to 87 years old (62.78±9.27, were recruited for this longitudinal study and underwent cognitive and clinical examinations at baseline and after three years. Blood samples were collected for apolipoprotein E (APOE genotyping and dual energy x-ray absorptiometry (DXA was conducted at the same day as cognitive assessment. Using hierarchical regression analysis, we found that BMD and lean body mass, as measured using DXA were significant predictors of episodic memory. Age, gender, APOE status and premorbid IQ were controlled for. Specifically, the List A learning from California Verbal Learning Test was significantly associated with BMD and lean mass both at baseline and at follow up assessment. Our findings indicate that there is a significant association between BMD and lean body mass and episodic verbal learning. While the involvement of modifiable lifestyle factors in human cognitive function has been examined in different studies, there is a need for further research to understand the potential underlying mechanisms.
Density functional theory and multiscale materials modeling
Indian Academy of Sciences (India)
One of the vital ingredients in the theoretical tools useful in materials modeling at all the length scales of interest is the concept of density. In the microscopic length scale, it is the electron density that has played a major role in providing a deeper understanding of chemical binding in atoms, molecules and solids.
Graphene on metals: A van der Waals density functional study
DEFF Research Database (Denmark)
Vanin, Marco; Mortensen, Jens Jørgen; Kelkkanen, Kari André
2010-01-01
We use density functional theory (DFT) with a recently developed van der Waals density functional (vdW-DF) to study the adsorption of graphene on Co, Ni, Pd, Ag, Au, Cu, Pt, and Al(111) surfaces. In contrast to the local-density approximation (LDA) which predicts relatively strong binding for Ni...
Synthesis, Crystal Structure, Density Function Theory, Molecular ...
African Journals Online (AJOL)
isoindoline-1,3-dione, was characterized by proton nuclear magnetic resonance spectroscopy (NMR) and single crystal x-ray diffraction method. The target compound was tested for its antimicrobial activities and computational studies including density ...
Dynamic density functional theory of solid tumor growth: Preliminary models
Directory of Open Access Journals (Sweden)
Arnaud Chauviere
2012-03-01
Full Text Available Cancer is a disease that can be seen as a complex system whose dynamics and growth result from nonlinear processes coupled across wide ranges of spatio-temporal scales. The current mathematical modeling literature addresses issues at various scales but the development of theoretical methodologies capable of bridging gaps across scales needs further study. We present a new theoretical framework based on Dynamic Density Functional Theory (DDFT extended, for the first time, to the dynamics of living tissues by accounting for cell density correlations, different cell types, phenotypes and cell birth/death processes, in order to provide a biophysically consistent description of processes across the scales. We present an application of this approach to tumor growth.
What Density Functional Theory could do for Quantum Information
Mattsson, Ann
2015-03-01
The Hohenberg-Kohn theorem of Density Functional Theory (DFT), and extensions thereof, tells us that all properties of a system of electrons can be determined through their density, which uniquely determines the many-body wave-function. Given access to the appropriate, universal, functionals of the density we would, in theory, be able to determine all observables of any electronic system, without explicit reference to the wave-function. On the other hand, the wave-function is at the core of Quantum Information (QI), with the wave-function of a set of qubits being the central computational resource in a quantum computer. While there is seemingly little overlap between DFT and QI, reliance upon observables form a key connection. Though the time-evolution of the wave-function and associated phase information is fundamental to quantum computation, the initial and final states of a quantum computer are characterized by observables of the system. While observables can be extracted directly from a system's wave-function, DFT tells us that we may be able to intuit a method for extracting them from its density. In this talk, I will review the fundamentals of DFT and how these principles connect to the world of QI. This will range from DFT's utility in the engineering of physical qubits, to the possibility of using it to efficiently (but approximately) simulate Hamiltonians at the logical level. The apparent paradox of describing algorithms based on the quantum mechanical many-body wave-function with a DFT-like theory based on observables will remain a focus throughout. The ultimate goal of this talk is to initiate a dialog about what DFT could do for QI, in theory and in practice. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Home range and density of three sympatric felids in the Southern Atlantic Forest, Brazil.
Kasper, C B; Schneider, A; Oliveira, T G
2016-02-01
Home range and minimal population densities of Southern tiger cat (Leopardus guttulus), margay (Lepardus wiedii) and jaguarundi (Puma yagouaroundi) were estimated between 2005 and 2006 in Taquari Valley, near the southern edge of the Atlantic Rainforest in Brazil. Home range data were collected by conventional radio telemetry (VHF) locations in a highly fragmented landscape. The average home range size, calculated using 95% kernel density estimates, was 16.01 km2 for Southern tiger cat, 21.85 km2 for margay and 51.45 km2 for jaguarundi. Telemetry data were used to obtain minimal density estimates of 0.08 Southern tiger cats / km2, and 0.04 jaguarundi / km2. The density estimates arise from areas where ocelot (Leopardus pardalis) and other larger-bodied carnivores were locally extinct, and they suggest a specific type of mesopredator release known as the ocelot effect, which is likely enabling the increase in smaller felid populations in this area.
Bioinorganic Chemistry Modeled with the TPSSh Density Functional
DEFF Research Database (Denmark)
Kepp, Kasper Planeta
2008-01-01
In this work, the TPSSh density functional has been benchmarked against a test set of experimental structures and bond energies for 80 transition-metal-containing diatomics. It is found that the TPSSh functional gives structures of the same quality as other commonly used hybrid and nonhybrid func...... promising density functional for use and further development within the field of bioinorganic chemistry....
Image potential states from the van der Waals density functional.
Hamada, Ikutaro; Hamamoto, Yuji; Morikawa, Yoshitada
2017-07-28
The image potential state is one of the fundamental surface electronic states and has a great relevance to many surface phenomena, but its accurate description is a great challenge for the semilocal density functional. Here, we use the nonlocal van der Waals density functional to describe the image potential states of graphene, graphite, and carbon nanotubes. We found that although it does not yield the correct image potential outside the surface, the van der Waals density functional improves the description of image potential states because of the nonlocal correlation potential. Our study demonstrates the usefulness of the van der Waals density functional to study the surface electronic properties.
Charge transfer in time-dependent density functional theory
Maitra, Neepa T.
2017-10-01
Charge transfer plays a crucial role in many processes of interest in physics, chemistry, and bio-chemistry. In many applications the size of the systems involved calls for time-dependent density functional theory (TDDFT) to be used in their computational modeling, due to its unprecedented balance between accuracy and efficiency. However, although exact in principle, in practise approximations must be made for the exchange-correlation functional in this theory, and the standard functional approximations perform poorly for excitations which have a long-range charge-transfer component. Intense progress has been made in developing more sophisticated functionals for this problem, which we review. We point out an essential difference between the properties of the exchange-correlation kernel needed for an accurate description of charge-transfer between open-shell fragments and between closed-shell fragments. We then turn to charge-transfer dynamics, which, in contrast to the excitation problem, is a highly non-equilibrium, non-perturbative, process involving a transfer of one full electron in space. This turns out to be a much more challenging problem for TDDFT functionals. We describe dynamical step and peak features in the exact functional evolving over time, that are missing in the functionals currently used. The latter underestimate the amount of charge transferred and manifest a spurious shift in the charge transfer resonance position. We discuss some explicit examples.
A Density Functional with Spherical Atom Dispersion Terms.
Austin, Amy; Petersson, George A; Frisch, Michael J; Dobek, Frank J; Scalmani, Giovanni; Throssell, Kyle
2012-12-11
A new hybrid density functional, APF, is introduced, which avoids the spurious long-range attractive or repulsive interactions that are found in most density functional theory (DFT) models. It therefore provides a sound baseline for the addition of an empirical dispersion correction term, which is developed from a spherical atom model (SAM). The APF-D empirical dispersion model contains nine adjustable parameters that were selected based on a very small training set (15 noble gas dimers and 4 small hydrocarbon dimers), along with two computed atomic properties (ionization potential and effective atomic polarizability) for each element. APF-D accurately describes a large portion of the potential energy surfaces of complexes of noble gas atoms with various diatomic molecules involving a wide range of elements and of dimers of small hydrocarbons, and it reproduces the relative conformational energies of organic molecules. The accuracy for these weak interactions is comparable to that of CCSD(T)/aug-cc-pVTZ calculations. The accuracy in predicting the geometry of hydrogen bond complexes is competitive with other models involving DFT and empirical dispersion.
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution
Shahmoradi, Amir
2015-01-01
What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of individual residues. Most importantly, there has been disagreement in the literature over the relative importance of solvent accessibility and local packing density for explaining site-specific sequence variability in proteins. We show here that this discussion has been confounded by the definition of local packing density. The most commonly used measures of local packing, such as the contact number and the weighted contact number, represent by definition the combined effects of local packing density and longer-range effects. As an alternative, we here propose a truly local measure of packing density around a single residue, based on the Voronoi cell volume. We show that the Voronoi cell volume, when calculated relative to the geometric center of amino-acid side chains, be...
Bone mineral density and menstrual function in adolescent female ...
African Journals Online (AJOL)
Bone mineral density and menstrual function in adolescent female long-distance runners - A prospective comparative study of bone structure and menstrual function in adolescent female endurance athletes from five secondary schools in Pretoria.
Density-dependent home-range size revealed by spatially explicit capture–recapture
Efford, M.G.; Dawson, Deanna K.; Jhala, Y.V.; Qureshi, Q.
2016-01-01
The size of animal home ranges often varies inversely with population density among populations of a species. This fact has implications for population monitoring using spatially explicit capture–recapture (SECR) models, in which both the scale of home-range movements σ and population density D usually appear as parameters, and both may vary among populations. It will often be appropriate to model a structural relationship between population-specific values of these parameters, rather than to assume independence. We suggest re-parameterizing the SECR model using kp = σp √Dp, where kp relates to the degree of overlap between home ranges and the subscript p distinguishes populations. We observe that kp is often nearly constant for populations spanning a range of densities. This justifies fitting a model in which the separate kp are replaced by the single parameter k and σp is a density-dependent derived parameter. Continuous density-dependent spatial variation in σ may also be modelled, using a scaled non-Euclidean distance between detectors and the locations of animals. We illustrate these methods with data from automatic photography of tigers (Panthera tigris) across India, in which the variation is among populations, from mist-netting of ovenbirds (Seiurus aurocapilla) in Maryland, USA, in which the variation is within a single population over time, and from live-trapping of brushtail possums (Trichosurus vulpecula) in New Zealand, modelling spatial variation within one population. Possible applications and limitations of the methods are discussed. A model in which kp is constant, while density varies, provides a parsimonious null model for SECR. The parameter k of the null model is a concise summary of the empirical relationship between home-range size and density that is useful in comparative studies. We expect deviations from this model, particularly the dependence of kp on covariates, to be biologically interesting.
Density functional theory study of vibrational spectra, and ...
Indian Academy of Sciences (India)
WINTEC
315. *For correspondence. Density functional theory study of vibrational spectra, and assignment of fundamental modes of ... FTIR; FT-Raman; density functional theory; dacarbazine. 1. Introduction. Dacarbazine, used as antineoplastic in ...... molecules (London: Chapman and Hall) vol 2. 18. Wiberg K B and Sharke A 1973 ...
Introduction to Classical Density Functional Theory by a Computational Experiment
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2014-01-01
We propose an in silico experiment to introduce the classical density functional theory (cDFT). Density functional theories, whether quantum or classical, rely on abstract concepts that are nonintuitive; however, they are at the heart of powerful tools and active fields of research in both physics and chemistry. They led to the 1998 Nobel Prize in…
Testing one-body density functionals on a solvable model
Benavides-Riveros, Carlos L
2012-01-01
There are several physically motivated density matrix functionals in the literature, built from the knowledge of the natural orbitals and the occupation numbers of the one-body reduced density matrix. With the help of the equivalent phase-space formalism, we thoroughly test some of the most popular of those functionals on a completely solvable model.
Testing one-body density functionals on a solvable model
Benavides-Riveros, C. L.; Várilly, J. C.
2012-10-01
There are several physically motivated density matrix functionals in the literature, built from the knowledge of the natural orbitals and the occupation numbers of the one-body reduced density matrix. With the help of the equivalent phase-space formalism, we thoroughly test some of the most popular of those functionals on a completely solvable model.
Asymptotic Theory for the Probability Density Functions in Burgers Turbulence
Weinan, E; Eijnden, Eric Vanden
1999-01-01
A rigorous study is carried out for the randomly forced Burgers equation in the inviscid limit. No closure approximations are made. Instead the probability density functions of velocity and velocity gradient are related to the statistics of quantities defined along the shocks. This method allows one to compute the anomalies, as well as asymptotics for the structure functions and the probability density functions. It is shown that the left tail for the probability density function of the velocity gradient has to decay faster than $|\\xi|^{-3}$. A further argument confirms the prediction of E et al., Phys. Rev. Lett. {\\bf 78}, 1904 (1997), that it should decay as $|\\xi|^{-7/2}$.
The probability density function of completed length of service (CLS ...
African Journals Online (AJOL)
By investigating the existing relationships between the probability density function of CLS distribution and some other wastage functions this paper estimates the functions for some secondary schools in Enugu State. Wastage probabilities are calculated, survivor functions estimated. The accompanying standard errors are ...
Local Covariance Functions and Density Distributions.
1984-06-01
function K(oR) will be virtually zero for large distances. We may therefore approximate sin 1, and obtain : 2Jz +1=P± f ’ K(,R) P (cos 4)do (2.30) - 2 0 The...Moritz, H.: Advanced physical geodesy. Herbert Wichman Verlag, Karlsruhe, 1980. - Nash, R.A. and S.K. Jordan: Statistical geodesy - an engineering
Avoiding self-repulsion in density functional description of biased molecular junctions
Energy Technology Data Exchange (ETDEWEB)
Baer, Roi [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: roi.baer@huji.ac.il; Livshits, Ester [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Neuhauser, Daniel [Department of Physical Chemistry and Lise Meitner Minerva-Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: dxn@chem.ucla.edu
2006-10-26
We examine the effects of self-repulsion on the predictions of charge distribution in biased molecular junctions by the local density functional theory methods. This is done using a functional with explicit long-range exchange term effects [R. Baer, D. Neuhauser, Phys. Rev. Lett. 94 (2005) 043002]. We discuss in detail the new density functional, pointing out some of the remaining difficulties in the theory. We find that in weakly coupled junctions (the typical molecular electronics case) local-density functionals fail to describe correctly the charge distribution in the intermediate bias regime.
Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura
2015-08-11
The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.
The Ionization Constant of Water over Wide Ranges of Temperature and Density
Bandura, Andrei V.; Lvov, Serguei N.
2006-03-01
A semitheoretical approach for the ionization constant of water, KW, is used to fit the available experimental data over wide ranges of density and temperature. Statistical thermodynamics is employed to formulate a number of contributions to the standard state chemical potential of the ionic hydration process. A sorption model is developed for calculating the inner-shell term, which accounts for the ion-water interactions in the immediate ion vicinity. A new analytical expression is derived using the Bragg-Williams approximation that reproduces the dependence of a mean ion solvation number on the solvent chemical potential. The proposed model was found to be correct at the zero-density limit. The final formulation has a simple analytical form, includes seven adjustable parameters, and provides good fitting of the collected KW data, within experimental uncertainties, for a temperature range of 0-800 °C and densities of 0-1.2 g cm-3.
Evaluating the impact of a wide range of vegetation densities on river channel pattern
Pattison, Ian; Roucou, Ron
2016-04-01
Braided rivers are very dynamic systems which have complex controls over their planform and flow dynamics. Vegetation is one variable which influences channel geometry and pattern, through its effect on local flow hydraulics and the process continuum of sediment erosion-transport-deposition. Furthermore, where in the braided floodplain stable vegetation develops depends on the temporal sequencing of the river discharge i.e. floods. Understanding the effect of vegetation in these highly dynamic systems has multiple consequences for human activity and floodplain management. This paper focusses on the specific role of vegetation density in controlling braided river form and processes. Previous research in this field has been contradictory; with Gran and Paola (2001) finding that increasing vegetation density decreased the number of active channels. In contrast, Coulthard (2005] observed that as vegetation become denser there was an increase in the number of channels. This was hypothesized to be caused by flow separation around vegetation and the development of bars immediately downstream of the plant. This paper reports the results from a set of experiments in a 4m by 1m flume, where discharge, slope and sediment size were kept constant. Artificial grass was used to represent vegetation with a density ranging from 50 plants/m2 to 400 plants/m2. Digital photographs, using a GoPro camera with a fish eye lens, were taken from ~1m above the flume at an interval of 30 seconds during the 3 hour experiment. The experiments showed that as the vegetation density increased from 50 to 150 plants/m2, the number of channel bars developing doubled from 12 to 24. At vegetation densities greater than 150 plants/m2 there was a decline in the number of bars created to a minimum of 8 bars for a density of 400 plants/m2. We attribute these patterns to the effect that the vegetation has on flow hydraulics, sediment transport processes and the spatial patterns of erosion and deposition. We
The Benchmark of Gutzwiller Density Functional Theory in Hydrogen Systems
Energy Technology Data Exchange (ETDEWEB)
Yao, Yongxin; Wang, Cai-Zhuang; Ho, Kai-Ming
2011-01-13
We propose an approximate form of the exchange-correlation energy functional for the Gutzwiller density functional theory. It satisfies certain physical constraints in both weak and strong electron correlation limits. We benchmark the Gutzwiller density functional approximation in the hydrogen systems, where the static correlation error is shown to be negligible. The good transferability is demonstrated by applications to the hydrogen molecule and some crystal structures. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
RANGE AND DENSITY OF ALIEN FISH IN WESTERN STREAMS AND RIVERS, US
Alien fish have become increasingly prevalent in Western U.S. waters. The EPA Environmental Monitoring and Assessment Program's Western Pilot (12 western states), which is based upon a probabilistic design, provides an opportunity to make inferences about the range and density of...
Energy Densities in the Strong-Interaction Limit of Density Functional Theory
Mirtschink, A.; Seidl, M.; Gori Giorgi, P.
2012-01-01
We discuss energy densities in the strong-interaction limit of density functional theory, deriving an exact expression within the definition (gauge) of the electrostatic potential of the exchange-correlation hole. Exact results for small atoms and small model quantum dots (Hooke's atoms) are
Home range and density of three sympatric felids in the Southern Atlantic Forest, Brazil
Directory of Open Access Journals (Sweden)
C. B. Kasper
Full Text Available Abstract Home range and minimal population densities of Southern tiger cat (Leopardus guttulus, margay (Lepardus wiedii and jaguarundi (Puma yagouaroundi were estimated between 2005 and 2006 in Taquari Valley, near the southern edge of the Atlantic Rainforest in Brazil. Home range data were collected by conventional radio telemetry (VHF locations in a highly fragmented landscape. The average home range size, calculated using 95% kernel density estimates, was 16.01 km2 for Southern tiger cat, 21.85 km2 for margay and 51.45 km2 for jaguarundi. Telemetry data were used to obtain minimal density estimates of 0.08 Southern tiger cats / km2, and 0.04 jaguarundi / km2. The density estimates arise from areas where ocelot (Leopardus pardalis and other larger-bodied carnivores were locally extinct, and they suggest a specific type of mesopredator release known as the ocelot effect, which is likely enabling the increase in smaller felid populations in this area.
Bond energy decomposition analysis for subsystem density functional theory
Beyhan, S.M.; Gotz, A.W.; Visscher, L.
2013-01-01
We employed an explicit expression for the dispersion (D) energy in conjunction with Kohn-Sham (KS) density functional theory and frozen-density embedding (FDE) to calculate interaction energies between DNA base pairs and a selected set of amino acid pairs in the hydrophobic core of a small protein
Energy dependence with the number of particles: Density and reduced density matrices functionals
Miranda-Quintana, Ramón A.; Bochicchio, Roberto C.
2014-02-01
The energy of a physical domain within a molecular system considered as a quantum open system is analyzed as a functional of the electron distribution dependence with the number of particles. Our attention is focused upon the constrained-search functionals of the electron density, the 1- and 2-reduced density matrices (1-, 2-RDMs) for grand-canonical states. It is shown that functionals of the 2-RDM depend on the number of particles if the ground state energy is not a convex function of them.
Making a happy match between orbital-free density functional theory and information energy density
Alipour, Mojtaba
2015-08-01
In the field of computational chemistry within density functional theory (DFT), the orbital-free DFT (OF-DFT) can be considered as a promising approach for simulating large systems. In OF-DFT, only a single relation, the Euler equation, has to be solved independently from the number of electrons. In this work, the Euler equation of OF-DFT is rewritten through a new partition scheme for energy density functional. Next, based on information theory, we reformulate the resulting equation in terms of Onicescu information energy density. Plus, the new forms of Euler equation based on Shannon entropy and Fisher information are presented.
Time-dependent quantum fluid density functional theory of hydrogen ...
Indian Academy of Sciences (India)
WINTEC
GNLSE) of motion was earlier derived in our laboratory by combining density functional theory and quantum fluid dynamics in three- dimensional space. In continuation of the work reported previously, the GNLSE is applied to provide addi-.
Simple Fully Nonlocal Density Functionals for Electronic Repulsion Energy.
Vuckovic, Stefan; Gori-Giorgi, Paola
2017-07-06
From a simplified version of the mathematical structure of the strong coupling limit of the exact exchange-correlation functional, we construct an approximation for the electronic repulsion energy at physical coupling strength, which is fully nonlocal. This functional is self-interaction free and yields energy densities within the definition of the electrostatic potential of the exchange-correlation hole that are locally accurate and have the correct asymptotic behavior. The model is able to capture strong correlation effects that arise from chemical bond dissociation, without relying on error cancellation. These features, which are usually missed by standard density functional theory (DFT) functionals, are captured by the highly nonlocal structure, which goes beyond the "Jacob's ladder" framework for functional construction, by using integrals of the density as the key ingredient. Possible routes for obtaining the full exchange-correlation functional by recovering the missing kinetic component of the correlation energy are also implemented and discussed.
Towards a kinetic energy density functional for the water molecule
Akin-Ojo, Omololu; Shittu, Doyin
Development of an accurate kinetic energy kinetic energy density functional (KEDF) is a holy grail. In this work, local KEDFS are parameterized for the water molecule in order to reproduce Kohn-Sham density functional theory (KS-DFT) results. Energies, forces and dipole moments from these KEDFs are presented. Problems with the convergence of the self-consistent-field (SCF) calculations are discussed together with possible solutions. and: Theoretical and Applied Physics Dept. African Univ. of Science and Technology (AUST) Abuja, Nigeria.
Reflection-asymmetric nuclear deformations within the Density Functional Theory
Olsen, E; Erler, J; Nazarewicz, W.; Stoitsov, M.
2013-01-01
Within the nuclear density functional theory (DFT) we study the effect of reflection-asymmetric shapes on ground-state binding energies and binding energy differences. To this end, we developed the new DFT solver AxialHFB that uses an approximate second-order gradient to solve the Hartree-Fock-Bogoliubov equations of superconducting DFT with the quasi-local Skyrme energy density functionals. Illustrative calculations are carried out for even-even isotopes of radium and thorium.
von Lilienfeld, O Anatole; Tavernelli, Ivano; Rothlisberger, Ursula; Sebastiani, Daniel
2004-10-08
We add an effective atom-centered nonlocal term to the exchange-correlation potential in order to cure the lack of London dispersion forces in standard density functional theory. Calibration of this long-range correction is performed using density functional perturbation theory and an arbitrary reference. Without any prior assignment of types and structures of molecular fragments, our corrected generalized gradient approximation density functional theory calculations yield correct equilibrium geometries and dissociation energies of argon-argon, benzene-benzene, graphite-graphite, and argon-benzene complexes.
Density functional theory for polymeric systems in 2D.
Słyk, Edyta; Roth, Roland; Bryk, Paweł
2016-06-22
We propose density functional theory for polymeric fluids in two dimensions. The approach is based on Wertheim's first order thermodynamic perturbation theory (TPT) and closely follows density functional theory for polymers proposed by Yu and Wu (2002 J. Chem. Phys. 117 2368). As a simple application we evaluate the density profiles of tangent hard-disk polymers at hard walls. The theoretical predictions are compared against the results of the Monte Carlo simulations. We find that for short chain lengths the theoretical density profiles are in an excellent agreement with the Monte Carlo data. The agreement is less satisfactory for longer chains. The performance of the theory can be improved by recasting the approach using the self-consistent field theory formalism. When the self-avoiding chain statistics is used, the theory yields a marked improvement in the low density limit. Further improvements for long chains could be reached by going beyond the first order of TPT.
Fromager, Emmanuel
2014-01-01
The exact formulation of multi-configuration density-functional theory (DFT) is discussed in this work. As an alternative to range-separated methods, where electron correlation effects are split in the coordinate space, the combination of Configuration Interaction methods with orbital occupation functionals is explored at the formal level through the separation of correlation effects in the orbital space. When applied to model Hamiltonians, this approach leads to an exact Site-Occupation Embedding Theory (SOET). An adiabatic connection expression is derived for the complementary bath functional and a comparison with Density Matrix Embedding Theory (DMET) is made. Illustrative results are given for the simple two-site Hubbard model. SOET is then applied to a quantum chemical Hamiltonian, thus leading to an exact Complete Active Space Site-Occupation Functional Theory (CASSOFT) where active electrons are correlated explicitly within the CAS and the remaining contributions to the correlation energy are described...
Mountain lions: preliminary findings on home-range use and density, central Sierra Nevada
Donald L. Neal; George N. Steger; Ronald C. Bertram
1987-01-01
Between August 1983 and December 1985, 19 mountain lions were captured, radio equipped, and monitored daily within a portion of the North Kings deer herd range on the west slope of the central Sierra Nevada in California. The density of adult mountain lions was estimated to be one per 33.3 km²; that of adults and kittens together was estimated to be one per 20...
Linear response of homogeneous nuclear matter with energy density functionals
Energy Technology Data Exchange (ETDEWEB)
Pastore, A. [Institut d’Astronomie et d’Astrophysique, CP 226, Université Libre de Bruxelles, B-1050 Bruxelles (Belgium); Davesne, D., E-mail: davesne@ipnl.in2p3.fr [Institut de Physique Nucléaire de Lyon, CNRS-IN2P3, UMR 5822, Université Lyon 1, F-69622 Villeurbanne (France); Navarro, J. [IFIC (CSIC University of Valencia), Apdo. Postal 22085, E-46071 Valencia (Spain)
2015-03-01
Response functions of infinite nuclear matter with arbitrary isospin asymmetry are studied in the framework of the random phase approximation. The residual interaction is derived from a general nuclear Skyrme energy density functional. Besides the usual central, spin–orbit and tensor terms it could also include other components as new density-dependent terms or three-body terms. Algebraic expressions for the response functions are obtained from the Bethe–Salpeter equation for the particle–hole propagator. Applications to symmetric nuclear matter, pure neutron matter and asymmetric nuclear matter are presented and discussed. Spin–isospin strength functions are analyzed for varying conditions of density, momentum transfer, isospin asymmetry, and temperature for some representative Skyrme functionals. Particular attention is paid to the discussion of instabilities, either real or unphysical, which could manifest in finite nuclei.
Reactivity of Graphene Investigated by Density-Functional Theory
Soni, Himadri; Gebhardt, Julian; Görling, Andreas; Chair of Theoretical Chemistry Team
Using spin-polarized density-functional theory, we study the adsorption and reaction of hydrogen and fluorine with graphene. Graphene has a bipartite lattice with two different sublattices and hence, due to Lieb's theorem, the inequality between two sublattices should lead to a net magnetic moment upon adsorption of hydrogen or fluorine. Our calculations using density-functional theory with the generalized gradient approximation predict a magnetic moment of 1 µB for a single hydrogen adsorbed on graphene but not for a single fluorine atom adsorbed on graphene. Switching to hybrid density-functional theory with the HSE functional, we obtain a magnetic moment of 1 µB for of a single fluorine atom adsorption on graphene. This is in line with work of Kim et al., who also found in density-functional theory calculations with the HSE exchange-correlation functional spin-polarization for a fluorine adatom on graphene. Here, we present a systematic study of the reactivity and relevant adsorption mechanism for single-sided graphene, i.e., a graphene sheet which is accessible by an adsorbate from only one side with hydrogen and fluorine using hybrid density-functional theory. German Research Council (DFG) by the Collaborative Research Center 953.
Uniform magnetic fields in density-functional theory.
Tellgren, Erik I; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M
2018-01-14
We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.
Uniform magnetic fields in density-functional theory
Tellgren, Erik I.; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M.
2018-01-01
We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.
Benchmark density functional theory calculations for nanoscale conductance
DEFF Research Database (Denmark)
Strange, Mikkel; Bækgaard, Iben Sig Buur; Thygesen, Kristian Sommer
2008-01-01
We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code...... a systematic downshift of the SIESTA transmission functions relative to the plane-wave results. The effect diminishes as the atomic orbital basis is enlarged; however, the convergence can be rather slow....
Range-Separated meta-GGA Functional Designed for Noncovalent Interactions.
Modrzejewski, Marcin; Chałasiński, Grzegorz; Szczęśniak, Małgorzata M
2014-10-14
The accuracy of applying density functional theory to noncovalent interactions is hindered by errors arising from low-density regions of interaction-induced change in the density gradient, error compensation between correlation and exchange functionals, and dispersion double counting. A new exchange-correlation functional designed for noncovalent interactions is proposed to address these problems. The functional consists of the range-separated PBEsol exchange considered in two variants, pure and hybrid, and the semilocal correlation functional of Modrzejewski et al. (J. Chem. Phys. 2012, 137, 204121) designed with the constraint satisfaction technique to smoothly connect with a dispersion term. Two variants of dispersion correction are appended to the correlation functional: the atom-atom pairwise additive DFT-D3 model and the density-dependent many-body dispersion with self-consistent screening (MBD-rsSCS). From these building blocks, a set of four functionals is created to systematically examine the role of pure versus hybrid exchange and the underlying models for dispersion. The new functional is extensively tested on benchmark sets with diverse nature and size. Truly outstanding performance is demonstrated for water clusters of varying size, ionic hydrogen bonds, and thermochemistry of isodesmic n-alkane fragmentation reactions. The merits of each component of the new functional are discussed.
Performance of density functional theory methods to describe ...
Indian Academy of Sciences (India)
Unknown
Abstract. The performance of three exchange and correlation density functionals, LDA, BLYP and B3LYP, with four basis sets is tested in three intramolecular hydrogen shift reactions. The best reaction and acti- vation energies come from the hybrid functional B3LYP with triple-ζ basis sets, when they are compared.
Higher-accuracy van der Waals density functional
DEFF Research Database (Denmark)
Lee, Kyuho; Murray, Éamonn D.; Kong, Lingzhu
2010-01-01
We propose a second version of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-N asymptote gradient correction in determining the vdW kernel. The predicted binding energy...
Time-Dependent (Current) Density Functional Theory for Periodic Systems
Kootstra, F.; Boeij, P.L. de; Leeuwen, R. van; Snijders, J.G.
2002-01-01
In this article we review time-dependent density functional theory for calculating the static and frequency-dependent dielectric function ε(ω) of nonmetallic crystals. We show that a real-space description becomes feasible for solids by using a combination of a lattice-periodic (microscopic) scalar
Density Functional Theory and Materials Modeling at Atomistic Length Scales
Directory of Open Access Journals (Sweden)
Swapan K. Ghosh
2002-04-01
Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.
Laser system range calculations and the Lambert W function.
Steinvall, Ove
2009-02-01
The knowledge of range performance versus atmospheric transmission, often given by the visibility, is critical for the design, use, and prediction of laser and passive electro-optic systems. I present a solution of the ladar-lidar equation based on Lambert's W function. This solution will reveal the dependence of the maximum range on the system and target parameters for different atmospheric attenuations and will also allow us to take the signal statistics into account by studying the influence on the threshold signal-to-noise ratio. The method is also applicable to many range calculations for passive systems where the atmospheric loss can be approximated by an exponential term.
Benchmarking Density Functionals for Chemical Bonds of Gold
DEFF Research Database (Denmark)
Kepp, Kasper Planeta
2017-01-01
Gold plays a major role in nanochemistry, catalysis, and electrochemistry. Accordingly, hundreds of studies apply density functionals to study chemical bonding with gold, yet there is no systematic attempt to assess the accuracy of these methods applied to gold. This paper reports a benchmark...... correlation produce weaker bonds to gold. Most functionals provide similar trend accuracy, though somewhat lower for M06 and M06L, but very different numerical accuracy. Notably, PBE and TPSS functionals with dispersion display the smallest numerical errors and very small mean signed errors (0-6 kJ/mol), i...... against 51 experimental bond enthalpies of AuX systems and seven additional polyatomic and cationic molecules. Twelve density functionals were tested, covering meta functionals, hybrids with variable HF exchange, double-hybrid, dispersion-corrected, and nonhybrid GGA functionals. The defined benchmark...
Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.
2017-08-01
Background: The central depression of nucleonic density, i.e., a reduction of density in the nuclear interior, has been attributed to many factors. For instance, bubble structures in superheavy nuclei are believed to be due to the electrostatic repulsion. In light nuclei, the mechanism behind the density reduction in the interior has been discussed in terms of shell effects associated with occupations of s orbits. Purpose: The main objective of this work is to reveal mechanisms behind the formation of central depression in nucleonic densities in light and heavy nuclei. To this end, we introduce several measures of the internal nucleonic density. Through the statistical analysis, we study the information content of these measures with respect to nuclear matter properties. Method: We apply nuclear density functional theory with Skyrme functionals. Using the statistical tools of linear least square regression, we inspect correlations between various measures of central depression and model parameters, including nuclear matter properties. We study bivariate correlations with selected quantities as well as multiple correlations with groups of parameters. Detailed correlation analysis is carried out for 34Si for which a bubble structure has been reported recently, 48Ca, and N =82 , 126, and 184 isotonic chains. Results: We show that the central depression in medium-mass nuclei is very sensitive to shell effects, whereas for superheavy systems it is firmly driven by the electrostatic repulsion. An appreciable semibubble structure in proton density is predicted for 294Og, which is currently the heaviest nucleus known experimentally. Conclusion: Our correlation analysis reveals that the central density indicators in nuclei below 208Pb carry little information on parameters of nuclear matter; they are predominantly driven by shell structure. On the other hand, in the superheavy nuclei there exists a clear relationship between the central nucleonic density and symmetry energy.
Filtered density function approach for reactive transport in groundwater
Suciu, Nicolae; Schüler, Lennart; Attinger, Sabine; Knabner, Peter
2016-04-01
Spatial filtering may be used in coarse-grained simulations (CGS) of reactive transport in groundwater, similar to the large eddy simulations (LES) in turbulence. The filtered density function (FDF), stochastically equivalent to a probability density function (PDF), provides a statistical description of the sub-grid, unresolved, variability of the concentration field. Besides closing the chemical source terms in the transport equation for the mean concentration, like in LES-FDF methods, the CGS-FDF approach aims at quantifying the uncertainty over the whole hierarchy of heterogeneity scales exhibited by natural porous media. Practically, that means estimating concentration PDFs on coarse grids, at affordable computational costs. To cope with the high dimensionality of the problem in case of multi-component reactive transport and to reduce the numerical diffusion, FDF equations are solved by particle methods. But, while trajectories of computational particles are modeled as stochastic processes indexed by time, the concentration's heterogeneity is modeled as a random field, with multi-dimensional, spatio-temporal sets of indices. To overcome this conceptual inconsistency, we consider FDFs/PDFs of random species concentrations weighted by conserved scalars and we show that their evolution equations can be formulated as Fokker-Planck equations describing stochastically equivalent processes in concentration-position spaces. Numerical solutions can then be approximated by the density in the concentration-position space of an ensemble of computational particles governed by the associated Itô equations. Instead of sequential particle methods we use a global random walk (GRW) algorithm, which is stable, free of numerical diffusion, and practically insensitive to the increase of the number of particles. We illustrate the general FDF approach and the GRW numerical solution for a reduced complexity problem consisting of the transport of a single scalar in groundwater
Assessing Density Functionals Using Many Body Theory for Hybrid Perovskites
Bokdam, Menno; Lahnsteiner, Jonathan; Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg
2017-10-01
Which density functional is the "best" for structure simulations of a particular material? A concise, first principles, approach to answer this question is presented. The random phase approximation (RPA)—an accurate many body theory—is used to evaluate various density functionals. To demonstrate and verify the method, we apply it to the hybrid perovskite MAPbI3 , a promising new solar cell material. The evaluation is done by first creating finite temperature ensembles for small supercells using RPA molecular dynamics, and then evaluating the variance between the RPA and various approximate density functionals for these ensembles. We find that, contrary to recent suggestions, van der Waals functionals do not improve the description of the material, whereas hybrid functionals and the strongly constrained appropriately normed (SCAN) density functional yield very good agreement with the RPA. Finally, our study shows that in the room temperature tetragonal phase of MAPbI3 , the molecules are preferentially parallel to the shorter lattice vectors but reorientation on ps time scales is still possible.
Perspective: Kohn-Sham density functional theory descending a staircase
Yu, Haoyu S.; Li, Shaohong L.; Truhlar, Donald G.
2016-10-01
This article presents a perspective on Kohn-Sham density functional theory (KS-DFT) for electronic structure calculations in chemical physics. This theory is in widespread use for applications to both molecules and solids. We pay special attention to several aspects where there are both concerns and progress toward solutions. These include: 1. The treatment of open-shell and inherently multiconfigurational systems (the latter are often called multireference systems and are variously classified as having strong correlation, near-degeneracy correlation, or high static correlation; KS-DFT must treat these systems with broken-symmetry determinants). 2. The treatment of noncovalent interactions. 3. The choice between developing new functionals by parametrization, by theoretical constraints, or by a combination. 4. The ingredients of the exchange-correlation functionals used by KS-DFT, including spin densities, the magnitudes of their gradients, spin-specific kinetic energy densities, nonlocal exchange (Hartree-Fock exchange), nonlocal correlation, and subshell-dependent corrections (DFT+U). 5. The quest for a universal functional, where we summarize some of the success of the latest Minnesota functionals, namely MN15-L and MN15, which were obtained by optimization against diverse databases. 6. Time-dependent density functional theory, which is an extension of DFT to treat time-dependent problems and excited states. The review is a snapshot of a rapidly moving field, and—like Marcel Duchamp—we hope to convey progress in a stimulating way.
Density and current profiles in Uq (A2(1)) zero range process
Kuniba, A.; Mangazeev, V. V.
2017-09-01
The stochastic R matrix for Uq (An(1)) introduced recently gives rise to an integrable zero range process of n classes of particles in one dimension. For n = 2 we investigate how finitely many first class particles fixed as defects influence the grand canonical ensemble of the second class particles. By using the matrix product stationary probabilities involving infinite products of q-bosons, exact formulas are derived for the local density and current of the second class particles in the large volume limit.
Density-functional calculations of magnetoplasmons in quantum rings
Emperador, A.; Barranco, M.; Lipparini, E.; Pi, M.; Serra, Ll.
1999-06-01
We have studied the structure and dipole charge-density response of nanorings as a function of the magnetic field using local-spin-density-functional theory. Two small rings consisting of 12 and 22 electrons confined by a positively charged background are used to represent the cases of narrow and wide rings. The results are qualitatively compared with experimental data existing on microrings and on antidots. A smaller ring containing five electrons is also analyzed to allow for a closer comparison with a recent experiment on a two-electron quantum ring.
Spin Propensities of Octahedral Complexes From Density Functional Theory
DEFF Research Database (Denmark)
Mortensen, Sara R.; Kepp, Kasper Planeta
2015-01-01
The fundamental balance between high- and low-spin states of transition metal systems depends on both the metal ion and the ligands surrounding it, as often visualized by the spectrochemical series. Most density functionals do not reproduce this balance, and real spin state propensities depend...... on orbital pairing and vibrational entropies absent in the spectrochemical series. Thus, we systematically computed the tendency toward high or low spin of "text-book" octahedral metal complexes versus ligand and metal type, using eight density functionals. Dispersion effects were generally
Embedding germanium in graphene: A density functional theory study
Energy Technology Data Exchange (ETDEWEB)
Xu, Zhuo; Li, Yangping, E-mail: liyp@nwpu.edu.cn; Tan, Tingting; Liu, Zhengtang
2017-03-31
Highlights: • Substitutional Ge in graphene is more stable in double vacancy site than in single vacancy site. • Metallic and semiconductor behaviors are obtained for Ge-substituted graphene depending on different substitution sites, concentrations, and vacancy types. • Tunable electronic and magnetic behaviors are observed in graphene sheet with Ge-chain impurity. - Abstract: Based on the density functional theory, we investigate the structural, electronic, and magnetic properties of graphene sheet with substitutional Ge atoms in both single and double vacancies, and graphene sheet with Ge-chain impurity. We find the substitutional Ge is chemically bonded to graphene, and is more stable in the double vacancy site. The electronic properties indicate that metallic and semiconductor states with a range of band gaps from 0 to 0.87 eV could be obtained depending on different substitution sites, concentrations, and vacancy types. Magnetic moment is observed in graphene with single vacancy. Tunable electronic behaviors are also observed in graphene sheet with Ge-chain impurity, and a magnetic moment of 2.9 μB is observed in single Ge-chain incorporated 4 × 4 graphene supercell. From these investigations, we conclude that by doping of Ge in vacancy-contained graphene, it could provide great advantages for its application in future nanoscale devices.
Effects of taurine and housing density on renal function in laying hens.
Ma, Zi-Li; Gao, Yang; Ma, Hai-Tian; Zheng, Liu-Hai; Dai, Bin; Miao, Jin-Feng; Zhang, Yuan-Shu
This study investigated the putative protective effects of supplemental 2-aminoethane sulfonic acid (taurine) and reduced housing density on renal function in laying hens. We randomly assigned fifteen thousand green-shell laying hens into three groups: a free range group, a low-density caged group, and a high-density caged group. Each group was further divided equally into a control group (C) and a taurine treatment group (T). After 15 d, we analyzed histological changes in kidney cells, inflammatory mediator levels, oxidation and anti-oxidation levels. Experimental data revealed taurine supplementation, and rearing free range or in low-density housing can lessen morphological renal damage, inflammatory mediator levels, and oxidation levels and increase anti-oxidation levels. Our data demonstrate that taurine supplementation and a reduction in housing density can ameliorate renal impairment, increase productivity, enhance health, and promote welfare in laying hens.
Density and Phonon-Stiffness Anomalies of Water and Ice in the Full Temperature Range.
Sun, Chang Q; Zhang, Xi; Fu, Xiaojian; Zheng, Weitao; Kuo, Jer-Lai; Zhou, Yichun; Shen, Zexiang; Zhou, Ji
2013-10-03
The specific-heat difference between the O:H van der Waals bond and the H-O polar-covalent bond and the Coulomb repulsion between electron pairs on adjacent oxygen atoms determine the angle-length-stiffness relaxation dynamics of the hydrogen bond (O:H-O), which is responsible for the density and phonon-stiffness oscillation of water ice over the full temperature range. Cooling shortens and stiffens the part of relatively lower specific-heat, and meanwhile lengthens and softens the other part of the O:H-O bond via repulsion. Length contraction/elongation of a specific part always stiffens/softens its corresponding phonon. In the liquid and in the solid phase, the O:H bond contracts more than the H-O elongates, hence, an O:H-O cooling contraction and the seemingly "regular" process of cooling densification take place. During freezing, the H-O contracts less than the O:H elongates, leading to an O:H-O elongation and volume expansion. At extremely low temperatures, the O:H-O angle stretching lowers the density slightly as the O:H and the H-O lengths change insignificantly. In ice, the O-O distance is longer than it is in water, resulting in a lower density, so that ice floats.
Dynamic density functional theory versus kinetic theory of simple fluids
Energy Technology Data Exchange (ETDEWEB)
Marini Bettolo Marconi, Umberto [Dipartimento di Fisica, Universita di Camerino and Istituto Nazionale di Fisica della Materia, Via Madonna delle Carceri, 62032, Camerino (Italy); Melchionna, Simone, E-mail: umberto.marinibettolo@unicam.i [Institute of Materials, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne (Switzerland)
2010-09-15
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as their hydrodynamic behavior. We focus on the evolution of the one-particle phase space distribution, rather than on the evolution of the average particle density which features in dynamic density functional theory. The resulting equation can be studied in two different physical limits: diffusive dynamics, typical of colloidal fluids without hydrodynamic interaction where particles are subject to overdamped motion resulting from coupling with a solvent at rest, and inertial dynamics, typical of molecular fluids. Finally, we propose an algorithm to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the lattice Boltzmann method.
Probability density functions of instantaneous Stokes parameters on weak scattering
Chen, Xi; Korotkova, Olga
2017-10-01
The single-point probability density functions (PDF) of the instantaneous Stokes parameters of a polarized plane-wave light field scattered from a three-dimensional, statistically stationary, weak medium with Gaussian statistics and Gaussian correlation function have been studied for the first time. Apart from the scattering geometry the PDF distributions of the scattered light have been related to the illumination's polarization state and the correlation properties of the medium.
On the discretization of probability density functions and the ...
Indian Academy of Sciences (India)
The probability density functions for the linear superposition of two coherent states is used for developing a representative example. Author Affiliations. Diógenes Campos1. Academia Colombiana de Ciencias Exactas, Físicas y Naturales, ACCEFYN, Bogotá, Colombia. Dates. Manuscript received: 27 June 2014; Manuscript ...
On the Probability Density Functions of Forster-Greer-Thorbecke ...
African Journals Online (AJOL)
This study considers the possibility of using Pearson system of distributions to approximate the probability density functions of. Forster-Greer-Thorbecke (FGT) poverty indices. The application of the Pearson system reveals the potentials of normal and four parameter distributions in poverty analysis. Keywords: Distributional ...
Density functional theory in surface science and heterogeneous catalysis
DEFF Research Database (Denmark)
Nørskov, Jens Kehlet; Scheffler, M.; Toulhoat, H.
2006-01-01
Solid surfaces are used extensively as catalysts throughout the chemical industry, in the energy sector, and in environmental protection. Recently, density functional theory has started providing new insight into the atomic-scale mechanisms of heterogeneous catalysis, helping to interpret the large...
Density functional study of ferromagnetism in alkali metal thin films
Indian Academy of Sciences (India)
2015-11-27
in/article/fulltext/pram/074/04/0653-0659 ... films of K and Cs, having thicknesses of one to seven layers, are calculated within the plane-wave projector augmented wave (PAW) formalism of the density functional theory (DFT), ...
Dynamic behavior of chemical reactivity indices in density functional ...
Indian Academy of Sciences (India)
Dynamic behaviors of chemical concepts in density functional theory such as frontier orbitals (HOMO/LUMO), chemical potential, hardness, and electrophilicity index have been investigated in this work in the context of Bohn-Oppenheimer quantum molecular dynamics in association with molecular conformation changes.
Density functional theory calculations of charge transport properties ...
Indian Academy of Sciences (India)
ZIRAN CHEN
2017-08-04
Aug 4, 2017 ... Abstract. Charge transport rate is one of the key parameters determining the performance of organic electronic devices. In this paper, we used density functional theory (DFT) at the M06-2X/6−31+G(d) level to compute the charge transport rates of nine coronene topological structures. The results show that ...
Density functional studies of molecular structures of N-methyl ...
Indian Academy of Sciences (India)
Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 1. Density functional studies of molecular structures of N-methyl formamide, N,N-dimethyl formamide, and N,N-dimethyl acetamide. V Renugopalakrishnan G Madrid G Cuevas A T Hagler. Physical and Theoretical Volume 112 Issue 1 February 2000 pp 35- ...
A density functional study on the adsorption of hydrogen molecule ...
Indian Academy of Sciences (India)
Abstract. An all-electron scalar relativistic calculation on the adsorption of hydrogen molecule onto small copper clusters has been performed by using density functional theory with the generalized gradient approxi- mation (GGA) at PW91 level. Our results reveal that after adsorption of H2 molecule, the Cu–Cu interaction.
The electron-propagator approach to conceptual density-functional ...
Indian Academy of Sciences (India)
Both electron propagator theory and density-functional theory provide conceptually useful information about chemical reactivity and, most especially, charge transfer. This paper elucidates thequalitative and quantitative links between the two theories, with emphasis on how the reactivity indicators of conceptual ...
Density functional study of : Electronic and optical properties
Indian Academy of Sciences (India)
K C Bhamu
2017-06-20
Jun 20, 2017 ... the refractive index in zero frequency limits is 2.42. The absorption coefficient predicts the applicability of AgScO2 in solar cells and flat panel liquid crystal display as a transparent top window layer. Keywords. Density functional theory; band structure; optical properties. PACS Nos 71.15.Mb; 71.20.−b; 78.20.
A comparative study of the performance of some density functionals ...
Indian Academy of Sciences (India)
CH SRIDHAR REDDY
Electronic absorption; finite temperature; vibronic spectra; density functionals; Gaussian wave packet propagation. 1. Introduction. Electronic excitation of a molecule is always accompa- nied by vibrational excitations due to the differences in the equilibrium structures and the hessian matrices in the two electronic states.
Density-functional theory of atoms and molecules
Parr, Robert G
1995-01-01
Provides an account of the fundamental principles of the density-functional theory of the electronic structure of matter and its applications to atoms and molecules. This book contains a discussion of the chemical potential and its derivatives. It is intended for physicists, chemists, and advanced students in chemistry.
A density functional study on the adsorption of hydrogen molecule ...
Indian Academy of Sciences (India)
An all-electron scalar relativistic calculation on the adsorption of hydrogen molecule onto small copper clusters has been performed by using density functional theory with the generalized gradient approximation (GGA) at PW91 level. Our results reveal that after adsorption of H2 molecule, the Cu-Cu interaction is ...
Peverati, Roberto; Truhlar, Donald G
2014-03-13
Kohn-Sham density functional theory is in principle an exact formulation of quantum mechanical electronic structure theory, but in practice we have to rely on approximate exchange-correlation (xc) functionals. The objective of our work has been to design an xc functional with broad accuracy across as wide an expanse of chemistry and physics as possible, leading--as a long-range goal--to a functional with good accuracy for all problems, i.e. a universal functional. To guide our path towards that goal and to measure our progress, we have developed-building on earlier work of our group-a set of databases of reference data for a variety of energetic and structural properties in chemistry and physics. These databases include energies of molecular processes, such as atomization, complexation, proton addition and ionization; they also include molecular geometries and solid-state lattice constants, chemical reaction barrier heights, and cohesive energies and band gaps of solids. For this paper, we gather many of these databases into four comprehensive databases, two with 384 energetic data for chemistry and solid-state physics and another two with 68 structural data for chemistry and solid-state physics, and we test two wave function methods and 77 density functionals (12 Minnesota meta functionals and 65 others) in a consistent way across this same broad set of data. We especially highlight the Minnesota density functionals, but the results have broader implications in that one may see the successes and failures of many kinds of density functionals when they are all applied to the same data. Therefore, the results provide a status report on the quest for a universal functional.
Kvaal, Simen; Helgaker, Trygve
2015-11-14
The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.
Estimating probability density functions and entropies of chua's circuit using b-spline functions
Savacı, Ferit Acar; Güngör, Mesut
2012-01-01
n this paper, first the probability density functions (PDFs) of the states of Chua's circuit have been estimated using B-spline functions and then the state entropies of Chua's circuit with respect to the bifurcation parameter have been obtained. The results of the proposed B-spline density estimator have been compared with the results obtained from the Parzen density estimator. © 2012 World Scientific Publishing Company.
Lei, Youming; Zheng, Fan
2016-12-01
Stochastic chaos induced by diffusion processes, with identical spectral density but different probability density functions (PDFs), is investigated in selected lightly damped Hamiltonian systems. The threshold amplitude of diffusion processes for the onset of chaos is derived by using the stochastic Melnikov method together with a mean-square criterion. Two quasi-Hamiltonian systems, namely, a damped single pendulum and damped Duffing oscillator perturbed by stochastic excitations, are used as illustrative examples. Four different cases of stochastic processes are taking as the driving excitations. It is shown that in such two systems the spectral density of diffusion processes completely determines the threshold amplitude for chaos, regardless of the shape of their PDFs, Gaussian or otherwise. Furthermore, the mean top Lyapunov exponent is employed to verify analytical results. The results obtained by numerical simulations are in accordance with the analytical results. This demonstrates that the stochastic Melnikov method is effective in predicting the onset of chaos in the quasi-Hamiltonian systems.
Astym therapy improves function and range of motion following mastectomy
Directory of Open Access Journals (Sweden)
Davies CC
2016-03-01
Full Text Available Claire C Davies,1 Dorothy Brockopp,2 Krista Moe2 1Baptist Health Rehabilitation, 2Research Department, Baptist Health Lexington, Lexington, KY, USA Abstract: Hypersensitive scar tissue formation along the incision line and drain site is a common side effect following mastectomy. If this scar tissue is not addressed, it can lead to decreased flexibility and function in the involved upper quadrant. Astym® treatment is a new approach to soft tissue injuries, and is evidenced in animal studies to promote the healing and regeneration of soft tissues. It has also been found to reduce pain and increase function in people with soft tissue dysfunction. The aim of Astym treatment is to engage the regenerative mechanisms of the body in order to resorb scar tissue, stimulate tissue turnover, and regenerate soft tissues. Handheld instrumentation is applied topically to locate and treat the underlying dysfunctional soft tissue through specific protocols for the application of particular pressures and shear forces. The purpose of this study was to examine the effects of Astym treatment on activities of daily living in women who had undergone a mastectomy following a diagnosis of breast cancer. A quasi-experiment involving 40 women, following a mastectomy, evaluated five outcome measures pre- and post-Astym treatment. All five measurement scores: Disabilities of the Arm, Shoulder, and Hand Outcome Measure; a clothing questionnaire on their ability to wear a bra; Patient-Specific Functional Scale; active range of motion of shoulder flexion; and active range of motion of abduction were also measured and all demonstrated significant changes. In this study, Astym treatment improved active range of motion in the involved quadrant and also improved function in patients following a mastectomy. Keywords: breast cancer, quality of life, scar tissue treatment, physical therapy
Measurement of individual loudness functions by trisection of loudness ranges.
Villchur, Edgar; Killion, Mead C
2008-10-01
Loudness-balance measurements with monaurally impaired subjects have shown that the shape of the loudness versus sound-pressure curve among hearing-impaired persons varies significantly. But the effectiveness of adjusting the compression characteristics of wide-dynamic-range compression hearing aids-the compression ratios, the variation of compression ratio with level, and the threshold of compression-to restore normal loudness growth for the individual patient has never been properly tested; individual loudness measurements have been too uncertain to permit meaningful individual adjustments. Recent investigators have reported standard deviations of such measurements in normal-hearing subjects of 6.4 dB and 7.8 dB. This investigation describes a method of measuring loudness function with a standard deviation in normal-hearing subjects of the order of 1 dB, both significantly lower than that of previous methods and sufficiently accurate for individual-subject adjustments. Each of nine normal-hearing subjects-seven of them inexperienced and one a 9-year-old was asked to make three successive loudness trisections within an amplitude range of 40 to 80 dB SPL, providing six points from which to plot a loudness-function curve between these limits. The individual and average curves were validated as accurate loudness functions by comparing them to the curve defined by the equation of loudness versus amplitude in current Standards. In a second validation experiment, the loudness functions of masked ears measured by trisection were compared to the loudness function of those ears measured by loudness balance between masked and unmasked ears. The difference between a loudness function based on the average of subject trisections and the loudness function defined by the ANSI Standard loudness equation was -1.92 dB at the lowest trisection level and +0.05 dB at the highest level. The standard deviations of subject responses were 1.63 dB for the lowest trisection level and 0.68 d
A numerical shallow-water model for gravity currents for a wide range of density differences
Shimizu, Hiroyuki A.; Koyaguchi, Takehiro; Suzuki, Yujiro J.
2017-12-01
Gravity currents with various contrasting densities play a role in mass transport in a number of geophysical situations. The ratio of the density of the current, ρ c, to the density of the ambient fluid, ρ a, can vary between 100 and 103. In this paper, we present a numerical method of simulating gravity currents for a wide range of ρ c/ ρ a using a shallow-water model. In the model, the effects of varying ρ c/ ρ a are taken into account via the front condition (i.e., factors describing the balance between the driving pressure and the ambient resistance pressure at the flow front). Previously, two types of numerical models have been proposed to solve the front condition. These are referred to here as the Boundary Condition (BC) model and the Artificial Bed (AB) model. The front condition is calculated as a boundary condition at each time step in the BC model, whereas it is calculated by setting a thin artificial bed ahead of the front in the AB model. We assessed the BC and AB models by comparing their numerical results with the analytical results for a simple case of homogeneous currents. The results from the BC model agree well with the analytical results when ρ c/ ρ a≲102, but the model tends to overestimate the speed of the front position when ρ c/ρ a≳102. In contrast, the AB model generates good approximations of the analytical results for ρ c/ρ a≳ 102, given a sufficiently small artificial bed thickness, but fails to reproduce the analytical results when ρ c/ ρ a≲102. Therefore, we propose a numerical method in which the BC model is used for currents with ρ c/ ρ a≲102 and the AB model is used for currents with ρ c/ρ a≳ 102.
Workhorse semilocal density functional for condensed matter physics and quantum chemistry.
Perdew, John P; Ruzsinszky, Adrienn; Csonka, Gábor I; Constantin, Lucian A; Sun, Jianwei
2009-07-10
Semilocal density functionals for the exchange-correlation energy are needed for large electronic systems. The Tao-Perdew-Staroverov-Scuseria (TPSS) meta-generalized gradient approximation (meta-GGA) is semilocal and usefully accurate, but predicts too-long lattice constants. Recent "GGA's for solids" yield good lattice constants but poor atomization energies of molecules. We show that the construction principle for one of them (restoring the density gradient expansion for exchange over a wide range of densities) can be used to construct a "revised TPSS" meta-GGA with accurate lattice constants, surface energies, and atomization energies for ordinary matter.
General framework for fluctuating dynamic density functional theory
Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim
2017-12-01
We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean–Kawasaki (DK) model, which resembles the stochastic Navier–Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier–Stokes equations, originally derived by Landau and
Nanda, B. R. K.; Sherafati, M.; Popović, Z. S.; Satpathy, S.
2012-08-01
We study the electronic structure of graphene with a single substitutional vacancy using a combination of the density-functional, tight-binding and impurity Green's function approaches. Density-functional studies are performed with the all-electron spin-polarized linear augmented plane wave (LAPW) method. The three sp2σ dangling bonds adjacent to the vacancy introduce localized states (Vσ) in the mid-gap region, which split due to the crystal field and a Jahn-Teller distortion, while the pzπ states introduce a sharp resonance state (Vπ) in the band structure. For a planar structure, symmetry strictly forbids hybridization between the σ and the π states, so that these bands are clearly identifiable in the calculated band structure. As to the magnetic moment of the vacancy, the Hund's rule coupling aligns the spins of the four localized Vσ1↑↓, Vσ2↑ and Vπ↑ electrons, resulting in an S = 1 state, with a magnetic moment of 2μB, which is reduced by about 0.3μB due to the anti-ferromagnetic spin polarization of the π band itinerant states in the vicinity of the vacancy. This results in the net magnetic moment of 1.7μB. Using the Lippmann-Schwinger equation, we reproduce the well-known ˜1/r decay of the localized Vπ wave function with distance, and in addition, find an interference term coming from the two Dirac points, previously unnoticed in the literature. The long-range nature of the Vπ wave function is a unique feature of the graphene vacancy and we suggest that this may be one of the reasons for the widely varying relaxed structures and magnetic moments reported from the supercell band calculations in the literature.
DEFF Research Database (Denmark)
Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.
2008-01-01
Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...
Density dependence of the stress relaxation function of a simple fluid
Hartkamp, Remco; Daivis, P.J.; Todd, B.D.
2013-01-01
We present accurate molecular dynamics calculations of the shear stress relaxation modulus of a simple atomic fluid over a wide range of densities. The high accuracy of the data enables us to study changes in the functional form of the shear relaxation modulus, and the properties that are derived
Reduced density matrix functional theory at finite temperature
Energy Technology Data Exchange (ETDEWEB)
Baldsiefen, Tim
2012-10-15
Density functional theory (DFT) is highly successful in many fields of research. There are, however, areas in which its performance is rather limited. An important example is the description of thermodynamical variables of a quantum system in thermodynamical equilibrium. Although the finite-temperature version of DFT (FT-DFT) rests on a firm theoretical basis and is only one year younger than its brother, groundstate DFT, it has been successfully applied to only a few problems. Because FT-DFT, like DFT, is in principle exact, these shortcomings can be attributed to the difficulties of deriving valuable functionals for FT-DFT. In this thesis, we are going to present an alternative theoretical description of quantum systems in thermal equilibrium. It is based on the 1-reduced density matrix (1RDM) of the system, rather than on its density and will rather cumbersomly be called finite-temperature reduced density matrix functional theory (FT-RDMFT). Its zero-temperature counterpart (RDMFT) proved to be successful in several fields, formerly difficult to address via DFT. These fields include, for example, the calculation of dissociation energies or the calculation of the fundamental gap, also for Mott insulators. This success is mainly due to the fact that the 1RDM carries more directly accessible ''manybody'' information than the density alone, leading for example to an exact description of the kinetic energy functional. This sparks the hope that a description of thermodynamical systems employing the 1RDM via FT-RDMFT can yield an improvement over FT-DFT. Giving a short review of RDMFT and pointing out difficulties when describing spin-polarized systems initiates our work. We then lay the theoretical framework for FT-RDMFT by proving the required Hohenberg-Kohn-like theorems, investigating and determining the domain of FT-RDMFT functionals and by deriving several properties of the exact functional. Subsequently, we present a perturbative method to
Zheng, Yulong; Liao, Zhiyong
2017-11-22
Invasive plant species often form dense mono-dominant stands in areas they have invaded, while having only sparse distribution in their native ranges, and the reasons behind this phenomenon are a key point of research in invasive species biology. Differences in species composition between native and invasive ranges may contribute to the difference in distribution status. In this study, we found that the high-density condition had a more negative effect on C. odorata than the low-density condition when co-grown with neighbor plants from its native range in Mexico, while this pattern was not in evidence when it was grown with neighbors from its invasive range in China. Different competitive ability and coevolutionary history with C. odorata between native-range neighbors and invasive-range neighbors may lead to the inconsistent patterns.
Energy Technology Data Exchange (ETDEWEB)
McKechnie, Scott [Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Booth, George H. [Theory and Simulation of Condensed Matter, King’s College London, The Strand, London WC2R 2LS (United Kingdom); Cohen, Aron J. [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Cole, Jacqueline M., E-mail: jmc61@cam.ac.uk [Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Argonne National Laboratory, 9700 S Cass Avenue, Argonne, Illinois 60439 (United States)
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.
Predicting species’ range limits from functional traits for the tree flora of North America
Stahl, Ulrike; Reu, Björn; Wirth, Christian
2014-01-01
Using functional traits to explain species’ range limits is a promising approach in functional biogeography. It replaces the idiosyncrasy of species-specific climate ranges with a generic trait-based predictive framework. In addition, it has the potential to shed light on specific filter mechanisms creating large-scale vegetation patterns. However, its application to a continental flora, spanning large climate gradients, has been hampered by a lack of trait data. Here, we explore whether five key plant functional traits (seed mass, wood density, specific leaf area (SLA), maximum height, and longevity of a tree)—indicative of life history, mechanical, and physiological adaptations—explain the climate ranges of 250 North American tree species distributed from the boreal to the subtropics. Although the relationship between traits and the median climate across a species range is weak, quantile regressions revealed strong effects on range limits. Wood density and seed mass were strongly related to the lower but not upper temperature range limits of species. Maximum height affects the species range limits in both dry and humid climates, whereas SLA and longevity do not show clear relationships. These results allow the definition and delineation of climatic “no-go areas” for North American tree species based on key traits. As some of these key traits serve as important parameters in recent vegetation models, the implementation of trait-based climatic constraints has the potential to predict both range shifts and ecosystem consequences on a more functional basis. Moreover, for future trait-based vegetation models our results provide a benchmark for model evaluation. PMID:25225398
High density, multi-range analog output Versa Module Europa board for control system applications
Singh, Kundan; Das, Ajit Lal
2014-01-01
A new VMEDAC64, 12-bit 64 channel digital-to-analog converter, a Versa Module Europa (VME) module, features 64 analog voltage outputs with user selectable multiple ranges, has been developed for control system applications at Inter University Accelerator Centre. The FPGA (Field Programmable Gate Array) is the module's core, i.e., it implements the DAC control logic and complexity of VMEbus slave interface logic. The VMEbus slave interface and DAC control logic are completely designed and implemented on a single FPGA chip to achieve high density of 64 channels in a single width VME module and will reduce the module count in the control system applications, and hence will reduce the power consumption and cost of overall system. One of our early design goals was to develop the VME interface such that it can be easily integrated with the peripheral devices and satisfy the timing specifications of VME standard. The modular design of this module reduces the amount of time required to develop other custom modules for control system. The VME slave interface is written as a single component inside FPGA which will be used as a basic building block for any VMEbus interface project. The module offers multiple output voltage ranges depending upon the requirement. The output voltage range can be reduced or expanded by writing range selection bits in the control register. The module has programmable refresh rate and by default hold capacitors in the sample and hold circuit for each channel are charged periodically every 7.040 ms (i.e., update frequency 284 Hz). Each channel has software controlled output switch which disconnects analog output from the field. The modularity in the firmware design on FPGA makes the debugging very easy. On-board DC/DC converters are incorporated for isolated power supply for the analog section of the board.
NbB{sub 2}: a density functional study
Energy Technology Data Exchange (ETDEWEB)
Islam, A.K.M.A. [International Islamic University Chittagong, 154/A College Road, Chittagong-4203 (Bangladesh)]. E-mail: azislam46@yahoo.com; Sikder, A.S. [Department of Physics, Rajshahi University, Rajshahi-6205 (Bangladesh); Islam, F.N. [Department of Physics, Rajshahi University, Rajshahi-6205 (Bangladesh)
2006-02-06
The ground state properties and electronic structure of NbB{sub 2} are studied by an ab initio density functional method using the gradient-corrected approximation. The structural and bonding properties and pressure effects are discussed and the results compared with other calculations and experiments where available. The five independent elastic constants have been calculated for the first time for NbB{sub 2}. In the absence of experimental data, the results are compared with those of other related diborides. The pressure dependence of T{sub c} is also discussed. The band structure is presented and the bonding nature is analysed using the charge density plot and density of state histogram.
SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS
Energy Technology Data Exchange (ETDEWEB)
Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J
2010-12-20
We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.
Density of states of two-dimensional systems with long-range logarithmic interactions
Energy Technology Data Exchange (ETDEWEB)
Somoza, Andrés M.; Ortuño, Miguel; Baturina, Tatyana I.; Vinokur, Valerii M.
2015-08-03
We investigate a single-particle density of states (DOS) in strongly disordered two- dimensional high dielectric permittivity systems with logarithmic Coulomb interaction between particles. We derive self-consistent DOS at zero temperature and show that it is appreciably suppressed as compared to the DOS expected from the Efros-Shklovskii approach.We carry out zero- and finite-temperature Monte Carlo numerical studies of the DOS and find the perfect agreement between the numerical and analytical results at zero temperature, observing, in particular, a hardening of the Coulomb gap with the increasing electrostatic screening length. At finite temperatures, we reveal a striking scaling of the DOS as a function of energy normalized to the temperature of the system.
Energy Technology Data Exchange (ETDEWEB)
Tao, Jianmin [Los Alamos National Laboratory; Perdew, John P [TULANE UNIV; Staroverov, Viktor N [UNIV OF WESTERN ONTARIO; Scuseria, Gustavo E [RICE UNIV
2008-01-01
We construct a nonlocal density functional approximation with full exact exchange, while preserving the constraint-satisfaction approach and justified error cancellations of simpler semilocal functionals. This is achieved by interpolating between different approximations suitable for two extreme regions of the electron density. In a 'normal' region, the exact exchange-correlation hole density around an electron is semilocal because its spatial range is reduced by correlation and because it integrates over a narrow range to -1. These regions are well described by popular semilocal approximations (many of which have been constructed nonempirically), because of proper accuracy for a slowly-varying density or because of error cancellation between exchange and correlation. 'Abnormal' regions, where non locality is unveiled, include those in which exchange can dominate correlation (one-electron, nonuniform high-density, and rapidly-varying limits), and those open subsystems of fluctuating electron number over which the exact exchange-correlation hole integrates to a value greater than -1. Regions between these extremes are described by a hybrid functional mixing exact and semi local exchange energy densities locally (i.e., with a mixing fraction that is a function of position r and a functional of the density). Because our mixing fraction tends to 1 in the high-density limit, we employ full exact exchange according to the rigorous definition of the exchange component of any exchange-correlation energy functional. Use of full exact exchange permits the satisfaction of many exact constraints, but the nonlocality of exchange also requires balanced nonlocality of correlation. We find that this nonlocality can demand at least five empirical parameters (corresponding roughly to the four kinds of abnormal regions). Our local hybrid functional is perhaps the first accurate size-consistent density functional with full exact exchange. It satisfies other known
Extending density functional embedding theory for covalently bonded systems.
Yu, Kuang; Carter, Emily A
2017-12-19
Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.
Kernel density estimators of home range: smoothing and the autocorrelation red herring.
Fieberg, John
2007-04-01
Two oft-cited drawbacks of kernel density estimators (KDEs) of home range are their sensitivity to the choice of smoothing parameter(s) and their need for independent data. Several simulation studies have been conducted to compare the performance of objective, data-based methods of choosing optimal smoothing parameters in the context of home range and utilization distribution (UD) estimation. Lost in this discussion of choice of smoothing parameters is the general role of smoothing in data analysis, namely, that smoothing serves to increase precision at the cost of increased bias. A primary goal of this paper is to illustrate this bias-variance trade-off by applying KDEs to sampled locations from simulated movement paths. These simulations will also be used to explore the role of autocorrelation in estimating UDs. Autocorrelation can be reduced (1) by increasing study duration (for a fixed sample size) or (2) by decreasing the sampling rate. While the first option will often be reasonable, for a fixed study duration higher sampling rates should always result in improved estimates of space use. Further, KDEs with typical data-based methods of choosing smoothing parameters should provide competitive estimates of space use for fixed study periods unless autocorrelation substantially alters the optimal level of smoothing.
Analyzing the financial crisis using the entropy density function
Oh, Gabjin; Kim, Ho-yong; Ahn, Seok-Won; Kwak, Wooseop
2015-02-01
The risk that is created by nonlinear interactions among subjects in economic systems is assumed to increase during an abnormal state of a financial market. Nevertheless, investigating the systemic risk in financial markets following the global financial crisis is not sufficient. In this paper, we analyze the entropy density function in the return time series for several financial markets, such as the S&P500, KOSPI, and DAX indices, from October 2002 to December 2011 and analyze the variability in the entropy value over time. We find that the entropy density function of the S&P500 index during the subprime crisis exhibits a significant decrease compared to that in other periods, whereas the other markets, such as those in Germany and Korea, exhibit no significant decrease during the market crisis. These findings demonstrate that the S&P500 index generated a regular pattern in the return time series during the financial crisis.
Modeling of nanoscale liquid mixture transport by density functional hydrodynamics.
Dinariev, Oleg Yu; Evseev, Nikolay V
2017-06-01
Modeling of multiphase compositional hydrodynamics at nanoscale is performed by means of density functional hydrodynamics (DFH). DFH is the method based on density functional theory and continuum mechanics. This method has been developed by the authors over 20 years and used for modeling in various multiphase hydrodynamic applications. In this paper, DFH was further extended to encompass phenomena inherent in liquids at nanoscale. The new DFH extension is based on the introduction of external potentials for chemical components. These potentials are localized in the vicinity of solid surfaces and take account of the van der Waals forces. A set of numerical examples, including disjoining pressure, film precursors, anomalous rheology, liquid in contact with heterogeneous surface, capillary condensation, and forward and reverse osmosis, is presented to demonstrate modeling capabilities.
Resveratrol preserves cerebrovascular density and cognitive function in aging mice
Directory of Open Access Journals (Sweden)
Charlotte A Oomen
2009-12-01
Full Text Available Resveratrol, a natural polyphenol abundant in grapes and red wine, has been reported to exert numerous beneficial health effects. Among others, acute neuroprotective effects of resveratrol have been reported in several models of neurodegeneration, both in vitro and in vivo. In the present study we examined the neuroprotective effects of long term dietary supplementation with resveratrol in mice on behavioral, neurochemical and cerebrovascular level. We report a preserved cognitive function in resveratrol treated aging mice, as shown by an enhanced acquisition of a spatial Y-maze task. This was paralleled by a higher microvascular density and a lower number of microvascular abnormalities in comparison to aging non-treated control animals. We found no effects of resveratrol supplementation on cholinergic cell number or fiber density. The present findings support the hypothesis that resveratrol exerts beneficial effects on the brain by maintaining cerebrovascular health. Via this mechanism resveratrol can contribute to the preservation of cognitive function during aging.
Inclusion of Dispersion Effects in Density Functional Theory
DEFF Research Database (Denmark)
Møgelhøj, Andreas
on fitting to high-level ab initio and experimental results. The fitting scheme, based on Baysian theory, focuses on the three aspects: a) model space, b) datasets, and c) model selection. The model space consists of a flexible expansion of the exchange enhancement factor in the generalized gradient...... approximation plus local density approximation, and the non-local Rutgers-Chalmers correlations. The datasets are chosen to represent gas phase chemistry, surface chemistry, solid state physics, and non-covalently bound systems in order to produce a generally applicable functional that is particularly useful......In this thesis, applications and development will be presented within the field of van der Waals interactions in density functional theory. The thesis is based on the three projects: i) van der Waals interactions effect on the structure of liquid water at ambient conditions, ii) development...
Non-Periodic Finite-Element Formulation of Orbital-Free Density Functional Theory
Energy Technology Data Exchange (ETDEWEB)
Gavini, V; Knap, J; Bhattacharya, K; Ortiz, M
2006-10-06
We propose an approach to perform orbital-free density functional theory calculations in a non-periodic setting using the finite-element method. We consider this a step towards constructing a seamless multi-scale approach for studying defects like vacancies, dislocations and cracks that require quantum mechanical resolution at the core and are sensitive to long range continuum stresses. In this paper, we describe a local real space variational formulation for orbital-free density functional theory, including the electrostatic terms and prove existence results. We prove the convergence of the finite-element approximation including numerical quadratures for our variational formulation. Finally, we demonstrate our method using examples.
On the discretization of probability density functions and the ...
Indian Academy of Sciences (India)
In probability theory, statistics, statistical mechanics, communication theory, and other fields of science, the calculation of Rényi and Tsallis entropies [1–3] for probability density function ρ(x) involves integral. ∫ b a [ρ(x)] q dx, where q ≥ 0 is a parameter. The aim of this paper is to present a procedure for the discretization of ...
Plato: A localised orbital based density functional theory code
Kenny, S. D.; Horsfield, A. P.
2009-12-01
The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summaryProgram title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available
Directory of Open Access Journals (Sweden)
A. Verhoef
1997-01-01
Full Text Available Values of the momentum roughness length, z0, and displacement height, d, derived from wind profiles and momentum flux measurements, are selected from the literature for a variety of sparse canopies. These include savannah, tiger-bush and several row crops. A quality assessment of these data, conducted using criteria such as available fetch, height of wind speed measurement and homogeneity of the experimental site, reduced the initial total of fourteen sites to eight. These datapoints, combined with values carried forward from earlier studies on the parameterization of z0 and d, led to a maximum number of 16 and 24 datapoints available for d and z0, respectively. The data are compared with estimates of roughness length and displacement height as predicted from a detailed drag partition model, R92 (Raupach, 1992, and a simplified version of this model, R94 (Raupach, 1994. A key parameter in these models is the roughness density or frontal area index, λ. Both the comprehensive and the simplified model give accurate predictions of measured z0 and d values, but the optimal model coefficients are significantly different from the ones originally proposed in R92 and R94. The original model coefficients are based predominantly on measured aerodynamic parameters of relatively closed canopies and they were fitted `by eye'. In this paper, best-fit coefficients are found from a least squares minimization using the z0 and d values of selected good-quality data for sparse canopies and for the added, mainly closed canopies. According to a statistical analysis, based on the coefficient of determination (r2, the number of observations and the number of fitted model coefficients, the simplified model, R94, is deemed to be the most appropriate for future z0 and d predictions. A CR value of 0.35 and a cd1 value of about 20 are found to be appropriate for a large range of canopies varying in density from closed to very sparse. In this case, 99% of the total variance
A density functional theory study on redox reaction of uranium
Energy Technology Data Exchange (ETDEWEB)
Toraishi, T.; Kawaguchi, M.; Tsuneda, T.; Tanaka, S. [Department of Quantum Engineering and Systems Science, School of Engineering, The University of Tokyo, Tokyo 113-8656 (Japan); Nagasaki, S. [Instutute of Environmental Studies, Faculty of Frontier Science, The University of Tokyo, Tokyo 113-8656 (Japan)
2005-07-01
Full text of publication follows: Redox reactions are key issues for predicting the migration behavior of actinides in the geosphere, and therefore the chemical processes have to be profoundly understood. However, redox reactions basically involve several elemental processes, and in many cases only limited chemical information can be obtained experimentally. A theoretical approach gives further information which never can be obtained by experiments, such as precise thermodynamic data or reaction pathways of very rapid charge transfer reactions. For this reason, ab initio MO calculations have been applied in the last 5-6 years to the elucidation of redox processes in the U(VI)-Fe(II) or U(VI)-U(IV) system [1- 3]. Those studies provided extremely important chemical information. Nevertheless, the 'huge' calculation costs of ab initio MO techniques now interfere with the extension of the calculation to the 'real' size system: In order to deal with the practically important chemical reactions such as the reduction of actinides at solid surfaces, a large chemical system involving many atoms (electrons) has to be treated. Present ab initio MO techniques at CASSCF, CASPT2 or MRCI level, however, do not allow to handle such a large systems because of the high calculation costs. Density functional theory (DFT) calculations should be also feasible for such systems. Nevertheless, there are very few reports on redox processes of actinides calculated by DFT. This fact was based on the argument that DFT could not treat charge transfer phenomena accurately since the two-electron exchange integral term is not explicitly involved [1-3]. However this is no longer correct: the long-range corrected (LC) energy function was recently developed, and now the charge transfer reaction can safely be calculated by DFT [4]. In the present work, we employ the DFT technique to treat the reduction of U(VI) to U(V) by Fe(II) via the bi-nuclear complex system, and confirm the
Spin-density functional for exchange anisotropic Heisenberg model
Energy Technology Data Exchange (ETDEWEB)
Prata, G.N.; Penteado, P.H.; Souza, F.C. [Departamento de Fisica e Informatica, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, CP 369, Sao Carlos - SP (Brazil); Libero, Valter L., E-mail: valter@if.sc.usp.b [Departamento de Fisica e Informatica, Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, CP 369, Sao Carlos - SP (Brazil)
2009-10-15
Ground-state energies for antiferromagnetic Heisenberg models with exchange anisotropy are estimated by means of a local-spin approximation made in the context of the density functional theory. Correlation energy is obtained using the non-linear spin-wave theory for homogeneous systems from which the spin functional is built. Although applicable to chains of any size, the results are shown for small number of sites, to exhibit finite-size effects and allow comparison with exact-numerical data from direct diagonalization of small chains.
Bayesian error estimation in density-functional theory
DEFF Research Database (Denmark)
Mortensen, Jens Jørgen; Kaasbjerg, Kristen; Frederiksen, Søren Lund
2005-01-01
We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies...... for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude...
Time-dependent density-functional theory concepts and applications
Ullrich, Carsten A
2011-01-01
Time-dependent density-functional theory (TDDFT) describes the quantum dynamics of interacting electronic many-body systems formally exactly and in a practical and efficient manner. TDDFT has become the leading method for calculating excitation energies and optical properties of large molecules, with accuracies that rival traditional wave-function based methods, but at a fraction of the computational cost.This book is the first graduate-level text on the concepts and applications of TDDFT, including many examples and exercises, and extensive coverage of the literature. The book begins with a s
Environmental determinants, liver function, and high density lipoprotein cholesterol levels.
Kuller, L H; Hulley, S B; LaPorte, R E; Neaton, J; Dai, W S
1983-04-01
High density lipoprotein cholesterol (HDL-chol) is negatively associated with coronary heart disease. Environmental heart disease risk factors may partially be related to coronary heart disease through alterations in HDL-chol concentrations. Little is known about the underlying mechanisms by which environmental factors are related to HDL-chol. The authors investigated a possible mechanism: changes in liver function as a mediating link between risk factors and HDL-chol concentrations in marathon runners, alcoholics, and participants in the Multiple Risk Factor Intervention Trial. Liver function, as measured by liver enzymes, was related to both coronary heart disease risk factors and alcohol consumption, suggesting that the increased levels of HDL-chol associated with alcohol were primarily the result of changes in liver function. The relationship of obesity to HDL-chol could not be explained by the alterations in liver function.
Energy Technology Data Exchange (ETDEWEB)
Franco-Pérez, Marco, E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx [Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 (Canada); Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340 (Mexico); Ayers, Paul W., E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx [Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 (Canada); Gázquez, José L., E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx [Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340 (Mexico); Vela, Alberto, E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx [Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), Av. Instituto Politécnico Nacional 2508, México, D.F. 07360 (Mexico)
2015-12-28
We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model.
Influence of dietary taurine and housing density on oviduct function in laying hens.
Dai, Bin; Zhang, Yuan-shu; Ma, Zi-li; Zheng, Liu-hai; Li, Shuang-jie; Dou, Xin-hong; Gong, Jian-sen; Miao, Jin-feng
2015-06-01
Experiments were conducted to study the effects of dietary taurine and housing density on oviduct function in laying hens. Green-shell laying hens were randomly assigned to a free range group and two caged groups, one with low-density and the other with high-density housing. Each group was further divided into control (C) and taurine treatment (T) groups. All hens were fed the same basic diet except that the T groups' diet was supplemented with 0.1% taurine. The experiment lasted 15 d. Survival rates, laying rates, daily feed consumption, and daily weight gain were recorded. Histological changes, inflammatory mediator levels, and oxidation and anti-oxidation levels were determined. The results show that dietary taurine supplementation and reduced housing density significantly attenuated pathophysiological changes in the oviduct. Nuclear factor-κB (NF-κB) DNA binding activity increased significantly in the high-density housing group compared with the two other housing groups and was reduced by taurine supplementation. Tumor necrosis factor-α (TNF-α) mRNA expression in the high-density and low-density C and T groups increased significantly. In the free range and low-density groups, dietary taurine significantly reduced the expression of TNF-α mRNA. Supplementation with taurine decreased interferon-γ (IFN-γ) mRNA expression significantly in the low-density groups. Interleukin 4 (IL-4) mRNA expression was significantly higher in caged hens. IL-10 mRNA expression was higher in the high-density C group than in the free range and low-density C groups. Supplementation with taurine decreased IL-10 mRNA expression significantly in the high-density group and increased superoxide dismutase (SOD) activity in the free range hens. We conclude that taurine has important protective effects against oviduct damage. Reducing housing density also results in less oxidative stress, less inflammatory cell infiltration, and lower levels of inflammatory mediators in the oviduct
Influence of dietary taurine and housing density on oviduct function in laying hens*
Dai, Bin; Zhang, Yuan-shu; Ma, Zi-li; Zheng, Liu-hai; Li, Shuang-jie; Dou, Xin-hong; Gong, Jian-sen; Miao, Jin-feng
2015-01-01
Experiments were conducted to study the effects of dietary taurine and housing density on oviduct function in laying hens. Green-shell laying hens were randomly assigned to a free range group and two caged groups, one with low-density and the other with high-density housing. Each group was further divided into control (C) and taurine treatment (T) groups. All hens were fed the same basic diet except that the T groups’ diet was supplemented with 0.1% taurine. The experiment lasted 15 d. Survival rates, laying rates, daily feed consumption, and daily weight gain were recorded. Histological changes, inflammatory mediator levels, and oxidation and anti-oxidation levels were determined. The results show that dietary taurine supplementation and reduced housing density significantly attenuated pathophysiological changes in the oviduct. Nuclear factor-κB (NF-κB) DNA binding activity increased significantly in the high-density housing group compared with the two other housing groups and was reduced by taurine supplementation. Tumor necrosis factor-α (TNF-α) mRNA expression in the high-density and low-density C and T groups increased significantly. In the free range and low-density groups, dietary taurine significantly reduced the expression of TNF-α mRNA. Supplementation with taurine decreased interferon-γ (IFN-γ) mRNA expression significantly in the low-density groups. Interleukin 4 (IL-4) mRNA expression was significantly higher in caged hens. IL-10 mRNA expression was higher in the high-density C group than in the free range and low-density C groups. Supplementation with taurine decreased IL-10 mRNA expression significantly in the high-density group and increased superoxide dismutase (SOD) activity in the free range hens. We conclude that taurine has important protective effects against oviduct damage. Reducing housing density also results in less oxidative stress, less inflammatory cell infiltration, and lower levels of inflammatory mediators in the oviduct
Recent developments in LIBXC - A comprehensive library of functionals for density functional theory
Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T.; Marques, Miguel A. L.
2018-01-01
LIBXC is a library of exchange-correlation functionals for density-functional theory. We are concerned with semi-local functionals (or the semi-local part of hybrid functionals), namely local-density approximations, generalized-gradient approximations, and meta-generalized-gradient approximations. Currently we include around 400 functionals for the exchange, correlation, and the kinetic energy, spanning more than 50 years of research. Moreover, LIBXC is by now used by more than 20 codes, not only from the atomic, molecular, and solid-state physics, but also from the quantum chemistry communities.
Interrogating the Becke'05 density functional for non-locality information
Dale, Stephen G.; Johnson, Erin R.; Becke, Axel D.
2017-10-01
In two papers, Becke [J. Chem. Phys. 119, 2972 (2003) and J. Chem. Phys. 122, 064101 (2005)] introduced Kohn-Sham density-functional approximations for static and dynamical correlation to be partnered with 100 percent exactly computed exchange. Known as "B05," this was the first non-local correlation model designed to work with the full non-locality of exact (or Hartree-Fock) exchange. Non-locality issues, often referred to as the "delocalization" problem, are among the most vexing problems in density-functional theory today. How much exact exchange should be used in a hybrid functional? What value of the range parameter should be used in a long-range corrected functional? Questions such as these abound, and the answers are system dependent. The physics of non-locality is built into the B05 functional in a natural way, and one wonders, therefore, if B05 might provide a mechanism to answer such questions. Here we explore a variational procedure, "B05min," to do so. We compute dipole moments of 52 small molecules and find that B05min delivers better moments than parent hybrid and long-range corrected functionals. Furthermore, B05min provides a priori optimum exact-exchange mixing fractions and range parameters for the parent functionals, whose values agree with literature values fit to experimental data.
A hybrid version of the SCAN functional including long-range dispersion interactions
Ko, Hsin-Yu; Calegari Andrade, Marcos F.; Santra, Biswajit; Selloni, Annabella; Car, Roberto
The recently developed meta-GGA density functional, called SCAN (strongly constrained and appropriately normed), provides an accurate description of the electronic structure in a broad class of systems characterized by different bonding interactions, including intermediate range van-der-Waals (vdW) bonding. Here we consider a hybrid version of the SCAN functional with inclusion of long-range vdW interactions via a re-parameterized Tkatchenko-Scheffler scheme. Calculations for the S22 molecular database, ice hexamer clusters, and bulk ice Ih indicate that this functional further improves the description of vdW and hydrogen bonding interactions. This work has been supported by the Department of Energy under Grants No. DE-SC0008626.
Gil de la Fe, Juan Miguel; Rodriguez Perez, Rafael; Florido, Ricardo; Garcia Rubiano, Jesus; Mendoza, M. A.; Nuez, A. de la; Espinosa, G.; Martel Escobar, Carlos; Mínguez Torres, Emilio
2013-01-01
In this work we present an analysis of the influence of the thermodynamic regime on the monochromatic emissivity, the radiative power loss and the radiative cooling rate for optically thin carbon plasmas over a wide range of electron temperature and density assuming steady state situations. Furthermore, we propose analytical expressions depending on the electron density and temperature for the average ionization and cooling rate based on polynomial fittings which are valid for the whole range...
Comparative studies of density-functional approximations for light atoms in strong magnetic fields
Zhu, Wuming; Zhang, Liang; Trickey, S. B.
2014-08-01
For a wide range of magnetic fields, 0≤B≤2000 a.u., we present a systematic comparative study of the performance of different types of density-functional approximations in light atoms (2≤Z≤6). Local, generalized-gradient approximation (GGA; semilocal), and meta-GGA ground-state exchange-correlation (xc) functionals are compared on an equal footing with exact-exchange, Hartree-Fock (HF), and current-density-functional-theory (CDFT) approximations. Comparison also is made with published quantum Monte Carlo data. Though all approximations give qualitatively reasonable results, the exchange energies from local and GGA functionals are too negative for large B. Results from the Perdew-Burke-Ernzerhof ground-state GGA and Tao-Perdew-Staroverov-Scuseria (TPSS) ground-state meta-GGA functionals are very close. Because of confinement, self-interaction error in such functionals is more severe at large B than at B =0, hence self-interaction correction is crucial. Exact exchange combined with the TPSS correlation functional results in a self-interaction-free (xc) functional, from which we obtain atomic energies of comparable accuracy to those from correlated wave-function methods. Specifically for the B and C atoms, we provide beyond-HF energies in a wide range of B fields. Fully self-consistent CDFT calculations were done with the Vignale-Rasolt-Geldart (VRG) functional in conjunction with the PW92 xc functional. Current effects turn out to be small, and the vorticity variable in the VRG functional diverges in some low-density regions. This part of the study suggests that nonlocal, self-interaction-free functionals may be better than local approximations as a starting point for CDFT functional construction and that some basic variable other than the vorticity could be helpful in making CDFT calculations practical.
Density-functional perturbation theory goes time-dependent
Directory of Open Access Journals (Sweden)
Gebauer, Ralph
2008-05-01
Full Text Available The scope of time-dependent density-functional theory (TDDFT is limited to the lowest portion of the spectrum of rather small systems (a few tens of atoms at most. In the static regime, density-functional perturbation theory (DFPT allows one to calculate response functions of systems as large as currently dealt with in ground-state simulations. In this paper we present an effective way of combining DFPT with TDDFT. The dynamical polarizability is first expressed as an off-diagonal matrix element of the resolvent of the Kohn-Sham Liouvillian super-operator. A DFPT representation of response functions allows one to avoid the calculation of unoccupied Kohn-Sham orbitals. The resolvent of the Liouvillian is finally conveniently evaluated using a newly developed non-symmetric Lanczos technique, which allows for the calculation of the entire spectrum with a single Lanczos recursion chain. Each step of the chain essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn-Sham Hamiltonian or, for that matter, as a single time step of a Car-Parrinello molecular dynamics run. The method will be illustrated with a few case molecular applications.
Density-dependence of functional spiking networks in vitro
Energy Technology Data Exchange (ETDEWEB)
Ham, Michael I [Los Alamos National Laboratory; Gintautuas, Vadas [Los Alamos National Laboratory; Rodriguez, Marko A [Los Alamos National Laboratory; Bettencourt, Luis M A [Los Alamos National Laboratory; Bennett, Ryan [UNIV OF NORTH TEXAS; Santa Maria, Cara L [UNIV OF NORTH TEXAS
2008-01-01
During development, the mammalian brain differentiates into specialized regions with unique functional abilities. While many factors contribute to this functional specialization, we explore the effect neuronal density can have on neuronal interactions. Two types of networks, dense (50,000 neurons and glia support cells) and sparse (12,000 neurons and glia support cells), are studied. A competitive first response model is applied to construct activation graphs that represent pairwise neuronal interactions. By observing the evolution of these graphs during development in vitro we observe that dense networks form activation connections earlier than sparse networks, and that link-!llltropy analysis of the resulting dense activation graphs reveals that balanced directional connections dominate. Information theoretic measures reveal in addition that early functional information interactions (of order 3) are synergetic in both dense and sparse networks. However, during development in vitro, such interactions become redundant in dense, but not sparse networks. Large values of activation graph link-entropy correlate strongly with redundant ensembles observed in the dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue also in vivo.
Performance of Density Functional Theory for Second Row (4d) Transition Metal Thermochemistry.
Laury, Marie L; Wilson, Angela K
2013-09-10
The performances of 22 density functionals, including generalized gradient approximation (GGA), hybrid GGAs, hybrid-meta GGAs, and range-separated and double hybrid functionals, in combination with the correlation consistent basis sets and effective core potentials, have been gauged for the prediction of gas phase enthalpies of formation for the TM-4d set, which contains 30 second row transition metal-containing molecules. The enthalpies of formation determined by the 22 density functionals were compared to those generated via the relativistic pseudopotential correlation consistent Composite Approach (rp-ccCA), which has a goal of reproducing energies akin to those from CCSD(T,FC1)-DK/aug-cc-pCV∞Z-DK calculations. B3LYP/cc-pVTZ-PP optimized geometries were used in this study, though structures determined by other functionals also were examined. Of the functionals employed, the double hybrid functionals, B2GP-PLYP and mPW2-PLYP, yielded the best overall results with mean absolute deviations (MADs) from experimental enthalpies of formation of 4.25 and 5.19 kcal mol(-1), respectively. The GGA functionals BP86 and PBEPBE resulted in deviations from experiment of nearly 100 kcal mol(-1) for molecules such as molybdenum carbonyls. The ωB97X-D functional, which includes the separation of exchange energy into long-range and short-range contributions and includes a dispersion correction, resulted in an MAD of 6.52 kcal mol(-1).
Formaldehyde adsorption on carbon nanotubes fragment by density functional theory
Chen, D.; Yuan, Yong J.
2017-07-01
The interaction between formaldehyde (HCOH) and pristine single-walled carbon nanotube (SWCNT) fragment was investigated by density functional theory (DFT) to evaluate the detection of HCOH. The simulation results demonstrated less adsorption on surface of SWCNT and doped CNTs, while a HCOH molecule tended to be chemisorbed to the C atom located on SWCNT’s edge positions with larger binding energy of 1.742 eV and smaller binding distance of 1.351 Å. Furthermore, charge transfer and density of states study indicated that the electronic properties changed evidently in the most stable HCOH-SWCNT system, and were mainly around the Fermi level. More importantly, the adsorption of HCOH affected the electronic conductance of SWCNT. It is expected that the results could provide a useful theoretical guidance for the investigation of molecular films interface bonding and design of HCOH sensing devices.
Probability density functions for use when calculating standardised drought indices
Svensson, Cecilia; Prosdocimi, Ilaria; Hannaford, Jamie
2015-04-01
Time series of drought indices like the standardised precipitation index (SPI) and standardised flow index (SFI) require a statistical probability density function to be fitted to the observed (generally monthly) precipitation and river flow data. Once fitted, the quantiles are transformed to a Normal distribution with mean = 0 and standard deviation = 1. These transformed data are the SPI/SFI, which are widely used in drought studies, including for drought monitoring and early warning applications. Different distributions were fitted to rainfall and river flow data accumulated over 1, 3, 6 and 12 months for 121 catchments in the United Kingdom. These catchments represent a range of catchment characteristics in a mid-latitude climate. Both rainfall and river flow data have a lower bound at 0, as rains and flows cannot be negative. Their empirical distributions also tend to have positive skewness, and therefore the Gamma distribution has often been a natural and suitable choice for describing the data statistically. However, after transformation of the data to Normal distributions to obtain the SPIs and SFIs for the 121 catchments, the distributions are rejected in 11% and 19% of cases, respectively, by the Shapiro-Wilk test. Three-parameter distributions traditionally used in hydrological applications, such as the Pearson type 3 for rainfall and the Generalised Logistic and Generalised Extreme Value distributions for river flow, tend to make the transformed data fit better, with rejection rates of 5% or less. However, none of these three-parameter distributions have a lower bound at zero. This means that the lower tail of the fitted distribution may potentially go below zero, which would result in a lower limit to the calculated SPI and SFI values (as observations can never reach into this lower tail of the theoretical distribution). The Tweedie distribution can overcome the problems found when using either the Gamma or the above three-parameter distributions. The
Density-functional method for nonequilibrium electron transport
DEFF Research Database (Denmark)
Brandbyge, Mads; Mozos, J.L.; Ordejon, P.
2002-01-01
We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented...... the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme...... wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects....
Directory of Open Access Journals (Sweden)
Daniel D Bjornlie
Full Text Available Changes in life history traits of species can be an important indicator of potential factors influencing populations. For grizzly bears (Ursus arctos in the Greater Yellowstone Ecosystem (GYE, recent decline of whitebark pine (WBP; Pinus albicaulis, an important fall food resource, has been paired with a slowing of population growth following two decades of robust population increase. These observations have raised questions whether resource decline or density-dependent processes may be associated with changes in population growth. Distinguishing these effects based on changes in demographic rates can be difficult. However, unlike the parallel demographic responses expected from both decreasing food availability and increasing population density, we hypothesized opposing behavioral responses of grizzly bears with regard to changes in home-range size. We used the dynamic changes in food resources and population density of grizzly bears as a natural experiment to examine hypotheses regarding these potentially competing influences on grizzly bear home-range size. We found that home-range size did not increase during the period of whitebark pine decline and was not related to proportion of whitebark pine in home ranges. However, female home-range size was negatively associated with an index of population density. Our data indicate that home-range size of grizzly bears in the GYE is not associated with availability of WBP, and, for female grizzly bears, increasing population density may constrain home-range size.
Bjornlie, Daniel D; Van Manen, Frank T; Ebinger, Michael R; Haroldson, Mark A; Thompson, Daniel J; Costello, Cecily M
2014-01-01
Changes in life history traits of species can be an important indicator of potential factors influencing populations. For grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem (GYE), recent decline of whitebark pine (WBP; Pinus albicaulis), an important fall food resource, has been paired with a slowing of population growth following two decades of robust population increase. These observations have raised questions whether resource decline or density-dependent processes may be associated with changes in population growth. Distinguishing these effects based on changes in demographic rates can be difficult. However, unlike the parallel demographic responses expected from both decreasing food availability and increasing population density, we hypothesized opposing behavioral responses of grizzly bears with regard to changes in home-range size. We used the dynamic changes in food resources and population density of grizzly bears as a natural experiment to examine hypotheses regarding these potentially competing influences on grizzly bear home-range size. We found that home-range size did not increase during the period of whitebark pine decline and was not related to proportion of whitebark pine in home ranges. However, female home-range size was negatively associated with an index of population density. Our data indicate that home-range size of grizzly bears in the GYE is not associated with availability of WBP, and, for female grizzly bears, increasing population density may constrain home-range size.
Density-functional computation of 99Ru NMR parameters
Buhl; Gaemers; Elsevier
2000-09-01
Gradient-corrected and hybrid variants of density-functional theory are used to compute the geometries and 99Ru chemical shifts of RuO4, [RuCp2], [K4Ru(CN)6], [Ru3(CO)12], [Ru(CO)3X3]- (X=Cl, I), [Ru(CO)2Cl4]2-, [Ru(bipy)3]2+, and [Ru(CO)2(iPr-DAB)(X)(Y)] [XY= Cl2, I2, MeCl, MeI, or (SnMe3)2]. For this set of compounds, substituent effects on delta(99Ru) are somewhat underestimated with the BPW91 pure density functional but are described well by the B3LYP hybrid functional, which can also be used to reproduce empirical trends in electric field gradients (EFGs) at the Ru nucleus qualitatively. In the [Ru(CO)2(iPr-DAB)XY] series, trends in the computed EFGs parallel those in the observed 99Ru NMR linewidths, in accordance with the quadrupolar relaxation mechanism expected for this nucleus. For this series of compounds, the use of X-ray-derived geometries affords a worse correlation between calculated EFGs and experimental linewidths than does the use of optimized geometries.
INTERACTIVE VISUALIZATION OF PROBABILITY AND CUMULATIVE DENSITY FUNCTIONS
Potter, Kristin
2012-01-01
The probability density function (PDF), and its corresponding cumulative density function (CDF), provide direct statistical insight into the characterization of a random process or field. Typically displayed as a histogram, one can infer probabilities of the occurrence of particular events. When examining a field over some two-dimensional domain in which at each point a PDF of the function values is available, it is challenging to assess the global (stochastic) features present within the field. In this paper, we present a visualization system that allows the user to examine two-dimensional data sets in which PDF (or CDF) information is available at any position within the domain. The tool provides a contour display showing the normed difference between the PDFs and an ansatz PDF selected by the user and, furthermore, allows the user to interactively examine the PDF at any particular position. Canonical examples of the tool are provided to help guide the reader into the mapping of stochastic information to visual cues along with a description of the use of the tool for examining data generated from an uncertainty quantification exercise accomplished within the field of electrophysiology.
Graphene oxide and adsorption of chloroform: A density functional study
Energy Technology Data Exchange (ETDEWEB)
Kuisma, Elena; Hansson, C. Fredrik; Lindberg, Th. Benjamin; Gillberg, Christoffer A.; Idh, Sebastian; Schröder, Elsebeth, E-mail: schroder@chalmers.se [Quantum Device Physics Laboratory, Microtechnology and Nanoscience (MC2), Chalmers University of Technology, SE-412 96 Göteborg (Sweden)
2016-05-14
Chlorinated hydrocarbon compounds are of environmental concerns, since they are toxic to humans and other mammals, and are widespread, and exposure is hard to avoid. Understanding and improving methods to reduce the amount of the substances are important. We present an atomic-scale calculational study of the adsorption of chlorine-based substance chloroform (CHCl{sub 3}) on graphene oxide, as a step in estimating the capacity of graphene oxide for filtering out such substances, e.g., from drinking water. The calculations are based on density functional theory, and the recently developed consistent-exchange functional for the van der Waals density-functional method is employed. We obtain values of the chloroform adsorption energy varying from roughly 0.2 to 0.4 eV per molecule. This is comparable to previously found results for chloroform adsorbed directly on clean graphene, using similar calculations. In a wet environment, like filters for drinking water, the graphene will not stay clean and will likely oxidize, and thus adsorption onto graphene oxide, rather than clean graphene, is a more relevant process to study.
Graphene oxide and adsorption of chloroform: a density functional study
Kuisma, Elena; Lindberg, Th Benjamin; Gillberg, Christoffer A; Idh, Sebastian; Schroder, Elsebeth
2016-01-01
Chlorinated hydrocarbon compounds are of environmental concerns, since they are toxic to humans and other mammals, are widespread, and exposure is hard to avoid. Understanding and improving methods to reduce the amount of the substances is important. We present an atomic-scale calculational study of the adsorption of chlorine-based substance chloroform (CHCl3) on graphene oxide, as a step in estimating the capacity of graphene oxide for filtering out such substances, e.g., from drinking water. The calculations are based on density functional theory (DFT), and the recently developed consistent-exchange functional for the van der Waals density-functional method (vdW-DF-cx) is employed. We obtain values of the chloroform adsorption energy varying from roughly 0.2 to 0.4 eV per molecule. This is comparable to previously found results for chloroform adsorbed directly on clean graphene, using similar calculations. In a wet environment, like filters for drinking water, the graphene will not stay clean and will likel...
Visualization techniques for spatial probability density function data
Directory of Open Access Journals (Sweden)
Udeepta D Bordoloi
2006-01-01
Full Text Available Novel visualization methods are presented for spatial probability density function data. These are spatial datasets, where each pixel is a random variable, and has multiple samples which are the results of experiments on that random variable. We use clustering as a means to reduce the information contained in these datasets; and present two different ways of interpreting and clustering the data. The clustering methods are used on two datasets, and the results are discussed with the help of visualization techniques designed for the spatial probability data.
Continuation of probability density functions using a generalized Lyapunov approach
Energy Technology Data Exchange (ETDEWEB)
Baars, S., E-mail: s.baars@rug.nl [Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, P.O. Box 407, 9700 AK Groningen (Netherlands); Viebahn, J.P., E-mail: viebahn@cwi.nl [Centrum Wiskunde & Informatica (CWI), P.O. Box 94079, 1090 GB, Amsterdam (Netherlands); Mulder, T.E., E-mail: t.e.mulder@uu.nl [Institute for Marine and Atmospheric research Utrecht, Department of Physics and Astronomy, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); Kuehn, C., E-mail: ckuehn@ma.tum.de [Technical University of Munich, Faculty of Mathematics, Boltzmannstr. 3, 85748 Garching bei München (Germany); Wubs, F.W., E-mail: f.w.wubs@rug.nl [Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, P.O. Box 407, 9700 AK Groningen (Netherlands); Dijkstra, H.A., E-mail: h.a.dijkstra@uu.nl [Institute for Marine and Atmospheric research Utrecht, Department of Physics and Astronomy, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY (United States)
2017-05-01
Techniques from numerical bifurcation theory are very useful to study transitions between steady fluid flow patterns and the instabilities involved. Here, we provide computational methodology to use parameter continuation in determining probability density functions of systems of stochastic partial differential equations near fixed points, under a small noise approximation. Key innovation is the efficient solution of a generalized Lyapunov equation using an iterative method involving low-rank approximations. We apply and illustrate the capabilities of the method using a problem in physical oceanography, i.e. the occurrence of multiple steady states of the Atlantic Ocean circulation.
Nuclear clustering in the energy density functional approach
Energy Technology Data Exchange (ETDEWEB)
Ebran, J.-P., E-mail: jean-paul.ebran@cea.fr [CEA,DAM,DIF, F-91297 Arpajon (France); Khan, E. [Institut de Physique Nucléaire, Université Paris-Sud CEA, IN2P3 CNRS, F-91406 Orsay Cedex (France); Nikšić, T.; Vretenar, D. [Physics Department, Faculty of Science, University of Zagreb, 10000 Zagreb (Croatia)
2015-10-15
Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.
Density-functional errors in ionization potential with increasing system size
Energy Technology Data Exchange (ETDEWEB)
Whittleton, Sarah R.; Sosa Vazquez, Xochitl A.; Isborn, Christine M., E-mail: cisborn@ucmerced.edu [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Johnson, Erin R., E-mail: erin.johnson@dal.ca [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2 (Canada)
2015-05-14
This work investigates the effects of molecular size on the accuracy of density-functional ionization potentials for a set of 28 hydrocarbons, including series of alkanes, alkenes, and oligoacenes. As the system size increases, delocalization error introduces a systematic underestimation of the ionization potential, which is rationalized by considering the fractional-charge behavior of the electronic energies. The computation of the ionization potential with many density-functional approximations is not size-extensive due to excessive delocalization of the incipient positive charge. While inclusion of exact exchange reduces the observed errors, system-specific tuning of long-range corrected functionals does not generally improve accuracy. These results emphasize that good performance of a functional for small molecules is not necessarily transferable to larger systems.
Self-consistent density functional calculation of the image potential at a metal surface
Energy Technology Data Exchange (ETDEWEB)
Jung, J [Departamento de Fisica Fundamental, Universidad Nacional de Educacion a Distancia, Apartado 60141, 28080 Madrid (Spain); Alvarellos, J E [Departamento de Fisica Fundamental, Universidad Nacional de Educacion a Distancia, Apartado 60141, 28080 Madrid (Spain); Chacon, E [Instituto de Ciencias de Materiales de Madrid, Consejo Superior de Investigaciones CientIficas, E-28049 Madrid (Spain); GarcIa-Gonzalez, P [Departamento de Fisica Fundamental, Universidad Nacional de Educacion a Distancia, Apartado 60141, 28080 Madrid (Spain)
2007-07-04
It is well known that the exchange-correlation (XC) potential at a metal surface has an image-like asymptotic behaviour given by -1/4(z-z{sub 0}), where z is the coordinate perpendicular to the surface. Using a suitable fully non-local functional prescription, we evaluate self-consistently the XC potential with the correct image behaviour for simple jellium surfaces in the range of metallic densities. This allows a proper comparison between the corresponding image-plane position, z{sub 0}, and other related quantities such as the centroid of an induced charge by an external perturbation. As a by-product, we assess the routinely used local density approximation when evaluating electron density profiles, work functions, and surface energies by focusing on the XC effects included in the fully non-local description.
Campbell, D L M; Lee, C; Hinch, G N; Roberts, J R
2017-09-01
Free-range laying hen systems are increasing in number within Australia. Variation in outdoor stocking densities has led to development of a national information standard on free-range egg labeling, including setting a maximum density of 10,000 hens per hectare. However, there are few data on the impacts of differing outdoor densities on production and egg quality. ISA Brown hens in small (150 hens) flocks were housed in identical indoor pens, each with access (from 21 weeks) to different sized ranges simulating one of three outdoor stocking densities (2 replicates each: 2,000 hens/hectare (ha), 10,000 hens/ha, 20,000 hens/ha). Hen-day production was tracked from 21 through 35 weeks with eggs visually graded daily for external deformities. All eggs laid on one day were weighed each week. Eggs were collected from each pen at 25, 30, and 36 weeks and analyzed for egg quality. There were no effects of outdoor stocking density on average hen-day percentage production (P = 0.67), egg weight (P = 0.09), percentages of deformed eggs (P = 0.30), shell reflectivity (P = 0.74), shell breaking strength (P = 0.07), shell deformation (P = 0.83), or shell thickness (P = 0.24). Eggs from hens in the highest density had the highest percentage shell weight (P = 0.004) and eggs from the lowest density had the highest yolk color score (P < 0.001). The amount of cuticle present did not differ between densities (P = 0.95) but some aspects of shell colors (P ≤ 0.01) and location of protoporphyrin IX (P = 0.046) varied. Hen age affected the majority of measurements. Stocking density differences may be related to hen diet as previous radio-frequency identification tracking of individual hens in these flocks showed birds used the range for longer in the lowest density and the least in the highest density, including depleting the range of vegetation sooner in the smaller ranges. An additional study assessing the relationship between individual hen range use, nutrition, and egg
Crystallization of supercooled liquid antimony: A density functional study
Ropo, M.; Akola, J.; Jones, R. O.
2017-11-01
Crystallization of liquid antimony has been studied at 600 K using six density functional/molecular dynamics simulations with up to 882 atoms and three scenarios: one completely disordered sample that did not crystallize even after 570 ps, four with fixed crystalline slab templates, and one with a fixed crystalline seed. Crystallization proceeded layer-by-layer in most cases and was rapid (˜36 m/s) with templates and somewhat slower with the seed. The seed simulation shows an unusual percolation asymmetry where the crystallite grows faster in the direction normal to the zigzag planes. Changes in pair distribution functions, bond angle distributions, ring statistics, nearest-neighbor distances, and cavity volumes were monitored. Diffusion plays a minor role in the process, and the evolution of bond lengths and ring statistics supports the bond-interchange model introduced to explain the rapid crystallization of Sb-rich phase change materials.
Energetics of cyclohexane isomers: a density-functional study
Lee, C Y
1999-01-01
The binding energies and the geometric structures of conformational isomers of cyclohexane (C sub 6 H sub 1 sub 2) are determined from the density-functional theory combined with ultrasoft pseudopotentials and gradient-corrected nonlocal exchange-correlation functionals. The ground-state chair conformation is found to have a binding energy of 99.457 eV, and the metastable twist-boat conformation has 99.161 eV. The chair conformation converts to another conformation via a half-chair conformation with an energy barrier of 0.507 eV whereas the twist-boat conformation converts to another twist-boat conformation via a boat conformation with a much smaller energy barrier of 0.015 eV.
Geometry-based density functional theory an overview
Schmidt, M
2003-01-01
An overview of recent developments and applications of a specific density functional approach that originates from Rosenfeld's fundamental measure theory for hard spheres is given. Model systems that were treated include penetrable spheres that interact with a step function pair potential, the Widom-Rowlinson model, the Asakura-Oosawa colloid-polymer mixture, ternary mixtures of spheres, needles, and globular polymers, hard-body amphiphilic mixtures, fluids in porous media, and random sequential adsorption that describes non-equilibrium processes such as colloidal deposition and random car parking. In these systems various physical phenomena were studied, such as correlations in liquids, freezing and demixing phase behaviour, the properties of fluid interfaces with and without orientational order, and wetting and layering phenomena at walls.
Building a universal nuclear energy density functional (UNEDF)
Energy Technology Data Exchange (ETDEWEB)
Nazarewicz, Witold [Univ. of Tennessee, Knoxville, TN (United States)
2012-07-01
The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: First, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties. Second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data. Third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory.
Uncertainty Quantification and Propagation in Nuclear Density Functional Theory
Energy Technology Data Exchange (ETDEWEB)
Schunck, N; McDonnell, J D; Higdon, D; Sarich, J; Wild, S M
2015-03-17
Nuclear density functional theory (DFT) is one of the main theoretical tools used to study the properties of heavy and superheavy elements, or to describe the structure of nuclei far from stability. While on-going eff orts seek to better root nuclear DFT in the theory of nuclear forces, energy functionals remain semi-phenomenological constructions that depend on a set of parameters adjusted to experimental data in fi nite nuclei. In this paper, we review recent eff orts to quantify the related uncertainties, and propagate them to model predictions. In particular, we cover the topics of parameter estimation for inverse problems, statistical analysis of model uncertainties and Bayesian inference methods. Illustrative examples are taken from the literature.
Nuclear charge radii: density functional theory meets Bayesian neural networks
Utama, R.; Chen, Wei-Chia; Piekarewicz, J.
2016-11-01
The distribution of electric charge in atomic nuclei is fundamental to our understanding of the complex nuclear dynamics and a quintessential observable to validate nuclear structure models. The aim of this study is to explore a novel approach that combines sophisticated models of nuclear structure with Bayesian neural networks (BNN) to generate predictions for the charge radii of thousands of nuclei throughout the nuclear chart. A class of relativistic energy density functionals is used to provide robust predictions for nuclear charge radii. In turn, these predictions are refined through Bayesian learning for a neural network that is trained using residuals between theoretical predictions and the experimental data. Although predictions obtained with density functional theory provide a fairly good description of experiment, our results show significant improvement (better than 40%) after BNN refinement. Moreover, these improved results for nuclear charge radii are supplemented with theoretical error bars. We have successfully demonstrated the ability of the BNN approach to significantly increase the accuracy of nuclear models in the predictions of nuclear charge radii. However, as many before us, we failed to uncover the underlying physics behind the intriguing behavior of charge radii along the calcium isotopic chain.
JDFTx: Software for joint density-functional theory
Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; Gunceler, Deniz; Ozhabes, Yalcin; Arias, T. A.
Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.
New approaches for the calibration of exchange-energy densities in local hybrid functionals.
Maier, Toni M; Haasler, Matthias; Arbuznikov, Alexei V; Kaupp, Martin
2016-08-21
The ambiguity of exchange-energy densities is a fundamental challenge for the development of local hybrid functionals, or of other functionals based on a local mixing of exchange-energy densities. In this work, a systematic construction of semi-local calibration functions (CFs) for adjusting the exchange-energy densities in local hybrid functionals is provided, which directly links a given CF to an underlying semi-local exchange functional, as well as to the second-order gradient expansion of the exchange hole. Using successive steps of integration by parts allows the derivation of correction terms of increasing order, resulting in more and more complicated but also more flexible CFs. We derive explicit first- and second-order CFs (pig1 and pig2) based on B88 generalized-gradient approximation (GGA) exchange, and a first-order CF (tpig1) based on τ-dependent B98 meta-GGA exchange. We combine these CFs with different long-range damping functions and evaluate them for calibration of LDA, B88 GGA, and TPSS meta-GGA exchange-energy densities. Based on a minimization of unphysical nondynamical correlation contributions in three noble-gas dimer potential-energy curves, free parameters in the CFs are optimized, and performance of various approaches in the calibration of different exchange-energy densities is compared. Most notably, the second-order pig2 CF provides the largest flexibility with respect to the diffuseness of the damping function. This suggests that higher-order CFs based on the present integration-by-parts scheme may be particularly suitable for the flexible construction of local hybrid functionals.
Nonequilibrium green functions in time-dependent current-density-functional theory
Bonitz, M; Semkat, D
2003-01-01
We give an overview of the underlying concepts of time-dependent current-density functional theory (TDCDFT). We show how the basic equations of TDCDFT can be elegantly derived using the time contour method of nonequilibrium Green function theory. We further demonstrate how the formalism can be used
DEFF Research Database (Denmark)
Bast, Radovan; Jensen, Hans Jørgen Aagaard; Saue, Trond
2009-01-01
We report an implementation of adiabatic time-dependent density functional theory based on the 4-component relativistic Dirac-Coulomb Hamiltonian and a closed-shell reference. The implementation includes noncollinear spin magnetization and full derivatives of functionals, including hybrid general...
Application of ferrofluid density separation to particles in the micrometer-size range
Energy Technology Data Exchange (ETDEWEB)
Strebin, R.S. Jr.; Johnson, J.W.; Robertson, D.M.
1976-02-01
A device designed and described by AVCO* as a ''Ferrofluid Density Separator''/sup (1)/ develops an apparent fluid density from nominally 2 to 20 g/cm/sup 3/ dependent on the magnitude of an imposed magnetic field gradient. The ferrofluid retains other normal properties of a liquid. One of these devices and a concentration series of ferrofluids were obtained in order to determine the practicality of separating groups of micrometer-size particles into density fractions. Such separations would be of enormous value in the study of various particle burdens because particles of interest are almost always diluted with overwhelming amounts of other particles. The results of a study of separations of micrometer-size particles with the ferrofluid density separator are presented.
Medium density polyethylene composites with functionalized carbon nanotubes
Pulikkathara, Merlyn X.; Kuznetsov, Oleksandr V.; Peralta, Ivana R. G.; Wei, Xin; Khabashesku, Valery N.
2009-05-01
A strong interface between the single-walled carbon nanotubes (SWNTs) and polymer matrix is necessary to achieve enhanced mechanical properties of composites. In this work a series of sidewall-functionalized SWNTs have been investigated in order to evaluate the effect of functionalization on SWNT aspect ratio and composite interfacial chemistry and their role on mechanical properties of a medium density polyethylene (MDPE) matrix. Fluorinated nanotubes (F-SWNTs) were used as precursors for subsequent sidewall functionalization with long chain alkyl groups to produce an F-SWNT- C11H23 derivative. The latter was refluorinated to yield a new perfluorinated derivative, F-SWNT- C11FxHy. The functionalized SWNTs as well as the pristine SWNTs were integrated into an MDPE matrix at a 1 wt% loading. The nanotubes and composite materials were characterized with FTIR, Raman spectroscopy, NMR, XPS, AFM, SEM, TGA, DSC and tensile tests. When incorporated into polyethylene, the new perfluorinated derivative, F-SWNT- C11FxHy, yielded the highest tensile strength value among all nanotube/MDPE composite samples, showing a 52% enhancement in comparison with the neat MDPE. The 1 wt% SWNT/MDPE composite contained nanotubes with a larger aspect ratio but, due to a lack of interfacial chemistry, it resulted in less improvement in mechanical properties compared to the composites made with the fluorinated SWNT derivatives.
Benchmarking Density Functionals for Chemical Bonds of Gold.
Kepp, Kasper P
2017-03-09
Gold plays a major role in nanochemistry, catalysis, and electrochemistry. Accordingly, hundreds of studies apply density functionals to study chemical bonding with gold, yet there is no systematic attempt to assess the accuracy of these methods applied to gold. This paper reports a benchmark against 51 experimental bond enthalpies of AuX systems and seven additional polyatomic and cationic molecules. Twelve density functionals were tested, covering meta functionals, hybrids with variable HF exchange, double-hybrid, dispersion-corrected, and nonhybrid GGA functionals. The defined benchmark data set probes all types of bonding to gold from very electronegative halides that force Au + electronic structure, via covalently bonded systems, hard and soft Lewis acids and bases that either work against or complement the softness of gold, the Au 2 molecule probing gold's bond with itself, and weak bonds between gold and noble gases. Zero-point vibrational corrections are relatively small for Au-X bonds, ∼ 11-12 kJ/mol except for Au-H bonds. Dispersion typically provides ∼5 kJ/mol of the total bond enthalpy but grows with system size and is 10 kJ/mol for AuXe and AuKr. HF exchange and LYP correlation produce weaker bonds to gold. Most functionals provide similar trend accuracy, though somewhat lower for M06 and M06L, but very different numerical accuracy. Notably, PBE and TPSS functionals with dispersion display the smallest numerical errors and very small mean signed errors (0-6 kJ/mol), i.e. no bias toward over- or under-binding. Errors are evenly distributed versus atomic number, suggesting that relativistic effects are treated fairly; the mean absolute error is almost halved from B3LYP (45 kJ/mol) to TPSS and PBE (23 kJ/mol, including difficult cases); 23 kJ/mol is quite respectable considering the diverse bonds to gold and the complication of relativistic effects. Thus, studies that use DFT with effective core potentials for gold chemistry, with no alternative due
The probability density function (PDF) of Lagrangian Turbulence
Birnir, B.
2012-12-01
The statistical theory of Lagrangian turbulence is derived from the stochastic Navier-Stokes equation. Assuming that the noise in fully-developed turbulence is a generic noise determined by the general theorems in probability, the central limit theorem and the large deviation principle, we are able to formulate and solve the Kolmogorov-Hopf equation for the invariant measure of the stochastic Navier-Stokes equations. The intermittency corrections to the scaling exponents of the structure functions require a multiplicative (multipling the fluid velocity) noise in the stochastic Navier-Stokes equation. We let this multiplicative noise, in the equation, consists of a simple (Poisson) jump process and then show how the Feynmann-Kac formula produces the log-Poissonian processes, found by She and Leveque, Waymire and Dubrulle. These log-Poissonian processes give the intermittency corrections that agree with modern direct Navier-Stokes simulations (DNS) and experiments. The probability density function (PDF) plays a key role when direct Navier-Stokes simulations or experimental results are compared to theory. The statistical theory of turbulence is determined, including the scaling of the structure functions of turbulence, by the invariant measure of the Navier-Stokes equation and the PDFs for the various statistics (one-point, two-point, N-point) can be obtained by taking the trace of the corresponding invariant measures. Hopf derived in 1952 a functional equation for the characteristic function (Fourier transform) of the invariant measure. In distinction to the nonlinear Navier-Stokes equation, this is a linear functional differential equation. The PDFs obtained from the invariant measures for the velocity differences (two-point statistics) are shown to be the four parameter generalized hyperbolic distributions, found by Barndorff-Nilsen. These PDF have heavy tails and a convex peak at the origin. A suitable projection of the Kolmogorov-Hopf equations is the
Flomenbom, Ophir; Silbey, Robert J
2007-07-21
The Green's function for the master equation and the generalized master equation in path representation is an infinite sum over the length of path probability density functions (PDFs). In this paper, the properties of path PDFs are studied both qualitatively and quantitatively. The results are used in building efficient approximations for Green's function in 1D, and are relevant in modeling and in data analysis.
Patra, Abhirup; Bates, Jefferson E; Sun, Jianwei; Perdew, John P
2017-10-31
We have computed the surface energies, work functions, and interlayer surface relaxations of clean (111), (100), and (110) surfaces of Al, Cu, Ru, Rh, Pd, Ag, Pt, and Au. We interpret the surface energy from liquid metal measurements as the mean of the solid-state surface energies over these three lowest-index crystal faces. We compare experimental (and random phase approximation) reference values to those of a family of nonempirical semilocal density functionals, from the basic local density approximation (LDA) to our most advanced general purpose meta-generalized gradient approximation, strongly constrained and appropriately normed (SCAN). The closest agreement is achieved by the simplest density functional LDA, and by the most sophisticated one, SCAN+rVV10 (Vydrov-Van Voorhis 2010). The long-range van der Waals interaction, incorporated through rVV10, increases the surface energies by about 10%, and increases the work functions by about 3%. LDA works for metal surfaces through two known error cancellations. The Perdew-Burke-Ernzerhof generalized gradient approximation tends to underestimate both surface energies (by about 24%) and work functions (by about 4%), yielding the least-accurate results. The amount by which a functional underestimates these surface properties correlates with the extent to which it neglects van der Waals attraction at intermediate and long range. Qualitative arguments are given for the signs of the van der Waals contributions to the surface energy and work function. A standard expression for the work function in Kohn-Sham (KS) theory is shown to be valid in generalized KS theory. Interlayer relaxations from different functionals are in reasonable agreement with one another, and usually with experiment. Published under the PNAS license.
Progress in Time-Dependent Density-Functional Theory
Casida, M E
2011-01-01
The classic density-functional theory (DFT) formalism introduced by Hohenberg, Kohn, and Sham in the mid-1960s, is based upon the idea that the complicated N-electron wavefunction can be replaced with the mathematically simpler 1-electron charge density in electronic struc- ture calculations of the ground stationary state. As such, ordinary DFT is neither able to treat time-dependent (TD) problems nor describe excited electronic states. In 1984, Runge and Gross proved a theorem making TD-DFT formally exact. Information about electronic excited states may be obtained from this theory through the linear response (LR) theory formalism. Begin- ning in the mid-1990s, LR-TD-DFT became increasingly popular for calculating absorption and other spectra of medium- and large-sized molecules. Its ease of use and relatively good accuracy has now brought LR-TD-DFT to the forefront for this type of application. As the number and the diversity of applications of TD-DFT has grown, so too has grown our understanding of the str...
Density functional theory and phytochemical study of 8-hydroxyisodiospyrin
Ullah, Zakir; Ata-ur-Rahman; Fazl-i-Sattar; Rauf, Abdur; Yaseen, Muhammad; Hassan, Waseem; Tariq, Muhammad; Ayub, Khurshid; Tahir, Asif Ali; Ullah, Habib
2015-09-01
Comprehensive theoretical and experimental studies of a natural product, 8-hydroxyisodiospyrin (HDO) have been carried out. Based on the correlation of experimental and theoretical data, an appropriate computational model was developed for obtaining the electronic, spectroscopic, and thermodynamic parameters of HDO. First of all, the exact structure of HDO is confirmed from the nice correlation of theory and experiment, prior to determination of its electroactive nature. Hybrid density functional theory (DFT) is employed for all theoretical simulations. The experimental and predicted IR and UV-vis spectra [B3LYP/6-31+G(d,p) level of theory] have excellent correlation. Inter-molecular non-covalent interaction of HDO with different gases such as NH3, CO2, CO, H2O is investigated through geometrical counterpoise (gCP) i.e., B3LYP-gCP-D3/6-31G∗ method. Furthermore, the inter-molecular interaction is also supported by geometrical parameters, electronic properties, thermodynamic parameters and charge analysis. All these characterizations have corroborated each other and confirmed the electroactive nature (non-covalent interaction ability) of HDO for the studied gases. Electronic properties such as Ionization Potential (IP), Electron Affinities (EA), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap of HDO have been estimated for the first time theoretically.
Density functional study of Pu2C3
Yang, Rong; Tang, Bin; Gao, Tao; Ao, Bing Yun
2017-08-01
The structural, magnetic, electronic, vibrational, thermodynamic and elastic properties of plutonium sesquicarbide (Pu2C3) are investigated based on density functional theory. The use of the Hubbard term to describe the 5 f electrons of plutonium is discussed according the lattice parameters and magnetism. The calculated lattice constants, magnetism and density of states agree well with the experimental data or other theoretical calculations. The Pu-C bonds of Pu2C3 have a mixture of covalent character and ionic character, while covalent character is stronger than ionic character. The phonon frequencies and the assignment of infrared-active, Raman-active and silent modes at Γ point are obtained. Furthermore, the enthalpy difference H-H298, entropy S, heat capacity and linear thermal expansion coefficient α of Pu2C3 have been calculated and compared with the available data. Lastly, the calculated elastic properties predict that Pu2C3 is ductile metal. In addition, the effect of spin-orbit coupling on the structural, magnetic, and electronic properties of Pu2C3 has been discussed. We hope that our results can provide a useful reference for further theoretical and experimental research on Pu2C3.
Wang, F.-F.; Jenness, G.; Al-Saidi, W. A.; Jordan, K. D.
2010-04-01
Localized molecular orbital energy decomposition analysis and symmetry-adapted perturbation theory (SAPT) calculations are used to analyze the two- and three-body interaction energies of four low-energy isomers of (H2O)6 in order to gain insight into the performance of several popular density functionals for describing the electrostatic, exchange-repulsion, induction, and short-range dispersion interactions between water molecules. The energy decomposition analyses indicate that all density functionals considered significantly overestimate the contributions of charge transfer to the interaction energies. Moreover, in contrast to some studies that state that density functional theory (DFT) does not include dispersion interactions, we adopt a broader definition and conclude that for (H2O)6 the short-range dispersion interactions recovered in the DFT calculations account about 75% or more of the net (short-range plus long-range) dispersion energies obtained from the SAPT calculations.
Building A Universal Nuclear Energy Density Functional (UNEDF)
Energy Technology Data Exchange (ETDEWEB)
Carlson, Joe [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Furnstahl, Dick [The Ohio State Univ., Columbus, OH (United States); Horoi, Mihai [Central Michigan Univ., Mount Pleasant, MI (United States); Lusk, Rusty [Argonne National Lab. (ANL), Argonne, IL (United States); Nazarewicz, Witek [Univ. of Tennessee, Knoxville, TN (United States); Ng, Esmond [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Thompson, Ian [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vary, James [Iowa State Univ., Ames, IA (United States)
2012-09-30
During the period of Dec. 1 2006 - Jun. 30, 2012, the UNEDF collaboration carried out a comprehensive study of all nuclei, based on the most accurate knowledge of the strong nuclear interaction, the most reliable theoretical approaches, the most advanced algorithms, and extensive computational resources, with a view towards scaling to the petaflop platforms and beyond. The long-term vision initiated with UNEDF is to arrive at a comprehensive, quantitative, and unified description of nuclei and their reactions, grounded in the fundamental interactions between the constituent nucleons. We seek to replace current phenomenological models of nuclear structure and reactions with a well-founded microscopic theory that delivers maximum predictive power with well-quantified uncertainties. Specifically, the mission of this project has been three-fold: first, to find an optimal energy density functional (EDF) using all our knowledge of the nucleonic Hamiltonian and basic nuclear properties; second, to apply the EDF theory and its extensions to validate the functional using all the available relevant nuclear structure and reaction data; third, to apply the validated theory to properties of interest that cannot be measured, in particular the properties needed for reaction theory. The main physics areas of UNEDF, defined at the beginning of the project, were: ab initio structure; ab initio functionals; DFT applications; DFT extensions; reactions.
Interactive design of probability density functions for shape grammars
Dang, Minh
2015-11-02
A shape grammar defines a procedural shape space containing a variety of models of the same class, e.g. buildings, trees, furniture, airplanes, bikes, etc. We present a framework that enables a user to interactively design a probability density function (pdf) over such a shape space and to sample models according to the designed pdf. First, we propose a user interface that enables a user to quickly provide preference scores for selected shapes and suggest sampling strategies to decide which models to present to the user to evaluate. Second, we propose a novel kernel function to encode the similarity between two procedural models. Third, we propose a framework to interpolate user preference scores by combining multiple techniques: function factorization, Gaussian process regression, autorelevance detection, and l1 regularization. Fourth, we modify the original grammars to generate models with a pdf proportional to the user preference scores. Finally, we provide evaluations of our user interface and framework parameters and a comparison to other exploratory modeling techniques using modeling tasks in five example shape spaces: furniture, low-rise buildings, skyscrapers, airplanes, and vegetation.
Efficient Density Functional Approximation for Electronic Properties of Conjugated Systems
Caldas, Marília J.; Pinheiro, José Maximiano, Jr.; Blum, Volker; Rinke, Patrick
2014-03-01
There is on-going discussion about reliable prediction of electronic properties of conjugated oligomers and polymers, such as ionization potential IP and energy gap. Several exchange-correlation (XC) functionals are being used by the density functional theory community, with different success for different properties. In this work we follow a recent proposal: a fraction α of exact exchange is added to the semi-local PBE XC aiming consistency, for a given property, with the results obtained by many-body perturbation theory within the G0W0 approximation. We focus the IP, taken as the negative of the highest occupied molecular orbital energy. We choose α from a study of the prototype family trans-acetylene, and apply this same α to a set of oligomers for which there is experimental data available (acenes, phenylenes and others). Our results indicate we can have excellent estimates, within 0,2eV mean ave. dev. from the experimental values, better than through complete EN - 1 -EN calculations from the starting PBE functional. We also obtain good estimates for the electrical gap and orbital energies close to the band edge. Work supported by FAPESP, CNPq, and CAPES, Brazil, and DAAD, Germany.
Density functional study of aqueous uranyl(VI) fluoride complexes
Bühl, Michael; Sieffert, Nicolas; Wipff, Georges
2009-01-01
Mixed uranyl aquo fluoro complexes [UO 2(H 2O) xF y] 2-y ( y = 1-4; x + y = 4, 5) have been optimized with BLYP and B3LYP density functionals in vacuo and in a polarizable continuum modeling bulk water, and have been studied at the BLYP level with Car-Parrinello molecular dynamics (MD) simulations. Using constrained MD simulations and thermodynamic integration, the computed free binding energy between aqueous uranyl and fluoride, affording [UO 2(H 2O) 4F] +, is in excellent agreement with experiment. With the same technique, five-coordinate [UO 2F 4(H 2O)] 2- is indicated to be unstable against loss of the water ligand, as the free energy for dissociation is computed to be ca. -7 kcal/mol in aqueous solution.
Density functional theory studies of transition metal nanoparticles in catalysis
DEFF Research Database (Denmark)
Greeley, Jeffrey Philip; Rankin, Rees; Zeng, Zhenhua
2013-01-01
Periodic Density Functional Theory calculations are capable of providing powerful insights into the structural, energetics, and electronic phenomena that underlie heterogeneous catalysis on transition metal nanoparticles. Such calculations are now routinely applied to single crystal metal surfaces...... and to subnanometer metal clusters. Descriptions of catalysis on truly nanosized structures, however, are generally not as well developed. In this talk, I will illustrate different approaches to analyzing nanocatalytic phenomena with DFT calculations. I will describe case studies from heterogeneous catalysis...... and electrocatalysis, in which single crystal models are combined with Wulff construction-based ideas to produce descriptions of average nanocatalyst behavior. Then, I will proceed to describe explicitly DFT-based descriptions of catalysis on truly nanosized particles (
Density functional theory and simulations of colloidal triangular prisms
Marechal, Matthieu; Dussi, Simone; Dijkstra, Marjolein
2017-03-01
Nanopolyhedra form a versatile toolbox to investigate the effect of particle shape on self-assembly. Here we consider rod-like triangular prisms to gauge the effect of the cross section of the rods on liquid crystal phase behavior. We also take this opportunity to implement and test a previously proposed version of fundamental measure density functional theory (0D-FMT). Additionally, we perform Monte Carlo computer simulations and we employ a simpler Onsager theory with a Parsons-Lee correction. Surprisingly and disappointingly, 0D-FMT does not perform better than the Tarazona and Rosenfeld's version of fundamental measure theory (TR-FMT). Both versions of FMT perform somewhat better than the Parsons-Lee theory. In addition, we find that the stability regime of the smectic phase is larger for triangular prisms than for spherocylinders and square prisms.
Nitrotyrosine adsorption on defective graphene: A density functional theory study
Majidi, R.; Karami, A. R.
2015-06-01
We have applied density functional theory to study adsorption of nitrotyrosine on perfect and defective graphene sheets. The graphene sheets with Stone-Wales (SW) defect, pentagon-nonagon (5-9) single vacancy, and pentagon-octagon-pentagon (5-8-5) double vacancy were considered. The calculations of adsorption energy showed that nitrotyrosine presents a more strong interaction with defective graphene rather than with perfect graphene sheet. The order of interaction strength is: SW>5-9>5-8-5>perfect graphene. It is found that the electronic properties of perfect and defective graphene are sensitive to the presence of nitrotyrosine. Hence, graphene sheets can be considered as a good sensor for detection of nitrotyrosine molecule which is observed in connection with several human disorders, such as Parkinson's and Alzheimer's disease.
Use of density functional theory in drug metabolism studies
DEFF Research Database (Denmark)
Rydberg, Patrik; Jørgensen, Flemming Steen; Olsen, Lars
2014-01-01
isoforms. This is probably due to the fact that the binding of the substrates is not the major determinant. When binding of the substrate plays a significant role, the well-known issue of determining the free energy of binding is the challenge. How approaches taking the protein environment into account......INTRODUCTION: The cytochrome P450 enzymes (CYPs) metabolize many drug compounds. They catalyze a wide variety of reactions, and potentially, a large number of different metabolites can be generated. Density functional theory (DFT) has, over the past decade, been shown to be a powerful tool...... to rationalize and predict the possible metabolites generated by the CYPs as well as other drug-metabolizing enzymes. AREAS COVERED: We review applications of DFT on reactions performed by the CYPs and other drug-metabolizing enzymes able to perform oxidation reactions, with an emphasis on predicting which...
Vibrational spectroscopy and density functional theory study of ninhydrin
Li, Ran; Sui, Huimin; Liu, Peipie; Chen, Lei; Cheng, Jianbo; Zhao, Bing
2015-02-01
In this paper, ninhydrin was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G** level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental values. The molecular electrostatic potential surface calculation was performed and the result suggested that the ninhydrin had two potential hydrogen bond donors and four potential hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311++G** level.
Study of spontaneous fission lifetimes using nuclear density functional theory
Directory of Open Access Journals (Sweden)
Sadhukhan Jhilam
2013-12-01
Full Text Available The spontaneous fission lifetimes have been studied microscopically by minimizing the collective action integral in a two-dimensional collective space of quadrupole moments (Q20, Q22 representing elongation and triaxiality. The microscopic collective potential and inertia tensor are obtained by solving the self-consistent Hartree-Fock-Bogoliubov (HFB equations with the Skyrme energy density functional and mixed pairing interaction. The mass tensor is computed within the perturbative Adiabatic Time-Dependent HFB (ATDHFB approach in the cranking approximation. The dynamic fission trajectories have been obtained by minimizing the collective action using two different numerical techniques. The values of spontaneous fission lifetimes obtained in this way are compared with the static results.
Density Functional Approach and Random Matrix Theory in Proteogenesis
Yamanaka, Masanori
2017-02-01
We study the energy-level statistics of amino acids by random matrix theory. The molecular orbital and the Kohn-Sham orbital energies are calculated using ab initio and density-functional formalisms for 20 different amino acids. To generate statistical data, we performed a multipoint calculation on 10000 molecular structures produced via a molecular dynamics simulation. For the valence orbitals, the energy-level statistics exhibit repulsion, but the universality in the random matrix cannot be determined. For the unoccupied orbitals, the energy-level statistics indicate an intermediate distribution between the Gaussian orthogonal ensemble and the semi-Poisson statistics for all 20 different amino acids. These amino acids are considered to be in a type of critical state.
Time-dependent density functional theory for quantum transport.
Zheng, Xiao; Chen, GuanHua; Mo, Yan; Koo, SiuKong; Tian, Heng; Yam, ChiYung; Yan, YiJing
2010-09-21
Based on our earlier works [X. Zheng et al., Phys. Rev. B 75, 195127 (2007); J. S. Jin et al., J. Chem. Phys. 128, 234703 (2008)], we propose a rigorous and numerically convenient approach to simulate time-dependent quantum transport from first-principles. The proposed approach combines time-dependent density functional theory with quantum dissipation theory, and results in a useful tool for studying transient dynamics of electronic systems. Within the proposed exact theoretical framework, we construct a number of practical schemes for simulating realistic systems such as nanoscopic electronic devices. Computational cost of each scheme is analyzed, with the expected level of accuracy discussed. As a demonstration, a simulation based on the adiabatic wide-band limit approximation scheme is carried out to characterize the transient current response of a carbon nanotube based electronic device under time-dependent external voltages.
Periodic Density Functional Theory Solver using Multiresolution Analysis with MADNESS
Harrison, Robert; Thornton, William
2011-03-01
We describe the first implementation of the all-electron Kohn-Sham density functional periodic solver (DFT) using multi-wavelets and fast integral equations using MADNESS (multiresolution adaptive numerical environment for scientific simulation; http://code.google.com/p/m-a-d-n-e-s-s). The multiresolution nature of a multi-wavelet basis allows for fast computation with guaranteed precision. By reformulating the Kohn-Sham eigenvalue equation into the Lippmann-Schwinger equation, we can avoid using the derivative operator which allows better control of overall precision for the all-electron problem. Other highlights include the development of periodic integral operators with low-rank separation, an adaptable model potential for nuclear potential, and an implementation for Hartree Fock exchange. This work was supported by NSF project OCI-0904972 and made use of resources at the Center for Computational Sciences at Oak Ridge National Laboratory under contract DE-AC05-00OR22725.
Density Functional Theory using Multiresolution Analysis with MADNESS
Thornton, Scott; Harrison, Robert
2012-02-01
We describe the first implementation of the all-electron Kohn-Sham density functional periodic solver (DFT) using multi-wavelets and fast integral equations using MADNESS (multiresolution adaptive numerical environment for scientific simulation; http://code.google.com/p/m-a-d-n-e-s-s). The multiresolution nature of a multi-wavelet basis allows for fast computation with guaranteed precision. By reformulating the Kohn-Sham eigenvalue equation into the Lippmann-Schwinger equation, we can avoid using the derivative operator which allows better control of overall precision for the all-electron problem. Other highlights include the development of periodic integral operators with low-rank separation, an adaptable model potential for the nuclear potential, and an implementation for Hartree-Fock exchange.
Density Functional Theory of Polymer Structure and Conformations
Directory of Open Access Journals (Sweden)
Zhaoyang Wei
2016-04-01
Full Text Available We present a density functional approach to quantitatively evaluate the microscopic conformations of polymer chains with consideration of the effects of chain stiffness, polymer concentration, and short chain molecules. For polystyrene (PS, poly(ethylene oxide (PEO, and poly(methyl methacrylate (PMMA melts with low-polymerization degree, as chain length increases, they display different stretching ratios and show non-universal scaling exponents due to their different chain stiffnesses. In good solvent, increase of PS concentration induces the decline of gyration radius. For PS blends containing short (m1 = 1 − 100 and long (m = 100 chains, the expansion of long chains becomes unobvious once m 1 is larger than 40, which is also different to the scaling properties of ideal chain blends.
Wellendorff, Jess; Lundgaard, Keld T.; Møgelhøj, Andreas; Petzold, Vivien; Landis, David D.; Nørskov, Jens K.; Bligaard, Thomas; Jacobsen, Karsten W.
2012-06-01
A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding the overfitting found when standard least-squares methods are applied to high-order polynomial expansions. A general-purpose density functional for surface science and catalysis studies should accurately describe bond breaking and formation in chemistry, solid state physics, and surface chemistry, and should preferably also include van der Waals dispersion interactions. Such a functional necessarily compromises between describing fundamentally different types of interactions, making transferability of the density functional approximation a key issue. We investigate this trade-off between describing the energetics of intramolecular and intermolecular, bulk solid, and surface chemical bonding, and the developed optimization method explicitly handles making the compromise based on the directions in model space favored by different materials properties. The approach is applied to designing the Bayesian error estimation functional with van der Waals correlation (BEEF-vdW), a semilocal approximation with an additional nonlocal correlation term. Furthermore, an ensemble of functionals around BEEF-vdW comes out naturally, offering an estimate of the computational error. An extensive assessment on a range of data sets validates the applicability of BEEF-vdW to studies in chemistry and condensed matter physics. Applications of the approximation and its Bayesian ensemble error estimate to two intricate surface science problems support this.
Comment on "Density functional theory is straying from the path toward the exact functional"
DEFF Research Database (Denmark)
Kepp, Kasper Planeta
2017-01-01
Medvedev et al (Reports, 6 January 2017, p. 49) argue that recent density functionals stray from the path toward exactness. This conclusion rests on very compact 1s2 and 1s22s2 systems favored by the Hartree-Fock picture. Comparison to actual energies for the same systems indicates that the "stra......Medvedev et al (Reports, 6 January 2017, p. 49) argue that recent density functionals stray from the path toward exactness. This conclusion rests on very compact 1s2 and 1s22s2 systems favored by the Hartree-Fock picture. Comparison to actual energies for the same systems indicates...
Do sex-specific densities affect local survival of free-ranging great tits?
Michler, Stephanie P. M.; Nicolaus, Marion; Ubels, Richard; van der Velde, Marco; Both, Christiaan; Tinbergen, Joost M.; Komdeur, Jan
2011-01-01
Competition within sexes is expected when resources are sex specific, whereas competition between sexes can occur when similar resources are exploited. Local population density and sex ratio will determine the amount of sex-specific interactions and thus the potential degree of sex-specific
Goerigk, Lars
2015-10-01
It is shown that the latest Minnesota density functionals (SOGGA11, M11-L, N12, MN12-L, SOGGA11-X, M11, N12-SX, and MN12-SX) do not properly describe London-dispersion interactions. Grimme's DFT-D3 correction can solve this problem partially; however, double-counting of medium-range electron correlation can occur. For the related M06-L functional, the alternative VV10 van der Waals kernel is tested, but it experiences similar double-counting. Most functionals give unphysical dissociation curves for the argon dimer, an indication for method-inherent problems, and further investigation is recommended. These results are further evidence that the London-dispersion problem in density functional theory approximations is unlikely to be solved by mere empirical optimization of functional parameters, unless the functionals contain components that ensure the correct asymptotic long-range behavior. London dispersion is ubiquitous, which is why the reported findings are not only important for theoreticians but also a reminder to the general chemist to carefully consider their choice of method before undertaking computational studies.
Wide host-range cloning for functional metagenomics.
Wexler, Margaret; Johnston, Andrew W B
2010-01-01
We describe how wide host-range cloning vectors can lead to more flexible and effective procedures to isolate novel genes by screening metagenomic libraries in a range of bacterial hosts, not just the conventionally used Escherichia coli. We give examples of various wide host-range plasmid, cosmid, and BAC cloning vectors and the types of genes and activities that have been successfully obtained to date. We present a detailed protocol that involves the construction and screening of a metagenomic library comprising fragments of bacterial DNA, obtained from a wastewater treatment plant and cloned in a wide host-range cosmid. We also consider future prospects and how techniques and tools can be improved.
Warshavsky, V B; Zeng, X C
2013-10-07
We have studied interfacial structure and properties of liquid-vapor interfaces of dipolar fluids and quadrupolar fluids, respectively, using the classical density functional theory (DFT). Towards this end, we employ the fundamental measure DFT for a reference hard-sphere (HS) part of free energy and the modified mean field approximation for the correlation function of dipolar or quadrupolar fluid. At low temperatures we find that both the liquid-vapor interfacial density profile and orientational order parameter profile exhibit weakly damped oscillatory decay into the bulk liquid. At high temperatures the decay of interfacial density and order parameter profiles is entirely monotonic. The scaled temperature τ = 1 - T/T(c) that separates the two qualitatively different interfacial structures is in the range 0.10-0.15. At a given (dimensionless) temperature, increasing the dipolar or quadrupolar moment enhances the density oscillations. Application of an electric field (normal to the interface) will damp the oscillations. Likewise, at the given temperature, increasing the strength of any multipolar moment also increases the surface tensions while increasing the strength of the applied electric field will reduce the surface tensions. The results are compared with those based on the local-density approximations (LDA) for the reference HS part of free energy as well as with results of numerical experiments.
Thyroid function and bone mineral density among Indian subjects
Directory of Open Access Journals (Sweden)
Raman K Marwaha
2012-01-01
Full Text Available Background : Thyroid hormones affect bone remodeling in patients with thyroid disease by acting directly or indirectly on bone cells. In view of limited information on correlation of thyroid function with bone mineral density (BMD in euthyroid subjects, we undertook this study to evaluate the correlation between thyroid function with BMD in subjects with normal thyroid function and subclinical hypothyroidism. Material and Methods : A total of 1290 subjects included in this cross sectional study, were divided in Group-1 with normal thyroid function and Group-2 with subclinical hypothyroidism. Fasting blood samples were drawn for the estimation of serum 25(OHD, intact parathyroid hormone, total and ionized calcium, inorganic phosphorus, and alkaline phosphatase. BMD at lumbar spine, femur, and forearm was measured. Results : BMD at all sites (radius, femur, and spine were comparable in both groups. There was no difference in BMD when subjects were divided in tertiles of TSH in either group. In group-1, FT4 and TSH were positively associated with BMD at 33% radius whereas FT3 was negatively associated with BMD at femoral neck in multiple regression analysis after adjustment for age, sex, BMI, 25(OHD and PTH levels. In group-2, there was no association observed between TSH and BMD at any site. Amongst all study subjects FT4 and FT3 were positively correlated with BMD at lumbar spine and radius respectively among all subjects. Conclusion: TSH does not affect BMD in euthyroid subjects and subjects with subclinical hypothyroidism. Thyroid hormones appear to have more pronounced positive effect on cortical than trabecular bone in euthyroid subjects.
DEFF Research Database (Denmark)
Sharma, S.; Pittalis, S.; Kurth, S.
2007-01-01
The relative merits of current-spin-density- and spin-density-functional theory are investigated for solids treated within the exact-exchange-only approximation. Spin-orbit splittings and orbital magnetic moments are determined at zero external magnetic field. We find that for magnetic (Fe, Co...
Antisites in III-V semiconductors: Density functional theory calculations
Energy Technology Data Exchange (ETDEWEB)
Chroneos, A., E-mail: alex.chroneos@open.ac.uk [Engineering and Innovation, The Open University, Milton Keynes MK7 6AA (United Kingdom); Tahini, H. A. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); PSE Division, KAUST, Thuwal 23955-6900 (Saudi Arabia); Schwingenschlögl, U., E-mail: udo.schwingenschlogl@kaust.edu.sa [PSE Division, KAUST, Thuwal 23955-6900 (Saudi Arabia); Grimes, R. W., E-mail: r.grimes@imperial.ac.uk [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom)
2014-07-14
Density functional based simulation, corrected for finite size effects, is used to investigate systematically the formation of antisite defects in III-V semiconductors (III = Al, Ga, and In and V = P, As, and Sb). Different charge states are modelled as a function of the Fermi level and under different growth conditions. The formation energies of group III antisites (III{sub V}{sup q}) decrease with increasing covalent radius of the group V atom though not group III radius, whereas group V antisites (V{sub III}{sup q}) show a consistent decrease in formation energies with increase in group III and group V covalent radii. In general, III{sub V}{sup q} defects dominate under III-rich conditions and V{sub III}{sup q} under V-rich conditions. Comparison with equivalent vacancy formation energy simulations shows that while antisite concentrations are always dominant under stoichiometric conditions, modest variation in growth or doping conditions can lead to a significantly higher concentration of vacancies.
Antisites in III-V semiconductors: Density functional theory calculations
Chroneos, A.
2014-07-14
Density functional based simulation, corrected for finite size effects, is used to investigate systematically the formation of antisite defects in III-V semiconductors (III=Al, Ga, and In and V=P, As, and Sb). Different charge states are modelled as a function of the Fermi level and under different growth conditions. The formation energies of group III antisites (III V q) decrease with increasing covalent radius of the group V atom though not group III radius, whereas group V antisites (V I I I q) show a consistent decrease in formation energies with increase in group III and group V covalent radii. In general, III V q defects dominate under III-rich conditions and V I I I q under V-rich conditions. Comparison with equivalent vacancy formation energy simulations shows that while antisite concentrations are always dominant under stoichiometric conditions, modest variation in growth or doping conditions can lead to a significantly higher concentration of vacancies. © 2014 AIP Publishing LLC.
Density functional steric analysis of linear and branched alkanes.
Ess, Daniel H; Liu, Shubin; De Proft, Frank
2010-12-16
Branched alkane hydrocarbons are thermodynamically more stable than straight-chain linear alkanes. This thermodynamic stability is also manifest in alkane bond separation energies. To understand the physical differences between branched and linear alkanes, we have utilized a novel density functional theory (DFT) definition of steric energy based on the Weizäcker kinetic energy. Using the M06-2X functional, the total DFT energy was partitioned into a steric energy term (E(s)[ρ]), an electrostatic energy term (E(e)[ρ]), and a fermionic quantum energy term (E(q)[ρ]). This analysis revealed that branched alkanes have less (destabilizing) DFT steric energy than linear alkanes. The lower steric energy of branched alkanes is mitigated by an equal and opposite quantum energy term that contains the Pauli component of the kinetic energy and exchange-correlation energy. Because the steric and quantum energy terms cancel, this leaves the electrostatic energy term that favors alkane branching. Electrostatic effects, combined with correlation energy, explains why branched alkanes are more stable than linear alkanes.
Peroxynitrous Acid Dimer: Ab Initio Density Functional Study
Pathak, Rajeev
2012-02-01
Peroxynitrous acid (PNA) HOONO, isomeric to nitric acid, is a very strong oxidant. A novel dimeric hydrogen-bonded cluster of peroxynitrous acid (PNA-D) is proposed herein; ab inito quantum chemical investigations performed whereupon lead to several stable structures that have a direct bearing on the reactivity of the participating monomers, quantified in terms of the molecular electrostatic potential. The electron-correlation lending stability to PNA and its dimers is gauged through several density functionals namely B3LYP, B3PW91, M06-2X, M06-L, and φ-B97X, etc.; as well as from popular wave-function based second order Møller-Plesset (MP2) perturbation theory, using the basis sets 6-311++G(d,p) and 6-311++G(2d,2p). The infra-red vibrational spectra reveal spectral shifts and intensity redistribution after dimerization. While the lowest energy PNA-D has a perfect inversion symmetry; the other stable dimers emerge as combinations of monomers in different orientation.
Czech Academy of Sciences Publication Activity Database
Šálek, Martin; Drahníková, L.; Tkadlec, Emil
2015-01-01
Roč. 45, č. 1 (2015), s. 1-14 ISSN 0305-1838 Institutional support: RVO:68081766 Keywords : Carnivores * home range size * natural–urban gradient * population density * review Subject RIV: EG - Zoology Impact factor: 4.116, year: 2015
Lipparini, Enrico; Pederiva, Francesco
2016-08-01
The time dependent local isospin density approximation (TDLIDA) has been extended to the study of the transverse isospin response function in nuclear matter with an arbitrary neutron-proton asymmetry parameter ξ . The energy density functional has been chosen in order to fit existing accurate quantum Monte Carlo calculations with a density dependent potential. The evolution of the response with ξ in the Δ Tz=±1 channels is quite different. While the strength of the Δ Tz=+1 channel disappears rather quickly by increasing the asymmetry, the Δ Tz=-1 channel develops a stronger and stronger collective mode that in the regime typical of neutron star matter at β equilibrium almost completely exhausts the excitation spectrum of the system. The neutrino mean free paths obtained from the TDLIDA responses are strongly dependent on ξ and on the presence of collective modes, leading to a sizable difference with respect to the prediction of the Fermi gas model.
Equation satisfied by electron-electron mutual Coulomb repulsion energy density functional
Joubert, Daniel P.
2011-01-01
The electron-electron mutual Coulomb repulsion energy density functional satisfies an equation that links functionals and functional derivatives at N-electron and (N-1)-electron densities for densities determined from the same adiabatic scaled external potential for the N-electron system.
Transport through correlated systems with density functional theory
Kurth, S.; Stefanucci, G.
2017-10-01
We present recent advances in density functional theory (DFT) for applications in the field of quantum transport, with particular emphasis on transport through strongly correlated systems. We review the foundations of the popular Landauer-Büttiker(LB) + DFT approach. This formalism, when using approximations to the exchange-correlation (xc) potential with steps at integer occupation, correctly captures the Kondo plateau in the zero bias conductance at zero temperature but completely fails to capture the transition to the Coulomb blockade (CB) regime as the temperature increases. To overcome the limitations of LB + DFT, the quantum transport problem is treated from a time-dependent (TD) perspective using TDDFT, an exact framework to deal with nonequilibrium situations. The steady-state limit of TDDFT shows that in addition to an xc potential in the junction, there also exists an xc correction to the applied bias. Open shell molecules in the CB regime provide the most striking examples of the importance of the xc bias correction. Using the Anderson model as guidance we estimate these corrections in the limit of zero bias. For the general case we put forward a steady-state DFT which is based on one-to-one correspondence between the pair of basic variables, steady density on and steady current across the junction and the pair local potential on and bias across the junction. Like TDDFT, this framework also leads to both an xc potential in the junction and an xc correction to the bias. Unlike TDDFT, these potentials are independent of history. We highlight the universal features of both xc potential and xc bias corrections for junctions in the CB regime and provide an accurate parametrization for the Anderson model at arbitrary temperatures and interaction strengths, thus providing a unified DFT description for both Kondo and CB regimes and the transition between them.
Transport through correlated systems with density functional theory.
Kurth, S; Stefanucci, G
2017-10-18
We present recent advances in density functional theory (DFT) for applications in the field of quantum transport, with particular emphasis on transport through strongly correlated systems. We review the foundations of the popular Landauer-Büttiker(LB) + DFT approach. This formalism, when using approximations to the exchange-correlation (xc) potential with steps at integer occupation, correctly captures the Kondo plateau in the zero bias conductance at zero temperature but completely fails to capture the transition to the Coulomb blockade (CB) regime as the temperature increases. To overcome the limitations of LB + DFT, the quantum transport problem is treated from a time-dependent (TD) perspective using TDDFT, an exact framework to deal with nonequilibrium situations. The steady-state limit of TDDFT shows that in addition to an xc potential in the junction, there also exists an xc correction to the applied bias. Open shell molecules in the CB regime provide the most striking examples of the importance of the xc bias correction. Using the Anderson model as guidance we estimate these corrections in the limit of zero bias. For the general case we put forward a steady-state DFT which is based on one-to-one correspondence between the pair of basic variables, steady density on and steady current across the junction and the pair local potential on and bias across the junction. Like TDDFT, this framework also leads to both an xc potential in the junction and an xc correction to the bias. Unlike TDDFT, these potentials are independent of history. We highlight the universal features of both xc potential and xc bias corrections for junctions in the CB regime and provide an accurate parametrization for the Anderson model at arbitrary temperatures and interaction strengths, thus providing a unified DFT description for both Kondo and CB regimes and the transition between them.
Large-scale density functional calculations of the surface properties of the Wigner crystal
Cortes-Huerto, R.; Ballone, P.
2010-05-01
The surface properties of the jellium model have been investigated by large supercell computations in the density functional theory-local spin-density (DFT-LSD) approach for planar slabs with up to 1000 electrons. A wide interval of densities has been explored, extending into the stability range of the Wigner crystal. Most computations have been carried out on nominally paramagnetic samples with an equal number of spin-up and spin-down electrons. The results show that within DFT-LSD spontaneous spin polarization and charge localization start nearly simultaneously at the surface for rs˜20 , then, with decreasing density, they progress toward the center of the slab. Electrons are fully localized and spin polarized at rs=30 . At this density the charge distribution is the superposition of disjoint charge blobs, each corresponding to one electron. The distribution of blobs displays both regularities and disorder, the first being represented by well-defined planes and simple in-plane geometries, and the latter by a variety of surface defects. The surface energy, surface dipole, electric polarisability, and magnetization pattern have been determined as a function of density. All these quantities display characteristic anomalies at the density of the localization transition. The analysis of the low-frequency electric conductivity shows that in the fluid paramagnetic regime the in-plane current preferentially flows in the central region of the slab and the two spin channels are equally conducting. In the charge localized, spin-polarized regime, conductivity is primarily a surface effect, and an apparent asymmetry is observed in the two spin currents.
Abnormal functional connectivity density in children with anisometropic amblyopia at resting-state.
Wang, Tianyue; Li, Qian; Guo, Mingxia; Peng, Yanmin; Li, Qingji; Qin, Wen; Yu, Chunshui
2014-05-14
Amblyopia is a developmental disorder resulting from anomalous binocular visual input in early life. Task-based neuroimaging studies have widely investigated cortical functional impairments in amblyopia, but changes in spontaneous neuronal functional activities in amblyopia remain largely unknown. In the present study, functional connectivity density (FCD) mapping, an ultrafast data-driven method based on fMRI, was applied for the first time to investigate changes in cortical functional connectivities in amblyopia during the resting-state. We quantified and compared both short- and long-range FCD in both the brains of children with anisometropic amblyopia (AAC) and normal sighted children (NSC). In contrast to the NSC, the AAC showed significantly decreased short-range FCD in the inferior temporal/fusiform gyri, parieto-occipital and rostrolateral prefrontal cortices, as well as decreased long-range FCD in the premotor cortex, dorsal inferior parietal lobule, frontal-insular and dorsal prefrontal cortices. Furthermore, most regions with reduced long-range FCD in the AAC showed decreased functional connectivity with occipital and posterior parietal cortices in the AAC. The results suggest that chronically poor visual input in amblyopia not only impairs the brain's short-range functional connections in visual pathways and in the frontal cortex, which is important for cognitive control, but also affects long-range functional connections among the visual areas, posterior parietal and frontal cortices that subserve visuomotor and visual-guided actions, visuospatial attention modulation and the integration of salient information. This study provides evidence for abnormal spontaneous brain activities in amblyopia. Copyright © 2014 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Nicholas Capel
2015-11-01
Full Text Available We present a comparative dispersion-corrected Density Functional Theory (DFT and Density Functional Tight Binding (DFTB-D study of several phases of nitrogen, including the well-known alpha, beta, and gamma phases as well as recently discovered highly energetic phases: covalently bound cubic gauche (cg nitrogen and molecular (vdW-bound N8 crystals. Among several tested parametrizations of N–N interactions for DFTB, we identify only one that is suitable for modeling of all these phases. This work therefore establishes the applicability of DFTB-D to studies of phases, including highly metastable phases, of nitrogen, which will be of great use for modelling of dynamics of reactions involving these phases, which may not be practical with DFT due to large required space and time scales. We also derive a dispersion-corrected DFT (DFT-D setup (atom-centered basis parameters and Grimme dispersion parameters tuned for accurate description simultaneously of several nitrogen allotropes including covalently and vdW-bound crystals and including high-energy phases.
Modrzejewski, Marcin; Chalasinski, Grzegorz; Szczesniak, Malgorzata M
2016-01-01
We devise a scheme for converting an existing exchange functional into its range-separated hybrid variant. The underlying exchange hole of the Becke-Roussel type has the exact second-order expansion in the interelectron distance. The short-range part of the resulting range-separated exchange energy depends on the kinetic energy density and the Laplacian even if the base functional lacks the dependence on these variables. The most successful practical realization of the scheme, named LC-PBETPSS, combines the range-separated PBE exchange lifted to the hybrid meta-GGA rung and the TPSS correlation. The value of the range-separation parameter is estimated theoretically and confirmed by empirical optimization. The D3 dispersion correction is recommended for all energy computations employing the presented functional. Numerical tests show remarkably robust performance of the method for noncovalent interaction energies, barrier heights, main-group thermochemistry, and excitation energies.
Jaffé, Rodolfo; Dietemann, Vincent; Allsopp, Mike H; Costa, Cecilia; Crewe, Robin M; Dall'olio, Raffaele; DE LA Rúa, Pilar; El-Niweiri, Mogbel A A; Fries, Ingemar; Kezic, Nikola; Meusel, Michael S; Paxton, Robert J; Shaibi, Taher; Stolle, Eckart; Moritz, Robin F A
2010-04-01
Although pollinator declines are a global biodiversity threat, the demography of the western honeybee (Apis mellifera) has not been considered by conservationists because it is biased by the activity of beekeepers. To fill this gap in pollinator decline censuses and to provide a broad picture of the current status of honeybees across their natural range, we used microsatellite genetic markers to estimate colony densities and genetic diversity at different locations in Europe, Africa, and central Asia that had different patterns of land use. Genetic diversity and colony densities were highest in South Africa and lowest in Northern Europe and were correlated with mean annual temperature. Confounding factors not related to climate, however, are also likely to influence genetic diversity and colony densities in honeybee populations. Land use showed a significantly negative influence over genetic diversity and the density of honeybee colonies over all sampling locations. In Europe honeybees sampled in nature reserves had genetic diversity and colony densities similar to those sampled in agricultural landscapes, which suggests that the former are not wild but may have come from managed hives. Other results also support this idea: putative wild bees were rare in our European samples, and the mean estimated density of honeybee colonies on the continent closely resembled the reported mean number of managed hives. Current densities of European honeybee populations are in the same range as those found in the adverse climatic conditions of the Kalahari and Saharan deserts, which suggests that beekeeping activities do not compensate for the loss of wild colonies. Our findings highlight the importance of reconsidering the conservation status of honeybees in Europe and of regarding beekeeping not only as a profitable business for producing honey, but also as an essential component of biodiversity conservation.
Nemiroski, Alex; Soh, Siowling; Kwok, Sen Wai; Yu, Hai-Dong; Whitesides, George M
2016-02-03
Magnetic levitation (MagLev) of diamagnetic or weakly paramagnetic materials suspended in a paramagnetic solution in a magnetic field gradient provides a simple method to measure the density of small samples of solids or liquids. One major limitation of this method, thus far, has been an inability to measure or manipulate materials outside of a narrow range of densities (0.8 g/cm(3) levitated magnetically. Tilting the MagLev device relative to the gravitational vector enables the magnetic force to be decreased (relative to the magnetic force) along the axis of measurement. This approach enables many practical measurements over the entire range of densities observed in matter at ambient conditions-from air bubbles (ρ ≈ 0) to osmium and iridium (ρ ≈ 23 g/cm(3)). The ability to levitate, simultaneously, objects with a broad range of different densities provides an operationally simple method that may find application to forensic science (e.g., for identifying the composition of miscellaneous objects or powders), industrial manufacturing (e.g., for quality control of parts), or resource-limited settings (e.g., for identifying and separating small particles of metals and alloys).
Density Functional Theory for Phase-Ordering Transitions
Energy Technology Data Exchange (ETDEWEB)
Wu, Jianzhong [Univ. of California, Riverside, CA (United States)
2016-03-30
Colloids display astonishing structural and dynamic properties that can be dramatically altered by modest changes in the solution condition or an external field. This complex behavior stems from a subtle balance of colloidal forces and intriguing mesoscopic and macroscopic phase transitions that are sensitive to the processing conditions and the dispersing environment. Whereas the knowledge on the microscopic structure and phase behavior of colloidal systems at equilibrium is now well-advanced, quantitative predictions of the dynamic properties and the kinetics of phase-ordering transitions in colloids are not always realized. Many important mesoscopic and off-equilibrium colloidal states remain poorly understood. The proposed research aims to develop a new, unifying approach to describe colloidal dynamics and the kinetics of phase-ordering transitions based on accomplishments from previous work for the equilibrium properties of both uniform and inhomogeneous systems and on novel concepts from the state-of-the-art dynamic density functional theory. In addition to theoretical developments, computational research is designed to address a number of fundamental questions on phase-ordering transitions in colloids, in particular those pertinent to a competition of the dynamic pathways leading to various mesoscopic structures, off-equilibrium states, and crystalline phases. By providing a generic theoretical framework to describe equilibrium, metastable as well as non-ergodic phase transitions concurrent with the colloidal self-assembly processes, accomplishments from this work will have major impacts on both fundamental research and technological applications.
Chiroptical Properties of Amino Acids: A Density Functional Theory Study
Directory of Open Access Journals (Sweden)
Martine Adrian-Scotto
2010-04-01
Full Text Available Amino acids are involved in many scientific theories elucidating possible origins of life on Earth. One of the challenges when discussing the evolutionary origin of biopolymers such as proteins and oligonucleotides in living organisms is the phenomenon that these polymers implement monomers of exclusively one handedness, a feature called biomolecular homochirality. Many attempts have been made to understand this process of racemic symmetry breaking. Assuming an extraterrestrial origin of the molecular building blocks of living organisms, their susceptibility to asymmetric photolysis by the absorption of circularly polarized electromagnetic radiation in interstellar space was proposed. In order to predict whether the interaction of circularly polarized light with various racemic amino acids can induce an enantiomeric excess, we investigated the electronic and chiroptical properties of the amino acids valine and isovaline by a molecular modelling approach based on quantum chemistry (Density Functional Theory. The average spectra of both L-valine and L-isovaline have been produced on the basis of Boltzmann population analysis using computed spectra for the various conformations of each amino acid.
Density Functional Studies of Molecular Polarizabilities. 10. Fulvenes and Fulvalenes
Directory of Open Access Journals (Sweden)
Humberto J. SoscÃƒÂºn Machado
2000-09-01
Full Text Available We report accurate Ab Initio Hartree Fock (HF and Density Functional Theory (DFT studies of the static dipole polarizabilities and first hyperpolarizabilities of the [n] fulvene and the [n,m] fulvalene series of molecules (with n, m = 3,5,7. Calculations are also reported for the parent cycloalkenes: cyclopropene, cyclopentadiene and cycloheptatriene (1-3 respectively. Geometries were optimized at the HF/6-311G(3d,2p level of theory. All the fulvenes (4-6 and the smaller fulvalenes (7, 9 and 10 are found to be planar. Pentaheptafulvalene (11 is slightly non-planar whilst heptafulvalene (12 has a folded C2h structure. Calculated C-C bond lengths are consistently smaller than the experimental values. Dipole polarizabilities and non-zero hyperpolarizabilities were calculated at the HF/6-311++G(3d,2p and BLYP/6-311++G(3d,2p levels of theory, using HF/6-311G(3d,2p geometries. Dipole polarizabilities correlate well with those given on the basis of atom additivity. Molecules (8, (9 and (11 show very large dipole hyperpolarizabilities.
Benchmark Study of Density Cumulant Functional Theory: Thermochemistry and Kinetics.
Copan, Andreas V; Sokolov, Alexander Yu; Schaefer, Henry F
2014-06-10
We present an extensive benchmark study of density cumulant functional theory (DCFT) for thermochemistry and kinetics of closed- and open-shell molecules. The performance of DCFT methods (DC-06, DC-12, ODC-06, and ODC-12) is compared to that of coupled-electron pair methods (CEPA0 and OCEPA0) and coupled-cluster theory (CCSD and CCSD(T)) for the description of noncovalent interactions (A24 database), barrier heights of hydrogen-transfer reactions (HTBH38), radical stabilization energies (RSE30), adiabatic ionization energies (AIE), and covalent bond stretching in diatomic molecules. Our results indicate that out of four DCFT methods the ODC-12 method is the most reliable and accurate DCFT formulation to date. Compared to CCSD, ODC-12 shows superior results for all benchmark tests employed in our study. With respect to coupled-pair theories, ODC-12 outperforms CEPA0 and shows similar accuracy to the orbital-optimized CEPA0 variant (OCEPA0) for systems at equilibrium geometries. For covalent bond stretching, ODC-12 is found to be more reliable than OCEPA0. For the RSE30 and AIE data sets, ODC-12 shows competitive performance with CCSD(T). In addition to benchmark results, we report new reference values for the RSE30 data set computed using coupled cluster theory with up to perturbative quadruple excitations.
Excess electrons in ice: a density functional theory study.
Bhattacharya, Somesh Kr; Inam, Fakharul; Scandolo, Sandro
2014-02-21
We present a density functional theory study of the localization of excess electrons in the bulk and on the surface of crystalline and amorphous water ice. We analyze the initial stages of electron solvation in crystalline and amorphous ice. In the case of crystalline ice we find that excess electrons favor surface states over bulk states, even when the latter are localized at defect sites. In contrast, in amorphous ice excess electrons find it equally favorable to localize in bulk and in surface states which we attribute to the preexisting precursor states in the disordered structure. In all cases excess electrons are found to occupy the vacuum regions of the molecular network. The electron localization in the bulk of amorphous ice is assisted by its distorted hydrogen bonding network as opposed to the crystalline phase. Although qualitative, our results provide a simple interpretation of the large differences observed in the dynamics and localization of excess electrons in crystalline and amorphous ice films on metals.
Time-dependent probability density function in cubic stochastic processes
Kim, Eun-jin; Hollerbach, Rainer
2016-11-01
We report time-dependent probability density functions (PDFs) for a nonlinear stochastic process with a cubic force using analytical and computational studies. Analytically, a transition probability is formulated by using a path integral and is computed by the saddle-point solution (instanton method) and a new nonlinear transformation of time. The predicted PDF p (x ,t ) in general involves a time integral, and useful PDFs with explicit dependence on x and t are presented in certain limits (e.g., in the short and long time limits). Numerical simulations of the Fokker-Planck equation provide exact time evolution of the PDFs and confirm analytical predictions in the limit of weak noise. In particular, we show that transient PDFs behave drastically differently from the stationary PDFs in regard to the asymmetry (skewness) and kurtosis. Specifically, while stationary PDFs are symmetric with the kurtosis smaller than 3, transient PDFs are skewed with the kurtosis larger than 3; transient PDFs are much broader than stationary PDFs. We elucidate the effect of nonlinear interaction on the strong fluctuations and intermittency in the relaxation process.
Aronsson, Malin; Low, Matthew; López-Bao, José V; Persson, Jens; Odden, John; Linnell, John D C; Andrén, Henrik
2016-05-01
Home range (HR) size variation is often linked to resource abundance, with sex differences expected to relate to sex-specific fitness consequences. However, studies generally fail to disentangle the effects of the two main drivers of HR size variation, food and conspecific density, and rarely consider how their relative influence change over spatiotemporal scales. We used location data from 77 Eurasian lynx (Lynx lynx) from a 16-year Scandinavian study to examine HR sizes variation relative to prey and conspecific density at different spatiotemporal scales. By varying the isopleth parameter (intensity of use) defining the HR, we show that sex-specific effects were conditional on the spatial scale considered. Males had larger HRs than females in all seasons. Females' total HR size declined as prey and conspecific density increased, whereas males' total HR was only affected by conspecific density. However, as the intensity of use within the HR increased (from 90% to 50% isopleth), the relationship between prey density and area showed opposing patterns for females and males; for females, the prey density effect was reduced, while for males, prey became increasingly important. Thus, prey influenced the size of key regions within male HRs, despite total HR size being independent of prey density. Males reduced their HR size during the mating season, likely to remain close to individual females in estrous. Females reduced their HR size postreproduction probably because of movement constrains imposed by dependent young. Our findings highlight the importance of simultaneously considering resources and intraspecific interactions as HR size determinants. We show that sex-specific demands influence the importance of prey and conspecific density on space use at different spatiotemporal scales. Thus, unless a gradient of space use intensity is examined, factors not related to total HR size might be disregarded despite their importance in determining size of key regions within
Brandenburg, J. G.; Bates, J. E.; Sun, J.; Perdew, J. P.
2016-09-01
The strongly constrained and appropriately normed (SCAN) semilocal density functional [J. Sun, A. Ruzsinszky, and J. P. Perdew, Phys. Rev. Lett. 115, 036402 (2015), 10.1103/PhysRevLett.115.036402] obeys all 17 known exact constraints for meta-generalized-gradient approximations (meta-GGAs), and it includes some medium-range correlation effects. Long-range London dispersion interactions are still missing, but they can be accounted for via an appropriate correction scheme. In this study, we combine SCAN with an efficient London dispersion correction and show that lattice energies of simple organic crystals can be improved with the applied correction by 50%. The London-dispersion corrected SCAN meta-GGA outperforms all other tested London-dispersion corrected meta-GGAs for molecular geometries. Our method yields mean absolute deviations (MADs) for main group bond lengths that are consistently below 1 pm, rotational constants with MADs of 0.2%, and noncovalent distances with MADs below 1%. For a large database of general main group thermochemistry and kinetics (˜800 chemical species), one of the lowest weighted mean absolute deviations for long-range corrected meta-GGA functionals is achieved. Noncovalent interactions are of average quality, and hydrogen bonded systems in particular seem to suffer from overestimated polarization related to the self-interaction error of SCAN. We also discuss some consequences of numerical sensitivity encountered for meta-GGAs.
Zahariev, F.; Leang, S. S.; Gordon, Mark S.
2013-06-01
Meta-generalized gradient approximation (meta-GGA) exchange-correlation density functionals depend on the Kohn-Sham (KS) orbitals through the kinetic energy density. The KS orbitals in turn depend functionally on the electron density. However, the functional dependence of the KS orbitals is indirect, i.e., not given by an explicit expression, and the computation of analytic functional derivatives of meta-GGA functionals with respect to the density imposes a challenge. The practical solution used in many computer implementations of meta-GGA density functionals for ground-state calculations is abstracted and generalized to a class of density functionals that is broader than meta-GGAs and to any order of functional differentiation. Importantly, the TDDFT working equations for meta-GGA density functionals are presented here for the first time, together with the technical details of their computer implementation. The analysis presented here also uncovers the implicit assumptions in the practical solution to computing functional derivatives of meta-GGA density functionals. The connection between the approximation that is invoked in taking functional derivatives of density functionals, the non-uniqueness with respect to the KS orbitals, and the non-locality of the resultant potential is also discussed.
Plant host range of Verticillium longisporum and microsclerotia density in Swedisch soils
Johansson, A.; Goud, J.C.; Dixelius, C.
2006-01-01
Verticillium longisporum is a soil-borne fungal pathogen causing vascular wilt of Brassica crops. This study was conducted to enhance our knowledge on the host range of V. longisporum. Seven crop species (barley, oat, oilseed rape, pea, red clover, sugar beet and wheat) and five weed species (barren
A novel approach for assessing density and range-wide abundance of prairie dogs
Aaron N. Facka; Paulette L. Ford; Gary W. Roemer
2008-01-01
Habitat loss, introduced disease, and government-sponsored eradication programs have caused population declines in all 5 species of prairie dogs. Black-tailed prairie dogs (Cynomys ludovicianus) currently occupy only about 2% of an extensive geographic range (160 million hectares) and were recently considered for listing under the United States...
Reducing Systematic Errors in Oxide Species with Density Functional Theory Calculations
DEFF Research Database (Denmark)
Christensen, Rune; Hummelshøj, Jens S.; Hansen, Heine Anton
2015-01-01
for different types of alkali and alkaline earth metal oxide species has been examined. Most examined functionals result in significant overestimation of the stability of superoxide species compared to peroxides and monoxides, which can result in erroneous prediction of reaction pathways. We show that if metal...... chlorides are used as reference structures instead of metals, the systematic errors are significantly reduced and functional variations decreased. Using a metal chloride reference, where the metal atoms are in the same oxidation state as in the oxide species, will provide a computationally inexpensive......Density functional theory calculations can be used to gain valuable insight into the fundamental reaction processes in metal−oxygen systems, e.g., metal−oxygen batteries. Here, the ability of a range of different exchange-correlation functionals to reproduce experimental enthalpies of formation...
Surfaces of complex intermetallic compounds: insights from density functional calculations.
Hafner, Jürgen; Krajčí, Marian
2014-11-18
CONSPECTUS: Complex intermetallic compounds are a class of ordered alloys consisting of quasicrystals and other ordered compounds with large unit cells; many of them are approximant phases to quasicrystals. Quasicrystals are the limiting case where the unit cell becomes infinitely large; approximants are series of periodic structures converging to the quasicrystal. While the unique properties of quasicrystals have inspired many investigations of their surfaces, relatively little attention has been devoted to the surface properties of the approximants. In general, complex intermetallic compounds display rather irregular, often strongly corrugated surfaces, making the determination of their atomic structure a very complex and challenging task. During recent years, scanning tunneling microscopy (STM) has been used to study the surfaces of several complex intermetallic compounds. If atomic resolution can be achieved, STM permits visualization of the local atomistic surface structure. However, the interpretation of the STM images is often ambiguous and sometimes even impossible without a realistic model of the structure of the surface and the distribution of the electronic density above the surface. Here we demonstrate that ab initio density functional theory (DFT) can be used to determine the energetics and the geometric and electronic structures of the stable surfaces of complex intermetallic compounds. Calculations for surfaces with different chemical compositions can be performed in the grand canonical ensemble. Simulated cleavage experiments permit us to determine the formation of the cleavage planes requiring the lowest energy. The investigation of the adsorption of molecular species permits a comparison with temperature-programmed thermal desorption experiments. Calculated surface electronic densities of state can be compared with the results of photoelectron spectroscopy. Simulations of detailed STM images can be directly confronted with the experimental results
Global cold curve. New representation for zero-temperature isotherm in whole density range
Iosilevskiy, Igor
2014-01-01
Non-standard representation for so-called "cold curve" of matter (i.e. isotherm $T = 0$) is proposed as Global Cold Curve (GCC). The main point is that chemical potential of substance, $\\mu$, plays role of ruling parameter in basic GCC-dependence of internal energy under compression, $U = U(\\mu)$, in contrast to the standard form $U = U(\\rho)$. This substitution changes radically low-density ("gaseous") part of GCC. Namely: ($i$) - physically meaningless part of standard cold curve $(U(\\rho)$ at $T \\rightarrow 0)$ disappears totally from new version of GCC. This deleted part corresponded to absolutely thermodynamically unstable states in standard representation $U(\\rho)$; ($ii$) - new gaseous branch of cold curve, $U = U(\\mu)$, comes in GCC. It describes in simple, schematic way thermodynamics of whole gas-like plasma in low-temperature limit (Iosilevskiy: arXiv:0902.3708) as combination of all ionization and dissociation processes available for equilibrium plasma at finite temperature. This gaseous branch co...
Weidinger, Lukas; Bauer, Florian; von Delft, Jan
2017-01-01
We introduce an equilibrium formulation of the functional renormalization group (fRG) for inhomogeneous systems capable of dealing with spatially finite-ranged interactions. In the general third-order truncated form of fRG, the dependence of the two-particle vertex is described by O (N4) independent variables, where N is the dimension of the single-particle system. In a previous paper [Bauer et al., Phys. Rev. B 89, 045128 (2014), 10.1103/PhysRevB.89.045128], the so-called coupled-ladder approximation (CLA) was introduced and shown to admit a consistent treatment for models with a purely onsite interaction, reducing the vertex to O (N2) independent variables. In this work, we introduce an extended version of this scheme, called the extended coupled ladder approximation (eCLA), which includes a spatially extended feedback between the individual channels, measured by a feedback length L , using O (N2L2) independent variables for the vertex. We apply the eCLA in a static approximation and at zero temperature to three types of one-dimensional model systems, focusing on obtaining the linear response conductance. First, we study a model of a quantum point contact (QPC) with a parabolic barrier top and on-site interactions. In our setup, where the characteristic length lx of the QPC ranges between approximately 4-10 sites, eCLA achieves convergence once L becomes comparable to lx. It also turns out that the additional feedback stabilizes the fRG flow. This enables us, second, to study the geometric crossover between a QPC and a quantum dot, again for a one-dimensional model with on-site interactions. Third, the enlarged feedback also enables the treatment of a finite-ranged interaction extending over up to L sites. Using a simple estimate for the form of such a finite-ranged interaction in a QPC with a parabolic barrier top, we study its effects on the conductance and the density. We find that for low densities and sufficiently large interaction ranges the conductance
Faber, C; Boulanger, P; Attaccalite, C; Duchemin, I; Blase, X
2014-03-13
Many-body Green's function perturbation theories, such as the GW and Bethe-Salpeter formalisms, are starting to be routinely applied to study charged and neutral electronic excitations in molecular organic systems relevant to applications in photovoltaics, photochemistry or biology. In parallel, density functional theory and its time-dependent extensions significantly progressed along the line of range-separated hybrid functionals within the generalized Kohn-Sham formalism designed to provide correct excitation energies. We give an overview and compare these approaches with examples drawn from the study of gas phase organic systems such as fullerenes, porphyrins, bacteriochlorophylls or nucleobases molecules. The perspectives and challenges that many-body perturbation theory is facing, such as the role of self-consistency, the calculation of forces and potential energy surfaces in the excited states, or the development of embedding techniques specific to the GW and Bethe-Salpeter equation formalisms, are outlined.
Rengers, Francis; McGuire, Luke; Coe, Jeffrey A.; Kean, Jason W.; Baum, Rex L.; Staley, Dennis M.; Godt, Jonathan W.
2016-01-01
We explored regional influences on debris-flow initiation throughout the Colorado Front Range (Colorado, USA) by exploiting a unique data set of more than 1100 debris flows that initiated during a 5 day rainstorm in 2013. Using geospatial data, we examined the influence of rain, hillslope angle, hillslope aspect, and vegetation density on debris-flow initiation. In particular we used a greenness index to differentiate areas of high tree density from grass and bare soil. The data demonstrated an overwhelming propensity for debris-flow initiation on south-facing hillslopes. However, when the debris-flow density was analyzed with respect to total rainfall and greenness we found that most debris flows occurred in areas of high rainfall and low tree density, regardless of hillslope aspect. These results indicate that present-day tree density exerts a stronger influence on debris-flow initiation locations than aspect-driven variations in soil and bedrock properties that developed over longer time scales.
Density functional study of condensation in capped capillaries.
Yatsyshin, P; Savva, N; Kalliadasis, S
2015-07-15
We study liquid adsorption in narrow rectangular capped capillaries formed by capping two parallel planar walls (a slit pore) with a third wall orthogonal to the two planar walls. The most important transition in confined fluids is arguably condensation, where the pore becomes filled with the liquid phase which is metastable in the bulk. Depending on the temperature T, the condensation in capped capillaries can be first-order (at T≤Tcw) or continuous (at T>Tcw), where Tcw is the capillary wetting temperature. At T>Tcw, the capping wall can adsorb mesoscopic amounts of metastable under-condensed liquid. The onset of condensation is then manifested by the continuous unbinding of the interface between the liquid adsorbed on the capping wall and the gas filling the rest of the capillary volume. In wide capped capillaries there may be a remnant of wedge filling transition, which is manifested by the adsorption of liquid drops in the corners. Our classical statistical mechanical treatment predicts a possibility of three-phase coexistence between gas, corner drops and liquid slabs adsorbed on the capping wall. In sufficiently wide capillaries we find that thick prewetting films of finite length may be nucleated at the capping wall below the boundary of the prewetting transition. Prewetting then proceeds in a continuous manner manifested by the unbinding interface between the thick and thin films adsorbed on the side walls. Our analysis is based on a detailed numerical investigation of the density functional theory for the fluid equilibria for a number of illustrative case studies.
Antioxidant Properties of Kynurenines: Density Functional Theory Calculations.
Directory of Open Access Journals (Sweden)
Aleksandr V Zhuravlev
2016-11-01
Full Text Available Kynurenines, the main products of tryptophan catabolism, possess both prooxidant and anioxidant effects. Having multiple neuroactive properties, kynurenines are implicated in the development of neurological and cognitive disorders, such as Alzheimer's, Parkinson's, and Huntington's diseases. Autoxidation of 3-hydroxykynurenine (3HOK and its derivatives, 3-hydroxyanthranilic acid (3HAA and xanthommatin (XAN, leads to the hyperproduction of reactive oxygen species (ROS which damage cell structures. At the same time, 3HOK and 3HAA have been shown to be powerful ROS scavengers. Their ability to quench free radicals is believed to result from the presence of the aromatic hydroxyl group which is able to easily abstract an electron and H-atom. In this study, the redox properties for kynurenines and several natural and synthetic antioxidants have been calculated at different levels of density functional theory in the gas phase and water solution. Hydroxyl bond dissociation enthalpy (BDE and ionization potential (IP for 3HOK and 3HAA appear to be lower than for xanthurenic acid (XAA, several phenolic antioxidants, and ascorbic acid. BDE and IP for the compounds with aromatic hydroxyl group are lower than for their precursors without hydroxyl group. The reaction rate for H donation to *O-atom of phenoxyl radical (Ph-O* and methyl peroxy radical (Met-OO* decreases in the following rankings: 3HOK ~ 3HAA > XAAOXO > XAAENOL. The enthalpy absolute value for Met-OO* addition to the aromatic ring of the antioxidant radical increases in the following rankings: 3HAA* < 3HOK* < XAAOXO* < XAAENOL*. Thus, the high free radical scavenging activity of 3HAA and 3HOK can be explained by the easiness of H-atom abstraction and transfer to O-atom of the free radical, rather than by Met-OO* addition to the kynurenine radical.
Density functional theory and phytochemical study of Pistagremic acid
Ullah, Habib; Rauf, Abdur; Ullah, Zakir; Fazl-i-Sattar; Anwar, Muhammad; Shah, Anwar-ul-Haq Ali; Uddin, Ghias; Ayub, Khurshid
2014-01-01
We report here for the first time a comparative theoretical and experimental study of Pistagremic acid (P.A). We have developed a theoretical model for obtaining the electronic and spectroscopic properties of P.A. The simulated data showed nice correlation with the experimental data. The geometric and electronic properties were simulated at B3LYP/6-31 G (d, p) level of density functional theory (DFT). The optimized geometric parameters of P.A were found consistent with those from X-ray crystal structure. Differences of about 0.01 and 0.15 Å in bond length and 0.19-1.30° degree in the angles, respectively; were observed between the experimental and theoretical data. The theoretical vibrational bands of P.A were found to correlate with the experimental IR spectrum after a common scaling factor of 0.963. The experimental and predicted UV-Vis spectra (at B3LYP/6-31+G (d, p)) have 36 nm differences. This difference from experimental results is because of the condensed phase nature of P.A. Electronic properties such as Ionization Potential (I.P), Electron Affinities (E.A), co-efficient of highest occupied molecular orbital (HOMO), co-efficient of lowest unoccupied molecular orbital (LUMO) of P.A were estimated for the first time however, no correlation can be made with experiment. Inter-molecular interaction and its effect on vibrational (IR), electronic and geometric parameters were simulated by using Formic acid as model for hydrogen bonding in P.A.
Energy Technology Data Exchange (ETDEWEB)
Fattebert, J
2008-07-29
We describe an iterative algorithm to solve electronic structure problems in Density Functional Theory. The approach is presented as a Subspace Accelerated Inexact Newton (SAIN) solver for the non-linear Kohn-Sham equations. It is related to a class of iterative algorithms known as RMM-DIIS in the electronic structure community. The method is illustrated with examples of real applications using a finite difference discretization and multigrid preconditioning.
Ziani, Ahmed
2015-09-03
We report a combined experimental and theoretical study on the optoelectronic properties of α-SnWO4 for UV-Vis excitation. The experimentally measured values for thin films were systematically compared with high-accuracy density functional theory and density functional perturbation theory using the HSE06 functional. The α-SnWO4 material shows an indirect bandgap of 1.52 eV with high absorption coefficient in the visible-light range (>2 × 105 cm−1). The results show relatively high dielectric constant (>30) and weak diffusion properties (large effective masses) of excited carriers.
Robust functional statistics applied to Probability Density Function shape screening of sEMG data.
Boudaoud, S; Rix, H; Al Harrach, M; Marin, F
2014-01-01
Recent studies pointed out possible shape modifications of the Probability Density Function (PDF) of surface electromyographical (sEMG) data according to several contexts like fatigue and muscle force increase. Following this idea, criteria have been proposed to monitor these shape modifications mainly using High Order Statistics (HOS) parameters like skewness and kurtosis. In experimental conditions, these parameters are confronted with small sample size in the estimation process. This small sample size induces errors in the estimated HOS parameters restraining real-time and precise sEMG PDF shape monitoring. Recently, a functional formalism, the Core Shape Model (CSM), has been used to analyse shape modifications of PDF curves. In this work, taking inspiration from CSM method, robust functional statistics are proposed to emulate both skewness and kurtosis behaviors. These functional statistics combine both kernel density estimation and PDF shape distances to evaluate shape modifications even in presence of small sample size. Then, the proposed statistics are tested, using Monte Carlo simulations, on both normal and Log-normal PDFs that mimic observed sEMG PDF shape behavior during muscle contraction. According to the obtained results, the functional statistics seem to be more robust than HOS parameters to small sample size effect and more accurate in sEMG PDF shape screening applications.
Ding, Ju-Rong; Ding, Xin; Hua, Bo; Xiong, Xingzhong; Wang, Qingsong; Chen, Huafu
2016-09-01
White matter lesions (WMLs) are frequently detected in elderly people. Previous structural and functional studies have demonstrated that WMLs are associated with cognitive and motor decline. However, the underlying mechanism of how WMLs lead to cognitive decline and motor disturbance remains unclear. We used functional connectivity density mapping (FCDM) to investigate changes in brain functional connectivity in 16 patients with ischemic WMLs and 13 controls. Both short- and long-range FCD maps were computed, and group comparisons were performed between the 2 groups. A correlation analysis was further performed between regions with altered FCD and cognitive test scores (Mini-Mental State Examination [MMSE] and Montreal Cognitive Assessment [MoCA]) in the patient group. We found that patients with ischemic WMLs showed reduced short-range FCD in the temporal cortex, primary motor cortex, and subcortical region, which may account for inadequate top-down attention, impaired motor, memory, and executive function associated with WMLs. The positive correlation between primary motor cortex and MoCA scores may provide evidence for the influences of cognitive function on behavioral performance. The inferior parietal cortex exhibited increased short-range FCD, reflecting a hyper bottom-up attention to compensate for the inadequate top-down attention for language comprehension and information retrieval in patients with WMLs. Moreover, the prefrontal and primary motor cortex showed increased long-range FCD and the former positively correlated with MoCA scores, which may suggest a strategy of cortical functional reorganization to compensate for motor and executive deficits. Our findings provide new insights into how WMLs cause cognitive and motor decline from cortical functional connectivity perspective.
Directory of Open Access Journals (Sweden)
Heena Kaushal
2017-08-01
Full Text Available Background: Menstruation being an inevitable part of a girl’s life and more so, an important indicator of normal physical, physiological and functional well-being. Female athlete who engages in high-intensity exercise is at risk as a consequence of the hormonal change, which results in menstrual dysfunction, subsequently; the athlete is at risk for compromised skeletal integrity. The objective of the study is to find the prevalence of menstrual dysfunction among female athletes of Punjabi University, Patiala, to assess the bone mineral density in female athletes and to examine the relationship of Bone Mineral Density with Menstrual dysfunction in female athletes. Methods: The present study evaluated the menstrual status and its association with Bone Mineral Density in 76 adolescent female athletes. Convenient random sampling was adopted to recruit athletes by inclusion and exclusion criteria. Result: The percentile analysis of menstrual dysfunction is found to be 59.3% Out of 59.3% population with menstrual dysfunction, 55.5 % have oligomenorrhea, 28.9% have amenorrhea, and 15.5% have polymenorrhea. In this study population, the mean age of menarche is 13.81. Out of 76 female athletes, 35 have normal BMD ranges whereas 41 are having lower BMD ranges. The association of bone mineral density was found to be non-significant with both stress fracture (X2 = 4.38, p= 0.3570, and epimenorrhea (X2 = 4.49, p = 0.3437. The analysis of Pearson's correlation coefficient (r suggested a negative association between menstrual function with Bone Mineral Density (-0.06292 at 0.05 levels. The result found to be statistically non-significant; therefore, any change in menstrual function is not associated with Bone mineral density. Conclusion: Common menstrual dysfunctions reported were: oligomenorrhea, polymenorrhea, amenorrhea, and amenorrhea. However, pre-menstrual syndrome (PMS and dysmenorrhea were specifically found to be very high in prevalence i.e. 94
Polymer density functional approach to efficient evaluation of path integrals
DEFF Research Database (Denmark)
Brukhno, Andrey; Vorontsov-Velyaminov, Pavel N.; Bohr, Henrik
2005-01-01
, the path integral problem can, in principle, be solved exactly by making use of the two-particle pair correlation function (2p-PCF) for the ends of an open polymer, half of the original. This way the exact data for one-dimensional quantum harmonic oscillator are reproduced in a wide range of temperatures....... The exact solution is not, though, reachable in three dimensions (3D) because of a vast amount of storage required for 2p-PCF. In order to treat closed paths in 3D, we introduce a so-called "open ring" approximation which proves to be rather accurate in the limit of long chains. We also employ a simple self......-consistent iteration so as to correctly account for the interparticle interactions. The algorithm is speeded up by taking convolutions with the aid of fast Fourier transforms. We apply this approximate path integral DFT (PI-DFT) method to systems within spherical symmetry: 3D harmonic oscillator, atoms of hydrogen...
Kowal, Virginia A.; Schmolke, Amelie; Kanagaraj, Rajapandian; Bruggeman, Douglas
2014-03-01
The gopher tortoise ( Gopherus polyphemus) is protected by conservation policy throughout its range. Efforts to protect the species from further decline demand detailed understanding of its habitat requirements, which have not yet been rigorously defined. Current methods of identifying gopher tortoise habitat typically rely on coarse soil and vegetation classifications, and are prone to over-prediction of suitable habitat. We used a logistic resource selection probability function in an information-theoretic framework to understand the relative importance of various environmental factors to gopher tortoise habitat selection, drawing on nationwide environmental datasets, and an existing tortoise survey of the Ft. Benning military base. We applied the normalized difference vegetation index (NDVI) as an index of vegetation density, and found that NDVI was strongly negatively associated with active burrow locations. Our results showed that the most parsimonious model included variables from all candidate model types (landscape features, topography, soil, vegetation), and the model groups describing soil or vegetation alone performed poorly. These results demonstrate with a rigorous quantitative approach that although soil and vegetation are important to the gopher tortoise, they are not sufficient to describe suitable habitat. More widely, our results highlight the feasibility of constructing highly accurate habitat suitability models from data that are widely available throughout the species' range. Our study shows that the widespread availability of national environmental datasets describing important components of gopher tortoise habitat, combined with existing tortoise surveys on public lands, can be leveraged to inform knowledge of habitat suitability and target recovery efforts range-wide.
Density Functional Theory Calculations of Mass Transport in UO2
Energy Technology Data Exchange (ETDEWEB)
Andersson, Anders D. [Los Alamos National Laboratory; Dorado, Boris [CEA; Uberuaga, Blas P. [Los Alamos National Laboratory; Stanek, Christopher R. [Los Alamos National Laboratory
2012-06-26
In this talk we present results of density functional theory (DFT) calculations of U, O and fission gas diffusion in UO{sub 2}. These processes all impact nuclear fuel performance. For example, the formation and retention of fission gas bubbles induce fuel swelling, which leads to mechanical interaction with the clad thereby increasing the probability for clad breach. Alternatively, fission gas can be released from the fuel to the plenum, which increases the pressure on the clad walls and decreases the gap thermal conductivity. The evolution of fuel microstructure features is strongly coupled to diffusion of U vacancies. Since both U and fission gas transport rates vary strongly with the O stoichiometry, it is also important to understand O diffusion. In order to better understand bulk Xe behavior in UO{sub 2{+-}x} we first calculate the relevant activation energies using DFT techniques. By analyzing a combination of Xe solution thermodynamics, migration barriers and the interaction of dissolved Xe atoms with U, we demonstrate that Xe diffusion predominantly occurs via a vacancy-mediated mechanism. Since Xe transport is closely related to diffusion of U vacancies, we have also studied the activation energy for this process. In order to explain the low value of 2.4 eV found for U migration from independent damage experiments (not thermal equilibrium) the presence of vacancy clusters must be included in the analysis. Next we investigate species transport on the (111) UO{sub 2} surface, which is motivated by the formation of small voids partially filled with fission gas atoms (bubbles) in UO{sub 2} under irradiation. Surface diffusion could be the rate-limiting step for diffusion of such bubbles, which is an alternative mechanism for mass transport in these materials. As expected, the activation energy for surface diffusion is significantly lower than for bulk transport. These results are further discussed in terms of engineering-scale fission gas release models
Lymphatic vessel density and function in experimental bladder cancer
Directory of Open Access Journals (Sweden)
Maier Julie
2007-11-01
Full Text Available Abstract Background The lymphatics form a second circulatory system that drains the extracellular fluid and proteins from the tumor microenvironment, and provides an exclusive environment in which immune cells interact and respond to foreign antigen. Both cancer and inflammation are known to induce lymphangiogenesis. However, little is known about bladder lymphatic vessels and their involvement in cancer formation and progression. Methods A double transgenic mouse model was generated by crossing a bladder cancer-induced transgenic, in which SV40 large T antigen was under the control of uroplakin II promoter, with another transgenic mouse harboring a lacZ reporter gene under the control of an NF-κB-responsive promoter (κB-lacZ exhibiting constitutive activity of β-galactosidase in lymphatic endothelial cells. In this new mouse model (SV40-lacZ, we examined the lymphatic vessel density (LVD and function (LVF during bladder cancer progression. LVD was performed in bladder whole mounts and cross-sections by fluorescent immunohistochemistry (IHC using LYVE-1 antibody. LVF was assessed by real-time in vivo imaging techniques using a contrast agent (biotin-BSA-Gd-DTPA-Cy5.5; Gd-Cy5.5 suitable for both magnetic resonance imaging (MRI and near infrared fluorescence (NIRF. In addition, IHC of Cy5.5 was used for time-course analysis of co-localization of Gd-Cy5.5 with LYVE-1-positive lymphatics and CD31-positive blood vessels. Results SV40-lacZ mice develop bladder cancer and permitted visualization of lymphatics. A significant increase in LVD was found concomitantly with bladder cancer progression. Double labeling of the bladder cross-sections with LYVE-1 and Ki-67 antibodies indicated cancer-induced lymphangiogenesis. MRI detected mouse bladder cancer, as early as 4 months, and permitted to follow tumor sizes during cancer progression. Using Gd-Cy5.5 as a contrast agent for MRI-guided lymphangiography, we determined a possible reduction of lymphatic
Zinc surface complexes on birnessite: A density functional theory study
Energy Technology Data Exchange (ETDEWEB)
Kwon, Kideok D.; Refson, Keith; Sposito, Garrison
2009-01-05
Biogeochemical cycling of zinc is strongly influenced by sorption on birnessite minerals (layer-type MnO2), which are found in diverse terrestrial and aquatic environments. Zinc has been observed to form both tetrahedral (Zn{sup IV}) and octahedral (Zn{sup VI}) triple-corner-sharing surface complexes (TCS) at Mn(IV) vacancy sites in hexagonal birnessite. The octahedral complex is expected to be similar to that of Zn in the Mn oxide mineral, chalcophanite (ZnMn{sub 3}O{sub 7} {center_dot} 3H{sub 2}O), but the reason for the occurrence of the four-coordinate Zn surface species remains unclear. We address this issue computationally using spin-polarized Density Functional Theory (DFT) to examine the Zn{sub IV}-TCS and Zn{sup VI}-TCS species. Structural parameters obtained by DFT geometry optimization were in excellent agreement with available experimental data on Zn-birnessites. Total energy, magnetic moments, and electron-overlap populations obtained by DFT for isolated Zn{sup IV}-TCS revealed that this species is stable in birnessite without a need for Mn(III) substitution in the octahedral sheet and that it is more effective in reducing undersaturation of surface O at a Mn vacancy than is Zn{sub VI}-TCS. Comparison between geometry-optimized ZnMn{sub 3}O{sub 7} {center_dot} 3H{sub 2}O (chalcophanite) and the hypothetical monohydrate mineral, ZnMn{sub 3}O{sub 7} {center_dot} H{sub 2}O, which contains only tetrahedral Zn, showed that the hydration state of Zn significantly affects birnessite structural stability. Finally, our study also revealed that, relative to their positions in an ideal vacancy-free MnO{sub 2}, Mn nearest to Zn in a TCS surface complex move toward the vacancy by 0.08-0.11 {angstrom}, while surface O bordering the vacancy move away from it by 0.16-0.21 {angstrom}, in agreement with recent X-ray absorption spectroscopic analyses.
Lin, Lin
The computational cost of standard Kohn-Sham density functional theory (KSDFT) calculations scale cubically with respect to the system size, which limits its use in large scale applications. In recent years, we have developed an alternative procedure called the pole expansion and selected inversion (PEXSI) method. The PEXSI method solves KSDFT without solving any eigenvalue and eigenvector, and directly evaluates physical quantities including electron density, energy, atomic force, density of states, and local density of states. The overall algorithm scales as at most quadratically for all materials including insulators, semiconductors and the difficult metallic systems. The PEXSI method can be efficiently parallelized over 10,000 - 100,000 processors on high performance machines. The PEXSI method has been integrated into a number of community electronic structure software packages such as ATK, BigDFT, CP2K, DGDFT, FHI-aims and SIESTA, and has been used in a number of applications with 2D materials beyond 10,000 atoms. The PEXSI method works for LDA, GGA and meta-GGA functionals. The mathematical structure for hybrid functional KSDFT calculations is significantly different. I will also discuss recent progress on using adaptive compressed exchange method for accelerating hybrid functional calculations. DOE SciDAC Program, DOE CAMERA Program, LBNL LDRD, Sloan Fellowship.
Directory of Open Access Journals (Sweden)
Tomasz A Leski
Full Text Available Rapid and effective detection and identification of emerging microbiological threats and potential biowarfare agents is very challenging when using traditional culture-based methods. Contemporary molecular techniques, relying upon reverse transcription and/or polymerase chain reaction (RT-PCR/PCR provide a rapid and effective alternative, however, such assays are generally designed and optimized to detect only a limited number of targets, and seldom are capable of differentiation among variants of detected targets. To meet these challenges, we have designed a broad-range resequencing pathogen microarray (RPM for detection of tropical and emerging infectious agents (TEI including biothreat agents: RPM-TEI v 1.0 (RPM-TEI. The scope of the RPM-TEI assay enables detection and differential identification of 84 types of pathogens and 13 toxin genes, including most of the class A, B and C select agents as defined by the Centers for Disease Control and Prevention (CDC, Atlanta, GA. Due to the high risks associated with handling these particular target pathogens, the sensitivity validation of the RPM-TEI has been performed using an innovative approach, in which synthetic DNA fragments are used as templates for testing the assay's limit of detection (LOD. Assay specificity and sensitivity was subsequently confirmed by testing with full-length genomic nucleic acids of selected agents. The LOD for a majority of the agents detected by RPM-TEI was determined to be at least 10(4 copies per test. Our results also show that the RPM-TEI assay not only detects and identifies agents, but is also able to differentiate near neighbors of the same agent types, such as closely related strains of filoviruses of the Ebola Zaire group, or the Machupo and Lassa arenaviruses. Furthermore, each RPM-TEI assay results in specimen-specific agent gene sequence information that can be used to assess pathogenicity, mutations, and virulence markers, results that are not generally
ECON-KG: A Code for Computation of Electrical Conductivity Using Density Functional Theory
2017-10-01
AND SUBTITLE ECON-KG: A Code for Computation of Electrical Conductivity Using Density Functional Theory 5a. CONTRACT NUMBER 5b. GRANT NUMBER ...Functional Theory by DeCarlos E Taylor Approved for public release; distribution is unlimited. NOTICES Disclaimers The...Computation of Electrical Conductivity Using Density Functional Theory by DeCarlos E Taylor Weapons and Materials Research Directorate, ARL
Density Functional Investigation of Graphene Doped with Amine-Based Organic Molecules
Directory of Open Access Journals (Sweden)
Yeun Hee Hwang
2015-01-01
Full Text Available To improve the electronic properties of graphene, many doping techniques have been studied. Herein, we investigate the electronic and molecular structure of doped graphene using density functional theory, and we report the effects of amine-based benzene dopants adsorbed on graphene. Density functional theory (DFT calculations were performed to determine the role of amine-based aromatic compounds in graphene doping. These organic molecules bind to graphene through long-range interactions such as π-π interactions and C-H⋯π hydrogen bonding. We compared the electronic structures of pristine graphene and doped graphene to understand the electronic structure of doped graphene at the molecular level. Also, work functions of doped graphene were obtained from electrostatic potential calculations. A decrease in the work function was observed when the amine-based organic compounds were adsorbed onto graphene. Because these systems are based on physisorption, there was no obvious band structure change at point K at the Fermi level after doping. However, the amine-based organic dopants did change the absolute Fermi energy levels. In this study, we showed that the Fermi levels of the doped graphene were affected by the HOMO energy level of the dopants and by the intermolecular charge transfer between the adsorbed molecules and graphene.
Stretched hydrogen molecule from a constrained-search density-functional perspective
Energy Technology Data Exchange (ETDEWEB)
Valone, Steven M [Los Alamos National Laboratory; Levy, Mel [DIKE UNIV.
2009-01-01
Constrained-search density functional theory gives valuable insights into the fundamentals of density functional theory. It provides exact results and bounds on the ground- and excited-state density functionals. An important advantage of the theory is that it gives guidance in the construction of functionals. Here they engage constrained search theory to explore issues associated with the functional behavior of 'stretched bonds' in molecular hydrogen. A constrained search is performed with familiar valence bond wavefunctions ordinarily used to describe molecular hydrogen. The effective, one-electron hamiltonian is computed and compared to the corresponding uncorrelated, Hartree-Fock effective hamiltonian. Analysis of the functional suggests the need to construct different functionals for the same density and to allow a competition among these functions. As a result the correlation energy functional is composed explicitly of energy gaps from the different functionals.
Energy Technology Data Exchange (ETDEWEB)
Khan, Shehryar, E-mail: sherkhan@fysik.su.se; Odelius, Michael, E-mail: odelius@fysik.su.se [Department of Physics, Stockholm University, AlbaNova University Center, S-106 91 Stockholm (Sweden); Kubica-Misztal, Aleksandra [Institute of Physics, Jagiellonian University, ul. Reymonta 4, PL-30-059 Krakow (Poland); Kruk, Danuta [Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Sloneczna 54, Olsztyn PL-10710 (Poland); Kowalewski, Jozef [Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm (Sweden)
2015-01-21
The zero-field splitting (ZFS) of the electronic ground state in paramagnetic ions is a sensitive probe of the variations in the electronic and molecular structure with an impact on fields ranging from fundamental physical chemistry to medical applications. A detailed analysis of the ZFS in a series of symmetric Gd(III) complexes is presented in order to establish the applicability and accuracy of computational methods using multiconfigurational complete-active-space self-consistent field wave functions and of density functional theory calculations. The various computational schemes are then applied to larger complexes Gd(III)DOTA(H{sub 2}O){sup −}, Gd(III)DTPA(H{sub 2}O){sup 2−}, and Gd(III)(H{sub 2}O){sub 8}{sup 3+} in order to analyze how the theoretical results compare to experimentally derived parameters. In contrast to approximations based on density functional theory, the multiconfigurational methods produce results for the ZFS of Gd(III) complexes on the correct order of magnitude.
Particle number and probability density functional theory and A-representability.
Pan, Xiao-Yin; Sahni, Viraht
2010-04-28
In Hohenberg-Kohn density functional theory, the energy E is expressed as a unique functional of the ground state density rho(r): E = E[rho] with the internal energy component F(HK)[rho] being universal. Knowledge of the functional F(HK)[rho] by itself, however, is insufficient to obtain the energy: the particle number N is primary. By emphasizing this primacy, the energy E is written as a nonuniversal functional of N and probability density p(r): E = E[N,p]. The set of functions p(r) satisfies the constraints of normalization to unity and non-negativity, exists for each N; N = 1, ..., infinity, and defines the probability density or p-space. A particle number N and probability density p(r) functional theory is constructed. Two examples for which the exact energy functionals E[N,p] are known are provided. The concept of A-representability is introduced, by which it is meant the set of functions Psi(p) that leads to probability densities p(r) obtained as the quantum-mechanical expectation of the probability density operator, and which satisfies the above constraints. We show that the set of functions p(r) of p-space is equivalent to the A-representable probability density set. We also show via the Harriman and Gilbert constructions that the A-representable and N-representable probability density p(r) sets are equivalent.
A density functional theory-based chemical potential equalisation ...
Indian Academy of Sciences (India)
Unknown
Abstract. The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the ...
A density functional theory-based chemical potential equalisation ...
Indian Academy of Sciences (India)
The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole ...
The functional response to prey density in an acarine system
Fransz, H.G.
1974-01-01
Predacious mites are considered to be important natural enemies of phytophagous mites. Their efficiency in the natural control of prey populations depends on the relationships of the number of prey killed per predator per time unit and the oviposition rate on the one hand and prey density on the
Density functional calculations of {sup 15}N chemical shifts in solvated dipeptides
Energy Technology Data Exchange (ETDEWEB)
Cai Ling; Fushman, David, E-mail: fushman@umd.edu; Kosov, Daniel S. [University of Maryland, Department of Chemistry and Biochemistry (United States)], E-mail: dkosov@umd.edu
2008-06-15
We performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on {sup 15}N chemical shielding in proteins. We used N-methylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from protein GB3. The conducting polarizable continuum model was employed to include the effect of solvent in the density functional calculations. Our calculations for NMA show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic {sup 15}N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard {beta}-sheet and {alpha}-helical conformations ranges from 0.8 to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the {sup 15}N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.
Cove, Michael V.; Gardner, Beth; Simons, Theodore R.; Kays, Roland; O'Connell, Allan F.
2017-01-01
Feral and free-ranging domestic cats (Felis catus) can have strong negative effects on small mammals and birds, particularly in island ecosystems. We deployed camera traps to study free-ranging cats in national wildlife refuges and state parks on Big Pine Key and Key Largo in the Florida Keys, USA, and used spatial capture–recapture models to estimate cat abundance, movement, and activities. We also used stable isotope analyses to examine the diet of cats captured on public lands. Top population models separated cats based on differences in movement and detection with three and two latent groups on Big Pine Key and Key Largo, respectively. We hypothesize that these latent groups represent feral, semi-feral, and indoor/outdoor house cats based on the estimated movement parameters of each group. Estimated cat densities and activity varied between the two islands, with relatively high densities (~4 cats/km2) exhibiting crepuscular diel patterns on Big Pine Key and lower densities (~1 cat/km2) exhibiting nocturnal diel patterns on Key Largo. These differences are most likely related to the higher proportion of house cats on Big Pine relative to Key Largo. Carbon and nitrogen isotope ratios from hair samples of free-ranging cats (n = 43) provided estimates of the proportion of wild and anthropogenic foods in cat diets. At the population level, cats on both islands consumed mostly anthropogenic foods (>80% of the diet), but eight individuals were effective predators of wildlife (>50% of the diet). We provide evidence that cat groups within a population move different distances, exhibit different activity patterns, and that individuals consume wildlife at different rates, which all have implications for managing this invasive predator.
Yang, Haibo; Yan, Fei; Lin, Ying; Wang, Tong; Wang, Fen
2017-08-18
A series of (1-x)Bi0.48La0.02Na0.48Li0.02Ti0.98Zr0.02O3-xNa0.73Bi0.09NbO3 ((1-x)LLBNTZ-xNBN) (x = 0-0.14) ceramics were designed and fabricated using the conventional solid-state sintering method. The phase structure, microstructure, dielectric, ferroelectric and energy storage properties of the ceramics were systematically investigated. The results indicate that the addition of Na0.73Bi0.09NbO3 (NBN) could decrease the remnant polarization (P r ) and improve the temperature stability of dielectric constant obviously. The working temperature range satisfying TCC 150 °C ≤±15% of this work spans over 400 °C with the compositions of x ≥ 0.06. The maximum energy storage density can be obtained for the sample with x = 0.10 at room temperature, with an energy storage density of 2.04 J/cm(3) at 178 kV/cm. In addition, the (1-x)LLBNTZ-xNBN ceramics exhibit excellent energy storage properties over a wide temperature range from room temperature to 90 °C. The values of energy storage density and energy storage efficiency is 0.91 J/cm(3) and 79.51%, respectively, for the 0.90LLBNTZ-0.10NBN ceramic at the condition of 100 kV/cm and 90 °C. It can be concluded that the (1-x)LLBNTZ-xNBN ceramics are promising lead-free candidate materials for energy storage devices over a broad temperature range.
Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald
2013-06-28
Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.
Performance of density functional theory methods to describe ...
Indian Academy of Sciences (India)
Fukui function shows a small dependence with both the exchange and correlation functional and the basis set. Evolution of the Fukui function along the reaction path describes important changes in the basic sites of the corresponding molecules. These results are in agreement with the chemical behavior of those species.
Zentel, Tobias; Kühn, Oliver
2016-12-21
The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared (IR) spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phases are shown to be comparable to the high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, IR absorption spectra are obtained using DFTB and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.
Zentel, Tobias
2016-01-01
The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phase are shown to be comparable to high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and regular DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, infrared (IR) absorption spectra are obtained and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.
Mclaren, Jason R W; Thomas, John C; Mackintosh, Jessica L; Mudge, Kerry A; Grant, Kenneth J; Clare, Bradley A; Cowley, William G
2012-09-01
A large number of model probability density functions (PDFs) are used to analyze atmospheric scintillation statistics. We have analyzed scintillation data from two different experimental setups covering a range of scintillation strengths to determine which candidate model PDFs best describe the experimental data. The PDFs were fitted to the experimental data using the method of least squares. The root-mean-squared fitting error was used to monitor the goodness of fit. The results of the fitting were found to depend strongly on the scintillation strength. We find that the log normally modulated Rician and the log normal PDFs are the best fit to the experimental data over the range of scintillation strengths encountered.
HI column density distribution function at z=0 : Connection to damped Ly alpha statistics
Zwaan, Martin; Verheijen, MAW; Briggs, FH
We present a measurement of the HI column density distribution function f(N-HI) at the present epoch for column densities > 10(20) cm(-2). These high column densities compare to those measured in damped Ly alpha lines seen in absorption against background quasars. Although observationally rare, it
Kemler, Sandra; Pospiech, Martin; Braun, Jens
2017-01-01
In nuclear physics, density functional theory (DFT) provides the basis for state-of-the art studies of ground-state properties of heavy nuclei. However, the direct relation of the density functional underlying these calculations and the microscopic nuclear forces is not yet fully understood. We present a combination of DFT and renormalization group (RG) techniques which allows to study selfbound many-body systems from microscopic interactions. We discuss its application with the aid of systems of identical fermions interacting via a long-range attractive and short-range repulsive two-body force in one dimension. We compute ground-state energies, intrinsic densities, and density correlation functions of these systems and compare our results to those obtained from other methods. In particular, we show how energies of excited states as well as the absolute square of the ground-state wave function can be extracted from the correlation functions within our approach. The relation between many-body perturbation theory and our DFT-RG approach is discussed and illustrated with the aid of the calculation of the second-order energy correction for a system of N identical fermions interacting via a general two-body interaction. Moreover, we discuss the control of spuriously emerging fermion self-interactions in DFT studies within our framework. In general, our approach may help to guide the development of energy functionals for future quantitative DFT studies of heavy nuclei from microscopic interactions.
Energy decomposition analysis of single bonds within Kohn-Sham density functional theory.
Levine, Daniel S; Head-Gordon, Martin
2017-11-28
An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.
Local thermodynamic mapping for effective liquid density-functional theory
Kyrlidis, Agathagelos; Brown, Robert A.
1992-01-01
The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.
A Density Functional Theory Study of New Boron Nanotubes
Chen, Zhao-Hua; Xie, Zun
2017-11-01
Using first-principles calculations, a series of new boron nanotubes (BNTs), which show various electronic properties, were theoretically predicted. Stable nanotubes with various chiral vectors and diameters can be formed by rolling up the boron sheet with relative stability [H. Tang and S. I. Beigi, Phys. Rev. B 82, 115412 (2010).]. By increasing the diameter for BNT, the stability is enhanced. The calculated density of states and band structures demonstrate that all the predicted BNTs are metallic, regardless of their diameter and chirality. The multicentre chemical bonds of the relatively stable boron sheet and BNTs are analysed using the deformation electron density. Within our study, the BNTs all have metallic conductive characteristics, in addition to having a low effective quality and high carrier concentration, which are very good nanoconductive material properties and could be combined to form high-power electrodes for lithium-ion batteries such as those used in many modern electronics.
Quantum mechanics in metric space: wave functions and their densities.
D'Amico, I; Coe, J P; França, V V; Capelle, K
2011-02-04
Hilbert space combines the properties of two different types of mathematical spaces: vector space and metric space. While the vector-space aspects are widely used, the metric-space aspects are much less exploited. Here we show that a suitable metric stratifies Fock space into concentric spheres on which maximum and minimum distances between states can be defined and geometrically interpreted. Unlike the usual Hilbert-space analysis, our results apply also to the reduced space of only ground states and to that of particle densities, which are metric, but not Hilbert, spaces. The Hohenberg-Kohn mapping between densities and ground states, which is highly complex and nonlocal in coordinate description, is found, for three different model systems, to be simple in metric space, where it becomes a monotonic and nearly linear mapping of vicinities onto vicinities.
Molecular density functional theory for water with liquid-gas coexistence and correct pressure.
Jeanmairet, Guillaume; Levesque, Maximilien; Sergiievskyi, Volodymyr; Borgis, Daniel
2015-04-21
The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.
Solovyeva, Alisa; Pavanello, Michele; Neugebauer, Johannes
2012-05-01
Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a π-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.
Energy Technology Data Exchange (ETDEWEB)
Solovyeva, Alisa [Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden (Netherlands); Technical University Braunschweig, Institute for Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig (Germany); Pavanello, Michele [Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden (Netherlands); Neugebauer, Johannes [Technical University Braunschweig, Institute for Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig (Germany)
2012-05-21
Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a {pi}-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.
Piyanzina, Irina; Minisini, Benoit; Tayurskii, Dmitrii; Bardeau, Jean-François
2015-02-01
Density functional theory (DFT) calculations have been used to investigate the structural properties, dipole moments, polarizabilities, Gibbs energies, hardness, electronegativity, HOMO/LUMO energies, and chemical potentials of trans and cis configurations of eight para-substituted azobenzene derivatives. All properties have been obtained using the B3LYP functional and 6-31++G(d,p) basis set. The planar structures have been obtained for all optimized trans configurations. The energy difference between trans and cis configurations for considered derivatives was found to be between 64.2-73.1 kJ/mole. It has been obtained that the p-aminodiazo-benzene (ADAB) has the difference in the dipole moments between trans and cis forms higher than for trans and cis azobenzene.
Treatment of Layered Structures Using a Semilocal meta-GGA Density Functional
DEFF Research Database (Denmark)
Madsen, Georg; Ferrighi, Lara; Hammer, Bjørk
2010-01-01
Density functional theory calculations on solids consisting of covalently bonded layers held together by dispersive interactions are presented. Utilizing the kinetic energy density in addition to the density and its gradients gives the meta-generalized gradient approximation (MGGA) M06-L enough f...... to discriminate between dispersive and covalent interactions and thereby prove that the performance of M06-L for dispersive interactions, as opposed to that for the local density approximation, is not based on an accidental cancellation of errors....
Spaak, Jurg W.; Baert, Jan M.; Baird, Donald J.; Eisenhauer, Nico; Maltby, Lorraine; Pomati, Francesco; Radchuk, Viktoriia; Rohr, Jason R.; Brink, van den Paul J.; Laender, De Frederik
2017-01-01
There has been considerable focus on the impacts of environmental change on ecosystem function arising from changes in species richness. However, environmental change may affect ecosystem function without affecting richness, most notably by affecting population densities and community
Łazarski, Roman; Burow, Asbjörn Manfred; Grajciar, Lukáš; Sierka, Marek
2016-10-30
A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn-Sham density functional theory using Gaussian-type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange-correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn-Sham matrix formation. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory
Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.
2017-07-01
We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.
Energy Technology Data Exchange (ETDEWEB)
Tabacchi, G; Hutter, J; Mundy, C
2005-04-07
A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density functional calculations.
Hellgren, M
2013-01-01
We present a detailed study of the exact-exchange (EXX) kernel of time-dependent density functional theory with an emphasis on its discontinuity at integer particle numbers. It was recently found that this exact property leads to sharp peaks and step features in the kernel that diverge in the dissociation limit of diatomic systems [Hellgren and Gross, Phys. Rev. A, 022514 (2012)]. To further analyze the discontinuity of the kernel we here make use of two different approximations to the EXX kernel: the PGG approximation and a common energy denominator approximation (CEDA). It is demonstrated that whereas the PGG approximation neglects the discontinuity the CEDA includes it explicitly. By studying model molecular systems it is shown that the so-called field counter-acting effect in the density functional description of molecular chains can be viewed in terms of the discontinuity of the static kernel. The role of the frequency dependence is also investigated, highlighting its importance for long-range charge tra...
Goel, Himanshu; Butler, Charles L; Windom, Zachary W; Rai, Neeraj
2016-07-12
Recent developments in dispersion corrected and nonlocal density functionals are aimed at accurately capturing dispersion interactions, a key shortcoming of local and semilocal approximations of density functional theory. These functionals have shown significant promise for dimers and small clusters of molecules as well as crystalline materials. However, their efficacy for predicting vapor liquid equilibria is largely unexplored. In this work, we examine the accuracy of dispersion-corrected and nonlocal van der Waals functionals by computing the vapor liquid coexistence curves (VLCCs) of hydrofluoromethanes. Our results indicate that the PBE-D3 functional performs significantly better in predicting saturated liquid densities than the rVV10 functional. With the PBE-D3 functional, we also find that as the number of fluorine atoms increase in the molecule, the accuracy of saturated liquid density prediction improves as well. All the functionals significantly underpredict the saturated vapor densities, which also result in an underprediction of saturated vapor pressure of all compounds. Despite the differences in the bulk liquid densities, the local microstructures of the liquid CFH3 and CF2H2 are relatively insensitive to the density functional employed. For CF3H, however, rVV10 predicts slightly more structured liquid than the PBE-D3 functional.
Statistics of adaptive optics speckles: From probability cloud to probability density function
Yaitskova, Natalia; Gladysz, Szymon
2016-01-01
The complex amplitude in the focal plane of adaptive optics system is modelled as an elliptical complex random variable. The geometrical properties of the probability density function of such variable relate directly to the statistics of the residual phase. Building solely on the twodimensional geometry, the expression for the probability density function of speckle intensity is derived.
Density Functional Study on the Morphology and Photoabsorption of CdSe Nanoclusters
Del Ben, Mauro; Havenith, Remco W. A.; Broer, Ria; Stener, Mauro
2011-01-01
The geometrical and electronic structures of a series of small CdSe quantum dots protected by various ligands have been studied by density functional theory. UV-vis spectra have been calculated by time-dependent density functional theory (TDDFT). The goal of this investigation is the rationalization
Energy Technology Data Exchange (ETDEWEB)
Baczewski, Andrew David; Shulenburger, Luke; Desjarlais, Michael Paul; Magyar, Rudolph J.
2014-02-01
In recent years, DFT-MD has been shown to be a useful computational tool for exploring the properties of WDM. These calculations achieve excellent agreement with shock compression experiments, which probe the thermodynamic parameters of the Hugoniot state. New X-ray Thomson Scattering diagnostics promise to deliver independent measurements of electronic density and temperature, as well as structural information in shocked systems. However, they require the development of new levels of theory for computing the associated observables within a DFT framework. The experimentally observable x-ray scattering cross section is related to the electronic density-density response function, which is obtainable using TDDFT - a formally exact extension of conventional DFT that describes electron dynamics and excited states. In order to develop a capability for modeling XRTS data and, more generally, to establish a predictive capability for rst principles simulations of matter in extreme conditions, real-time TDDFT with Ehrenfest dynamics has been implemented in an existing PAW code for DFT-MD calculations. The purpose of this report is to record implementation details and benchmarks as the project advances from software development to delivering novel scienti c results. Results range from tests that establish the accuracy, e ciency, and scalability of our implementation, to calculations that are veri ed against accepted results in the literature. Aside from the primary XRTS goal, we identify other more general areas where this new capability will be useful, including stopping power calculations and electron-ion equilibration.
Borpuzari, Manash Protim; Boruah, Abhijit; Kar, Rahul
2016-04-28
Recently, the range-separated density functionals have been reported to reproduce gas phase orbital and excitation energies with good accuracy. In this article, we have revisited the ionisation potential theorem in the presence of external electric field. Numerical results on six linear molecules are presented and the performance of the range-separated density functionals in reproducing highest occupied molecular orbital (HOMO) energies, LUMO energies, HOMO-LUMO gaps in the presence of the external electric field is assessed. In addition, valence and Rydberg excitation energies in the presence of the external electric field are presented. It is found that the range-separated density functionals reproduce orbital and excitation energies accurately in the presence of the electric field. Moreover, we have performed fractional occupation calculation using cubic spline equation and tried to explain the performance of the functional.
Yedukondalu, N.; Vaitheeswaran, G.
2014-06-01
Silver fulminate (AgCNO) is a primary explosive, which exists in two polymorphic phases, namely, orthorhombic (Cmcm) and trigonal (Rbar{3}) forms at ambient conditions. In the present study, we have investigated the effect of pressure and temperature on relative phase stability of the polymorphs using planewave pseudopotential approaches based on Density Functional Theory (DFT). van der Waals interactions play a significant role in predicting the phase stability and they can be effectively captured by semi-empirical dispersion correction methods in contrast to standard DFT functionals. Based on our total energy calculations using DFT-D2 method, the Cmcm structure is found to be the preferred thermodynamic equilibrium phase under studied pressure and temperature range. Hitherto Cmcm and Rbar{3} phases denoted as α- and β-forms of AgCNO, respectively. Also a pressure induced polymorphic phase transition is seen using DFT functionals and the same was not observed with DFT-D2 method. The equation of state and compressibility of both polymorphic phases were investigated. Electronic structure and optical properties were calculated using full potential linearized augmented plane wave method within the Tran-Blaha modified Becke-Johnson potential. The calculated electronic structure shows that α, β phases are indirect bandgap insulators with a bandgap values of 3.51 and 4.43 eV, respectively. The nature of chemical bonding is analyzed through the charge density plots and partial density of states. Optical anisotropy, electric-dipole transitions, and photo sensitivity to light of the polymorphs are analyzed from the calculated optical spectra. Overall, the present study provides an early indication to experimentalists to avoid the formation of unstable β-form of AgCNO.
Yedukondalu, N; Vaitheeswaran, G
2014-06-14
Silver fulminate (AgCNO) is a primary explosive, which exists in two polymorphic phases, namely, orthorhombic (Cmcm) and trigonal (R3) forms at ambient conditions. In the present study, we have investigated the effect of pressure and temperature on relative phase stability of the polymorphs using planewave pseudopotential approaches based on Density Functional Theory (DFT). van der Waals interactions play a significant role in predicting the phase stability and they can be effectively captured by semi-empirical dispersion correction methods in contrast to standard DFT functionals. Based on our total energy calculations using DFT-D2 method, the Cmcm structure is found to be the preferred thermodynamic equilibrium phase under studied pressure and temperature range. Hitherto Cmcm and R3 phases denoted as α- and β-forms of AgCNO, respectively. Also a pressure induced polymorphic phase transition is seen using DFT functionals and the same was not observed with DFT-D2 method. The equation of state and compressibility of both polymorphic phases were investigated. Electronic structure and optical properties were calculated using full potential linearized augmented plane wave method within the Tran-Blaha modified Becke-Johnson potential. The calculated electronic structure shows that α, β phases are indirect bandgap insulators with a bandgap values of 3.51 and 4.43 eV, respectively. The nature of chemical bonding is analyzed through the charge density plots and partial density of states. Optical anisotropy, electric-dipole transitions, and photo sensitivity to light of the polymorphs are analyzed from the calculated optical spectra. Overall, the present study provides an early indication to experimentalists to avoid the formation of unstable β-form of AgCNO.
Element orbitals for Kohn-Sham density functional theory
Energy Technology Data Exchange (ETDEWEB)
Lin, Lin; Ying, Lexing
2012-05-08
We present a method to discretize the Kohn-Sham Hamiltonian matrix in the pseudopotential framework by a small set of basis functions automatically contracted from a uniform basis set such as planewaves. Each basis function is localized around an element, which is a small part of the global domain containing multiple atoms. We demonstrate that the resulting basis set achieves meV accuracy for 3D densely packed systems with a small number of basis functions per atom. The procedure is applicable to insulating and metallic systems.
Linear density response function in the projector augmented wave method
DEFF Research Database (Denmark)
Yan, Jun; Mortensen, Jens Jørgen; Jacobsen, Karsten Wedel
2011-01-01
functions of Si, C, SiC, AlP, and GaAs compare well with previous calculations. While optical properties of semiconductors, in particular excitonic effects, are generally not well described by ALDA, we obtain excellent agreement with experiments for the surface loss function of graphene and the Mg(0001......) surface with plasmon energies deviating by less than 0.2 eV. Finally, the method is applied to study the influence of substrates on the plasmon excitations in graphene....
Dimakis, Nicholas; Valdez, Danielle; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade; Vargas, Sarah; Saenz, Justin
2017-08-01
The adsorption of the alkali Li, K, and Na and the alkaline Ca on graphene is studied using periodic density functional theory (DFT) under various adatom coverages. The charge transfers between the adatom and the graphene sheet and the almost unchanged densities-of-states spectra in the energy region near and below the Fermi level support an ionic bond pattern between the adatom and the graphene atoms. However, the presence of small orbital overlap between the metal and the nearest graphene atom is indicative of small covalent bonding. Van der Waals interactions are examined through a semiempirical correction in the DFT functional and by comparing adatom-graphene calculations between 3% and 1.4% adatom coverages. Optimized adatom-graphene geometries identify the preferred adatom sites, whereas the adatom-graphene strength is correlated with the adsorption energy and the adatom distance from the graphene plane. Calculated electronic properties and structural parameters are obtained using hybrid functionals and a generalized gradient approximation functional paired with basis sets of various sizes. We found that due to long range electrostatic forces between the alkali/alkaline adatoms and the graphene monolayer, the adatom-graphene structural and electronic properties could be well-described by specific DFT functionals paired with high-quality adatom basis sets. For Li, K, and Na adsorbed on graphene, increased adatom surface coverage weakens the adatom-graphene interaction. However, this statement does not apply for Ca adsorbed on graphene. In this case, the Ca adsorption strength, which is stronger at higher coverages, is opposite to increases in the Ca-4s orbital population.
Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura
2015-01-13
Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.
Formation energies of rutile metal dioxides using density functional theory
DEFF Research Database (Denmark)
Martinez, Jose Ignacio; Hansen, Heine Anton; Rossmeisl, Jan
2009-01-01
the formation energy of the oxygen molecule and the electron self-interaction for localized d and f electrons are known shortcomings. In this paper we show that despite the known problems, it is possible to calculate the stability of a wide range of rutile oxides MO2, with M being Pt, Ru, Ir, Os, Pb, Re, Mn, Se...
Surface effects on mean inner potentials studied using density functional theory
Energy Technology Data Exchange (ETDEWEB)
Pennington, Robert S., E-mail: robert.pennington@uni-ulm.de [Institute for Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm (Germany); Boothroyd, Chris B.; Dunin-Borkowski, Rafal E. [Ernst Ruska-Centre and Peter Grüneberg Institute, Forschungzentrum Jülich, 52425 Jülich (Germany)
2015-12-15
Quantitative materials characterization using electron holography frequently requires knowledge of the mean inner potential, but reported experimental mean inner potential measurements can vary widely. Using density functional theory, we have simulated the mean inner potential for materials with a range of different surface conditions and geometries. We use both “thin-film” and “nanowire” specimen geometries. We consider clean bulk-terminated surfaces with different facets and surface reconstructions using atom positions from both structural optimization and experimental data and we also consider surfaces both with and without adsorbates. We find that the mean inner potential is surface-dependent, with the strongest dependency on surface adsorbates. We discuss the outlook and perspective for future mean inner potential measurements. - Highlights: • Density functional theory (DFT) is used to simulate mean inner potentials (MIP). • Applications for MIP electron holography measurements are considered. • MIPs are found to be surface-dependent, for thin-film and nanowire geometries. • The DFT simulation precision is extensively tested for multiple materials. • Surface adsorbates can create a strong positive or negative effect.
Thyroid Function within the Reference Range and the Risk of Stroke
DEFF Research Database (Denmark)
Chaker, Layal; Baumgartner, Christine; den Elzen, Wendy P J
2016-01-01
CONTEXT: The currently applied reference ranges for thyroid function are under debate. Despite evidence that thyroid function within the reference range is related with several cardiovascular disorders, its association with the risk of stroke has not been evaluated previously. DESIGN AND SETTING:...
Chaker, Layal; Baumgartner, Christine; den Elzen, Wendy P. J.; Collet, Tinh-Hai; Ikram, M. Arfan; Blum, Manuel R.; Dehghan, Abbas; Drechsler, Christiane; Luben, Robert N.; Portegies, Marileen L. P.; Lervasi, Giorgio; Medici, Marco; Stott, David J.; Dullaart, Robin P.; Ford, Ian; Bremner, Alexandra; Newman, Anne B.; Wanner, Christoph; Sgarbi, Jose A.; Dorr, Marcus; Longstreth, W. T.; Psaty, Bruce M.; Ferrucci, Luigi; Maciel, Rui M. B.; Westendorp, Rudi G.; Jukema, J. Wouter; Ceresini, Graziano; Imaizumi, Misa; Hofman, Albert; Bakker, Stephan J. L.; Franklyn, Jayne A.; Khaw, Kay-Tee; Bauer, Douglas C.; Walsh, John P.; Razvi, Salman; Gussekloo, Jacobijn; Volzke, Henry; Franco, Oscar H.; Cappola, Anne R.; Rodondi, Nicolas; Peeters, Robin P.
2016-01-01
Context: The currently applied reference ranges for thyroid function are under debate. Despite evidence that thyroid function within the reference range is related with several cardiovascular disorders, its association with the risk of stroke has not been evaluated previously. Design and Setting: We
Evaluation of Density Functionals and Basis Sets for Carbohydrates
Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of alpha and beta-D-allopyranose, 15 of ...
A density functional model for the surface properties of liquid sup 4 He
Energy Technology Data Exchange (ETDEWEB)
Guirao, A.; Centelles, M.; Barranco, M.; Pi, M.; Polls, A.; Vinas, X. (Barcelona Univ. (Spain). Dept. d' Estructura i Constituents de la Materia)
1992-01-20
A density functional approach is proposed to study the {sup 4}He liquid-gas interface. The free energy density, which depends on the particle density and temperature, has been adjusted to reproduce the liquid density and the vapour pressure along the liquid-gas coexistence line, as well as the zero-temperature surface tension. After achieving a fairly good description of the phase transition, the calculated surface tension agrees well with the experimental results. The calculated density profile is used to discuss a recent experimental determination of the surface thickness. (author).
Fedorov, Dmitri G; Kitaura, Kazuo
2018-02-15
Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.
Farzaneh, Saeed; Forootan, Ehsan
2017-11-01
The computerized ionospheric tomography is a method for imaging the Earth's ionosphere using a sounding technique and computing the slant total electron content (STEC) values from data of the global positioning system (GPS). The most common approach for ionospheric tomography is the voxel-based model, in which (1) the ionosphere is divided into voxels, (2) the STEC is then measured along (many) satellite signal paths, and finally (3) an inversion procedure is applied to reconstruct the electron density distribution of the ionosphere. In this study, a computationally efficient approach is introduced, which improves the inversion procedure of step 3. Our proposed method combines the empirical orthogonal function and the spherical Slepian base functions to describe the vertical and horizontal distribution of electron density, respectively. Thus, it can be applied on regional and global case studies. Numerical application is demonstrated using the ground-based GPS data over South America. Our results are validated against ionospheric tomography obtained from the constellation observing system for meteorology, ionosphere, and climate (COSMIC) observations and the global ionosphere map estimated by international centers, as well as by comparison with STEC derived from independent GPS stations. Using the proposed approach, we find that while using 30 GPS measurements in South America, one can achieve comparable accuracy with those from COSMIC data within the reported accuracy (1 × 1011 el/cm3) of the product. Comparisons with real observations of two GPS stations indicate an absolute difference is less than 2 TECU (where 1 total electron content unit, TECU, is 1016 electrons/m2).
Long-range weight functions in fundamental measure theory of the non-uniform hard-sphere fluid.
Hansen-Goos, Hendrik
2016-06-22
We introduce long-range weight functions to the framework of fundamental measure theory (FMT) of the non-uniform, single-component hard-sphere fluid. While the range of the usual weight functions is equal to the hard-sphere radius R, the modified weight functions have range 3R. Based on the augmented FMT, we calculate the radial distribution function g(r) up to second order in the density within Percus' test particle theory. Consistency of the compressibility and virial routes on this level allows us to determine the free parameter γ of the theory. As a side result, we obtain a value for the fourth virial coefficient B 4 which deviates by only 0.01% from the exact result. The augmented FMT is tested for the dense fluid by comparing results for g(r) calculated via the test particle route to existing results from molecular dynamics simulations. The agreement at large distances (r > 6R) is significantly improved when the FMT with long-range weight functions is used. In order to improve agreement close to contact (r = 2R) we construct a free energy which is based on the accurate Carnahan-Starling equation of state, rather than the Percus-Yevick compressibility equation underlying standard FMT.
Pastore, Mariachiara; Assfeld, Xavier; Mosconi, Edoardo; Monari, Antonio; Etienne, Thibaud
2017-07-01
We report a theoretical study on the analysis of the relaxed one-particle difference density matrix characterizing the passage from the ground to the excited state of a molecular system, as obtained from time-dependent density functional theory. In particular, this work aims at using the physics contained in the so-called Z-vector, which differentiates between unrelaxed and relaxed difference density matrices to analyze excited states' nature. For this purpose, we introduce novel quantum-mechanical quantities, based on the detachment/attachment methodology, for analysing the Z-vector transformation for different molecules and density functional theory functionals. A derivation pathway of these novel descriptors is reported, involving a numerical integration to be performed in the Euclidean space on the density functions. This topological analysis is then applied to two sets of chromophores, and the correlation between the level of theory and the behavior of our descriptors is properly rationalized. In particular, the effect of range-separation on the relaxation amplitude is discussed. The relaxation term is finally shown to be system-specific (for a given level of theory) and independent of the number of electrons (i.e., the relaxation amplitude is not simply the result of a collective phenomenon).
Density Functional Theory (DFT Study of Edaravone Derivatives as Antioxidants
Directory of Open Access Journals (Sweden)
Walace G. Leal
2012-06-01
Full Text Available Quantum chemical calculations at the B3LYP/6–31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E, ionization potential (IP, bond dissociation energy (BDE, and stabilization energies (∆E_{iso}. Spin density calculations were also performed for the proposed antioxidant activity mechanism. The electron abstraction is related to electron-donating groups (EDG at position 3, decreasing the IP when compared to substitution at position 4. The hydrogen abstraction is related to electron-withdrawing groups (EDG at position 4, decreasing the BDE_{CH} when compared to other substitutions, resulting in a better antioxidant activity. The unpaired electron formed by the hydrogen abstraction from the C–H group of the pyrazole ring is localized at 2, 4, and 6 positions. The highest scavenging activity prediction is related to the lowest contribution at the carbon atom. The likely mechanism is related to hydrogen transfer. It was found that antioxidant activity depends on the presence of EDG at the C_{2} and C_{4} positions and there is a correlation between IP and BDE. Our results identified three different classes of new derivatives more potent than edaravone.
Gao, Qing; Xu, Fei; Jiang, Cui; Chen, Zhifeng; Chen, Huafu; Liao, Huaqiang; Zhao, Ling
2016-02-01
Migraine is one of the most prevalent neurological disorders which is suggested to be associated with dysfunctions of the central nervous system. The purpose of the present study was to detect the altered functional connectivity architecture in the large-scale network of the whole brain in migraine without aura (MWoA). Meanwhile, the brain functional hubs which are targeted by MWoA could be identified. A new voxel-based method named functional connectivity density (FCD) mapping was applied to resting-state functional magnetic resonance imaging data of 55 female MWoA patients and 44 age-matched female healthy controls (HC). Comparing to HC, MWoA patients showed abnormal short-range FCD values in bilateral hippocampus, bilateral insula, right amygdale, right anterior cingulate cortex, bilateral putamen, bilateral caudate nucleus and the prefrontal cortex. The results suggested decreased intraregional connectivity of these pain-related brain regions in female MWoA. In addition, short-range FCD values in left prefrontal cortex, putamen and caudate nucleus were significantly negatively correlated with duration of disease in MWoA group, implying the repeated migraine attacks over time may consistently affect the resting-state functional connectivity architecture of these brain hubs. Our findings revealed the dysfunction of brain hubs in female MWoA, and suggested the left prefrontal cortex, putamen and caudate nucleus served as sensitive neuroimaging markers for reflecting the disease duration of female MWoA. This may provide us new insights into the changes in the organization of the large-scale brain network in MWoA. Copyright © 2015 Elsevier B.V. All rights reserved.
A density functional theory investigation of the electronic structure and spin moments of magnetite
Noh, Junghyun
2014-08-01
We present the results of density functional theory (DFT) calculations on magnetite, Fe3O4, which has been recently considered as electrode in the emerging field of organic spintronics. Given the nature of the potential applications, we evaluated the magnetite room-temperature cubic phase in terms of structural, electronic, and magnetic properties. We considered GGA (PBE), GGA + U (PBE + U), and range-separated hybrid (HSE06 and HSE(15%)) functionals. Calculations using HSE06 and HSE(15%) functionals underline the impact that inclusion of exact exchange has on the electronic structure. While the modulation of the band gap with exact exchange has been seen in numerous situations, the dramatic change in the valence band nature and states near the Fermi level has major implications for even a qualitative interpretation of the DFT results. We find that HSE06 leads to highly localized states below the Fermi level while HSE(15%) and PBE + U result in delocalized states around the Fermi level. The significant differences in local magnetic moments and atomic charges indicate that describing room-temperature bulk materials, surfaces and interfaces may require different functionals than their low-temperature counterparts.
Structure and bonding of propyne on Cu(111) from density functional periodic and cluster models
Valcarcel, A.; Ricart, J. M.; Clotet, A.; Markovits, A.; Minot, C.; Illas, F.
2002-01-01
The interaction of propyne on Cu(111) has been studied by periodic and cluster model density functional based methods. The structure of adsorbed propyne predicted by the different models and methods is almost indistinguishable and in very good agreement with experiment. This is a highly distorted propyne with C1 and C2 in nearly sp2 hybridization. The adsorption site predicted by both surface models is also in agreement with experiment provided the cluster innermost region has the correct environment. The use of different functionals does not appear to have a noticeable effect on the adsorption geometry and position of the adsorbate relative to the surface. However, the adsorption energies computed by different exchange-correlation functionals may differ in roughly 0.35 eV. Periodic calculations carried out for different unit cells confirms the experimental long-range structure. Finally, a comparison of cluster and periodic adsorption energies permits to establish that the influence of the surface model on the predicted adsorption energies is much larger than the incertitude due to the choice of a particular exchange correlation functional.
Multiple exciton generation in chiral carbon nanotubes: Density functional theory based computation
Kryjevski, Andrei; Mihaylov, Deyan; Kilina, Svetlana; Kilin, Dmitri
2017-10-01
We use a Boltzmann transport equation (BE) to study time evolution of a photo-excited state in a nanoparticle including phonon-mediated exciton relaxation and the multiple exciton generation (MEG) processes, such as exciton-to-biexciton multiplication and biexciton-to-exciton recombination. BE collision integrals are computed using Kadanoff-Baym-Keldysh many-body perturbation theory based on density functional theory simulations, including exciton effects. We compute internal quantum efficiency (QE), which is the number of excitons generated from an absorbed photon in the course of the relaxation. We apply this approach to chiral single-wall carbon nanotubes (SWCNTs), such as (6,2) and (6,5). We predict efficient MEG in the (6,2) and (6,5) SWCNTs within the solar spectrum range starting at the 2Eg energy threshold and with QE reaching ˜1.6 at about 3Eg, where Eg is the electronic gap.
Bi, Gang; Kang, Jun; Wang, Lin-Wang
2017-03-29
Liquid lithium is often used as a coating material in fusion reaction chambers, where it is under constant bombardment from high speed neutrons and protons. However, numerous fundamental questions are unanswered, for example whether a single proton impact can cause Li atom sputtering, and what is the electron excitation energy profile after a collision particularly for extremely high energy projectiles. Herein, we use a real-time dependent density functional method to study these questions for proton energies in the range of 30 eV to 1 MeV. The calculated stopping power agrees well with experiment, and it is found that the stopping power cannot be described by the single electron exciting spectrum based on the adiabatic eigen energies, and Li atom sputtering is not observed within our simulation time.
Directory of Open Access Journals (Sweden)
Brandon B. Dale
2017-05-01
Full Text Available Bare and guanine-complexed silver clusters Ag n z (n = 2-6; z = 0-2 are examined using density functional theory to elucidate the geometries and binding motifs that are present experimentally. Whereas the neutral systems remain planar in this size range, a 2D-3D transition occurs at Ag 5 + for the cationic system and at Ag 4 2 + for the dicationic system. Neutral silver clusters can bind with nitrogen 3 or with the pi system of the base. However, positively charged clusters interact with nitrogen 7 and the neighboring carbonyl group. Thus, the cationic silver-DNA clusters present experimentally may preferentially interact at these sites.
Directory of Open Access Journals (Sweden)
Bin Liu
2018-01-01
Full Text Available Glycerol has been utilized in an extremely diversified manner throughout human civilization—ranging from food, to various consumer products, to pharmaceuticals, and even explosives. Large surplus in glycerol supply thanks to biodiesel production and biomass processing has created a demand to further boost its utility. One growing area is to expand the use of glycerol as an alternative feedstock to supplement fuels and chemicals production. Various catalytic processes have been developed. This review summarizes catalytic materials for glycerol reforming, hydrodeoxygenation, and oxidation. In particular, rationale for catalyst selection and new catalyst design will be discussed aided by the knowledge of reaction mechanisms. The role of theoretical density functional theory (DFT in elucidating complex glycerol conversion chemistries is particularly emphasized.
Time-dependent spin-density-functional-theory description of He+-He collisions
Baxter, Matthew; Kirchner, Tom; Engel, Eberhard
2017-09-01
Theoretical total cross-section results for all ionization and capture processes in the He+-He collision system are presented in the approximate impact energy range of 10-1000 keV/amu. Calculations were performed within the framework of time-dependent spin-density functional theory. The Krieger-Li-Iafrate approximation was used to determine an accurate exchange-correlation potential in the exchange-only limit. The results of two models, one where electron translation factors in the orbitals used to calculate the potential are ignored and another where partial electron translation factors are included, are compared with available experimental data as well as a selection of previous theoretical calculations.
Goal-Oriented Probability Density Function Methods for Uncertainty Quantification
2015-12-11
residual formulation, - in particular an alternating direction Galerkin method . In this way, the computational cost of solving high-dimensional PDF...UCSC - $2,445.65 5. 6/26/15 - Workshop at Woods Hole Oceanographic Institute - $149.23 • Indirect Costs - $22,138.96 • Total Costs : $57,561.29 8...function methods for uncertainty quantification Grant/Contract Number AFOSR assigned control number. It must begin with "FA9550" or "F49620" or "FA2386
Hallin, Sara; Welsh, Allana; Stenström, John; Hallet, Stephanie; Enwall, Karin; Bru, David; Philippot, Laurent
2012-01-01
Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.
Bartel, J.; Bencheikh, K.; Meyer, J.
2008-02-01
For a one-body Hamiltonian obtained from the energy-density functional associated with a Skyrme effective interaction, including a tensor force, semiclassical functional densities are derived in the framework of the Extended Thomas-Fermi method, in spherical symmetry, for the kinetic energy and spin-orbit density. The structure of the self-consistent mean-field potentials constructed with such semiclassical functionals is studied. The impact of the tensor force in particular on the spin-orbit form factor clearly indicates the necessity of including such tensor-force terms in the theoretical description of atomic nuclei and their possible influence on the shell structure of exotic nuclei.
Vyboishchikov, Sergei F
2017-09-03
We propose a simple method of calculating the electron correlation energy density ec (r) and the correlation potential Vc (r) from second-order Møller-Plesset amplitudes and its generalization for the case of a configuration interaction wavefunction, based on Nesbet's theorem. The correlation energy density obtained by this method for free and spherically confined Be and He atoms was employed to fit a local analytical density functional based on Wigner's functional. The functional is capable of producing a strong increase in the correlation energy with decreasing confined radius for the Be atom. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Pozorski, Jacek; Wacławczyk, Marta; Minier, Jean-Pierre
2003-05-01
A joint velocity-scalar probability density function (PDF) method is presented to model and simulate turbulent flows with passive inert scalars (here temperature). The full PDF approach is applied for wall-bounded flows. In the present work, the boundary conditions are imposed in the logarithmic region and the modeling is therefore performed in the wall-function spirit. The PDF equation is solved by a Monte Carlo method and the whole approach appears as a Lagrangian simulation using stochastic particles. The purpose of the work is to analyze the behavior of classical PDF models in the near-wall region and to develop new particle boundary conditions for the velocity and scalars attached to each particle. First of all, the logarithmic region is described as an equilibrium zone and resulting analytical formulas for second-order temperature-velocity statistics , , are derived. Boundary conditions for scalars are then developed and formulated in terms of instantaneous particle variables. These results are useful to discuss consistency issues between the formulation of scalar mixing models and the statement of boundary conditions. Finally, heated channel flow is simulated with a stand-alone PDF code for two different heat-flux conditions and results are compared with available direct numerical simulation and experimental data.
Configurational study of amino-functionalized silica surfaces: A density functional theory modeling.
Hozhabr Araghi, Samira; Entezari, Mohammad H; Sadeghi Googheri, Mohammad Sadegh
2015-06-01
Despite extensive studies of the amino-functionalized silica surfaces, a comprehensive investigation of the effects of configuration and hydrolysis of 3-aminopropyltriethoxysilan (APTES) molecules attached on silica has not been studied yet. Therefore, the methods of quantum mechanics were used for the study of configuration and hydrolysis forms of APTES molecules attached on the surface. For this purpose, five different categories based on the number of hydrolyzed ethoxy groups including 16 configurations were designed and analyzed by the density functional theory (DFT) method. The steric hindrance as an effective factor on the stability order was extracted from structural analysis. Other impressive parameters such as the effects of hydrogen bond and electron delocalization energy were obtained by using the atoms in molecules (AIM) and natural bond orbitals (NBO) theories. Consequently, it was found that the stability of configurations was attributed to steric effects, hydrogen bond numbers and electron delocalization energy. The maximum stability was achieved when at least two of these parameters cooperate with each other. Copyright © 2015 Elsevier Inc. All rights reserved.
Haataja, Mikko; Gránásy, László; Löwen, Hartmut
2010-08-01
-liquid interface properties, glassy dynamics, nucleation and growth, and diffusive phase transformations at the nano- and mesoscales [8-16]. The appealing feature of DDFT (as applied to solid-state systems) is that it automatically incorporates diffusive dynamics with atomic scale spatial resolution, and it naturally incorporates multiple components, elastic strains, dislocations, free surfaces, and multiple crystalline orientations; all of these features are critical in modeling the behavior of solid-state systems. Similarities between the problems of interest to the two communities and the complementary nature of the methods they apply suggest that a direct interaction between them should be highly beneficial for both parties. Here we summarize some of the discussions during a three-day CECAM workshop in Lausanne (21-23 October 2009) which was organized in order to bring together researchers from the complex fluids and materials science communities and to foster the exchange of ideas between these two communities. During the course of the workshop, several open problems relevant to both fields (DFT and PFC) were identified, including developing better microscopically-informed density functionals, incorporating stochastic fluctuations, and accounting for hydrodynamic interactions. The goal of this special issue is to highlight recent progress in DFT and PFC approaches, and discuss key outstanding problems for future work. The rest of this introductory paper is organized as follows. In section 2, we give a brief overview of the current research topics addressed in this special issue. Then, in section 3, we present a collection of outstanding problems, which have been identified as important for further developments of the two fields and intensely debated at the CECAM workshop. Finally, we close the paper with a few concluding remarks. 2. Research topics addressed in this special issue This special issue consists of research papers that cover a broad range of interesting subjects
Kremens, R.; Dickinson, M. B.; Hardy, C.; Skowronski, N.; Ellicott, E. A.; Schroeder, W.
2016-12-01
We have developed a wide dynamic range (24-bit) data acquisition system for collection of radiant flux density (FRFD) data from wildland fires. The data collection subsystem was designed as an Arduino `shield' and incorporates a 24-bit analog-to-digital converter, precision voltage reference, real time clock, microSD card interface, audible annuciator and interface for various digital communication interfaces (RS232, I2C, SPI, etc.). The complete radiometer system consists of our custom-designed `shield', a commercially available Arduino MEGA computer circuit board and a thermopile sensor -amplifier daughter board. Software design and development is greatly assisted by the availability of a library of public-domain, user-implemented software. The daughter board houses a 5-band radiometer using thermopiles designed for this experiment (Dexter Research Corp., Dexter, MI) to allow determination of the total FRFD from the fire (using a wide band thermopile with a KRS-5 window, 0.1 - 30 um), the FRFD as would be received by an orbital asset like MODIS (3.95 um center wavelength (CWL) and 10.95 CWL, corresponding to MODIS bands 21/22 and 31, respectively) and wider bandpass (0.1-5.5 um and 8-14 um) corresponding to the FRFD recorded by `MWIR' and `LWIR' imaging systems. We required a very wide dynamic range system in order to be able to record the flux density from `cold' ground before the fire, through the `hot' flaming combustion stage, to the `cool' phase after passage of the fire front. The recording dynamic range required (with reasonable resolution at the lowest temperatures) is on the order of 106, which is not currently available in commercial instrumentation at a price point, size or feature set that is suitable for wildland fire investigations. The entire unit, along with rechargeable battery power supply is housed in a fireproof aluminum chassis box, which is then mounted on a mast at a height of 5 - 7 m above the fireground floor. We will report initial
Screened van der Waals correction to density functional theory for solids
Tao, Jianmin; Zheng, Fan; Gebhardt, Julian; Perdew, John P.; Rappe, Andrew M.
2017-07-01
Lattice constant and cohesive energy are basic properties in the design of materials and devices. However, due to neglect of long-range van der Waals (vdW) interactions, density functional approximations (DFAs) often yield unusually large errors for ionic solids and heavy metals. Here, we propose a model for the dynamically screened vdW correction, including the leading order as well as higher-order contributions. The striking feature of this model is that important screening effects and higher-order contributions are properly considered and that its contribution to the short-range part is removed by a novel damping function for the avoidance of double counting. As a result, the model dramatically reduces the error of the DFA-GGA in lattice constant and cohesive energy. We also find that the three-body interactions are small, due to the screening effects. These observations greatly improve our fundamental understanding of vdW interactions and enhance the applicability of efficient semilocal DFAs.
Filatov, M; Cremer, D
2005-01-01
It is demonstrated that the LYP correlation functional is not suited to be used for the calculation of electron spin resonance hyperfine structure (HFS) constants, nuclear magnetic resonance spin-spin coupling constants, magnetic, shieldings and other properties that require a balanced account of
Energy Technology Data Exchange (ETDEWEB)
Dimakis, Nicholas, E-mail: nicholas.dimakis@utrgv.edu [Department of Physics, University of Texas Rio Grande Valley, Edinburg, TX (United States); Valdez, Danielle; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade [Department of Physics, University of Texas Rio Grande Valley, Edinburg, TX (United States); Vargas, Sarah; Saenz, Justin [Robert Vela High School, Edinburg, TX (United States)
2017-08-15
Highlights: • Li, K, Na, and Ca graphene interaction is primarily ionic, whereas small covalent interactions also co-exist in these cases. • Van der Waals interactions are revealed by comparing adatom-graphene geometries between 1.4% and 3% adatom coverages and using Grimme corrections. • The Li, K, Na graphene interactions are accurately described by both PBE0 and PBE functionals. For Ca/graphene, the PBE0 functional should not be used. • For Li, K, and Na adsorbed on graphene, adatom-graphene interaction weakens as the adatom coverages increases. • The Ca-graphene interaction strength, which is stronger at high coverages, is opposite to increases in the Ca–4s orbital population. - Abstract: The adsorption of the alkali Li, K, and Na and the alkaline Ca on graphene is studied using periodic density functional theory (DFT) under various adatom coverages. The charge transfers between the adatom and the graphene sheet and the almost unchanged densities-of-states spectra in the energy region near and below the Fermi level support an ionic bond pattern between the adatom and the graphene atoms. However, the presence of small orbital overlap between the metal and the nearest graphene atom is indicative of small covalent bonding. Van der Waals interactions are examined through a semiempirical correction in the DFT functional and by comparing adatom-graphene calculations between 3% and 1.4% adatom coverages. Optimized adatom-graphene geometries identify the preferred adatom sites, whereas the adatom-graphene strength is correlated with the adsorption energy and the adatom distance from the graphene plane. Calculated electronic properties and structural parameters are obtained using hybrid functionals and a generalized gradient approximation functional paired with basis sets of various sizes. We found that due to long range electrostatic forces between the alkali/alkaline adatoms and the graphene monolayer, the adatom-graphene structural and electronic
2007-03-01
relativistic, truncated calculation is smaller yet, with a Hamiltonian with dimension of the order of 1010 configurations, barely within reach of modern...exact exchange with density functional approximations,” Journal of Chemical Physics, 105 (22) (1996). 103. Perdew, John P. and Karla Schmidt. Density
Putz, Mihai V
2009-11-10
The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr's quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions - all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.
Density functional theory studies of screw dislocation core structures in bcc metals
DEFF Research Database (Denmark)
Frederiksen, Søren Lund; Jacobsen, Karsten Wedel
2003-01-01
The core structures of (I 11) screw dislocations in bee metals are studied using density functional theory in the local-density approximation. For Mo and Fe, direct calculations of the core structures show the cores to be symmetric with respect to 180degrees rotations around an axis perpendicular...
Directory of Open Access Journals (Sweden)
Mihai V. Putz
2009-11-01
Full Text Available The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving many-electronic systems.
Li, Junfu; O'Shea, James; Hou, Xianghui; Chen, George Z
2017-09-25
The study of electron delocalisation in oxygen atom segregated zones in graphene, aided by the first-principles density functional theory, has revealed extra energy bands of ≥2 eV wide around the Fermi level, predicting Faradaic charge storage occurring in a wide range of potentials, which disagrees with Nernst's law but accounts well for the so called pseudocapacitance of heteroatom-modified graphene based electrode materials in supercapacitors.
Introduction to Density Functional Theory: Calculations by Hand on the Helium Atom
Baseden, Kyle A.; Tye, Jesse W.
2014-01-01
Density functional theory (DFT) is a type of electronic structure calculation that has rapidly gained popularity. In this article, we provide a step-by-step demonstration of a DFT calculation by hand on the helium atom using Slater's X-Alpha exchange functional on a single Gaussian-type orbital to represent the atomic wave function. This DFT…
Towards a Microscopic Reaction Description Based on Energy Density Functionals
Energy Technology Data Exchange (ETDEWEB)
Nobre, G A; DIetrich, F S; Escher, J E; Thompson, I J; Dupuis, M; Terasaki, J; Engel, J
2011-09-26
A microscopic calculation of reaction cross sections for nucleon-nucleus scattering has been performed by explicitly coupling the elastic channel to all particle-hole excitations in the target and one-nucleon pickup channels. The particle-hole states may be regarded as doorway states through which the flux flows to more complicated configurations, and subsequently to long-lived compound nucleus resonances. Target excitations for {sup 40,48}Ca, {sup 58}Ni, {sup 90}Zr and {sup 144}Sm were described in a random-phase framework using a Skyrme functional. Reaction cross sections obtained agree very well with experimental data and predictions of a state-of-the-art fitted optical potential. Couplings between inelastic states were found to be negligible, while the pickup channels contribute significantly. The effect of resonances from higher-order channels was assessed. Elastic angular distributions were also calculated within the same method, achieving good agreement with experimental data. For the first time observed absorptions are completely accounted for by explicit channel coupling, for incident energies between 10 and 70 MeV, with consistent angular distribution results.
Density functional theory calculations of defect and fission gas properties in U-Si fuels
Energy Technology Data Exchange (ETDEWEB)
Andersson, Anders David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-02-03
Accident tolerant fuels (ATF) are being developed in response to the Fukushima Daiichi accident in Japan. One of the options being pursued is U-Si fuels, such as the U_{3}Si_{2} and U_{3}Si_{5} compounds, which benefit from high thermal conductivity (metallic) compared to the UO_{2} fuel (insulator or semi-conductor) used in current Light Water Reactors (LWRs). The U-Si fuels also have higher fissile density. In order to perform meaningful engineering scale nuclear fuel performance simulations, the material properties of the fuel, including the response to irradiation environments, must be known. Unfortunately, the data available for U-Si fuels are rather limited, in particular for the temperature range where LWRs would operate. The ATF HIP is using multi-scale modeling and simulations to address this knowledge gap. The present study investigates point defect and fission gas properties in U_{3}Si_{2}, which is one of the main fuel candidates, using density functional theory (DFT) calculations. Based on a few assumption regarding entropy contributions, defect and fission diffusivities are predicted. Even though uranium silicides have been shown to amorphize easily at low temperature, we assume that U_{3}Si_{2} remains crystalline under the conditions expected in Light Water Reactors (LWRs). The temperature and dose where amorphization occurs has not yet been well established.
Pressure and surface tension of soild-liquid interface using Tarazona density functional theory
Directory of Open Access Journals (Sweden)
M. M.
2000-12-01
Full Text Available The weighted density functional theory proposed by Tarazona is applied to study the solid-liquid interface. In the last two decades the weighted density functional became a useful tool to consider the properties of inhomogeneous liquids. In this theory, the role of the size of molecules or the particles of which the matter is composed, was found to be important. In this resarch we study a hard sphere fluid beside a hard wall. For this study the liquid is an inhomogeneous system. We use the definition of the direct correlation function as a second derivative of free energy with respect to the density. We use this definition and the definition of the weighting function, then we minimize the grand potential with respect to the density to get the Euler Lagrange equation and we obtain an integral equation to find the inhomogeneous density profile. The obtained density profile as a function of the distance from the wall, for different bulk density is plotted in three dimensions. We also calculate the pressure and compare it with the Carnahan-starling results, and finally we obtained the surface tension at liquid-solid interface and compared it with the results of Monte Carlo simulation.
Density-functional calculation of van der Waals forces for free-electron-like surfaces
DEFF Research Database (Denmark)
Hult, E.; Hyldgaard, P.; Rossmeisl, Jan
2001-01-01
A recently proposed general density functional for asymptotic van der Waals forces is used to calculate van der Waals coefficients and reference-plane positions for realistic low-indexed Al surfaces. Results are given for a number of atoms and molecules outside the surfaces, as well...... as for the interaction between the surfaces themselves. The densities and static image-plane positions that are needed as input in the van der Waals functional are calculated self-consistently within density-functional theory using the generalized-gradient approximation, pseudopotentials, and plane waves. This study...... shows that the van der Waals density functional is applicable to realistic surfaces. The need for physically correct surface models, especially for open surfaces, is also illustrated. Finally the parameters for the anisotropic interaction of O-2 with Al are calculated....
Object performance as a function of pileup density for CMS PhaseII
CMS Collaboration
2017-01-01
This document collects the performance of physics objects (electrons, muons, taus, jets, MET) reconstructed with the CMS Phase-2 upgraded detector as a function of the pileup density for the High Luminosity LHC environment of 200 PU.
Directory of Open Access Journals (Sweden)
Yoshiyuki Kawazoe
2009-04-01
Full Text Available Li adsorption on isoreticular MOFs with metal Fe, Cu, Co, Ni and Zn was studied using density function theory. Li functionalization shows a considerable structural change associated with a volume change in isoreticular MOF-5 except for the Zn metal center. Hydrogen binding energies on Li functionalized MOFs are seen to be in the range of 0.2 eV, which is the desired value for an ideal reversible storage system. This study has clearly shown that Li doping is possible only in Zn-based MOF-5, which would be better candidate to reversibly store hydrogen.
Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.
Tao, Jianmin; Mo, Yuxiang
2016-08-12
Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.
DEFF Research Database (Denmark)
Wellendorff, Jess; Lundgård, Keld Troen; Møgelhøj, Andreas
2012-01-01
A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding the overfit......A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We demonstrate that such methods enable well-behaved exchange-correlation approximations in very flexible model spaces, thus avoiding...
Drăghici, S.; Proştean, O.; Răduca, E.; Haţiegan, C.; Hălălae, I.; Pădureanu, I.; Nedeloni, M.; (Barboni Haţiegan, L.
2017-01-01
In this paper a method with which a set of characteristic functions are associated to a LDPC code is shown and also functions that represent the evolution density of messages that go along the edges of a Tanner graph. Graphic representations of the density evolution are shown respectively the study and simulation of likelihood threshold that render asymptotic boundaries between which there are decodable codes were made using MathCad V14 software.
Towards a filtered density function approach for reactive transport in groundwater
Suciu, N.; Schüler, L.; Attinger, S.; Knabner, P.
2016-04-01
Evolution equations for probability density functions (PDFs) and filtered density functions (FDFs) of random species concentrations weighted by conserved scalars are formulated as Fokker-Planck equations describing stochastically equivalent processes in concentration-position spaces. This approach provides consistent numerical PDF/FDF solutions, given by the density in the concentration-position space of an ensemble of computational particles governed by the associated Itô equations. The solutions are obtained by a global random walk (GRW) algorithm, which is stable, free of numerical diffusion, and practically insensitive to the increase of the number of particles. The general FDF approach and the GRW numerical solution are illustrated for a reduced complexity problem consisting of the transport of a single scalar in groundwater. Randomness is induced by the stochastic parameterization of the hydraulic conductivity, characterized by short range correlations and small variance. The objective is to infer the statistics of the random concentration sampled at the plume center of mass, integrated over the transverse dimension of a two-dimensional spatial domain. The PDF/FDF problem can therefore be formulated in a two-dimensional domain as well, a spatial dimension and one in the concentration space. The upscaled drift and diffusion coefficients describing the PDF transport in the physical space are estimated on single-trajectories of diffusion in velocity fields with short-range correlations, owing to their self-averaging property. The mixing coefficients describing the PDF transport in concentration spaces are parameterized by the trend and the noise inferred from the statistical analysis of an ensemble of simulated concentration time series, as well as by classical mixing models. A Gaussian spatial filter applied to a Kraichnan velocity field generator is used to construct coarse-grained simulations (CGS) for FDF problems. The purposes of the CGS simulations are
DEFF Research Database (Denmark)
Hedegård, Erik D.; Olsen, Jógvan Magnus Haugaard; Knecht, Stefan
2015-01-01
-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory......, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linear response have been implemented in a development version of Dalton. To benchmark the PE-MC-srDFT approach against the literature data, we have...... investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies...
Gabay, D.; Wang, X.; Lomakin, V.; Boag, A.; Jain, M.; Natan, A.
2017-12-01
We use an efficient projection scheme for the Fock operator to analyze the size dependence of silicon quantum dots (QDs) electronic properties. We compare the behavior of hybrid, screened hybrid and local density functionals as a function of the dot size up to ∼800 silicon atoms and volume of up to ∼20 nm3. This allows comparing the calculations of hybrid and screened hybrid functionals to experimental results over a wide range of QD sizes. We demonstrate the size dependent behavior of the band gap, density of states, ionization potential and HOMO level shift after ionization. We also demonstrate how the use of Graphical Processing Units (GPUs) can further accelerate such calculations.
Romaniello, P; de Boeij, P L
2005-04-22
We included relativistic effects in the formulation of the time-dependent current-density-functional theory for the calculation of linear response properties of metals [P. Romaniello and P. L. de Boeij, Phys. Rev. B (to be published)]. We treat the dominant scalar-relativistic effects using the zeroth-order regular approximation in the ground-state density-functional theory calculations, as well as in the time-dependent response calculations. The results for the dielectric function of gold calculated in the spectral range of 0-10 eV are compared with experimental data reported in literature and recent ellipsometric measurements. As well known, relativistic effects strongly influence the color of gold. We find that the onset of interband transitions is shifted from around 3.5 eV, obtained in a nonrelativistic calculation, to around 1.9 eV when relativity is included. With the inclusion of the scalar-relativistic effects there is an overall improvement of both real and imaginary parts of the dielectric function over the nonrelativistic ones. Nevertheless some important features in the absorption spectrum are not well reproduced, but can be explained in terms of spin-orbit coupling effects. The remaining deviations are attributed to the underestimation of the interband gap (5d-6sp band gap) in the local-density approximation and to the use of the adiabatic local-density approximation in the response calculation.
Calculation of semiconductor band gaps with the M06-L density functional.
Zhao, Yan; Truhlar, Donald G
2009-02-21
The performance of the M06-L density functional has been tested for band gaps in seven semiconductors plus diamond and MgO. Comparison with the local spin density approximation (LSDA), Becke-Lee-Yang-Parr (BLYP), Perdew-Burke-Eernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and Heyd-Scuseria-Ernzerhof (HSE) functionals shows that M06-L has improved performance for calculating band gaps as compared to other local functionals, but it is less accurate than the screened hybrid HSE functional for band gaps.
An improved theoretical approach to the empirical corrections of density functional theory.
Lii, Jenn-Huei; Hu, Ching-Han
2012-02-01
An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization-dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond (1,2-) and angle (1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported ΔH ( f ) values of the training set containing alkane, alcohol and ether molecules. The ΔH ( f ) of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in ΔH ( f ) were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.
On the derivation of the Nakajima-Zwanzig probability density function via white noise analysis
Butanas, Bienvenido M.; Caballar, Roland C. F.
2017-08-01
This paper presents an application of white noise analysis in obtaining the probability density function associated with Nakajima-Zwanzig equation. We revisit the derivation of the Nakajima-Zwanzig equation and solve the probability density function. Moreover, with the parametrization, x (t )=xO+∫t0t ∫so sκ (s',s)ω (s')d s'd s , we show that in the absence of memory effects, κ(t, s) ≈ δ(t - s), the obtained probability density for the Nakajima-Zwanzig equation reduces to that of the Gaussian distribution with σ2 = (t-t0).
Lan, Chen-Chia; Tsai, Shih-Jen; Huang, Chu-Chung; Wang, Ying-Hsiu; Chen, Tong-Ru; Yeh, Heng-Liang; Liu, Mu-En; Lin, Ching-Po; Yang, Albert C.
2016-01-01
Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood. Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form (GDS) and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD) mapping was performed to delineate short-range FCD (SFCD) and long-range FCD (LFCD). Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model (GLM), with age incorporated as a covariate and depressive symptoms and loneliness as predictors. Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus. Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male. PMID:26793101
Directory of Open Access Journals (Sweden)
Chen-Chia eLan
2016-01-01
Full Text Available Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood.Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD mapping was performed to delineate short-range FCD (SFCD and long-range FCD (LFCD. Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model, with age incorporated as a covariate and depressive symptoms and loneliness as predictors.Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus.Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male.
Chemical short range order obtained from the atomic pair distribution function
Proffen, Th.; Petkov, V.; Billinge, S. J. L.; Vogt, T.
2002-01-01
Many crystalline materials show chemical short range order and relaxation of neighboring atoms. Local structural information can be obtained by analyzing the atomic pair distribution function (PDF) obtained from powder diffraction data. In this paper, we present the successful extraction of chemical short range order parameters from the x-ray PDF of a quenched Cu_3Au sample.
Hakun, Jonathan G; Johnson, Nathan F
2017-11-01
Older adults tend to over-activate regions throughout frontoparietal cortices and exhibit a reduced range of functional modulation during WM task performance compared to younger adults. While recent evidence suggests that reduced functional modulation is associated with poorer task performance, it remains unclear whether reduced range of modulation is indicative of general WM capacity-limitations. In the current study, we examined whether the range of functional modulation observed over multiple levels of WM task difficulty (N-Back) predicts in-scanner task performance and out-of-scanner psychometric estimates of WM capacity. Within our sample (60-77years of age), age was negatively associated with frontoparietal modulation range. Individuals with greater modulation range exhibited more accurate N-Back performance. In addition, despite a lack of significant relationships between N-Back and complex span task performance, range of frontoparietal modulation during the N-Back significantly predicted domain-general estimates of WM capacity. Consistent with previous cross-sectional findings, older individuals with less modulation range exhibited greater activation at the lowest level of task difficulty but less activation at the highest levels of task difficulty. Our results are largely consistent with existing theories of neurocognitive aging (e.g. CRUNCH) but focus attention on dynamic range of functional modulation asa novel marker of WM capacity-limitations in older adults. Copyright © 2017 Elsevier Inc. All rights reserved.
Malheiro, Carine; Mendiboure, Bruno; Plantier, Frédéric; Blas, Felipe J.; Miqueu, Christelle
2014-04-01
As a first step of an ongoing study of thermodynamic properties and adsorption of complex fluids in confined media, we present a new theoretical description for spherical monomers using the Statistical Associating Fluid Theory for potential of Variable Range (SAFT-VR) and a Non-Local Density Functional Theory (NLDFT) with Weighted Density Approximations (WDA). The well-known Modified Fundamental Measure Theory is used to describe the inhomogeneous hard-sphere contribution as a reference for the monomer and two WDA approaches are developed for the dispersive terms from the high-temperature Barker and Henderson perturbation expansion. The first approach extends the dispersive contributions using the scalar and vector weighted densities introduced in the Fundamental Measure Theory (FMT) and the second one uses a coarse-grained (CG) approach with a unique weighted density. To test the accuracy of this new NLDFT/SAFT-VR coupling, the two versions of the theoretical model are compared with Grand Canonical Monte Carlo (GCMC) molecular simulations using the same molecular model. Only the version with the "CG" approach for the dispersive terms provides results in excellent agreement with GCMC calculations in a wide range of conditions while the "FMT" extension version gives a good representation solely at low pressures. Hence, the "CG" version of the theoretical model is used to reproduce methane adsorption isotherms in a Carbon Molecular Sieve and compared with experimental data after a characterization of the material. The whole results show an excellent agreement between modeling and experiments. Thus, through a complete and consistent comparison both with molecular simulations and with experimental data, the NLDFT/SAFT-VR theory has been validated for the description of monomers.
Energy Technology Data Exchange (ETDEWEB)
Malheiro, Carine; Mendiboure, Bruno; Plantier, Frédéric; Miqueu, Christelle [Université Pau et Pays Adour, CNRS, TOTAL - UMR 5150 – LFC-R – Laboratoire des Fluides Complexes et leurs Réservoirs, BP 1155 – PAU, F-64013 (France); Blas, Felipe J. [Departamento de Física Aplicada, and Centro de Física Teórica y Matemática FIMAT, Universidad de Huelva, 21071 Huelva (Spain)
2014-04-07
As a first step of an ongoing study of thermodynamic properties and adsorption of complex fluids in confined media, we present a new theoretical description for spherical monomers using the Statistical Associating Fluid Theory for potential of Variable Range (SAFT-VR) and a Non-Local Density Functional Theory (NLDFT) with Weighted Density Approximations (WDA). The well-known Modified Fundamental Measure Theory is used to describe the inhomogeneous hard-sphere contribution as a reference for the monomer and two WDA approaches are developed for the dispersive terms from the high-temperature Barker and Henderson perturbation expansion. The first approach extends the dispersive contributions using the scalar and vector weighted densities introduced in the Fundamental Measure Theory (FMT) and the second one uses a coarse-grained (CG) approach with a unique weighted density. To test the accuracy of this new NLDFT/SAFT-VR coupling, the two versions of the theoretical model are compared with Grand Canonical Monte Carlo (GCMC) molecular simulations using the same molecular model. Only the version with the “CG” approach for the dispersive terms provides results in excellent agreement with GCMC calculations in a wide range of conditions while the “FMT” extension version gives a good representation solely at low pressures. Hence, the “CG” version of the theoretical model is used to reproduce methane adsorption isotherms in a Carbon Molecular Sieve and compared with experimental data after a characterization of the material. The whole results show an excellent agreement between modeling and experiments. Thus, through a complete and consistent comparison both with molecular simulations and with experimental data, the NLDFT/SAFT-VR theory has been validated for the description of monomers.
Nobel Prize in Chemistry 1998 "for his development of the density-functional theory" : Walter Kohn
1999-01-01
Prof. Walter Kohn presents "Electronic structure of matter : wave functions and density functionals".Since the 1920's Schroedinger wave functions have been the principal theoretical concept for understanding and computing the electronic structure of matter. More recently, Density Functional Theory (DFT), couched in terms of the electronic density distribution, n(r), has provided a new perspective and new computational possibilities, especially for systems consisting of very many (up to ~1000) atoms. In this talk some fundamental limitations of wave function methods for very-many-atom-systems will be discussed. The DFT approach will be explained together with some physical/chemical applications and a discussion of its strenghts and weaknesses. W Kohn has received the prize with J A Pople for his development of computational methods in quantum chemistr.
Gaiduk, Alex P; Gygi, François; Galli, Giulia
2015-08-06
We determined the equilibrium density and compressibility of water and ice from first-principles molecular dynamics simulations using gradient-corrected (PBE) and hybrid (PBE0) functionals. Both functionals predicted the density of ice to be larger than that of water, by 15 (PBE) and 35% (PBE0). The PBE0 functional yielded a lower density of both ice and water with respect to PBE, leading to better agreement with experiment for ice but not for liquid water. Approximate inclusion of dispersion interactions on computed molecular-dynamics trajectories led to a substantial improvement of the PBE0 results for the density of liquid water, which, however, resulted to be slightly lower than that of ice.
Su, Neil Qiang; Chen, Jun; Sun, Zhigang; Zhang, Dong H.; Xu, Xin
2015-02-01
The potential energy surfaces for the H + H2 exchange reaction are determined, using the standard Becke-3_parameter-Lee-Yang-Parr (B3LYP) hybrid exchange-correlation functional and the recently developed XYG3 type (xDH) doubly hybrid functionals. Quantum dynamical results calculated on these density functional theory surfaces revealed that the accuracy for the surfaces from the xDH functionals is quite satisfactory as compared to the benchmark Boothroyd-Keogh-Martin-Peterson-2 surface, whereas B3LYP is wholly inadequate in describing this simplest reaction despite the fact that it has been widely used to study reactions in complex systems. It is shown that further improvements can be achieved if the xDH functional parameters are fine-tuned to be reaction specific.
Periodic Density Functional Theory Study of Water Adsorption on the a-Quartz (101) Surface.
Energy Technology Data Exchange (ETDEWEB)
Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Kubicki, James D. [Pennsylvania State University; Sofo, Jorge O. [Pennsylvania State University
2011-01-01
Plane wave density functional theory (DFT) calculations have been performed to study the atomic structure, preferred H2O adsorption sites, adsorption energies, and vibrational frequencies for water adsorption on the R-quartz (101) surface. Surface energies and atomic displacements on the vacuum-reconstructed, hydrolyzed, and solvated surfaces have been calculated and compared with available experimental and theoretical data. By considering different initial positions of H2O molecules, the most stable structures of water adsorption at different coverages have been determined. Calculated H2O adsorption energies are in the range -55 to -65 kJ/mol, consistent with experimental data. The lowest and the highest O-H stretching vibrational bands may be attributed to different states of silanol groups on the watercovered surface. The dissociation energy of the silanol group on the surface covered by the adsorption monolayer is estimated to be 80 kJ/mol. The metastable states for the protonated surface bridging O atoms (Obr), which may lead to hydrolysis of siloxane bonds, have been investigated. The calculated formation energy of a Q2 center from a Q3 center on the (101) surface with 2/3 dense monolayer coverage is equal to 70 kJ/mol which is in the range of experimental activation energies for quartz dissolution.
A minimal model for excitons within time-dependent density-functional theory.
Yang, Zeng-hui; Li, Yonghui; Ullrich, Carsten A
2012-07-07
The accurate description of the optical spectra of insulators and semiconductors remains an important challenge for time-dependent density-functional theory (TDDFT). Evidence has been given in the literature that TDDFT can produce bound as well as continuum excitons for specific systems, but there are still many unresolved basic questions concerning the role of dynamical exchange and correlation (xc). In particular, the roles of the long spatial range and the frequency dependence of the xc kernel f(xc) for excitonic binding are still not very well explored. We present a minimal model for excitons in TDDFT, consisting of two bands from a one-dimensional (1D) Kronig-Penney model and simple approximate xc kernels, providing an easily accessible model system for studying excitonic effects in TDDFT. For the 1D model system, it is found that adiabatic xc kernels can produce at most two bound excitons, confirming that the long spatial range of f(xc) is not a necessary condition. It is shown how the Wannier model, featuring an effective electron-hole interaction, emerges from TDDFT. The collective, many-body nature of excitons is explicitly demonstrated.
Newcomb, Sandra
2010-01-01
Children who are identified as visually impaired frequently have a functional vision assessment as one way to determine how their visual impairment affects their educational performance. The CVI Range is a functional vision assessment for children with cortical visual impairment. The purpose of the study presented here was to examine the…
Shen, Xianjun; Yi, Li; Yi, Yang; Yang, Jincai; He, Tingting; Hu, Xiaohua
2015-01-01
The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules have a common defect -- once a protein node is assigned to a functional module, there is no chance to move the protein to the other functional modules during the follow-up processes, which lead the erroneous partitioning occurred at previous step to accumulate till to the end. In this paper, we design a new algorithm ADM (Adaptive Density Modularity) to detect protein functional modules based on adaptive density modularity. In ADM algorithm, according to the comparison between external closely associated degree and internal closely associated degree, the partitioning of a protein-protein interaction network into functional modules always evolves quickly to increase the density modularity of the network. The integration of density modularity into the new algorithm not only overcomes the drawback mentioned above, but also contributes to identifying protein functional modules more effectively. The experimental result reveals that the performance of ADM algorithm is superior to many state-of-the-art protein functional modules detection techniques in aspect of the accuracy of prediction. Moreover, the identified protein functional modules are statistically significant in terms of "Biological Process" annotated in Gene Ontology, which provides substantial support for revealing the principles of cellular organization.
Minenkov, Yury
2017-11-29
We tested a battery of density functional theory (DFT) methods ranging from generalized gradient approximation (GGA) via meta-GGA to hybrid meta-GGA schemes as well as Møller–Plesset perturbation theory of the second order and a single and double excitation coupled-cluster (CCSD) theory for their ability to reproduce accurate gas-phase structures of di- and triatomic molecules derived from microwave spectroscopy. We obtained the most accurate molecular structures using the hybrid and hybrid meta-GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion interactions play an insignificant role. The structures that the CCSD method predicts are of similar quality although at considerably larger computational cost. The structures that GGA and meta-GGA schemes predict are less accurate with the largest absolute errors detected with BLYP and M11-L, suggesting that these methods should not be used if accurate three-dimensional molecular structures are required. Because of numerical problems related to the integration of the exchange–correlation part of the functional and large scattering of errors, most of the Minnesota models tested, particularly MN12-L, M11, M06-L, SOGGA11, and VSXC, are also not recommended for geometry optimization. When maintaining a low computational budget is essential, the nonseparable gradient functional N12 might work within an acceptable range of error. As expected, the DFT-D3 dispersion correction had a negligible effect on the internuclear distances when combined with the functionals tested on nonweakly bonded di- and triatomic inorganic molecules. By contrast, the dispersion correction for the APF-D functional has been found to shorten the bonds significantly, up to 0.064 Å (AgI), in Ag halides, BaO, BaS, BaF, BaCl, Cu halides, and Li and
Distortion range of filter synthetic discriminant function binary phase-only filters
Jared, David A.
1989-11-01
This paper considers the performance of filter synthetic-discriminant-function binary-phase-only filters (fSDF-BPOFs) with images in the distortion range that were not members of the training set. This evaluation was performed to understand better the distortion range that can be effectively covered by fSDF-BPOFs. The peak correlation and peak clutter responses were measured over various distortion ranges for in-plane and out-of-plane rotations. The peak correlation initially decreased rapidly as the distortion range increased but decreased gradually as the distortion range became larger for the images used in this study. The distortion ranges that can be effectively covered by fSDF-BPOFs appear to be modest: 0-30 deg for in-plane rotation and 0-10 deg for out-of-plane rotation. The results indicate that a temporal multiplexing scheme will be required to cover a large distortion range when BPOFs are used.
New Y-function based MOSFET parameter extraction method from weak to strong inversion range
Henry, J. B.; Rafhay, Q.; Cros, A.; Ghibaudo, G.
2016-09-01
A new Y-function based MOSFET parameter extraction method is proposed. This method relies on explicit expressions of inversion charge and drain current versus Yc(=Qi√Cgc)-function and Y(=Id/√gm)-function, respectively, applicable from weak to strong inversion range. It enables a robust MOSFET parameter extraction even for low gate voltage overdrive, whereas conventional extraction techniques relying on strong inversion approximation fail.
Quest of thermoelectricity in topological insulators: A density functional theory study
Singh, Sukhwinder; Kaur, Kulwinder; Kumar, Ranjan
2017-10-01
In this Paper, we have studied the structural, electronic and thermoelectric properties of LuAuPb and YAuPb compound respectively with frame work of density functional theory and Boltzmann equations. Our calculations show that both these compounds are gapless materials. Under strain, electronic and thermoelectric properties of these compounds are also studied. Under 5% strain, the maximum energy band gap opens up in LuAuPb compound. The thermoelectric properties of these compounds are studied between temperature range of 100-1000 K. Thermoelectric properties of these compound as a function of temperature are studied for the first time in this work. Seebeck measurements indicate that both these compounds are n-type in nature. The calculated electrical conductivity of these compounds under 5% strain increases with increase in temperature. The trends of electrical conductivity confirms that these compounds are semiconductor in nature. As temperature increases the electronic thermal conductivity of these compounds also increase. The maximum figure of merit is achieved for LuAuPb compound which is equal to 0.4.
Partial ionization in dense plasmas: comparisons among average-atom density functional models.
Murillo, Michael S; Weisheit, Jon; Hansen, Stephanie B; Dharma-wardana, M W C
2013-06-01
Nuclei interacting with electrons in dense plasmas acquire electronic bound states, modify continuum states, generate resonances and hopping electron states, and generate short-range ionic order. The mean ionization state (MIS), i.e, the mean charge Z of an average ion in such plasmas, is a valuable concept: Pseudopotentials, pair-distribution functions, equations of state, transport properties, energy-relaxation rates, opacity, radiative processes, etc., can all be formulated using the MIS of the plasma more concisely than with an all-electron description. However, the MIS does not have a unique definition and is used and defined differently in different statistical models of plasmas. Here, using the MIS formulations of several average-atom models based on density functional theory, we compare numerical results for Be, Al, and Cu plasmas for conditions inclusive of incomplete atomic ionization and partial electron degeneracy. By contrasting modern orbital-based models with orbital-free Thomas-Fermi models, we quantify the effects of shell structure, continuum resonances, the role of exchange and correlation, and the effects of different choices of the fundamental cell and boundary conditions. Finally, the role of the MIS in plasma applications is illustrated in the context of x-ray Thomson scattering in warm dense matter.
Chen, Zehua; Zhang, Du; Jin, Ye; Yang, Yang; Su, Neil Qiang; Yang, Weitao
2017-09-21
To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of the physical system consists of two parts: the energy of the auxiliary system, which is determined with a chosen density functional approximation (DFA), and the excitation energy from an approximate linear response theory that restores the symmetry to that of the physical system, thus rigorously leading to a multideterminant description of the physical system. The electron density of the physical system is different from that of the auxiliary system and is uniquely determined from the functional derivative of the total energy with respect to the external potential. Our energy functional is thus an implicit functional of the physical system density, but an explicit functional of the auxiliary system density. We show that the total energy minimum and stationary states, describing the ground and excited states of the physical system, can be obtained by a self-consistent optimization with respect to the explicit variable, the generalized Kohn-Sham noninteracting density matrix. We have developed the generalized optimized effective potential method for the self-consistent optimization. Among options of the auxiliary system and the associated linear response theory, reformulated versions of the particle-particle random phase approximation (pp-RPA) and the spin-flip time-dependent density functional theory (SF-TDDFT) are selected for illustration of principle. Numerical results show that our multireference DFT successfully describes static correlation in bond dissociation and double bond rotation.
Methane dissociation on Pt(111): Searching for a specific reaction parameter density functional
Energy Technology Data Exchange (ETDEWEB)
Nattino, Francesco, E-mail: f.nattino@chem.leidenuniv.nl; Migliorini, Davide; Kroes, Geert-Jan [Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden (Netherlands); Bonfanti, Matteo [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)
2016-01-28
The theoretical description of methane dissociating on metal surfaces is a current frontier in the field of gas-surface dynamics. Dynamical models that aim at achieving a highly accurate description of this reaction rely on potential energy surfaces based on density functional theory calculations at the generalized gradient approximation. We focus here on the effect that the exchange-correlation functional has on the reactivity of methane on a metal surface, using CHD{sub 3} + Pt(111) as a test case. We present new ab initio molecular dynamics calculations performed with various density functionals, looking also at functionals that account for the van der Waals (vdW) interaction. While searching for a semi-empirical specific reaction parameter density functional for this system, we find that the use of a weighted average of the PBE and the RPBE exchange functionals together with a vdW-corrected correlation functional leads to an improved agreement with quantum state-resolved experimental data for the sticking probability, compared to previous PBE calculations. With this semi-empirical density functional, we have also investigated the surface temperature dependence of the methane dissociation reaction and the influence of the rotational alignment on the reactivity, and compared our results with experiments.
Time-dependent current-density-functional theory for the metallic response of solids
Romaniello, P; de Boeij, PL
We extend the formulation of time-dependent current-density-functional theory for the linear response properties of dielectric and semi-metallic solids [Kootstra , J. Chem. Phys. 112, 6517 (2000)] to treat metals as well. To achieve this, the Kohn-Sham response functions have to include both
The Keldysh formalism applied to time-dependent current-density-functional theory
Gidopoulos, NI; Wilson, S
2003-01-01
In this work we demonstrate how to derive the Kohn-Sham equations of time-dependent current-density functional theory from a generating action functional defined on a Keldysh time contour. These Kohn-Sham equations contain an exchange-correlation contribution to the vector potential. For this
Phase diagram of two-dimensional hard rods from fundamental mixed measure density functional theory.
Wittmann, René; Sitta, Christoph E; Smallenburg, Frank; Löwen, Hartmut
2017-10-07
A density functional theory for the bulk phase diagram of two-dimensional orientable hard rods is proposed and tested against Monte Carlo computer simulation data. In detail, an explicit density functional is derived from fundamental mixed measure theory and freely minimized numerically for hard discorectangles. The phase diagram, which involves stable isotropic, nematic, smectic, and crystalline phases, is obtained and shows good agreement with the simulation data. Our functional is valid for a multicomponent mixture of hard particles with arbitrary convex shapes and provides a reliable starting point to explore various inhomogeneous situations of two-dimensional hard rods and their Brownian dynamics.
Improved description of soft layered materials with van der Waals density functional theory.
Graziano, Gabriella; Klimeš, Jiří; Fernandez-Alonso, Felix; Michaelides, Angelos
2012-10-24
The accurate description of van der Waals forces within density functional theory is currently one of the most active areas of research in computational physics and chemistry. Here we report results on the structural and energetic properties of graphite and hexagonal boron nitride, two layered materials where interlayer binding is dominated by van der Waals forces. Results from several density functionals are reported, including the optimized Becke88 van der Waals (optB88-vdW) and the optimized PBE van der Waals (optPBE-vdW) (Klimeš et al 2010 J. Phys.: Condens. Matter 22 022201) functionals. Where comparison to experiment and higher-level theory is possible, the results obtained from the two new van der Waals density functionals are in good agreement. An analysis of the physical nature of the interlayer binding in both graphite and hexagonal boron nitride is also reported.
Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation
Energy Technology Data Exchange (ETDEWEB)
Kühn, Michael [Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe (Germany); Weigend, Florian, E-mail: florian.weigend@kit.edu [Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe (Germany); Institut für Nanotechnologie, Karlsruher Institut für Technologie, Postfach 3640, 76021 Karlsruhe (Germany)
2015-01-21
We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy){sub 3} (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its “spin-forbidden” triplet-singlet transition.
Time-dependent density functional theory for many-electron systems interacting with cavity photons.
Tokatly, I V
2013-06-07
Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles. We suggest possible approximations for the exchange-correlation potentials and discuss implications of this approach for the theory of open quantum systems. In particular we show that it naturally leads to time-dependent density functional theory for systems coupled to the Caldeira-Leggett bath.
Relativistic coupled-cluster and density-functional studies of argon at high pressure
Schwerdtfeger, Peter; Steenbergen, Krista G.; Pahl, Elke
2017-06-01
The equation of state P (V ,T ) for solid argon is determined by the calculation of accurate static and vibrational terms in the free energy. The static component comes from a quantum theoretical many-body expansion summing over all energetic contributions from two-, three-, and four-body fragments treated with relativistic coupled cluster theory, while the lattice vibrations are described at an anharmonic level including two- and three-body forces as well as temperature effects. The dynamic part is calculated within the Debye and Einstein approximation, as well as by a more accurate phonon treatment where the vibrational motions in the lattice are coupled. Our results are in good agreement with room-temperature high-pressure experimental data up to ˜20 GPa. In the 20-100 GPa pressure range, however, we see considerable deviations between experiment and theory, perhaps indicating missing four-body contributions (beyond the quadruple dipole terms included here), missing five and higher-body effects, and the need to go beyond the coupled cluster singles-doubles with perturbative triples treatment in such higher-body forces. This contrasts with the results for solid neon, where excellent agreement has been achieved taking only two- and three-body forces into account [P. Schwerdtfeger and A. Hermann, Phys. Rev. B 80, 064106 (2009), 10.1103/PhysRevB.80.064106]. We demonstrate that the phase transition from fcc to hcp cannot account for the large discrepancies observed. Density functional calculations give very mixed results in the high-pressure region, but some functionals such as optB88-vdW (proposed by Lundqvist and co-workers) describe the many-body forces in argon reasonably well over the range of pressures investigated. Theoretical investigations of the heavier rare gas solids reaching experimental accuracy in the high-pressure regime therefore remain a significant challenge.
Pagnini, Gianni; Mura, Antonio; Mainardi, Francesco
2013-05-13
Two-particle dispersion is investigated in the context of anomalous diffusion. Two different modelling approaches related to time subordination are considered and unified in the framework of self-similar stochastic processes. By assuming a single-particle fractional Brownian motion and that the two-particle correlation function decreases in time with a power law, the particle relative separation density is computed for the cases with time sub-ordination directed by a unilateral M-Wright density and by an extremal Lévy stable density. Looking for advisable mathematical properties (for instance, the stationarity of the increments), the corresponding self-similar stochastic processes are represented in terms of fractional Brownian motions with stochastic variance, whose profile is modelled by using the M-Wright density or the Lévy stable density.
van der Waals forces in density functional theory: a review of the vdW-DF method.
Berland, Kristian; Cooper, Valentino R; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T; Hyldgaard, Per; Lundqvist, Bengt I
2015-06-01
A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.
Normal Parathyroid Function with Decreased Bone Mineral Density in Treated Celiac Disease
Directory of Open Access Journals (Sweden)
Bernard Lemieux
2001-01-01
Full Text Available Decreased bone mineral density (BMD has been reported in patients with celiac disease in association with secondary hyperparathyroidism. The present study investigated whether basal parathyroid hormone (PTH remained elevated and whether abnormalities of parathyroid function were still present in celiac disease patients treated with a gluten-free diet. Basal seric measurements of calcium and phosphate homeostasis and BMD were obtained in 17 biopsy-proven patients under treatment for a mean period of 5.7±3.7 years (range 1.1 to 15.9. In addition, parathyroid function was studied with calcium chloride and sodium citrate infusions in seven patients. Basal measurements of patients were compared with those of 26 normal individuals, while parathyroid function results were compared with those of seven sex- and age-matched controls. Basal results were similar in patients and controls except for intact PTH (I-PTH (3.77±0.88 pmol/L versus 2.28±0.63 pmol/L, P<0.001, which was higher in the former group but still within normal limits. Mean 25-hydroxy vitamin D and 1,25-dihydroxy vitamin D values were normal in patients. Parathyroid function results were also found to be similar in both groups. Compared with a reference population of the same age (Z score, patients had significantly lower BMDs of the hip (-0.60±0.96 SDs, P<0.05 and lumbar spine (-0.76±1.15 SDs, P<0.05. T scores were also decreased for the hip (-1.3±0.9 SDs, P<0.0001 and lumbar spine (-1.4±1.35 SDs, P<0.0001, with two to three patients being osteoporotic (T score less than -2.5 SDs and seven to eight osteopenic (T score less than -1 SDs but greater than or equal to -2.5 SDs in at least one site. Height and weight were the only important determinants of BMD values by multivariate or logistical regression analysis in these patients. The results show higher basal I-PTH values with normal parathyroid function in treated celiac disease. Height and weight values are, but I-PTH values are not
Spin orbit coupling in the spin-current-density-functional theory
Bencheikh, K.
2003-12-01
Starting from the spin-current-density-functional theory for electronic systems, we extend the formulation to include spin-orbit coupling. Particular attention is devoted to the symmetry of the problem. Here we show that the exchange-correlation energy functional is invariant by the U(1)em × SU(2)spin gauge transformations. We give the transformation laws of the paramagnetic current and also the paramagnetic spin current density by the U(1)em × SU(2)spin gauge transformations. For the case where the spin-orbit coupling is taken into account, we generalize the equations of continuity satisfied by the current density and the spin current density, derived by Vignale and Rasolt.
Energy Technology Data Exchange (ETDEWEB)
Franz Gross, Alfred Stadler
2010-09-01
We present the effective range expansions for the 1S0 and 3S1 scattering phase shifts, and the relativistic deuteron wave functions that accompany our recent high precision fits (with \\chi^2/N{data} \\simeq 1) to the 2007 world np data below 350 MeV. The wave functions are expanded in a series of analytical functions (with the correct asymptotic behavior at both large and small arguments) that can be Fourier-transformed from momentum to coordinate space and are convenient to use in any application. A fortran subroutine to compute these wave functions can be obtained from the authors.
Density-functional calculations of the surface tension of liquid Al and Na
Stroud, D.; Grimson, M. J.
1984-01-01
Calculations of the surface tensions of liquid Al and Na are described using the full ionic density functional formalism of Wood and Stroud (1983). Surface tensions are in good agreement with experiment in both cases, with results substantially better for Al than those found previously in the gradient approximation. Preliminary minimization with respect to surface profile leads to an oscillatory profile superimposed on a nearly steplike ionic density disribution; the oscillations have a wavellength of about a hardsphere diameter.
Cavallo, A; Cosenza, F; De Cesare, L
2001-12-10
The two-time retarded and advanced Green's function technique is formulated in nonextensive classical statistical mechanics within the optimal Lagrange multiplier framework. The main spectral properties are presented and a spectral decomposition for the spectral density is obtained. Finally, the nonextensive version of the spectral density method is given and its effectiveness is tested by exploring the equilibrium properties of a classical ferromagnetic spin chain.
Corsini, NR; Greco, A.; Hine, ND; Molteni, C.; Haynes, PD
2013-01-01
We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)], it supports both geometry optimizations and molecular dynamics simula...
Directory of Open Access Journals (Sweden)
Zhe Zhang
2017-12-01
Full Text Available Several neuropsychiatric diseases have been found to influence the frequency-specific spontaneous functional brain organization (SFBO in resting state, demonstrating that the abnormal brain activities of different frequency bands are associated with various physiological and psychological dysfunctions. However, little is known about the frequency specificities of SFBO in adolescent generalized anxiety disorder (GAD. Here, a novel complete ensemble empirical mode decomposition with adaptive noise method was applied to decompose the time series of each voxel across all participants (31 adolescent patients with GAD and 28 matched healthy controls; HCs into four frequency-specific bands with distinct intrinsic oscillation. The functional connectivity density (FCD of different scales (short-range and long-range was calculated to quantify the SFBO changes related to GAD within each above frequency-specific band and the conventional frequency band (0.01–0.08 Hz. Support vector machine classifier was further used to examine the discriminative ability of the frequency-specific FCD values. The results showed that adolescent GAD patients exhibited abnormal alterations of both short-range and long-range FCD (S-FCD and L-FCD in widespread brain regions across three frequency-specific bands. Positive correlation between the State Anxiety Inventory (SAI score and increased L-FCD in the fusiform gyrus in the conventional frequency band was found in adolescents with GAD. Both S-FCD and L-FCD in the insula in the lower frequency band (0.02–0.036 Hz had the highest classification performance compared to all other brain regions with inter-group difference. Furthermore, a satisfactory classification performance was achieved by combining the discrepant S-FCD and L-FCD values in all frequency bands, with the area under the curve (AUC value of 0.9414 and the corresponding sensitivity, specificity, and accuracy of 87.15, 92.92, and 89.83%, respectively. This study
The correlation function for density perturbations in an expanding universe. II - Nonlinear theory
Mcclelland, J.; Silk, J.
1977-01-01
A formalism is developed to find the two-point and higher-order correlation functions for a given distribution of sizes and shapes of perturbations which are randomly placed in three-dimensional space. The perturbations are described by two parameters such as central density and size, and the two-point correlation function is explicitly related to the luminosity function of groups and clusters of galaxies
Directory of Open Access Journals (Sweden)
Guo-Jun Kang
2016-11-01
Full Text Available The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH3-YD2 and TPhe-YD were systematically investigated by density functional theory (DFT and time-dependent density functional theory (TD-DFT to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO2 cluster were fully investigated. From the analyses of natural bond orbital (NBO, extended charge decomposition analysis (ECDA, and electron density variations (Δρ between the excited state and ground state, it was found that the introduction of N(CH32 and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH32 and 1,1,2-triphenylethene groups. NCH3-YD2 with N(CH32 groups in the donor part is an effective way to improve the interactions between the dyes and TiO2 surface, light having efficiency (LHE, and free energy change (ΔGinject, which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs.
Parry, A O; Rascón, C; Willis, G; Evans, R
2014-09-03
We study the density-density correlation function G(r, r') in the interfacial region of a fluid (or Ising-like magnet) with short-ranged interactions using square gradient density functional theory. Adopting a simple double parabola approximation for the bulk free-energy density, we first show that the parallel Fourier transform G(z, z'; q) and local structure factor S(z; q) separate into bulk and excess contributions. We attempt to account for both contributions by deriving an interfacial Hamiltonian, characterised by a wavevector dependent surface tension σ(q), and then reconstructing density correlations from correlations in the interface position. We show that the standard crossing criterion identification of the interface, as a surface of fixed density (or magnetization), does not explain the separation of G(z, z'; q) and the form of the excess contribution. We propose an alternative definition of the interface position based on the properties of correlations between points that 'float' with the surface and show that this describes the full q and z dependence of the excess contributions to both G and S. However, neither the 'crossing-criterion' nor the new 'floating interface' definition of σ(q) are quantities directly measurable from the total structure factor S(tot)(q) which contains additional q dependence arising from the non-local relation between fluctuations in the interfacial position and local density. Since it is the total structure factor that is measured experimentally or in simulations, our results have repercussions for earlier attempts to extract and interpret σ(q).
Boslough, M.
2011-12-01
Climate-related uncertainty is traditionally presented as an error bar, but it is becoming increasingly common to express it in terms of a probability density function (PDF). PDFs are a necessary component of probabilistic risk assessments, for which simple "best estimate" values are insufficient. Many groups have generated PDFs for climate sensitivity using a variety of methods. These PDFs are broadly consistent, but vary significantly in their details. One axiom of the verification and validation community is, "codes don't make predictions, people make predictions." This is a statement of the fact that subject domain experts generate results using assumptions within a range of epistemic uncertainty and interpret them according to their expert opinion. Different experts with different methods will arrive at different PDFs. For effective decision support, a single consensus PDF would be useful. We suggest that market methods can be used to aggregate an ensemble of opinions into a single distribution that expresses the consensus. Prediction markets have been shown to be highly successful at forecasting the outcome of events ranging from elections to box office returns. In prediction markets, traders can take a position on whether some future event will or will not occur. These positions are expressed as contracts that are traded in a double-action market that aggregates price, which can be interpreted as a consensus probability that the event will take place. Since climate sensitivity cannot directly be measured, it cannot be predicted. However, the changes in global mean surface temperature are a direct consequence of climate sensitivity, changes in forcing, and internal variability. Viable prediction markets require an undisputed event outcome on a specific date. Climate-related markets exist on Intrade.com, an online trading exchange. One such contract is titled "Global Temperature Anomaly for Dec 2011 to be greater than 0.65 Degrees C." Settlement is based
Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.
Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas
2017-01-17
The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than
Wierzcholski, Krzysztof
2014-01-01
The present paper is concerned with the calculation of the human hip joint parameters for periodic, stochastic unsteady, motion with asymmetric probability density function for gap height. The asymmetric density function indicates that the stochastic probabilities of gap height decreasing are different in comparison with the probabilities of the gap height increasing. The models of asymmetric density functions are considered on the grounds of experimental observations. Some methods are proposed for calculation of pressure distributions and load carrying capacities for unsteady stochastic conditions in a super thin layer of biological synovial fluid inside the slide biobearing gap limited by a spherical bone acetabulum. Numerical calculations are performed in Mathcad 12 Professional Program, by using the method of finite differences. This method assures stability of numerical solutions of partial differential equations and gives proper values of pressure and load carrying capacity forces occurring in human hip joints.
Failure of popular density functionals: Torsional potential of conjugated hetero double bonds
Tahchieva, Diana; von Lilienfeld, Anatole
Accurate predictions of torsional potential energy profiles are crucial to correctly sample conformational degrees of freedom. Using most of currently popular density functionals we have investigated many small organic closed shell molecules with conjugated hetero double bonds. Typically, density functional theory (DFT) is assumed to provide reasonable energy estimates for such systems and properties. In comparison to CCSD(T), however, all functionals fail to quantitatively reproduce the correct potential, except for M0(5,6)2X and CAM-B3LYP. For molecules containing CO or CS double bonds and heavy halogene atoms even qualitative trends can not be recovered. Analysis of the results reveals that the deviations are due to large errors in the electrostatic potential originating in a failures to generate correct electron densities. Empirical atom centered corrections can rectify some of the short-comings for PBE and BLYP.
Microscopic description of a liquid film on a solid substrate using density functional theory
Nold, Andreas; Pereira, Antonio; Malijewsky, Alexandr; Kalliadasis, Serafim
2010-11-01
We examine the wetting properties of planar and spherical substrates using a mean-field density functional theory. Equilibrium density profiles of a fluid close to an attractive wall are obtained by solving an integral equation resulting from the minimization of the grand potential. Using a novel pseudo-arc length continuation scheme, we compute the complete bifurcation diagram of the adsorption as a function of the chemical potential. For a spherical substrate we demonstrate a second unstable branch approaching saturation from the right, absent in the planar case. Our numerical results are in excellent agreement with analytical predictions obtained from a piecewise function approximation in which the density profile is assumed to be everywhere constant except near the wall-liquid and the liquid-gas interfaces. We also show that the sharp-interface approximation, used often to predict wetting behavior on planar substrates, is inadequate to describe wetting on a spherical substrate.
International Workshop on Electronic Density Functional Theory : Recent Progress and New Directions
Vignale, Giovanni; Das, Mukunda
1998-01-01
This book is an outcome of the International Workshop on Electronic Density Functional Theory, held at Griffith University in Brisbane, Australia, in July 1996. Density functional theory, standing as it does at the boundary between the disciplines of physics, chemistry, and materials science, is a great mixer. Invited experts from North America, Europe, and Australia mingled with students from several disciplines, rapidly taking up the informal style for which Australia is famous. A list of participants is given at the end of the book. Density functional theory (DFT) is a subtle approach to the very difficult problem of predicting the behavior of many interacting particles. A major application is the study of many-electron systems. This was the workshop theme, embracing inter alia computational chemistry and condensed matter physics. DFT circumvents the more conceptually straightforward (but more computationally intensive) approach in which one solves the many-body Schrodinger equation. It relies instead on r...
Archer, A J
2009-01-07
In recent years, a number of dynamical density functional theories (DDFTs) have been developed for describing the dynamics of the one-body density of both colloidal and atomic fluids. In the colloidal case, the particles are assumed to have stochastic equations of motion and theories exist for both the case when the particle motion is overdamped and also in the regime where inertial effects are relevant. In this paper, we extend the theory and explore the connections between the microscopic DDFT and the equations of motion from continuum fluid mechanics. In particular, starting from the Kramers equation, which governs the dynamics of the phase space probability distribution function for the system, we show that one may obtain an approximate DDFT that is a generalization of the Euler equation. This DDFT is capable of describing the dynamics of the fluid density profile down to the scale of the individual particles. As with previous DDFTs, the dynamical equations require as input the Helmholtz free energy functional from equilibrium density functional theory (DFT). For an equilibrium system, the theory predicts the same fluid one-body density profile as one would obtain from DFT. Making further approximations, we show that the theory may be used to obtain the mode coupling theory that is widely used for describing the transition from a liquid to a glassy state.
Lucero, Melissa J.; Henderson, Thomas M.; Scuseria, Gustavo E.
2011-01-01
We show that the middle-range exchange-correlation hybrid of Henderson, Izmaylov, Scuseria and Savin (HISS) performs extremely well for elemental and binary semiconductors with narrow or visible spectrum band gaps, as well as some wider gap or more ionic systems used commercially. The lattice parameters are superior to those predicted by the screened hybrid functional of Heyd, Scuseria and Ernzerhof (HSE), and provide a significant improvement over geometries predicted by semilocal functional...
Ghosh, Soumen; Cramer, Christopher J; Truhlar, Donald G; Gagliardi, Laura
2017-04-01
Predicting ground- and excited-state properties of open-shell organic molecules by electronic structure theory can be challenging because an accurate treatment has to correctly describe both static and dynamic electron correlation. Strongly correlated systems, i.e., systems with near-degeneracy correlation effects, are particularly troublesome. Multiconfigurational wave function methods based on an active space are adequate in principle, but it is impractical to capture most of the dynamic correlation in these methods for systems characterized by many active electrons. We recently developed a new method called multiconfiguration pair-density functional theory (MC-PDFT), that combines the advantages of wave function theory and density functional theory to provide a more practical treatment of strongly correlated systems. Here we present calculations of the singlet-triplet gaps in oligoacenes ranging from naphthalene to dodecacene. Calculations were performed for unprecedently large orbitally optimized active spaces of 50 electrons in 50 orbitals, and we test a range of active spaces and active space partitions, including four kinds of frontier orbital partitions. We show that MC-PDFT can predict the singlet-triplet splittings for oligoacenes consistent with the best available and much more expensive methods, and indeed MC-PDFT may constitute the benchmark against which those other models should be compared, given the absence of experimental data.
Martínez-Ruiz, Francisco José; Blas, Felipe J; Moreno-Ventas Bravo, A Ignacio; Míguez, José Manuel; MacDowell, Luis G
2017-05-17
The statistical associating fluid theory for attractive potentials of variable range (SAFT-VR) density functional theory (DFT) developed by [Gloor et al., J. Chem. Phys., 2004, 121, 12740-12759] is used to predict the interfacial behaviour of molecules modelled as fully-flexible square-well chains formed from tangentially-bonded monomers of diameter σ and potential range λ = 1.5σ. Four different model systems, comprising 4, 8, 12, and 16 monomers per molecule, are considered. In addition to that, we also compute a number of interfacial properties of molecular chains from direct simulation of the vapour-liquid interface. The simulations are performed in the canonical ensemble, and the vapour-liquid interfacial tension is evaluated using the wandering interface (WIM) method, a technique based on the thermodynamic definition of surface tension. Apart from surface tension, we also obtain density profiles, coexistence densities, vapour pressures, and critical temperature and density, paying particular attention to the effect of the chain length on these properties. According to our results, the main effect of increasing the chain length (at fixed temperature) is to sharpen the vapour-liquid interface and to increase the width of the biphasic coexistence region. As a result, the interfacial thickness decreases and the surface tension increases as the molecular chains get longer. The interfacial thickness and surface tension appear to exhibit an asymptotic limiting behaviour for long chains. A similar behaviour is also observed for the coexistence densities and critical properties. Agreement between theory and simulation results indicates that SAFT-VR DFT is only able to predict qualitatively the interfacial properties of the model. Our results are also compared with simulation data taken from the literature, including the vapour-liquid coexistence densities, vapour pressures, and surface tension.
Computationally efficient double hybrid density functional theory using dual basis methods
Byrd, Jason N
2015-01-01
We examine the application of the recently developed dual basis methods of Head-Gordon and co-workers to double hybrid density functional computations. Using the B2-PLYP, B2GP-PLYP, DSD-BLYP and DSD-PBEP86 density functionals, we assess the performance of dual basis methods for the calculation of conformational energy changes in C$_4$-C$_7$ alkanes and for the S22 set of noncovalent interaction energies. The dual basis methods, combined with resolution-of-the-identity second-order M{\\o}ller-Plesset theory, are shown to give results in excellent agreement with conventional methods at a much reduced computational cost.
A-centers in silicon studied with hybrid density functional theory
Wang, Hao
2013-07-29
Density functional theory employing hybrid functional is used to gain fundamental insight into the interaction of vacancies with oxygen interstitials to form defects known as A-centers in silicon. We calculate the formation energy of the defect with respect to the Fermi energy for all possible charge states. It is found that the neutral and doubly negatively charged A-centers dominate. The findings are analyzed in terms of the density of states and discussed in view of previous experimental and theoretical studies.
Modelling the Probability Density Function of IPTV Traffic Packet Delay Variation
Directory of Open Access Journals (Sweden)
Michal Halas
2012-01-01
Full Text Available This article deals with modelling the Probability density function of IPTV traffic packet delay variation. The use of this modelling is in an efficient de-jitter buffer estimation. When an IP packet travels across a network, it experiences delay and its variation. This variation is caused by routing, queueing systems and other influences like the processing delay of the network nodes. When we try to separate these at least three types of delay variation, we need a way to measure these types separately. This work is aimed to the delay variation caused by queueing systems which has the main implications to the form of the Probability density function.
Yao, Kun
2015-01-01
We demonstrate a convolutional neural network trained to reproduce the Kohn-Sham kinetic energy of hydrocarbons from electron density. The output of the network is used as a non-local correction to the conventional local and semi-local kinetic functionals. We show that this approximation qualitatively reproduces Kohn-Sham potential energy surfaces when used with conventional exchange correlation functionals. Numerical noise inherited from the non-linearity of the neural network is identified as the major challenge for the model. Finally we examine the features in the density learned by the neural network to anticipate the prospects of generalizing these models.
Optical Absorption in Molecular Crystals from Time-Dependent Density Functional Theory
2017-04-23
from time-dependent density functional theory 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-15-1-0290 5c. PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S...AFRL-AFOSR-UK-TR-2017-0030 Optical absorption in molecular crystals from time-dependent density functional theory Leeor Kronik WEIZMANN INSTITUTE OF...does not display a currently valid OMB control number . PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 1. REPORT DATE (DD-MM-YYYY) 23
Mohamed, Nasser J.
1990-05-01
A generalization of a previously published ambiguity function that applies to radar known as large-relative-bandwidth radar, carrier-free radar, impulse radar, or nonsinusoidal radar is discussed. This radar has recently attracted attention because of its ability to penetrate absorbing materials used in the stealth technology. Another good application is the detection of moving targets with a small radar cross section by a look-down radar, which calls for a thumbtack ambiguity function. Since a small radar cross section in this application is typically due to the small size of the target that is coated with absorbing material, the antistealth feature of the nonsinusoidal radar is implicitly being used. The principle is presented of a resolution function (tentatively called the range-velocity or the range-Doppler resolution function) based on processing a nonsinusoidal signal consisting of N characters with a time separation TD and each character consisting of a sequence of L binary pulses of duration T. It is shown that range-velocity resolution functions approaching the ideal thumbtack function are easy to obtain. The blind speeds of the pulse-Doppler radar with sinusoidal carrier do not inherently occur, and all velocities are observed as true velocities rather than as velocities modulo the first blind speed (velocity ambiguity).
Keyes, T.; Morita, Terumitsu
1981-11-01
Our modification of the method of Peralta and Zwanzig for the calculation of the drag on a sphere is applied at high and low bath densities. We obtain Stokes law at high density and 0.82 times the exact result at low density. Thus, our theory gives a unified framework for calculation of the drag as a function of density.
Directory of Open Access Journals (Sweden)
Tao Liu
2016-12-01
Full Text Available Objective: Addiction is a chronic relapsing brain disease. Brain structural abnormalities may constitute an abnormal neural network that underlies the risk of drug dependence. We hypothesized that individuals with Betel Quid Dependence (BQD have functional connectivity alterations that can be described by long- and short-range functional connectivity density(FCD maps. Methods: We tested this hypothesis using functional magnetic resonance imaging (fMRI data from subjects of the Han ethnic group in Hainan, China. Here, we examined BQD individuals (n = 33 and age-, sex-, and education-matched healthy controls (HCs (n = 32 in a rs-fMRI study to observe FCD alterations associated with the severity of BQD. Results: Compared with HCs, long-range FCD was decreased in the right anterior cingulate cortex (ACC and increased in the left cerebellum posterior lobe (CPL and bilateral inferior parietal lobule (IPL in the BQD group. Short-range FCD was reduced in the right ACC and left dorsolateral prefrontal cortex (dlPFC, and increased in the left CPL. The short-range FCD alteration in the right ACC displayed a negative correlation with the Betel Quid Dependence Scale (BQDS (r=-0.432, P=0.012, and the long-range FCD alteration of left IPL showed a positive correlation with the duration of BQD(r=0.519, P=0.002 in BQD individuals. Conclusions: fMRI revealed differences in long- and short- range FCD in BQD individuals, and these alterations might be due to BQ chewing, BQ dependency, or risk factors for developing BQD.
A new Skyrme energy density functional for a better description of spin-isospin resonances
Energy Technology Data Exchange (ETDEWEB)
Roca-Maza, X., E-mail: xavier.roca.maza@mi.infn.it [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Milano, via Celoria 16, 20133 Milano (Italy); Colò, G. [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Milano, via Celoria 16, 20133 Milano (Italy); Kavli Institute for Theoretical Physics China, CAS, Beijing 100190 (China); Cao, Li-Gang [Kavli Institute for Theoretical Physics China, CAS, Beijing 100190 (China); School of Mathematics and Physics, North China Electric Power University, Beijing 102206 (China); State Key Laboratory of Theoretical Physics, ITP, Chinese Academy of Sciences, Beijing 100190 (China); National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000 (China); Sagawa, H. [Kavli Institute for Theoretical Physics China, CAS, Beijing 100190 (China); Center for Mathematics and Physics, University of Aizu, Aizu-Wakamatsu, Fukushima 965-8580 (Japan); RIKEN, Nishina Center, Wako, 351-0198 (Japan)
2015-10-15
A correct determination of the isospin and spin-isospin properties of the nuclear effective interaction should lead to an accurate description of the Gamow-Teller resonance (GT), the Spin Dipole Resonance (SDR), the Giant Dipole Resonance (GDR) or the Antianalog Giant Dipole Resonance (AGDR), among others. A new Skyrme energy density functional named SAMi is introduced with the aim of going a step forward in setting the bases for a more precise description of spin-isospin resonances [1, 2]. In addition, we will discuss some new features of our analysis on the AGDR in {sup 208}Pb [3] as compared with available experimental data on this resonance [4, 5, 6], and on the GDR [7]. Such study, guided by a simple yet physical pocket formula, has been developed by employing the so called SAMi-J family of systematically varied interactions. This set of interactions is compatible with experimental data for values of the symmetry energy at saturation J and slope parameter L falling in the ranges 31−33 MeV and 75−95 MeV, respectively.
Using Sandia's Z Machine and Density Functional Theory Simulations to Understand Planetary Materials
Root, Seth
2017-06-01
The use of Z, NIF, and Omega have produced many breakthrough results in high pressure physics. One area that has greatly benefited from these facilities is the planetary sciences. The high pressure behavior of planetary materials has implications for numerous geophysical and planetary processes. The continuing discovery of exosolar super-Earths demonstrates the need for accurate equation of state data to better inform our models of their interior structures. Planetary collision processes, such as the moon-forming giant impact, require understanding planetary materials over a wide-range of pressures and temperatures. Using Z, we examined the shock compression response of some common planetary materials: MgO, Mg2SiO4, and Fe2O3 (hematite). We compare the experimental shock compression measurements with density functional theory (DFT) based quantum molecular dynamics (QMD) simulations. The combination of experiment and theory provides clearer understanding of planetary materials properties at extreme conditions. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics.
von Rudorff, Guido Falk; Jakobsen, Rasmus; Rosso, Kevin M; Blumberger, Jochen
2016-10-05
The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O(-)) and doubly protonated oxygens (-OH[Formula: see text]) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.
Wu, Tao; Deng, Kaiming; Deng, Wei-Qiao; Lu, Ruifeng
2017-09-19
BNCX monolayer as a kind of two-dimensional material has numerous chemical atomic ratios and arrangements with different electronic structures. Via calculations on the basis of density functional theory and Boltzmann transport theory under deformation potential approximation, the band structures and carrier mobilities of BNCX (x=1,2,3,4) nanosheets are systematically investigated. The calculated results show that BNC2-1 is a material with very small band gap (0.02 eV) among all the structures while other BNCX monolayers are semiconductors with band gap ranging from 0.51 to 1.32 eV. The carrier mobility of BNCX varies considerably from tens to millions of cm2 V-1 s-1. For BNC2-1, the hole mobility and electron mobility along both x and y directions can reach 105 orders of magnitude, which is similar to the carrier mobility of graphene. Besides, all studied BNCX monolayers obviously have anisotropic hole mobility and electron mobility. In particular, for semiconductor BNC4, its hole mobility along y direction and electron mobility along x direction unexpectedly reach 106 orders of magnitude, even higher than that of graphene. Our findings suggest that BNCX layered materials with proper ratio and arrangement of carbon atoms will possess desirable charge transport properties, exhibiting potential applications in nanoelectronic devices. © 2017 IOP Publishing Ltd.
Calculation of electronic excitations using wave-function in wave-function frozen-density embedding
Hoefener, S.; Visscher, L.
2012-01-01
Recently, a general framework suitable for general frozen-density embedding (FDE) methods was published [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)]10.1063/1.3675845. In the present article, we report the fragmentation of a supermolecule while treating all
Exercise induced effects on muscle function and range of motion in patients with hip osteoarthritis
DEFF Research Database (Denmark)
Bieler, Theresa; Siersma, Volkert; Magnusson, S Peter
2017-01-01
BACKGROUND AND PURPOSE: Patients with hip osteoarthritis have impairments in muscle function (muscle strength and power) and hip range of motion (ROM), and it is commonly believed that effective clinical management of osteoarthritis should address these impairments to reduce pain and disability. ...
Density of biofuel in function of temperature; Densidade de biocombustiveis em funcao da temperatura
Energy Technology Data Exchange (ETDEWEB)
Oliveira, Melina C.J.; Lopes, Afonso [Universidade Estadual Paulista Julio de Mesquita Filho (FCAV/UNESP), Jaboticabal, SP (Brazil). Fac. de Ciencias Agrarias e Veterinarias. Dept. de Engenharia Rural], email: melina_cais@yahoo.com.br; Camara, Felipe T. [Universidade Federal do Ceara (UFC), Cariri, CE (Brazil); Lima, Leomar P. [Instituto Federal do Triangulo Mineiro (IFTM), Uberlandia, MG (Brazil)
2011-07-01
Considering the oil a non-renewable natural resource, Biodiesel is an alternative fuel, the same being renewable, biodegradable and made from vegetable oil or residual transesterified with anhydrous alcohol in the presence of a catalyst. This study aimed to evaluate the density of biodiesel methyl filtered residual oil from the university cafeteria, biodiesel methyl filtered hydrogenated fat residual McDonald's and the density of the mixture of 50% of residual oil from the university cafeteria with 50% of hydrogenated fat residual McDonald's all a function of temperature (10 deg C to 70 deg C). The experiment was conducted at the Agricultural Engineering Department of UNESP-Jaboticabal, SP. Was used 3x13x7 factorial experimental design, which represent three types of biodiesel, 13 July and the temperatures of the mixtures. We conclude that the residual oil biodiesel university restaurant density was lower, while biodiesel from hydrogenated fat from McDonald's and the mixture had higher densities, but differ from each other. The diesel (B0) had the lowest density and Biodiesel (B100) the largest. The B0 and B5 blends did not differ regarding density, but differed from the mix B15, B25, B50, B75 and B100. For all the mixtures tested, with the increase of temperature decreased the density. (author)
Bhambure, Rahul; Angelo, James M; Gillespie, Christopher M; Phillips, Michael; Graalfs, Heiner; Lenhoff, Abraham M
2017-07-14
The effect of ligand density was studied on protein adsorption and transport behavior in tentacular cation-exchange sorbents at different ionic strengths. Results were obtained for lysozyme, lactoferrin and a monoclonal antibody (mAb) in order to examine the effects of protein size and charge. The combination of ligand density and ionic strength results in extensive variability of the static and dynamic binding capacities, transport rate and binding affinity of the proteins. Uptake and elution experiments were performed to quantify the transport behavior of selected proteins, specifically to estimate intraparticle protein diffusivities. The observed trend of decreasing uptake diffusivities with an increase in ligand density was correlated to structural properties of the ligand-density variants, particularly the accessible porosity. Increasing the ionic strength of the equilibration buffer led to enhanced mass transfer during uptake, independent of the transport model used, and specifically for larger proteins like lactoferrin and mAb, the most significant effects were evident in the sorbent of the highest ligand density. For lysozyme, higher ligand density leads to higher static and dynamic binding capacities whereas for lactoferrin and the mAb, the binding capacity is a complex function of accessible porosity due to ionic strength-dependent changes. Ligand density has a less pronounced effect on the elution rate, presumably due to ionic strength-dependent changes in the pore architecture of the sorbents. Copyright © 2017 Elsevier B.V. All rights reserved.
Ensemble Averaged Probability Density Function (APDF) for Compressible Turbulent Reacting Flows
Shih, Tsan-Hsing; Liu, Nan-Suey
2012-01-01
In this paper, we present a concept of the averaged probability density function (APDF) for studying compressible turbulent reacting flows. The APDF is defined as an ensemble average of the fine grained probability density function (FG-PDF) with a mass density weighting. It can be used to exactly deduce the mass density weighted, ensemble averaged turbulent mean variables. The transport equation for APDF can be derived in two ways. One is the traditional way that starts from the transport equation of FG-PDF, in which the compressible Navier- Stokes equations are embedded. The resulting transport equation of APDF is then in a traditional form that contains conditional means of all terms from the right hand side of the Navier-Stokes equations except for the chemical reaction term. These conditional means are new unknown quantities that need to be modeled. Another way of deriving the transport equation of APDF is to start directly from the ensemble averaged Navier-Stokes equations. The resulting transport equation of APDF derived from this approach appears in a closed form without any need for additional modeling. The methodology of ensemble averaging presented in this paper can be extended to other averaging procedures: for example, the Reynolds time averaging for statistically steady flow and the Reynolds spatial averaging for statistically homogeneous flow. It can also be extended to a time or spatial filtering procedure to construct the filtered density function (FDF) for the large eddy simulation (LES) of compressible turbulent reacting flows.
DEFF Research Database (Denmark)
Baumgartner, Christine; da Costa, Bruno R.; Collet, Tinh-Hai
2017-01-01
variations in thyroid function within the normal range or subclinical hypothyroidism are also associated with AF. Methods -We conducted a systematic review and obtained individual participant data from prospective cohort studies that measured thyroid function at baseline and assessed incident AF. Studies...... were identified from MEDLINE and EMBASE databases from inception to July 27, 2016. The euthyroid state was defined as thyroid-stimulating hormone (TSH) 0.45 to 4.49 mIU/L, and subclinical hypothyroidism as TSH 4.5 to 19.9 mIU/L with free thyroxine (fT4) levels within reference range. The association...... of TSH levels in the euthyroid and subclinical hypothyroid range with incident AF was examined by using Cox proportional hazards models. In euthyroid participants, we additionally examined the association between fT4 levels and incident AF. Results -Of 30 085 participants from 11 cohorts (278 955 person...
Xu, Zhijun; Yang, Yang; Wang, Ziqiu; Mkhonto, Donald; Shang, Cheng; Liu, Zhi-Pan; Cui, Qiang; Sahai, Nita
2014-01-05
The unique, plate-like morphology of hydroxyapatite (HAP) nanocrystals in bone lends to the hierarchical structure and functions of bone. Proteins enriched in phosphoserine (Ser-OPO3) and glutamic acid (Glu) residues have been proposed to regulate crystal morphology; however, the atomic-level mechanisms remain unclear. Previous molecular dynamics studies addressing biomineralization have used force fields with limited benchmarking, especially at the water/mineral interface, and often limited sampling for the binding free energy profile. Here, we use the umbrella sampling/weighted histogram analysis method to obtain the adsorption free energy of Ser-OPO3 and Glu on HAP (100) and (001) surfaces to understand organic-mediated crystal growth. The calculated organic-water-mineral interfacial energies are carefully benchmarked to density functional theory calculations, with explicit inclusion of solvating water molecules around the adsorbate plus the Poisson-Boltzmann continuum model for long-range solvation effects. Both amino acids adsorb more strongly on the HAP (100) face than the (001) face. Growth rate along the [100] direction should then be slower than in the [001] direction, resulting in plate-like crystal morphology with greater surface area for the (100) than the (001) face, consistent with bone HAP crystal morphology. Thus, even small molecules are capable of regulating bone crystal growth by preferential adsorption in specific directions. Furthermore, Ser-OPO3 is a more effective growth modifier by adsorbing more strongly than Glu on the (100) face, providing one possible explanation for the energetically expensive process of phosphorylation of some proteins involved in bone biomineralization. The current results have broader implications for designing routes for biomimetic crystal synthesis. Copyright © 2013 Wiley Periodicals, Inc.
Relating the defect band gap and the density functional band gap
Schultz, Peter; Edwards, Arthur
2014-03-01
Density functional theory (DFT) is an important tool to probe the physics of materials. The Kohn-Sham (KS) gap in DFT is typically (much) smaller than the observed band gap for materials in nature, the infamous ``band gap problem.'' Accurate prediction of defect energy levels is often claimed to be a casualty--the band gap defines the energy scale for defect levels. By applying rigorous control of boundary conditions in size-converged supercell calculations, however, we compute defect levels in Si and GaAs with accuracies of ~0.1 eV, across the full gap, unhampered by a band gap problem. Using GaAs as a theoretical laboratory, we show that the defect band gap--the span of computed defect levels--is insensitive to variations in the KS gap (with functional and pseudopotential), these KS gaps ranging from 0.1 to 1.1 eV. The defect gap matches the experimental 1.52 eV gap. The computed defect gaps for several other III-V, II-VI, I-VII, and other compounds also agree with the experimental gap, and show no correlation with the KS gap. Where, then, is the band gap problem? This talk presents these results, discusses why the defect gap and the KS gap are distinct, implying that current understanding of what the ``band gap problem'' means--and how to ``fix'' it--need to be rethought. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy's NNSA under contract DE-AC04-94AL85000.
Ramya, K. R.; Pavan Kumar, G. V.; Venkatnathan, Arun
2012-05-01
The sI type methane clathrate hydrate lattice is formed during the process of nucleation where methane gas molecules are encapsulated in the form of dodecahedron (512CH4) and tetrakaidecahedron (51262CH4) water cages. The characterization of change in the vibrational modes which occur on the encapsulation of CH4 in these cages plays a key role in understanding the formation of these cages and subsequent growth to form the hydrate lattice. In this present work, we have chosen the density functional theory (DFT) using the dispersion corrected B97-D functional to characterize the Raman frequency vibrational modes of CH4 and surrounding water molecules in these cages. The symmetric and asymmetric C-H stretch in the 512CH4 cage is found to shift to higher frequency due to dispersion interaction of the encapsulated CH4 molecule with the water molecules of the cages. However, the symmetric and asymmetric O-H stretch of water molecules in 512CH4 and 51262CH4 cages are shifted towards lower frequency due to hydrogen bonding, and interactions with the encapsulated CH4 molecules. The CH4 bending modes in the 512CH4 and 51262CH4 cages are blueshifted, though the magnitude of the shifts is lower compared to modes in the high frequency region which suggests bending modes are less affected on encapsulation of CH4. The low frequency librational modes which are collective motion of the water molecules and CH4 in these cages show a broad range of frequencies which suggests that these modes largely contribute to the formation of the hydrate lattice.
Energy Technology Data Exchange (ETDEWEB)
Anas, M. M.; Othman, A. P.; Gopir, G. [School of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor (Malaysia)
2014-09-03
Density functional theory (DFT), as a first-principle approach has successfully been implemented to study nanoscale material. Here, DFT by numerical basis-set was used to study the quantum confinement effect as well as electronic properties of silicon quantum dots (Si-QDs) in ground state condition. Selection of quantum dot models were studied intensively before choosing the right structure for simulation. Next, the computational result were used to examine and deduce the electronic properties and its density of state (DOS) for 14 spherical Si-QDs ranging in size up to ∼ 2 nm in diameter. The energy gap was also deduced from the HOMO-LUMO results. The atomistic model of each silicon QDs was constructed by repeating its crystal unit cell of face-centered cubic (FCC) structure, and reconstructed until the spherical shape obtained. The core structure shows tetrahedral (T{sub d}) symmetry structure. It was found that the model need to be passivated, and hence it was noticed that the confinement effect was more pronounced. The model was optimized using Quasi-Newton method for each size of Si-QDs to get relaxed structure before it was simulated. In this model the exchange-correlation potential (V{sub xc}) of the electrons was treated by Local Density Approximation (LDA) functional and Perdew-Zunger (PZ) functional.
2017-05-05
are characterized by many different geometries, which potentially can be optimized with respect to specific materials design criteria, i.e., molecular...19,20] and basis function 6-311+G(d) [21,22]. These basis functions designate the 6-311G basis set 5 supplemented by diffuse...Functional Theory,” Brazilian Journal of Physics 44, 154 (2014) [25] E. Runge and E.K.U. Gross, “Density-Functional Theory for Time-Dependent
Energy Technology Data Exchange (ETDEWEB)
Curro, John G.; McCoy, John Dwane (New Mexico Tech, Socorro, NM); Nath, Shyamal K. (New Mexico Tech, Socorro, NM); Frischknecht, Amalie Lucile
2005-05-01
Classical density functional theory (DFT) is applied to study properties of fully detailed, realistic models of poly(dimethylsiloxane) liquids near silica surfaces and compared to results from molecular dynamics simulations. In solving the DFT equations, the direct correlation functions are obtained from the polymer reference interaction site model (PRISM) theory for the repulsive parts of the interatomic interactions, and the attractions are treated via the random-phase approximation (RPA). Good agreement between density profiles calculated from DFT and from the simulations is obtained with empirical scaling of the direct correlation functions. Separate scaling factors are required for the PRISM and RPA parts of the direct correlation functions. Theoretical predictions of stress profiles, normal pressure, and surface tensions are also in reasonable agreement with simulation results.
DEFF Research Database (Denmark)
Lacevic, N.; Starr, F. W.; Schrøder, Thomas
2003-01-01
correlation function g4(r,t) and corresponding "structure factor" S4(q,t) which measure the spatial correlations between the local liquid density at two points in space, each at two different times, and so are sensitive to dynamical heterogeneity. We study g4(r,t) and S4(q,t) via molecular dynamics......Relaxation in supercooled liquids above their glass transition and below the onset temperature of "slow" dynamics involves the correlated motion of neighboring particles. This correlated motion results in the appearance of spatially heterogeneous dynamics or "dynamical heterogeneity." Traditional...... two-point time-dependent density correlation functions, while providing information about the transient "caging" of particles on cooling, are unable to provide sufficiently detailed information about correlated motion and dynamical heterogeneity. Here, we study a four-point, time-dependent density...
Density functional theory for crystal-liquid interfaces of Lennard-Jones fluid.
Wang, Xin; Mi, Jianguo; Zhong, Chongli
2013-04-28
A density functional approach is presented to describe the crystal-liquid interfaces and crystal nucleations of Lennard-Jones fluid. Within the theoretical framework, the modified fundamental measure theory is applied to describe the free energy functional of hard sphere repulsion, and the weighted density method based on first order mean spherical approximation is used to describe the free energy contribution arising from the attractive interaction. The liquid-solid equilibria, density profiles within crystal cells and at liquid-solid interfaces, interfacial tensions, nucleation free energy barriers, and critical cluster sizes are calculated for face-centered-cubic and body-centered-cubic nucleus. Some results are in good agreement with available simulation data, indicating that the present model is quantitatively reliable in describing nucleation thermodynamics of Lennard-Jones fluid.
Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon
2017-08-03
Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF-. The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pKa's, optimized geometries, and reaction paths.
Filtered Mass Density Function for Large Eddy Simulation of Turbulent Reacting Flows
Jaberi, F. A.; Colucci, P. J.; James, S.; Givi, P.; Pope, S. B.
1997-11-01
A new methodology termed the ``filtered mass density function'' (FMDF) is developed and implemented for large eddy simulation (LES) of variable density chemically reacting turbulent flows at low Mach numbers. The FMDF represents the single point joint probability density function of the subgrid scale scalar quantities and is governed by its modeled transport equation. In this equation, the effects of chemical reaction appear in closed form but the influences of scalar mixing and convection within the subgrid are modeled. The stochastic differential equations (SDEs) which yield statistically equivalent results to that of the FMDF transport equation are derived and are solved via a Lagrangian Monte Carlo scheme. The consistency, the convergence, and the accuracy of FMDF and the Monte Carlo solution of its equivalent SDEs are demonstrated. The performance of the model is assessed by extensive comparisons with DNS and laboratory experimental data in two-dimensional (2D) and 3D reacting turbulent shear flows.
Ab-initio density functional study of O on the Ag(001) surface
Gajdos, M.; A. Eichler; Hafner, J.
2003-01-01
The adsorption of oxygen on the Ag(001) is investigated by means of density functional techniques. Starting from a characterization of the clean silver surfaces oxygen adsorption in several modifications (molecularly, on-surface, sub-surface, Ag$_2$O) for varying coverage was studied. Besides structural parameters and adsorption energies also work-function changes, vibrational frequencies and core level energies were calculated for a better characterization of the adsorption structures and an...
Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity.
Domingo, Luis R; Ríos-Gutiérrez, Mar; Pérez, Patricia
2016-06-09
Theoretical reactivity indices based on the conceptual Density Functional Theory (DFT) have become a powerful tool for the semiquantitative study of organic reactivity. A large number of reactivity indices have been proposed in the literature. Herein, global quantities like the electronic chemical potential μ, the electrophilicity ω and the nucleophilicity N indices, and local condensed indices like the electrophilic P k + and nucleophilic P k - Parr functions, as the most relevant indices for the study of organic reactivity, are discussed.
Neutron-star matter within the energy-density functional theory and neutron-star structure
Energy Technology Data Exchange (ETDEWEB)
Fantina, A. F.; Chamel, N.; Goriely, S. [Institut d' Astronomie et d' Astrophysique, CP226, Université Libre de Bruxelles (ULB), 1050 Brussels (Belgium); Pearson, J. M. [Dépt. de Physique, Université de Montréal, Montréal (Québec), H3C 3J7 (Canada)
2015-02-24
In this lecture, we will present some nucleonic equations of state of neutron-star matter calculated within the nuclear energy-density functional theory using generalized Skyrme functionals developed by the Brussels-Montreal collaboration. These equations of state provide a consistent description of all regions of a neutron star. The global structure of neutron stars predicted by these equations of state will be discussed in connection with recent astrophysical observations.
Loco-regional differences in pulmonary function and density after partial rat lung irradiation.
Wiegman, E M; Meertens, H; Konings, A W T; Kampinga, H H; Coppes, R P
2003-10-01
The purpose of this study was to explore regional differences in radiosensitivity of rat lung using lung function and computed tomography (CT) density as endpoints. At first, CT scans were used to determine rat lung volumes. The data obtained enabled the design of accurate collimators to irradiate 50% of the total lung volume for the apex, base, left, right, mediastinal and lateral part of the lung. Male Wistar rats were irradiated with a single dose of 18 Gy of orthovoltage X-rays. Further rat thorax CT scans were made before and 4, 16, 26, and 52 weeks after irradiation to measure in vivo lung density changes indicative of lung damage. To evaluate overall lung function, breathing frequencies were measured biweekly starting 1 week before irradiation. Qualitative analysis of the CT scans showed clear density changes for all irradiated lung volumes, with the most prominent changes present in the mediastinal and left group at 26 weeks after radiation. Quantitative analysis using average density changes of whole lungs did not adequately describe the differences in radiation response between the treated groups. However, analysis of the density changes of the irradiated and non-irradiated regions of interest (ROI) more closely matched with the qualitative observations. Breathing frequencies (BF) were only increased after 50% left lung irradiation, indicating that the hypersensitivity of the mediastinal part as assessed by CT analysis, does not result in functional changes. For both BF and CT (best described by ROI analysis), differences in regional lung radiosensitivity were observed. The presentation of lung damage either as function loss or density changes do not necessarily coincide, meaning that for each endpoint the regional sensitivity may be different.
DEFF Research Database (Denmark)
Jacobsen, C.J.H.; Dahl, Søren; Boisen, A.
2002-01-01
For ammonia synthesis catalysts a volcano-type relationship has been found experimentally. We demonstrate that by combining density functional theory calculations with a microkinetic model the position of the maximum of the volcano curve is sensitive to the reaction conditions. The catalytic...
DEFF Research Database (Denmark)
Kitchin, J.R.; Nørskov, Jens Kehlet; Barteau, M.A.
2005-01-01
In this paper we present density functional theory (DFT) investigations of the physical, chemical and electronic structure properties of several close-packed surfaces of early transition metal carbides, including beta-Mo2C(0 0 0 1), and the (1 1 1) surfaces of TiC, VC, NbC, and TaC. The results a...
Dynamic Graphics in Excel for Teaching Statistics: Understanding the Probability Density Function
Coll-Serrano, Vicente; Blasco-Blasco, Olga; Alvarez-Jareno, Jose A.
2011-01-01
In this article, we show a dynamic graphic in Excel that is used to introduce an important concept in our subject, Statistics I: the probability density function. This interactive graphic seeks to facilitate conceptual understanding of the main aspects analysed by the learners.
Frederick C. Meinzer; Paula I. Campanello; Jean-Christophe Domec; M. Genoveva Gatti; Guillermo Goldstein; Randol Villalobos-Vega; David R. Woodruff
2008-01-01
This study examined how leaf and stem functional traits related to gas exchange and water balance scale with two potential proxies for tree hydraulic architecture: the leaf area:sapwood area ratio (AL:AS) and wood density (W). We studied the upper crowns of individuals of 15 tropical forest...
The accuracy of geometries for iron porphyrin complexes from density functional theory
DEFF Research Database (Denmark)
Rydberg, Patrik Åke Anders; Olsen, Lars
2009-01-01
Iron porphyrin complexes are cofactors in many important proteins such as cytochromes P450, hemoglobin, heme peroxidases, etc. Many computational studies on these systems have been done over the past decade. In this study, the performance of some of the most commonly used density functional theory...
Directory of Open Access Journals (Sweden)
L. da Rocha
Full Text Available This study evaluated the functional response of the predator Cosmoclopius nigroannulatus on first instar nymphae of Spartocera dentiventris, both species associated with Nicotina tabacum. The experiment was carried out in laboratory conditions: 27 ± 1ºC; 80 ± 5%, RH; 12 h, photophase. Ten newly emerged adults of each sex of C. nigroannulatus were used in each of five densities (5, 15, 25, 35, and 45 individuals of S. dentiventris nymphae. The predators were observed every 24 h for five days, when the number of dead and/or consumed nymphae was recorded. The results showed a positive correlation between the number of ingested nymphae and the increase in prey density. Females ingested more nymphae than the males. The estimated handling time per prey (Th was higher in males (3.07 h than in females (1.93 h, with total handling time (Th x Na increased with density. Other components of the functional response, such as attack rate (a', searching time (Ts, and search efficiency (E showed, in neither males nor females, a negative correlation regarding density. The results indicated a higher predatory efficiency in the females. The components of the functional response fitted significantly the randomic model of the Holling discs equation (Na = N {1 - exp[- a'(T - ThNa]}, evidencing a functional response of type II.
DEFF Research Database (Denmark)
Dohn, Asmus Ougaard; Møller, Klaus Braagaard; Sauer, Stephan P. A.
2013-01-01
The geometry of tetracyanoplatinate(II) (TCP) has been optimized with density functional theory (DFT) calculations in order to compare different computational strategies. Two approximate scalar relativistic methods, i.e. the scalar zeroth-order regular approximation (ZORA) and non-relativistic ca...
Some late-term thoughts of a density-functional theorist
Indian Academy of Sciences (India)
Unknown
The most appropriate density-functional language does not come easily. It is not just telling how to calculate better ... of the exchange energy. Explore its applications to molecules, and try to single it out of exact ... One never knows to where a study will lead. Computation will be involved in most of these problems, but their ...
Gold Nanowires : A Time-Dependent Density Functional Assessment of Plasmonic Behavior
Piccini, GiovanniMaria; Havenith, Remco W. A.; Broer, Ria; Stener, Mauro
2013-01-01
The surface plasmon resonance has been theoretically investigated in gold nanowires by means of time-dependent density functional theory. Linear chains of Au atoms and nanowires with the structure of the fcc bulk gold grown along the <110 > and <111 > directions have been considered. The effects of
Point Defects in 2D and 3D Nanomaterials: A Density Functional Theory Exploration
Li, W.F.
2017-01-01
In this thesis, a large number of point defects was studied in both 2D and 3D nanomaterials that are of utmost importance to nanoscience by means of first principles density functional theory calculations. First, we focused on the lead chalcogenide family: PbS, PbSe, and PbTe that are frequently
DEFF Research Database (Denmark)
Falk, Anne Katrine Vinther; Gryning, Sven-Erik
1997-01-01
In this model for atmospheric dispersion particles are simulated by the Langevin Equation, which is a stochastic differential equation. It uses the probability density function (PDF) of the vertical velocity fluctuations as input. The PDF is constructed as an expansion after Hermite polynomials. ...