Energy Technology Data Exchange (ETDEWEB)
Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fedorov, Dmitri G. [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Yokojima, Satoshi [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 (Japan); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Sakurai, Minoru [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)
2014-04-14
We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.
Mussard, Bastien; Angyan, Janos; Toulouse, Julien
2015-01-01
We consider several spin-unrestricted random-phase approximation (RPA) variants for calculating correlation energies, with and without range separation, and test them on datasets of atomization energies and reaction barrier heights. We show that range separation greatly improves the accuracy of all RPA variants for these properties. Moreover, we show that a RPA variant with exchange, hereafter referred to as RPAx-SO2, first proposed by Sz-abo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)] in a spin-restricted closed-shell formalism, and extended here to a spin-unrestricted formalism, provides on average the most accurate range-separated RPA variant for atomization energies and reaction barrier heights. Since this range-separated RPAx-SO2 method had already been shown to be among the most accurate range-separated RPA variants for weak intermolecular interactions [J. Toulouse, W. Zhu, A. Savin, G. Jansen, and J. G. {\\'A}ngy{\\'a}n, J. Chem. Phys. 135, 084119 (2011)], this works confirms...
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.
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...
SYNTHESIS, CHARACTERIZATION AND DENSITY FUNCTIONAL ...
African Journals Online (AJOL)
Preferred Customer
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 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
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.
Bao, Junwei Lucas; Odoh, Samuel O; Gagliardi, Laura; Truhlar, Donald G
2017-02-14
We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.
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 ...
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...
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).
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 ...
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...
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.
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.
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.)
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.
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
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.
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.
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 ...
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.
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)
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 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
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
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
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...
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.
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.
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.
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.
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....
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.
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.
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.
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.
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.
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
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 ...
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...
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 ...
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.
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.
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...
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 ...
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.
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.)
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
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...
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
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.
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.
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...
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.
Hermes, Matthew R.; Hirata, So
2015-09-01
One-dimensional (1D) solids exhibit a number of striking electronic structures including charge-density wave (CDW) and spin-density wave (SDW). Also, the Peierls theorem states that at zero temperature, a 1D system predicted by simple band theory to be a metal will spontaneously dimerize and open a finite fundamental bandgap, while at higher temperatures, it will assume the equidistant geometry with zero bandgap (a Peierls transition). We computationally study these unique electronic structures and transition in polyyne and all-trans polyacetylene using finite-temperature generalizations of ab initio spin-unrestricted Hartree-Fock (UHF) and spin-restricted coupled-cluster doubles (CCD) theories, extending upon previous work [He et al., J. Chem. Phys. 140, 024702 (2014)] that is based on spin-restricted Hartree-Fock (RHF) and second-order many-body perturbation (MP2) theories. Unlike RHF, UHF can predict SDW as well as CDW and metallic states, and unlike MP2, CCD does not diverge even if the underlying RHF reference wave function is metallic. UHF predicts a gapped SDW state with no dimerization at low temperatures, which gradually becomes metallic as the temperature is raised. CCD, meanwhile, confirms that electron correlation lowers the Peierls transition temperature. Furthermore, we show that the results from all theories for both polymers are subject to a unified interpretation in terms of the UHF solutions to the Hubbard-Peierls model using different values of the electron-electron interaction strength, U/t, in its Hamiltonian. The CCD wave function is shown to encompass the form of the exact solution of the Tomonaga-Luttinger model and is thus expected to describe accurately the electronic structure of Luttinger liquids.
Energy Technology Data Exchange (ETDEWEB)
Hermes, Matthew R. [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); Hirata, So, E-mail: sohirata@illinois.edu [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)
2015-09-14
One-dimensional (1D) solids exhibit a number of striking electronic structures including charge-density wave (CDW) and spin-density wave (SDW). Also, the Peierls theorem states that at zero temperature, a 1D system predicted by simple band theory to be a metal will spontaneously dimerize and open a finite fundamental bandgap, while at higher temperatures, it will assume the equidistant geometry with zero bandgap (a Peierls transition). We computationally study these unique electronic structures and transition in polyyne and all-trans polyacetylene using finite-temperature generalizations of ab initio spin-unrestricted Hartree–Fock (UHF) and spin-restricted coupled-cluster doubles (CCD) theories, extending upon previous work [He et al., J. Chem. Phys. 140, 024702 (2014)] that is based on spin-restricted Hartree–Fock (RHF) and second-order many-body perturbation (MP2) theories. Unlike RHF, UHF can predict SDW as well as CDW and metallic states, and unlike MP2, CCD does not diverge even if the underlying RHF reference wave function is metallic. UHF predicts a gapped SDW state with no dimerization at low temperatures, which gradually becomes metallic as the temperature is raised. CCD, meanwhile, confirms that electron correlation lowers the Peierls transition temperature. Furthermore, we show that the results from all theories for both polymers are subject to a unified interpretation in terms of the UHF solutions to the Hubbard–Peierls model using different values of the electron-electron interaction strength, U/t, in its Hamiltonian. The CCD wave function is shown to encompass the form of the exact solution of the Tomonaga–Luttinger model and is thus expected to describe accurately the electronic structure of Luttinger liquids.
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.
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
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.
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.
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.
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.
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.
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.
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....
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.
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.
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.
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.
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.
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...
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.
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.
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.
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...
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.
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.
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
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.
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
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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
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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.
Embedding germanium in graphene: A density functional theory study
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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.
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.
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
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.
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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.
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.
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.
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
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
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
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.
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
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.
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
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...
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.
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
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.
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.
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.
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.
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
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....
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.
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.
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.
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.
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).
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.
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
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.
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.
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
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.
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…
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...
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.
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.
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.
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.
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...
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).
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.
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.
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
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.
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.
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.
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.
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...
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.
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.
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.
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.
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.
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
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.
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.
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
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
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.
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.
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.
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.
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.
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...
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
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. ...
Fission properties of the Barcelona-Catania-Paris energy density functional
Energy Technology Data Exchange (ETDEWEB)
Robledo, L M [Dep. Fisica Teorica (Modulo 15), Universidad Autonoma de Madrid, E-28049 Madrid (Spain); 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, F-91406 Orsay (France); Vinas, X, E-mail: luis.robledo@uam.es [Departament d' Estructura i Constituents de la Materia and Institut de Ciencies del Cosmos, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)
2011-09-16
Fission properties of the Barcelona-Catania-Paris (BCP) energy density functional are explored by performing constrained mean field Hartree-Fock-Bogoliubov (HFB) calculations along the fission path. These calculations provide us with the quantities required to estimate the spontaneous fission half lives and fragment mass distribution. The results obtained are compared to experimental data and other calculations.
Analysis of the photophysical properties of zearalenone using density functional theory
The intrinsic photophysical properties of the resorcylic acid moiety of zearalenone offer a convenient label free method to determine zearalenone levels in contaminated agricultural products. Density functional theory and steady-state fluorescence methods were applied to investigate the role of stru...
Density functional theory study of the concerted pyrolysis mechanism for lignin models
Thomas Elder; Ariana Beste
2014-01-01
ABSTRACT: Studies on the pyrolysis mechanisms of lignin model compounds have largely focused on initial homolytic cleavage reactions. It has been noted, however, that concerted mechanisms may also account for observed product formation. In the current work, the latter processes are examined and compared to the former, by the application of density functional theory...
DEFF Research Database (Denmark)
Pennington, Robert S.
to analyze diffraction effects on the amplitude and the phase. There is relatively good comparison between image simulation and experimental data, but the experimental absorption parameter is found to differ between strongly and weakly diffracting conditions. Density functional theory simulations of the mean...
Some late-term thoughts of a density-functional theorist
Indian Academy of Sciences (India)
term thoughts of a density-functional theorist. Robert G Parr. Volume 117 Issue 5 September 2005 pp 613-615. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jcsc/117/05/0613-0615. Keywords.
Some late-term thoughts of a density-functional theorist
Indian Academy of Sciences (India)
term thoughts of a density-functional theorist. Robert G Parr. Erratum Volume 117 Issue 6 November 2005 pp 685-685. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jcsc/117/06/0685-0685 ...
Comparative study of patulin, ascladiol, and neopatulin by Density Functional Theory
Patulin, a secondary metabolite produced by several fungal species, is a potential contaminant of fruit and vegetable products. To better understand the structure and electronic properties of this mycotoxin and its biosynthetic precursors, a density functional theory (DFT) study was performed on co...
In this study density functional theory (DFT) was used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previously reported Brønsted–Evans–Polanyi (BEP) correlations for small open chain molecules are found to be inadequate in estimating the reaction...
Lourens, Aris; van Geer, F.C.
2016-01-01
In many fields of study, and certainly in hydrogeology, uncertainty propagation is a recurring subject. Usually, parametrized probability density functions (PDFs) are used to represent data uncertainty, which limits their use to particular distributions. Often, this problem is solved by Monte Carlo
Awuah, Joel B.; Dzade, N.Y.; Tia, Richard; Adei, Evans; Kwakye-Awuah, Bright; Catlow, C. Richard A.; de Leeuw, Nora H.
2016-01-01
We present density functional theory calculations of the adsorption of arsenic acid (AsO(OH)3) and arsenous acid (As(OH)3) on the Al(III)-modified natural zeolite clinoptilolite under anhydrous and hydrated conditions. From our calculated adsorption energies, we show that adsorption of both arsenic
Tapavicza, Enrico; Tavernelli, Ivano; Rothlisberger, Ursula; Filippi, Claudia; Casida, Mark E.
2008-01-01
We present a mixed time-dependent density-functional theory (TDDFT)/classical trajectory surface hopping (SH) study of the photochemical ring opening in oxirane. Previous preparatory work limited to the symmetric CC ring-opening pathways of oxirane concluded that the Tamm-Dancoff approximation (TDA)
Corrections to the density-functional theory electronic spectrum: Copper phthalocyanine
DEFF Research Database (Denmark)
Vazquez, Hector; Jelinek, P.; Brandbyge, Mads
2009-01-01
A method for improving the electronic spectrum of standard Density-Functional Theory (DFT) calculations (i.e., LDA or GGA approximations) is presented, and its application is discussed for the case of the copper phthalocyanine (CuPc) molecule. The method is based on a treatment of exchange...
Loco-regional differences in pulmonary function and density after partial rat lung irradiation
Wiegman, EM; Meertens, H; Konings, AWT; Kampinga, HH; Coppes, RP
2003-01-01
Purpose: 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. Methods: At first, CT scans were used to determine rat lung, volumes. The data obtained enabled the design of accurate
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.
Tao, Jianmin; Perdew, John P.; Almeida, Luís Miguel; Fiolhais, Carlos; Kümmel, Stephan
2008-06-01
Jellium, a simple model of metals, is a standard testing ground for density functionals both for bulk and for surface properties. Earlier tests show that the Tao-Perdew-Staroverov-Scuseria (TPSS) nonempirical metageneralized gradient approximation (meta-GGA) for the exchange-correlation energy yields more accurate surface energies than the local spin density (LSD) approximation for spin-unpolarized jellium. In this study, work functions and surface energies of a jellium metal in the presence of “internal” and external magnetic fields are calculated with LSD, Perdew-Burke-Ernzerhof (PBE) GGA, and TPSS meta-GGA and its predecessor, the nearly nonempirical Perdew-Kurth-Zupan-Blaha meta-GGA, using self-consistent LSD orbitals and densities. The results show that (i) For normal bulk densities, the surface correlation energy is the same in TPSS as in PBE, as it should be since TPSS strives to represent a self-correlation correction to PBE; (ii) Normal surface density profiles can be scaled uniformly to the low-density or strong-interaction limit, and TPSS provides an estimate for that limit that is consistent with (but probably more accurate than) other estimates; (iii) For both normal and low densities, TPSS provides the same description of surface magnetism as PBE, suggesting that these approximations may be generally equivalent for magnetism. The energies of jellium spheres with up to 106 electrons are calculated using density functionals and compared to those obtained with diffusion quantum Monte Carlo data, including our estimate for the fixed-node correction. Typically, while PBE energies are too low for spheres with more than about two electrons, LSD and TPSS are accurate there. We confirm that curvature energies are lower in PBE and TPSS than in LSD. Finally, we calculate the linear response of bulk jellium using these density functionals and find that not only LSD but also PBE GGA and TPSS meta-GGA yield a linear response in good agreement with that of the
Kanungo, Bikash
2016-01-01
We present a computationally efficient approach to perform large-scale all-electron density functional theory calculations by enriching the classical finite element basis with compactly supported atom-centered numerical basis functions that are constructed from the solution of the Kohn-Sham (KS) problem for single atoms. We term these numerical basis functions as enrichment functions, and the resultant basis as the enriched finite element basis. The enrichment functions are compactly supported through the use of smooth cutoff functions, which enhances the conditioning and maintains the locality of the basis. The integrals involved in the evaluation of the discrete KS Hamiltonian and overlap matrix in the enriched finite element basis are computed using an adaptive quadrature grid based on the characteristics of enrichment functions. Further, we propose an efficient scheme to invert the overlap matrix by using a block-wise matrix inversion in conjunction with special reduced-order quadrature rules to transform...
Energy Technology Data Exchange (ETDEWEB)
Schmidt, J; VandeVondele, J; Kuo, I W; Sebastiani, D; Siepmann, J I; Hutter, J; Mundy, C J
2009-03-06
We present herein a comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric-isothermal ensemble. Our results indicate that both PBE and BLYP functionals under predict the density and over structure the liquid. Adding the dispersion correction due to Grimme(1, 2) improves the predicted densities for both BLYP and PBE in a significant manner. Moreover, the addition of the dispersion correction for BLYP yields an oxygen-oxygen radial distribution function in excellent agreement with experiment. Thus, we conclude that one can obtain a very satisfactory model for water using BLYP and a correction for dispersion.
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.
Fukui and dual-descriptor matrices within the framework of spin-polarized density functional theory.
Alcoba, Diego R; Lain, Luis; Torre, Alicia; Oña, Ofelia B; Chamorro, Eduardo
2013-06-28
This work deals with the Fukui and dual reactivity descriptors within the framework of the spin-polarized density functional theory. The first and second derivatives of the electron density and the spin density with respect to the total number of electrons N = Nα + Nβ and with respect to the spin number NS = Nα-Nβ have been formulated by means of reduced density matrices in the representation of the spin-orbitals of a given basis set, providing the matrix extension of those descriptors. The analysis of the eigenvalues and eigenvectors of the Fukui and dual-descriptor matrices yields information on the role played by the molecular orbitals in charge-transfer and spin-polarization processes. This matrix formulation enables determining similarity indices which allows one to evaluate quantitatively the quality of the simple frontier molecular orbital model in conceptual density functional theory. Selected closed- and open-shell systems in different spin symmetries have been studied with this matrix formalism at several levels of electronic correlation. The results confirm the suitability of this approach.
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.
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).
Performance of density functionals for modeling vapor liquid equilibria of CO2 and SO2.
Goel, Himanshu; Windom, Zachary W; Jackson, Amber A; Rai, Neeraj
2017-11-21
Vapor liquid equilibria (VLE) and condensed phase properties of carbon dioxide and sulfur dioxide are calculated using first principles Monte Carlo (FPMC) simulations to assess the performance of several density functionals, notably PBE-D3, BLYP-D3, PBE0-D3, M062X-D3, and rVV10. GGA functionals were used to compute complete vapor liquid coexistence curves (VLCCs) to estimate critical properties, while the hybrid and nonlocal van der Waals functionals were used only for computing density at a single state point due to the high computational cost. Our results show that the BLYP-D3 functional performs well in predicting VLE properties for both molecules when compared with other functionals. In the liquid phase, pair correlation functions reveal that there is not a significant difference in the location of the peak for the first solvation shell while the peak heights are different for different functionals. Overall, the BLYP-D3 functional is a good choice for modeling VLE of acidic gases with significant environmental implications such as CO2 and SO2 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Su, Neil Qiang; Zhang, Igor Ying; Xu, Xin
2013-07-30
We present a theoretical development of the equations required to perform an analytic geometry optimization of a molecular system using the XYG3 type of doubly hybrid (xDH) functionals. In contrast to the well-established B2PLYP type of DH functionals, the energy expressions in the xDH functionals are constructed by using density and orbital information from another standard Kohn-Sham (KS) functional (e.g., B3LYP) for doing the self-consistent field calculations. Thus, the xDH functionals are nonvariational in both the hybrid density functional part and the second-order perturbation part, each of which requires formally to solve a coupled-perturbed KS equation. An implementation is reported here which combines the two parts by defining a total Lagrangian such that only a single set of the Z-vector equations need to be solved. The computational cost with our implementation is of the same order as those for the conventional Møller-Plesset theory to the second order (MP2) and B2PLYP. Systematic test calculations are provided for covalently bonded molecules as well as compounds involving the intramolecular nonbonded interactions for the main group elements. Satisfactory performance of the xDH functionals demonstrates that the extra computer time on top of the conventional KS procedure is well-invested, in particular, when the standard KS functionals and MP2 as well, are problematic. Copyright © 2013 Wiley Periodicals, Inc.
Artificial cognitive memory—changing from density driven to functionality driven
Shi, L. P.; Yi, K. J.; Ramanathan, K.; Zhao, R.; Ning, N.; Ding, D.; Chong, T. C.
2011-03-01
Increasing density based on bit size reduction is currently a main driving force for the development of data storage technologies. However, it is expected that all of the current available storage technologies might approach their physical limits in around 15 to 20 years due to miniaturization. To further advance the storage technologies, it is required to explore a new development trend that is different from density driven. One possible direction is to derive insights from biological counterparts. Unlike physical memories that have a single function of data storage, human memory is versatile. It contributes to functions of data storage, information processing, and most importantly, cognitive functions such as adaptation, learning, perception, knowledge generation, etc. In this paper, a brief review of current data storage technologies are presented, followed by discussions of future storage technology development trend. We expect that the driving force will evolve from density to functionality, and new memory modules associated with additional functions other than only data storage will appear. As an initial step toward building a future generation memory technology, we propose Artificial Cognitive Memory (ACM), a memory based intelligent system. We also present the characteristics of ACM, new technologies that can be used to develop ACM components such as bioinspired element cells (silicon, memristor, phase change, etc.), and possible methodologies to construct a biologically inspired hierarchical system.
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.
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....
Magnetic circular dichroism in real-time time-dependent density functional theory
Lee, K -M; Bertsch, G F
2010-01-01
We apply the adiabatic time-dependent density functional theory to magnetic ci the real-space, real-time computational method. The standard formulas for the MCD response and its A and B terms are derived from the observables in the time-dependent wave function. We find the real time method is well suited for calculating the overall spectrum, particularly at higher excitation energies where individual excited states are numerous and overlapping. The MCD sum rules are derived and interpreted in the real-time formalism; we find that they are very useful for normalization purposes and assessing the accuracy of the theory. The method is applied to MCD spectrum of C-60 using the adiabatic energy functional from the local density approximation. The theory correctly predicts the signs of the A and B terms for the lowest allowed excitations. However, the magnitudes of the terms only show qualitative agreement with experiment.
Developing density functional theory for Bose-Einstein condensates. The case of chemical bonding
Energy Technology Data Exchange (ETDEWEB)
Putz, Mihai V., E-mail: mvputz@cbg.uvt.ro [Laboratory of Physical and Computational Chemistry, Chemistry Department, West University of Timisoara, Str. Pestalozzi No. 16, 300115 Timisoara, Romania and Theoretical Physics Institute, Free University Berlin, Arnimallee 14, 14195 Berlin (Germany)
2015-01-22
Since the nowadays growing interest in Bose-Einstein condensates due to the expanded experimental evidence on various atomic systems within optical lattices in weak and strong coupling regimes, the connection with Density Functional Theory is firstly advanced within the mean field framework at three levels of comprehension: the many-body normalization condition, Thomas-Fermi limit, and the chemical hardness closure with the inter-bosonic strength and universal Hohenberg-Kohn functional. As an application the traditional Heitler-London quantum mechanical description of the chemical bonding for homopolar atomic systems is reloaded within the non-linear Schrödinger (Gross-Pitaevsky) Hamiltonian; the results show that a two-fold energetic solution is registered either for bonding and antibonding states, with the bosonic contribution being driven by the square of the order parameter for the Bose-Einstein condensate density in free (gas) motion, while the associate wave functions remain as in classical molecular orbital model.
Progress of cardioprotective effects of high density lipoprotein: function and mechanism
Directory of Open Access Journals (Sweden)
Hai-ge SUN
2015-01-01
Full Text Available The high density lipoprotein (HDL in human plasma is a heterogeneous lipoprotein consisting of roughly equal contents of lipid and protein in roughly equal content, and it consists of several subtypes. HDL possesses several well-documented functions, including anti-atherosclerosis by promoting reverse cholesterol transport, inhibiting the oxidative modification of low density lipoproteins (LDLs, inhibiting vascular inflammation, preventing thrombosis and apoptosis, and promoting endothelial repair. Recently, more cardiovascular protective functions of HDL have been found, mainly including the ability of suppressing immune inflammatory reaction, inhibiting the proliferation of hematopoietic stem cells, and regulating the plasma glucose level. It is of great importance to understand how different HDL subtypes contribute to the potentially cardioprotective functions. DOI: 10.11855/j.issn.0577-7402.2014.11.13
Is there a change in water proton density associated with functional magnetic resonance imaging?
Jochimsen, Thies H; Norris, David G; Möller, Harald E
2005-02-01
In a recent series of studies (see, for example, Stroman et al. Magn Reson Imag 2001; 19:827-831), an increase of water proton density has been suggested to correlate with neuronal activity. Owing to the significant implications of such a mechanism for other functional experiments, the functional signal changes in humans at very short echo times were re-examined by spin-echo EPI at 3 T. The results do not confirm the previous hypothesis of a significant increase in extravascular proton density at TE = 0. Instead, an alternative explanation of the effect is offered: The use of a low threshold to identify activated voxels may generate an artificial offset in functional contrast due to the inclusion of false-positives in the analysis.
The adsorption of NO, NH3, N2 on carbon surface: a density functional theory study.
Wang, Jiayong; Yang, Mo; Deng, Debing; Qiu, Shuxia
2017-08-11
To explore the adsorption mechanism of NO, NH3, N2 on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N2 physisorption, and N2 is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH3 physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface. Graphical abstract NH3, N2, NO adsortion on carbon surface.
Structure of solvent-free grafted nanoparticles: Molecular dynamics and density-functional theory
Chremos, Alexandros
2011-01-01
The structure of solvent-free oligomer-grafted nanoparticles has been investigated using molecular dynamics simulations and density-functional theory. At low temperatures and moderate to high oligomer lengths, the qualitative features of the core particle pair probability, structure factor, and the oligomer brush configuration obtained from the simulations can be explained by a density-functional theory that incorporates the configurational entropy of the space-filling oligomers. In particular, the structure factor at small wave numbers attains a value much smaller than the corresponding hard-sphere suspension, the first peak of the pair distribution function is enhanced due to entropic attractions among the particles, and the oligomer brush expands with decreasing particle volume fraction to fill the interstitial space. At higher temperatures, the simulations reveal effects that differ from the theory and are likely caused by steric repulsions of the expanded corona chains. © 2011 American Institute of Physics.
Farzanehpour, Mehdi; Tokatly, Ilya; Nano-Bio Spectroscopy Group; ETSF Scientific Development Centre Team
2015-03-01
We present a rigorous formulation of the time-dependent density functional theory for interacting lattice electrons strongly coupled to cavity photons. We start with an example of one particle on a Hubbard dimer coupled to a single photonic mode, which is equivalent to the single mode spin-boson model or the quantum Rabi model. For this system we prove that the electron-photon wave function is a unique functional of the electronic density and the expectation value of the photonic coordinate, provided the initial state and the density satisfy a set of well defined conditions. Then we generalize the formalism to many interacting electrons on a lattice coupled to multiple photonic modes and prove the general mapping theorem. We also show that for a system evolving from the ground state of a lattice Hamiltonian any density with a continuous second time derivative is locally v-representable. Spanish Ministry of Economy and Competitiveness (Grant No. FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13), COST Actions CM1204 (XLIC) and MP1306 (EUSpec).
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...
da Rocha, L; Redaelli, L R
2004-05-01
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 +/- 1 degree C; 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)
Cavallo, A; Cosenza, F; De Cesare, L
2008-05-01
We extend the formalism of the thermodynamic two-time Green's functions to nonextensive quantum statistical mechanics. Working in the optimal Lagrangian multiplier representation, the q -spectral properties and the methods for a direct calculation of the two-time q Green's functions and the related q -spectral density ( q measures the nonextensivity degree) for two generic operators are presented in strict analogy with the extensive (q=1) counterpart. Some emphasis is devoted to the nonextensive version of the less known spectral density method whose effectiveness in exploring equilibrium and transport properties of a wide variety of systems has been well established in conventional classical and quantum many-body physics. To check how both the equations of motion and the spectral density methods work to study the q -induced nonextensivity effects in nontrivial many-body problems, we focus on the equilibrium properties of a second-quantized model for a high-density Bose gas with strong attraction between particles for which exact results exist in extensive conditions. Remarkably, the contributions to several thermodynamic quantities of the q -induced nonextensivity close to the extensive regime are explicitly calculated in the low-temperature regime by overcoming the calculation of the q grand-partition function.
G-centers in irradiated silicon revisited: A screened hybrid density functional theory approach
Wang, H.
2014-05-13
Electronic structure calculations employing screened hybrid density functional theory are used to gain fundamental insight into the interaction of carbon interstitial (Ci) and substitutional (Cs) atoms forming the CiCs defect known as G-center in silicon (Si). The G-center is one of the most important radiation related defects in Czochralski grown Si. We systematically investigate the density of states and formation energy for different types of CiCs defects with respect to the Fermi energy for all possible charge states. Prevalence of the neutral state for the C-type defect is established.
DEFF Research Database (Denmark)
Gavnholt, Jeppe; Rubio, Angel; Olsen, Thomas
2009-01-01
Using time-evolution time-dependent density functional theory (TDDFT) within the adiabatic local-density approximation, we study the interactions between single electrons and molecular resonances at surfaces. Our system is a nitrogen molecule adsorbed on a ruthenium surface. The surface is modeled...... at two levels of approximation, first as a simple external potential and later as a 20-atom cluster. We perform a number of calculations on an electron hitting the adsorbed molecule from inside the surface and establish a picture, where the resonance is being probed by the hot electron. This enables us...
Current-density-functional approach to large quantum dots in intense magnetic fields
Pi, M.; Barranco, M.; Emperador, A.; Lipparini, E.; Serra, Ll.
1998-06-01
Within current-density-functional theory, we have studied a quantum dot made of 210 electrons confined in a disk geometry. The ground state of this large dot exhibits some features as a function of the magnetic field (B) that can be attributed in a clear way to the formation of compressible and incompressible states of the system. The orbital and spin angular momenta, the total energy, ionization and electron chemical potentials of the ground state, as well as the frequencies of far-infrared edge modes are calculated as a function of B, and compared with available experimental and theoretical results.
Using zero-norm constraint for sparse probability density function estimation
Hong, X.; Chen, S.; Harris, C. J.
2012-11-01
A new sparse kernel probability density function (pdf) estimator based on zero-norm constraint is constructed using the classical Parzen window (PW) estimate as the target function. The so-called zero-norm of the parameters is used in order to achieve enhanced model sparsity, and it is suggested to minimize an approximate function of the zero-norm. It is shown that under certain condition, the kernel weights of the proposed pdf estimator based on the zero-norm approximation can be updated using the multiplicative nonnegative quadratic programming algorithm. Numerical examples are employed to demonstrate the efficacy of the proposed approach.
Probability density and scaling exponents of longitudinal structure functions in strong turbulence
Yakhot, V
1997-01-01
The advective terms in the Navier-Stokes and Burgers equations are similar. It is proposed that the longitudinal structure functions $S_{n}(r)$ in homogeneous and isotropic three- dimensional turbulence are goverened by a one-dimensional equation of motion, resembling the 1D-Burgers equation, with the strongly non-local pressure contributions accounted for by galilean-invariance-breaking terms. The resulting equations give both scaling exponents and amplitudes of the structure functions in an excellent agreement with experimental data. The derived probability density function $P(\\Delta u,r)\
VV and VO2 defects in silicon studied with hybrid density functional theory
Christopoulos, Stavros Richard G
2014-12-07
The formation of VO (A-center), VV and VO2 defects in irradiated Czochralski-grown silicon (Si) is of technological importance. Recent theoretical studies have examined the formation and charge states of the A-center in detail. Here we use density functional theory employing hybrid functionals to analyze the formation of VV and VO2 defects. The formation energy as a function of the Fermi energy is calculated for all possible charge states. For the VV and VO2 defects double negatively charged and neutral states dominate, respectively.
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...
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.
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.
Weng, Meng-Hsiung; Ju, Shin-Pon; Chen, Hsin-Tsung; Chen, Hui-Lung; Lu, Jian-Ming; Lin, Ken-Huang; Lin, Jenn-Sen; Hsieh, Jin-Yuan; Yang, Hsi-Wen
2013-02-01
The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk.
Density functional study of AgScO_2: Electronic and optical properties
Bhamu, K. C.; Sahariya, Jagrati; Vyas, Rishi; Priolkar, K. R.
2017-07-01
This paper focusses on the electronic and optical properties of scandium-based silver delafossite (AgScO_2) semiconductor. The density functional theory (DFT) in the framework of full potential linearized augmented plane wave (FP-LAPW) scheme has been used for the present calculations with local density approximation (LDA) and generalized gradient approximation (GGA). Electronic properties deal with energy bands and density of states (DOSs), while optical properties describe refractive index and absorption coefficient. The energy bands are interpreted in terms of DOSs. The computed value of band gap is in agreement with that reported in the literature. Our results predict AgScO_2 as indirect band-gap semiconductor. Our calculated value of the refractive index in zero frequency limits is 2.42. The absorption coefficient predicts the applicability of AgScO_2 in solar cells and flat panel liquid crystal display as a transparent top window layer.
Haataja, Mikko; Gránásy, László; Löwen, Hartmut
2010-08-01
Herein we provide a brief summary of the background, events and results/outcome of the CECAM workshop 'Classical density functional theory methods in soft and hard matter held in Lausanne between October 21 and October 23 2009, which brought together two largely separately working communities, both of whom employ classical density functional techniques: the soft-matter community and the theoretical materials science community with interests in phase transformations and evolving microstructures in engineering materials. After outlining the motivation for the workshop, we first provide a brief overview of the articles submitted by the invited speakers for this special issue of Journal of Physics: Condensed Matter, followed by a collection of outstanding problems identified and discussed during the workshop. 1. Introduction Classical density functional theory (DFT) is a theoretical framework, which has been extensively employed in the past to study inhomogeneous complex fluids (CF) [1-4] and freezing transitions for simple fluids, amongst other things. Furthermore, classical DFT has been extended to include dynamics of the density field, thereby opening a new avenue to study phase transformation kinetics in colloidal systems via dynamical DFT (DDFT) [5]. While DDFT is highly accurate, the computations are numerically rather demanding, and cannot easily access the mesoscopic temporal and spatial scales where diffusional instabilities lead to complex solidification morphologies. Adaptation of more efficient numerical methods would extend the domain of DDFT towards this regime of particular interest to materials scientists. In recent years, DFT has re-emerged in the form of the so-called 'phase-field crystal' (PFC) method for solid-state systems [6, 7], and it has been successfully employed to study a broad variety of interesting materials phenomena in both atomic and colloidal systems, including elastic and plastic deformations, grain growth, thin film growth, solid
Interactions between copper and transition metal dichalcogenides: A density functional theory study
Helfrecht, Benjamin A.; Guzman, David M.; Onofrio, Nicolas; Strachan, Alejandro H.
2017-08-01
We characterized the interface between fcc Cu and various single-layer transition metal dichalcogenides (TMDs) using density functional theory calculations. We found that monolayer Mo, W, Nb, Ti, and V disulfides, diselenides, and ditellurides are stable on Cu(111) with binding energies higher than those of h -BN and graphene. An analysis of the electronic structure of the interfaces indicates partial covalent bonding and a complex redistribution of electronic density, consisting of electron accumulation in the gap region, depletion near the Cu and TMD surfaces, and charge density oscillations within both materials. The resulting net electric dipoles significantly alter the electron work function of the Cu surface. Interestingly, capping Cu(111) surfaces with group-IV and -V TMDs leads to an increase in the work function of up to 1 eV, while group-VI TMDs can decrease the work function by up to 1 eV. Finally, the complex charge distributions at the Cu/TMD interfaces include opposing dipoles and explain the fact that net dipoles associated with Cu/TMD interfaces are comparable to or smaller than those of Cu/graphene and Cu/h -BN, even though the Cu/TMD binding energies are significantly higher.
Chen, Chien-Chang; Juan, Hung-Hui; Tsai, Meng-Yuan; Lu, Henry Horng-Shing
2018-01-11
By introducing the methods of machine learning into the density functional theory, we made a detour for the construction of the most probable density function, which can be estimated by learning relevant features from the system of interest. Using the properties of universal functional, the vital core of density functional theory, the most probable cluster numbers and the corresponding cluster boundaries in a studying system can be simultaneously and automatically determined and the plausibility is erected on the Hohenberg-Kohn theorems. For the method validation and pragmatic applications, interdisciplinary problems from physical to biological systems were enumerated. The amalgamation of uncharged atomic clusters validated the unsupervised searching process of the cluster numbers and the corresponding cluster boundaries were exhibited likewise. High accurate clustering results of the Fisher's iris dataset showed the feasibility and the flexibility of the proposed scheme. Brain tumor detections from low-dimensional magnetic resonance imaging datasets and segmentations of high-dimensional neural network imageries in the Brainbow system were also used to inspect the method practicality. The experimental results exhibit the successful connection between the physical theory and the machine learning methods and will benefit the clinical diagnoses.
DEFF Research Database (Denmark)
Hammer, Bjørk; Hansen, Lars Bruno; Nørskov, Jens Kehlet
1999-01-01
A simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE) [Phys. Rev. Lett. 77, 3865 (1996)]. Subsequently Zhang and Yang [Phys. Rev. Lett. 80, 890 (1998)] have shown that a slight...... revision of the PBE functional systematically improves the atomization energies for a large database of small molecules. In the present work, we show that the Zhang and Yang functional (revPBE) also improves the chemisorption energetics of atoms and molecules on transition-metal surfaces. Our test systems...
Energy Technology Data Exchange (ETDEWEB)
Holthaus, Svea große; Köppen, Susan, E-mail: koeppen@hmi.uni-bremen.de; Frauenheim, Thomas; Ciacchi, Lucio Colombi [Bremen Centre for Computational Materials Science, University of Bremen, 28359 Bremen (Germany)
2014-06-21
We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.
Sander, Tobias; Kresse, Georg
2017-02-01
Linear optical properties can be calculated by solving the time-dependent density functional theory equations. Linearization of the equation of motion around the ground state orbitals results in the so-called Casida equation, which is formally very similar to the Bethe-Salpeter equation. Alternatively one can determine the spectral functions by applying an infinitely short electric field in time and then following the evolution of the electron orbitals and the evolution of the dipole moments. The long wavelength response function is then given by the Fourier transformation of the evolution of the dipole moments in time. In this work, we compare the results and performance of these two approaches for the projector augmented wave method. To allow for large time steps and still rely on a simple difference scheme to solve the differential equation, we correct for the errors in the frequency domain, using a simple analytic equation. In general, we find that both approaches yield virtually indistinguishable results. For standard density functionals, the time evolution approach is, with respect to the computational performance, clearly superior compared to the solution of the Casida equation. However, for functionals including nonlocal exchange, the direct solution of the Casida equation is usually much more efficient, even though it scales less beneficial with the system size. We relate this to the large computational prefactors in evaluating the nonlocal exchange, which renders the time evolution algorithm fairly inefficient.
Water monomer interaction with gold nanoclusters from van der Waals density functional theory.
Xue, Yongqiang
2012-01-14
We investigate the interaction between water molecules and gold nanoclusters Au(n) through a systematic density functional theory study within both the generalized gradient approximation and the nonlocal van der Waals (vdW) density functional theory. Both planar (n = 6-12) and three-dimensional (3D) clusters (n = 17-20) are studied. We find that applying vdW density functional theory leads to an increase in the Au-Au bond length and a decrease in the cohesive energy for all clusters studied. We classify water adsorption on nanoclusters according to the corner, edge, and surface adsorption geometries. In both corner and edge adsorptions, water molecule approaches the cluster through the O atom. For planar clusters, surface adsorption occurs in a O-up/H-down geometry with water plane oriented nearly perpendicular to the cluster. For 3D clusters, water instead favors a near-flat surface adsorption geometry with the water O atom sitting nearly atop a surface Au atom, in agreement with previous study on bulk surfaces. Including vdW interaction increases the adsorption energy for the weak surface adsorption but reduces the adsorption energy for the strong corner adsorption due to increased water-cluster bond length. By analyzing the adsorption induced charge rearrangement through Bader's charge partitioning and electron density difference and the orbital interaction through the projected density of states, we conclude that the bonding between water and gold nanocluster is determined by an interplay between electrostatic interaction and covalent interaction involving both the water lone-pair and in-plane orbitals and the gold 5d and 6s orbitals. Including vdW interaction does not change qualitatively the physical picture but does change quantitatively the adsorption structure due to the fluxionality of gold nanoclusters.
Petascale Orbital-Free Density Functional Theory Enabled by Small-Box Algorithms.
Chen, Mohan; Jiang, Xiang-Wei; Zhuang, Houlong; Wang, Lin-Wang; Carter, Emily A
2016-06-14
Orbital-free density functional theory (OFDFT) is a quantum-mechanics-based method that utilizes electron density as its sole variable. The main computational cost in OFDFT is the ubiquitous use of the fast Fourier transform (FFT), which is mainly adopted to evaluate the kinetic energy density functional (KEDF) and electron-electron Coulomb interaction terms. We design and implement a small-box FFT (SBFFT) algorithm to overcome the parallelization limitations of conventional FFT algorithms. We also propose real-space truncation of the nonlocal Wang-Teter KEDF kernel. The scalability of the SBFFT is demonstrated by efficiently simulating one full optimization step (electron density, energies, forces, and stresses) of 1,024,000 lithium (Li) atoms on up to 65,536 cores. We perform other tests using Li as a test material, including calculations of physical properties of different phases of bulk Li, geometry optimizations of nanocrystalline Li, and molecular dynamics simulations of liquid Li. All of the tests yield excellent agreement with the original OFDFT results, suggesting that the OFDFT-SBFFT algorithm opens the door to efficient first-principles simulations of materials containing millions of atoms.
Density functional theory of gas-liquid phase separation in dilute binary mixtures.
Okamoto, Ryuichi; Onuki, Akira
2016-06-22
We examine statics and dynamics of phase-separated states of dilute binary mixtures using density functional theory. In our systems, the difference of the solvation chemical potential between liquid and gas [Formula: see text] (the Gibbs energy of transfer) is considerably larger than the thermal energy [Formula: see text] for each solute particle and the attractive interaction among the solute particles is weaker than that among the solvent particles. In these conditions, the saturated vapor pressure increases by [Formula: see text], where [Formula: see text] is the solute density added in liquid. For [Formula: see text], phase separation is induced at low solute densities in liquid and the new phase remains in gaseous states, even when the liquid pressure is outside the coexistence curve of the solvent. This explains the widely observed formation of stable nanobubbles in ambient water with a dissolved gas. We calculate the density and stress profiles across planar and spherical interfaces, where the surface tension decreases with increasing interfacial solute adsorption. We realize stable solute-rich bubbles with radius about 30 nm, which minimize the free energy functional. We then study dynamics around such a bubble after a decompression of the surrounding liquid, where the bubble undergoes a damped oscillation. In addition, we present some exact and approximate expressions for the surface tension and the interfacial stress tensor.
Measuring response saturation in human MT and MST as a function of motion density.
Durant, Szonya; Furlan, Michele
2014-07-24
The human brain areas MT and MST have been studied in great detail using fMRI with regards to their motion processing properties; however, to what extent this corresponds with single cell recordings remains to be fully described. Average response over human MT+ has been shown to increase linearly with motion coherence, similar to single cell responses. In response to motion density some single cell data however suggest a rapid saturation. We ask how the combination of these responses is reflected in the population response. We measured the blood oxygen level dependent (BOLD) response function of MT and MST using a motion density signal, comparing with area V1. We used spatially fixed apertures containing motion stimuli to manipulate the area covered by motion. We found that MT and MST responded above baseline to a very minimal amount of motion and showed a rather flat response to motion density, indicative of saturation. We discuss how this may be related to the size of the receptive fields and inhibitory interactions, although necessarily residual attention effects also need to be considered. We then compared different types of motion and found no difference between coherent and random motion at any motion density, suggesting that when combining response over several motion stimuli covering the visual field, a linear relationship of MT and MST population response as a function of motion coherence might not hold. © 2014 ARVO.
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.
CO2 adsorption on the copper surfaces: van der Waals density functional and TPD studies
Muttaqien, Fahdzi; Hamamoto, Yuji; Hamada, Ikutaro; Inagaki, Kouji; Shiozawa, Yuichiro; Mukai, Kozo; Koitaya, Takanori; Yoshimoto, Shinya; Yoshinobu, Jun; Morikawa, Yoshitada
2017-09-01
We investigated the adsorption of CO2 on the flat, stepped, and kinked copper surfaces from density functional theory calculations as well as the temperature programmed desorption and X-ray photoelectron spectroscopy. Several exchange-correlation functionals have been considered to characterize CO2 adsorption on the copper surfaces. We used the van der Waals density functionals (vdW-DFs), i.e., the original vdW-DF (vdW-DF1), optB86b-vdW, and rev-vdW-DF2, as well as the Perdew-Burke-Ernzerhof (PBE) with dispersion correction (PBE-D2). We have found that vdW-DF1 and rev-vdW-DF2 functionals slightly underestimate the adsorption energy, while PBE-D2 and optB86b-vdW functionals give better agreement with the experimental estimation for CO2 on Cu(111). The calculated CO2 adsorption energies on the flat, stepped, and kinked Cu surfaces are 20-27 kJ/mol, which are compatible with the general notion of physisorbed species on solid surfaces. Our results provide a useful insight into appropriate vdW functionals for further investigation of related CO2 activation on Cu surfaces such as methanol synthesis and higher alcohol production.
Maslennikova, Yu. S.; Nugmanov, I. S.
2016-08-01
The problem of probability density function estimation for a random process is one of the most common in practice. There are several methods to solve this problem. Presented laboratory work uses methods of the mathematical statistics to detect patterns in the realization of random process. On the basis of ergodic theory, we construct algorithm for estimating univariate probability density distribution function for a random process. Correlational analysis of realizations is applied to estimate the necessary size of the sample and the time of observation. Hypothesis testing for two probability distributions (normal and Cauchy) is used on the experimental data, using χ2 criterion. To facilitate understanding and clarity of the problem solved, we use ELVIS II platform and LabVIEW software package that allows us to make the necessary calculations, display results of the experiment and, most importantly, to control the experiment. At the same time students are introduced to a LabVIEW software package and its capabilities.
Guidez, Emilie B; Gordon, Mark S
2015-03-12
The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.
Tempel, David G; Aspuru-Guzik, Alán
2012-01-01
We prove that the theorems of TDDFT can be extended to a class of qubit Hamiltonians that are universal for quantum computation. The theorems of TDDFT applied to universal Hamiltonians imply that single-qubit expectation values can be used as the basic variables in quantum computation and information theory, rather than wavefunctions. From a practical standpoint this opens the possibility of approximating observables of interest in quantum computations directly in terms of single-qubit quantities (i.e. as density functionals). Additionally, we also demonstrate that TDDFT provides an exact prescription for simulating universal Hamiltonians with other universal Hamiltonians that have different, and possibly easier-to-realize two-qubit interactions. This establishes the foundations of TDDFT for quantum computation and opens the possibility of developing density functionals for use in quantum algorithms.
Lagrangian filtered density function for LES-based stochastic modelling of turbulent dispersed flows
Innocenti, A; Chibbaro, S
2016-01-01
The Eulerian-Lagrangian approach based on Large-Eddy Simulation (LES) is one of the most promising and viable numerical tools to study turbulent dispersed flows when the computational cost of Direct Numerical Simulation (DNS) becomes too expensive. The applicability of this approach is however limited if the effects of the Sub-Grid Scales (SGS) of the flow on particle dynamics are neglected. In this paper, we propose to take these effects into account by means of a Lagrangian stochastic SGS model for the equations of particle motion. The model extends to particle-laden flows the velocity-filtered density function method originally developed for reactive flows. The underlying filtered density function is simulated through a Lagrangian Monte Carlo procedure that solves for a set of Stochastic Differential Equations (SDEs) along individual particle trajectories. The resulting model is tested for the reference case of turbulent channel flow, using a hybrid algorithm in which the fluid velocity field is provided b...
Wesolowski, Tomasz A
2013-01-01
This is a comprehensive overview of state-of-the-art computational methods based on orbital-free formulation of density functional theory completed by the most recent developments concerning the exact properties, approximations, and interpretations of the relevant quantities in density functional theory. The book is a compilation of contributions stemming from a series of workshops which had been taking place since 2002. It not only chronicles many of the latest developments but also summarises some of the more significant ones. The chapters are mainly reviews of sub-domains but also include original research. Readership: Graduate students, academics and researchers in computational chemistry. Atomic & molecular physicists, theoretical physicists, theoretical chemists, physical chemists and chemical physicists.
Conjugate-gradient optimization method for orbital-free density functional calculations.
Jiang, Hong; Yang, Weitao
2004-08-01
Orbital-free density functional theory as an extension of traditional Thomas-Fermi theory has attracted a lot of interest in the past decade because of developments in both more accurate kinetic energy functionals and highly efficient numerical methodology. In this paper, we developed a conjugate-gradient method for the numerical solution of spin-dependent extended Thomas-Fermi equation by incorporating techniques previously used in Kohn-Sham calculations. The key ingredient of the method is an approximate line-search scheme and a collective treatment of two spin densities in the case of spin-dependent extended Thomas-Fermi problem. Test calculations for a quartic two-dimensional quantum dot system and a three-dimensional sodium cluster Na216 with a local pseudopotential demonstrate that the method is accurate and efficient. (c) 2004 American Institute of Physics.
DEFF Research Database (Denmark)
Leth, Rasmus; Rydberg, Patrik; Jørgensen, Flemming Steen
2015-01-01
Many drug compounds are oxidized by cytochrome P450 (CYP) enzymes to form reactive metabolites. This study presents density functional theory calculations of the CYP-mediated metabolism of acetaminophen and a series of related compounds that can form reactive metabolites by hydrogen abstraction. ...... as an in silico method in the design of new compounds with improved metabolic stability.......Many drug compounds are oxidized by cytochrome P450 (CYP) enzymes to form reactive metabolites. This study presents density functional theory calculations of the CYP-mediated metabolism of acetaminophen and a series of related compounds that can form reactive metabolites by hydrogen abstraction...... the porphyrin model to determine the activation energies. We have used this correlation on monosubstituted phenols to rationalize the effect of the various substituents in the drug compounds. In addition to facilitating a chemical interpretation, the approach is sufficiently fast and reliable to be used...
A density functional theory study of the benzene-water complex.
Li, Shen; Cooper, Valentino R; Thonhauser, T; Puzder, Aaron; Langreth, David C
2008-09-25
The intermolecular interaction of the benzene-water complex is calculated using real-space pseudopotential density functional theory utilizing a van der Waals density functional. Our results for the intermolecular potential energy surface clearly show a stable configuration with the water molecule standing above or below the benzene with one or both of the H atoms pointing toward the benzene plane, as predicted by previous studies. However, when the water molecule is pulled outside the perimeter of the ring, the configuration of the complex becomes unstable, with the water molecule attaching in a saddle point configuration to the rim of the benzene with its O atom adjacent to a benzene H. We find that this structural change is connected to a change in interaction from H (water)/pi cloud (benzene) to O (water)/H (benzene). We compare our results for the ground-state structure with results from experiments and quantum-chemical calculations.
A comparison of different methods to implement higher order derivatives of density functionals
Energy Technology Data Exchange (ETDEWEB)
van Dam, Hubertus J.J. [Brookhaven National Lab. (BNL), Upton, NY (United States)
2016-05-18
Density functional theory is the dominant approach in electronic structure methods today. To calculate properties higher order derivatives of the density functionals are required. These derivatives might be implemented manually,by automatic differentiation, or by symbolic algebra programs. Different authors have cited different reasons for using the particular method of their choice. This paper presents work where all three approaches were used and the strengths and weaknesses of each approach are considered. It is found that all three methods produce code that is suffficiently performanted for practical applications, despite the fact that our symbolic algebra generated code and our automatic differentiation code still have scope for significant optimization. The automatic differentiation approach is the best option for producing readable and maintainable code.
Study of Parton Density Function Uncertainties with LHAPDF and PYTHIA at LHC
Bourilkov, D
2003-01-01
The experimental errors in current and future hadron colliders are expected to decrease to a level that will challenge the uncertainties in the theoretical calculations. One important component in the prediction uncertainties comes from the Parton Density Functions of the (anti)proton. In this work we develop an interface from the Les Houches Accord Parton Density Functions (LHAPDF) package to the very popular Monte Carlo generator {\\tt PYTHIA} version 6.2. Then we proceed to estimate the PDF uncertainties for the production of Drell-Yan pairs from the Z pole to masses above 1 $\\TeV$ and for Higgs bosons at LHC. The measurement of the electro-weak mixing angle at LHC as a particularly difficult case is studied.
Janesko, Benjamin G.; Proynov, Emil
2017-02-01
Density functional approximations (DFAs) often suffer from self-repulsion and delocalization errors which are reduced by exact (Hartree-Fock-like) exchange admixture. Oyeyemi and co-workers recently showed that several DFAs with little exact exchange incorrectly predict bent alkynyl radical geometries, giving errors in ab initio composite methods using density functional theory geometries [V. B. Oyeyemi et al., J. Phys. Chem. Lett. 3, 289 (2012)]. We show that the simple Hartree-Fock-Slater and Xα DFAs, which have substantial delocalization error, predict linear alkynyl radical geometries without incorporating exact exchange. Our Rung 3.5 DFAs, and rescaled generalized gradient approximations, can give either linear σ, bent σ -π , or nearly linear π radicals, all without incorporating exact exchange. This highlights the complexity of delocalization error, the utility of accurate empirical DFA geometries for ab initio composite methods, and the insights to be gained from Rung 3.5 DFAs.
National Research Council Canada - National Science Library
deGoma, Emil M; deGoma, Rolando L; Rader, Daniel J
2008-01-01
A number of therapeutic strategies targeting high-density lipoprotein (HDL) cholesterol and reverse cholesterol transport are being developed to halt the progression of atherosclerosis or even induce regression...
Density functional investigations of the properties and thermochemistry of UFn and UCln (n=1,...,6).
Batista, Enrique R; Martin, Richard L; Hay, P Jeffrey
2004-12-08
The structural properties and thermochemistry of the UF(n) and UCl(n) (n=1,...,6) molecules have been investigated using hybrid density functional theory and a small-core (60 electrons) relativistic effective core potential for the uranium atom. For the first time Bond dissociation energies for this whole series are computed and shown to be in good agreement with experiment. The geometry and electronic structure of each molecule was characterized. (c) 2004 American Institute of Physics.
No relationship between low-density lipoproteins and endothelial function in hemodialysis patients.
Dalton, Brad S; Fassett, Rob G; Geraghty, Dominic P; De Ryke, Rex; Coombes, Jeff S
2005-03-18
Relationships between low-density lipoprotein cholesterol and endothelial function in hemodialysis patients have yet to be investigated. Furthermore, current reporting of endothelial function data using flow-mediated dilatation has recognised limitations. The aims of the study were to determine the relationship between low-density lipoproteins and endothelial function in hemodialysis patients and to investigate the validity of determining the area under the curve for data collected during the flow-mediated dilatation technique. Brachial artery responses to reactive hyperemia (endothelial-dependent) and glyceryl trinitrate (endothelial-independent) were assessed in 19 hemodialysis patients using high-resolution ultrasound. Lipid profiles and other factors known to effect brachial artery reactivity were also measured prior to the flow-mediated dilatation technique. There were no significant relationships between serum low-density lipoproteins and endothelial-dependent or -independent vasodilation using absolute change (mm), relative change (%), time to peak change (s) or area under the curve (mm x s). In hemodialysis patients with atherosclerosis, area under the curve analysis showed a significantly (p<0.05) decreased endothelial-dependent response (mean+/-S.D.: 19.2+/-17.4) compared to non-atherosclerotic patients (42.3+/-28.6). However, when analysing these data using absolute change, relative change or time to peak dilatation, there were no significant differences between the two groups. In summary, there was no relationship between low-density lipoproteins and endothelial function in hemodialysis patients. In addition, area under the curve analysis of flow-mediated vasodilatation data may be a useful method of determining the temporal vascular response during the procedure.
DEFF Research Database (Denmark)
Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens
2006-01-01
Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported......, and it is argued how these processes may lead to different nanofiber structures. The proposed growth model is found to be in good agreement with previous findings....
Yedukondalu, N.; Vaitheeswaran, G.
2014-01-01
Silver fulminate (AgCNO) is a primary explosive, which exists in two polymorphic phases namely orthorhombic (\\emph{Cmcm}) and trigonal (\\emph{R$\\bar{3}$}) 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...
Time-dependent density-functional theory in the projector augmented-wave method
DEFF Research Database (Denmark)
Walter, Michael; Häkkinen, Hannu; Lehtovaara, Lauri
2008-01-01
We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we...... surfaces for a set of atoms and molecules with the linear-response method and by calculating nonlinear emission spectra using the time-propagation method....
Optical properties of Al nanostructures from time dependent density functional theory
Mokkath, Junais Habeeb
2016-04-05
The optical properties of Al nanostructures are investigated by means of time dependent density functional theory, considering chains of varying length and ladders/stripes of varying aspect ratio. The absorption spectra show redshifting for increasing length and aspect ratio. For the chains the absorption is dominated by HOMO → LUMO transitions, whereas ladders and stripes reveal more complex spectra of plasmonic nature above a specific aspect ratio.
Calculating joint confidence bands for impulse response functions using highest density regions
Lütkepohl, Helmut; Staszewska-Bystrova, Anna; Winker, Peter
2016-01-01
This paper proposes a new non-parametric method of constructing joint confidence bands for impulse response functions of vector autoregressive models. The estimation uncertainty is captured by means of bootstrapping and the highest density region (HDR) approach is used to construct the bands. A Monte Carlo comparison of the HDR bands with existing alternatives shows that the former are competitive with the bootstrap-based Bonferroni and Wald confidence regions. The relative tightness of the H...
Calculating Joint Bands for Impulse Response Functions using Highest Density Regions
Winker, Peter; Lütkepohl, Helmut; Staszewska-Bystrova, Anna
2016-01-01
This paper proposes a new non-parametric method of constructing joint confidence bands for impulse response functions of vector autoregressive models. The estimation uncertainty is captured by means of bootstrapping and the highest density region (HDR) approach is used to construct the bands. A Monte Carlo comparison of the HDR bands with existing alternatives shows that the former are competitive with the bootstrap-based Bonferroni and Wald confidence regions. The relative tightness of the H...
Mo, Yirong; Bao, Peng; Gao, Jiali
2011-01-01
An interaction energy decomposition analysis method based on the block-localized wavefunction (BLW-ED) approach is described. The first main feature of the BLW-ED method is that it combines concepts of valence bond and molecular orbital theories such that the intermediate and physically intuitive electron-localized states are variationally optimized by self-consistent field calculations. Furthermore, the block-localization scheme can be used both in wave function theory and in density functio...
Octupole deformation properties of the Barcelona-Catania-Paris energy density functionals
Robledo, L. M.; Baldo, M.; Schuck, P.; Viñas, X.
2010-01-01
We discuss the octupole deformation properties of the recently proposed Barcelona-Catania-Paris (BCP) energy density functionals for two sets of isotopes, those of radium and barium, where it is believed that octupole deformation plays a role in the description of the ground state. The analysis is carried out in the mean field framework (Hartree- Fock- Bogoliubov approximation) by using the axially symmetric octupole moment as a constraint. The main ingredients entering the octupole collectiv...
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 used in quantum dots. Defects including monovacancies, interstitials, Schottky and Frenkel type defects were considered. We found that monovacancies and Schottky defects are more favorable as indicate...
Cristofaro, S.; Friedl, R.; Fantz, U.
2017-08-01
Negative hydrogen ion sources rely on the surface conversion of neutral atomic hydrogen and positive hydrogen ions to H-. The efficiency of this process depends on the actual work function of the converter surface. By introducing caesium into the source the work function decreases, enhancing the negative ion yield. In order to study the impact of the work function on the H- surface production at similar conditions to the ones in ion sources for fusion devices like ITER and DEMO, fundamental investigations are performed in a flexible laboratory experiment. The work function of the converter surface can be absolutely measured by photoelectric effect, while a newly installed cavity ring-down spectroscopy system (CRDS) measures the H- density. The CRDS is firstly tested and characterized by investigations on H- volume production. Caesiation of a stainless steel sample is then performed in vacuum and the plasma effect on the Cs layer is investigated also for long plasma-on times. A minimum work function of (1.9±0.1) eV is reached after some minutes of plasma treatment, resulting in a reduction by a value of 0.8 eV compared to vacuum measurements. The H- density above the surface is (2.1±0.5)×1015 m-3. With further plasma exposure of the caesiated surface, the work function increases up to 3.75 eV, due to the impinging plasma particles which gradually remove the Cs layer. As a result, the H- density decreases by a factor of at least 2.
Energy Technology Data Exchange (ETDEWEB)
Betzinger, Markus
2011-12-14
In this thesis, we extended the applicability of the full-potential linearized augmented-plane-wave (FLAPW) method, one of the most precise, versatile and generally applicable electronic structure methods for solids working within the framework of density-functional theory (DFT), to orbital-dependent functionals for the exchange-correlation (xc) energy. Two different schemes that deal with orbital-dependent functionals, the Kohn-Sham (KS) and the generalized Kohn-Sham (gKS) formalism, have been realized. Hybrid functionals, combining some amount of the orbital-dependent exact exchange energy with local or semi-local functionals of the density, are implemented within the gKS scheme. We work in particular with the PBE0 hybrid of Perdew, Burke, and Ernzerhof. Our implementation relies on a representation of the non-local exact exchange potential - its calculation constitutes the most time consuming step in a practical calculation - by an auxiliary mixed product basis (MPB). In this way, the matrix elements of the Hamiltonian corresponding to the non-local potential become a Brillouin-zone (BZ) sum over vector-matrix-vector products. Several techniques are developed and explored to further accelerate our numerical scheme. We show PBE0 results for a variety of semiconductors and insulators. In comparison with experiment, the PBE0 functional leads to improved band gaps and an improved description of localized states. Even for the ferromagnetic semiconductor EuO with localized 4f electrons, the electronic and magnetic properties are correctly described by the PBE0 functional. Subsequently, we discuss the construction of the local, multiplicative exact exchange (EXX) potential from the non-local, orbital-dependent exact exchange energy. For this purpose we employ the optimized effective potential (OEP) method. Central ingredients of the OEP equation are the KS wave-function response and the single-particle density response function. We show that a balance between the LAPW
Sundararaman, Ravishankar; Goddard, William A.; Arias, Tomas A.
2017-03-01
First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Finally, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.
On the Analysis of the Discretized Kohn-Sham Density Functional Theory
Liu, Xin; Wang, Xiao; Ulbrich, Michael; Yuan, Yaxiang
2014-01-01
In this paper, we study a few theoretical issues in the discretized Kohn-Sham (KS) density functional theory (DFT). The equivalence between either a local or global minimizer of the KS total energy minimization problem and the solution to the KS equation is established under certain assumptions. The nonzero charge densities of a strong local minimizer are shown to be bounded below by a positive constant uniformly. We analyze the self-consistent field (SCF) iteration by formulating the KS equation as a fixed point map with respect to the potential. The Jacobian of these fixed point maps is derived explicitly. Both global and local convergence of the simple mixing scheme can be established if the gap between the occupied states and unoccupied states is sufficiently large. This assumption can be relaxed if the charge density is computed using the Fermi-Dirac distribution and it is not required if there is no exchange correlation functional in the total energy functional. Although our assumption on the gap is ver...
Sui, Ning; Li, Min; He, Ping
2014-12-01
In this work, we investigate the statistical computation of the Boltzmann entropy of statistical samples. For this purpose, we use both histogram and kernel function to estimate the probability density function of statistical samples. We find that, due to coarse-graining, the entropy is a monotonic increasing function of the bin width for histogram or bandwidth for kernel estimation, which seems to be difficult to select an optimal bin width/bandwidth for computing the entropy. Fortunately, we notice that there exists a minimum of the first derivative of entropy for both histogram and kernel estimation, and this minimum point of the first derivative asymptotically points to the optimal bin width or bandwidth. We have verified these findings by large amounts of numerical experiments. Hence, we suggest that the minimum of the first derivative of entropy be used as a selector for the optimal bin width or bandwidth of density estimation. Moreover, the optimal bandwidth selected by the minimum of the first derivative of entropy is purely data-based, independent of the unknown underlying probability density distribution, which is obviously superior to the existing estimators. Our results are not restricted to one-dimensional, but can also be extended to multivariate cases. It should be emphasized, however, that we do not provide a robust mathematical proof of these findings, and we leave these issues with those who are interested in them.
Singh, Niraj Kumar; Jha, Raghav Hira; Gargeshwari, Aditi; Kumar, Prawin
2018-01-01
Alteration in the process of bone remodelling is associated with falls and fractures due to increased bone fragility and altered calcium functioning. The auditory system consists of skeletal structures and is, therefore, prone to getting affected by altered bone remodelling. In addition, the vestibule consists of huge volumes of calcium (CaCO3) in the form of otoconia crystals and alteration in functioning calcium levels could, therefore, result in vestibular symptoms. Thus, the present study aimed at compiling information from various studies on assessment of auditory or vestibular systems in individuals with reduced bone mineral density (BMD). A total of 1977 articles were searched using various databases and 19 full-length articles which reported auditory and vestibular outcomes in persons with low BMD were reviewed. An intricate relationship between altered BMD and audio-vestibular function was evident from the studies; nonetheless, how one aspect of hearing or balance affects the other is not clear. Significant effect of reduced bone mineral density could probably be due to the metabolic changes at the level of cochlea, secondary to alterations in BMD. One could also conclude that sympathetic remodelling is associated with vestibular problems in individual; however, whether vestibular problems lead to altered BMD cannot be ascertained with confidence. The studies reviewed in the article provide an evidence of possible involvement of hearing and vestibular system abnormalities in individuals with reduced bone mineral density. Hence, the assessment protocol for these individuals must include hearing and balance evaluation as mandatory for planning appropriate management.
Energy Technology Data Exchange (ETDEWEB)
Lau, Kah Chun; Curtiss, Larry A.; Greeley, Jeffrey P.
2011-12-01
Density functional theory is used together with classical statistical mechanical analyses to investigate the thermodynamic stability of bulk crystalline LiO2, Li2 O, and Li2O2 as a function of the oxygen environment. The results indicate that lithium peroxide (Li2O2(s)) and superoxide (LiO2(s)) are likely to be stable only under O2-rich conditions with high oxygen partial pressures (PΟ2), whereas Li2O is the most stable at ambient conditions. Additionally, the trends in the density functional calculated equilibrium potential for an ideal reversible Li-O2 couple can be described by an analytical equation as a function of pressure and temperature. As part of this work, we have also calculated the structure and thermodynamics for lithium superoxide. It is found to be stable with respect to lattice vibrations, with an O-O stretching vibration mode very similar to that of the isolated LiO2 molecule and to the O2 - ion radical.
Energy Technology Data Exchange (ETDEWEB)
Lau, K. C.; Curtiss, L. A.; Greeley, J. (Center for Nanoscale Materials); ( MSD)
2011-01-01
Density functional theory is used together with classical statistical mechanical analyses to investigate the thermodynamic stability of bulk crystalline LiO{sub 2}, Li{sub 2}O, and Li{sub 2}O{sub 2} as a function of the oxygen environment. The results indicate that lithium peroxide (Li{sub 2}O{sub 2(s)}) and superoxide (LiO{sub 2(s)}) are likely to be stable only under O{sub 2}-rich conditions with high oxygen partial pressures (P?{sub 2}), whereas Li{sub 2}O is the most stable at ambient conditions. Additionally, the trends in the density functional calculated equilibrium potential for an ideal reversible Li-O{sub 2} couple can be described by an analytical equation as a function of pressure and temperature. As part of this work, we have also calculated the structure and thermodynamics for lithium superoxide. It is found to be stable with respect to lattice vibrations, with an O-O stretching vibration mode very similar to that of the isolated LiO{sub 2} molecule and to the O{sub 2}{sup -} ion radical.
Vacancy formation in MoO3: hybrid density functional theory and photoemission experiments
Salawu, Omotayo Akande
2016-09-29
Molybdenum oxide (MoO3) is an important material that is being considered for numerous technological applications, including catalysis and electrochromism. In the present study, we apply hybrid density functional theory to investigate O and Mo vacancies in the orthorhombic phase. We determine the vacancy formation energies of different defect sites as functions of the electron chemical potential, addressing different charge states. In addition, we investigate the consequences of defects for the material properties. Ultraviolet photoemission spectroscopy is employed to study the valence band of stoichiometric and O defective MoO3. We show that O vacancies result in occupied in-gap states.
Standard hydrogen electrode and potential of zero charge in density functional calculations
DEFF Research Database (Denmark)
Tripkovic, Vladimir; Björketun, Mårten; Skúlason, Egill
2011-01-01
Methods to explicitly account for half-cell electrode potentials have recently appeared within the framework of density functional theory. The potential of the electrode relative to the standard hydrogen electrode is typically determined by subtracting the experimental value of the absolute...... functional setups. By analyzing a dozen different water structures, built up from water hexamers, in their uncharged [potential of zero charge (PZC)] states on Pt(111), we then determine three different criteria (no net dipole, no charge transfer, and high water flexibility) that a water structure should...
Determan, John J; Poole, Katelyn; Scalmani, Giovanni; Frisch, Michael J; Janesko, Benjamin G; Wilson, Angela K
2017-10-10
The utility of several nonhybrid density functional approximations (DFAs) is considered for the prediction of gas phase enthalpies of formation for a large set of 3d transition metal-containing molecules. Nonhybrid DFAs can model thermochemical values for 3d transition metal-containing molecules with accuracy comparable to that of hybrid functionals. The GAM-generalized gradient approximation (GGA); the TPSS, M06-L, and MN15-L meta-GGAs; and the Rung 3.5 PBE+ΠLDA(s) DFAs all give root-mean-square deviations below that of the widely used B3LYP hybrid. Modern nonhybrid DFAs continue to show utility for transition metal thermochemistry.
Zhang, Ying; Xu, Xin; Goddard, William A.
2009-01-01
We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size. PMID:19276116
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...
Density functional theory analysis of hexagonal close-packed elemental metal photocathodes
Directory of Open Access Journals (Sweden)
Tuo Li
2015-07-01
Full Text Available A density function theory based analysis of photoemission from hexagonal close packed (hcp metals is presented and the calculated values of the rms transverse momentum (Δp_{T} are in good agreement with the available experimental data on Be [Phys. Rev. Lett. 111, 237401 (2013] and Mg [Proceedings of LINAC 2002, Gyeongju, Korea (2002]. The lattice constants and work functions of the hcp metals are also examined and are consistent with the available experimental values. In addition, emission from (0001-oriented Be is examined due to the presence of a strong surface state.
Modeling butadiene adsorption on oxidized graphene surface using density functional theory
Akimenko, Ju. Y.; Akimenko, S. S.; Gorbunov, V. A.
2017-08-01
In this paper, the process of chemisorption of cis-butadiene rubber on the surface of oxidized graphene was studied using the density functional theory. The polymer is interacting to a quinone group, an oxygen bridge, and an OH group which was differently located on the surface of the graphene sheet. Based on the calculated value of ΔG298, the possibility of spontaneous formation of the bond between butadiene rubber and these functional groups was estimated. The features of the temperature dependence of the change in free Gibbs energy for thermodynamically possible coupled systems are considered.
On the calculation of Δ for electronic excitations in time-dependent density-functional theory
Myneni, Hemanadhan; Casida, Mark E.
2017-04-01
Excited states are often treated within the context of time-dependent (TD) density-functional theory (DFT), making it important to be able to assign the excited spin-state symmetry. While there is universal agreement on how Δ , the difference between for ground and excited states, should be calculated in a wave-function-like formalism such as the Tamm-Dancoff approximation (TDA), confusion persists as to how to determine the spin-state symmetry of excited states in TD-DFT. We try to clarify the origins of this confusion by examining various possibilities for the parameters (σ1 ,σ2) in the formula
A Dynamic Density Functional Theory Approach to Diffusion in White Dwarfs and Neutron Star Envelopes
Diaw, A.; Murillo, M. S.
2016-09-01
We develop a multicomponent hydrodynamic model based on moments of the Born-Bogolyubov-Green-Kirkwood-Yvon hierarchy equations for physical conditions relevant to astrophysical plasmas. These equations incorporate strong correlations through a density functional theory closure, while transport enters through a relaxation approximation. This approach enables the introduction of Coulomb coupling correction terms into the standard Burgers equations. The diffusive currents for these strongly coupled plasmas is self-consistently derived. The settling of impurities and its impact on cooling can be greatly affected by strong Coulomb coupling, which we show can be quantified using the direct correlation function.
Yen, Tsung-Wen; Lim, Thong-Leng; Yoon, Tiem-Leong; Lai, S. K.
2017-11-01
We combined a new parametrized density functional tight-binding (DFTB) theory (Fihey et al. 2015) with an unbiased modified basin hopping (MBH) optimization algorithm (Yen and Lai 2015) and applied it to calculate the lowest energy structures of Au clusters. From the calculated topologies and their conformational changes, we find that this DFTB/MBH method is a necessary procedure for a systematic study of the structural development of Au clusters but is somewhat insufficient for a quantitative study. As a result, we propose an extended hybridized algorithm. This improved algorithm proceeds in two steps. In the first step, the DFTB theory is employed to calculate the total energy of the cluster and this step (through running DFTB/MBH optimization for given Monte-Carlo steps) is meant to efficiently bring the Au cluster near to the region of the lowest energy minimum since the cluster as a whole has explicitly considered the interactions of valence electrons with ions, albeit semi-quantitatively. Then, in the second succeeding step, the energy-minimum searching process will continue with a skilledly replacement of the energy function calculated by the DFTB theory in the first step by one calculated in the full density functional theory (DFT). In these subsequent calculations, we couple the DFT energy also with the MBH strategy and proceed with the DFT/MBH optimization until the lowest energy value is found. We checked that this extended hybridized algorithm successfully predicts the twisted pyramidal structure for the Au40 cluster and correctly confirms also the linear shape of C8 which our previous DFTB/MBH method failed to do so. Perhaps more remarkable is the topological growth of Aun: it changes from a planar (n =3-11) → an oblate-like cage (n =12-15) → a hollow-shape cage (n =16-18) and finally a pyramidal-like cage (n =19, 20). These varied forms of the cluster's shapes are consistent with those reported in the literature.
An efficient algorithm for classical density functional theory in three dimensions: ionic solutions.
Knepley, Matthew G; Karpeev, Dmitry A; Davidovits, Seth; Eisenberg, Robert S; Gillespie, Dirk
2010-03-28
Classical density functional theory (DFT) of fluids is a valuable tool to analyze inhomogeneous fluids. However, few numerical solution algorithms for three-dimensional systems exist. Here we present an efficient numerical scheme for fluids of charged, hard spheres that uses O(N log N) operations and O(N) memory, where N is the number of grid points. This system-size scaling is significant because of the very large N required for three-dimensional systems. The algorithm uses fast Fourier transforms (FFTs) to evaluate the convolutions of the DFT Euler-Lagrange equations and Picard (iterative substitution) iteration with line search to solve the equations. The pros and cons of this FFT/Picard technique are compared to those of alternative solution methods that use real-space integration of the convolutions instead of FFTs and Newton iteration instead of Picard. For the hard-sphere DFT, we use fundamental measure theory. For the electrostatic DFT, we present two algorithms. One is for the "bulk-fluid" functional of Rosenfeld [Y. Rosenfeld, J. Chem. Phys. 98, 8126 (1993)] that uses O(N log N) operations. The other is for the "reference fluid density" (RFD) functional [D. Gillespie et al., J. Phys.: Condens. Matter 14, 12129 (2002)]. This functional is significantly more accurate than the bulk-fluid functional, but the RFD algorithm requires O(N(2)) operations.
Energy Technology Data Exchange (ETDEWEB)
Sato, Kunihiko; Saito, Shun; Yanase, Satoshi; Oi, Takao [Sophia Univ., Tokyo (Japan). Faculty of Science and Technology
2014-03-15
The reduced partition function ratio (RPFR) of lithium in lithium-graphite intercalation compounds (Li-GICs) was evaluated at the UB3LYP/6-311G(d) level of theory. The partition functions were written in the usual rigid-rotor harmonic oscillator approximation. With a C{sub 24}H{sub 12} coronene molecule as the model of graphene, lithium-coronene sandwich, and club sandwich compounds were considered as models of Li-GICs. The estimated value of the {sup 6}Li-to-{sup 7}Li RPFR was 1.0402 at 25 C, which yielded 1.034 as the value of the equilibrium constant, K, of the lithium isotope exchange reaction between a lithium ion in an ethylene carbonate/ethylmethyl carbonate mixed solvent and a lithium atom in interlayer space of graphite. The estimated value of K was larger than the experimental value of 1.025. The unsatisfactory agreement between the estimated and experimental K values suggested that larger molecules should be used as models of graphene and that the vibrational anharmonicity should also be taken into consideration. (orig.)
Wu, Jun; Gygi, François
2012-06-01
We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.
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...
The role of paraoxonase 1 in regulating high-density lipoprotein functionality during aging.
Khalil, Abdelouahed; Kamtchueng Simo, Olivier; Ikhlef, Souade; Berrougui, Hicham
2017-10-01
Pharmacological interventions to increase the concentration of high-density lipoprotein (HDL) have led to disappointing results and have contributed to the emergence of the concept of HDL functionality. The anti-atherogenic activity of HDLs can be explained by their functionality or quality. The capacity of HDLs to maintain cellular cholesterol homeostasis and to transport cholesterol from peripheral cells to the liver for elimination is one of their principal anti-atherogenic activities. However, HDLs possess several other attributes that contribute to their protective effect against cardiovascular diseases. HDL functionality is regulated by various proteins and lipids making up HDL particles. However, several studies investigated the role of paraoxonase 1 (PON1) and suggest a significant role of this protein in the regulation of the functionality of HDLs. Moreover, research on PON1 attracted much interest following several studies indicating that it is involved in cardiovascular protection. However, the mechanisms by which PON1 exerts these effects remain to be elucidated.
Directory of Open Access Journals (Sweden)
Guocai Tian
2017-06-01
Full Text Available The accurate first-principles prediction of the energetic properties of molecules and clusters from efficient semilocal density functionals is of broad interest. Here we study the performance of a non-empirical Tao-Mo (TM density functional on binding energies and excitation energies of titanium dioxide and water clusters, as well as reaction barrier heights. To make a comparison, a combination of the TM exchange part with the TPSS (Tao–Perdew–Staroverov–Scuseria correlation functional—called TMTPSS—is also included in this study. Our calculations show that the best binding energies of titanium dioxide are predicted by PBE0 (Perdew–Burke–Ernzerhof hybrid functional, TM, and TMTPSS with nearly the same accuracy, while B3LYP (Beck’s three-parameter exchange part with Lee-Yang-Parr correlation, TPSS, and PBE (Perdew–Burke–Ernzerhof yield larger mean absolute errors. For excitation energies of titanium and water clusters, PBE0 and B3LYP are the most accurate functionals, outperforming the performance of semilocal functionals due to the nonlocality problem suffered by the latter. Nevertheless, TMTPSS and TM functionals are still good accurate semilocal methods, improving upon the commonly-used TPSS and PBE functionals. We also find that the best reaction barrier heights are predicted by PBE0 and B3LYP, thanks to the nonlocality incorporated into these two hybrid functionals, but TMTPSS and TM are obviously more accurate than SCAN (Strongly Constrained and Appropriately Normed, TPSS, and PBE, suggesting the good performance of TM and TMTPSS for physically different systems and properties.
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.
DEFF Research Database (Denmark)
Stradi, Daniele; Martinez, Umberto; Blom, Anders
2016-01-01
Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... this method to characterize an Ag/Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as a function of the semiconductor doping. We also demonstrate that the standard “activation energy” method for the analysis of I-Vbias data might be inaccurate for nonideal...
A second-order unconstrained optimization method for canonical-ensemble density-functional methods.
Nygaard, Cecilie R; Olsen, Jeppe
2013-03-07
A second order converging method of ensemble optimization (SOEO) in the framework of Kohn-Sham Density-Functional Theory is presented, where the energy is minimized with respect to an ensemble density matrix. It is general in the sense that the number of fractionally occupied orbitals is not predefined, but rather it is optimized by the algorithm. SOEO is a second order Newton-Raphson method of optimization, where both the form of the orbitals and the occupation numbers are optimized simultaneously. To keep the occupation numbers between zero and two, a set of occupation angles is defined, from which the occupation numbers are expressed as trigonometric functions. The total number of electrons is controlled by a built-in second order restriction of the Newton-Raphson equations, which can be deactivated in the case of a grand-canonical ensemble (where the total number of electrons is allowed to change). To test the optimization method, dissociation curves for diatomic carbon are produced using different functionals for the exchange-correlation energy. These curves show that SOEO favors symmetry broken pure-state solutions when using functionals with exact exchange such as Hartree-Fock and Becke three-parameter Lee-Yang-Parr. This is explained by an unphysical contribution to the exact exchange energy from interactions between fractional occupations. For functionals without exact exchange, such as local density approximation or Becke Lee-Yang-Parr, ensemble solutions are favored at interatomic distances larger than the equilibrium distance. Calculations on the chromium dimer are also discussed. They show that SOEO is able to converge to ensemble solutions for systems that are more complicated than diatomic carbon.
Ramasubramaniam, Ashwin
2010-06-01
The size-dependent electronic structure of oxygen-terminated zigzag graphene nanoribbons is investigated using standard density functional theory (DFT) with an exchange-correlation functional of the generalized gradient approximation form as well as hybrid DFT calculations with two different exchange-correlation functionals. Hybrid DFT calculations, which typically provide more accurate band gaps than standard DFT, are found to predict semiconducting behavior in oxygen-terminated zigzag graphene nanoribbons; this is in distinct contrast to standard DFT with (semi)local exchange-correlation functionals, which have been widely employed in previous studies and shown to predict metallic behavior. (Semi)local exchange-correlation functionals employed in standard DFT calculations cause unphysical delocalization of lone pairs from the oxygen atoms due to self-interaction errors and lead to metallic behavior. Hybrid DFT calculations do not suffer from this spurious effect and produce a clear size-dependent band gap. Appreciable fundamental band gaps (˜1eV) are found for the smallest ribbons (two zigzag rows); the band gap decreases rapidly with increasing ribbon width, resulting eventually in a zero band-gap semiconductor at about 4-5 zigzag rows. This finding could have useful implications for molecular electronics, in particular, since oxygen-terminated zigzag graphene nanoribbons are thermodynamically stable unlike their hydrogenated counterparts. More generally, through a concrete example, this study suggests caution when employing (semi)local functionals in DFT studies of functionalized graphene/graphene derivatives when the functional groups contain electron lone pairs.
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
Culpitt, Tanner; Brorsen, Kurt R.
2017-01-01
Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT. PMID:28576084
Energy Technology Data Exchange (ETDEWEB)
Buecking, N.
2007-11-05
In this work a new theoretical formalism is introduced in order to simulate the phononinduced relaxation of a non-equilibrium distribution to equilibrium at a semiconductor surface numerically. The non-equilibrium distribution is effected by an optical excitation. The approach in this thesis is to link two conventional, but approved methods to a new, more global description: while semiconductor surfaces can be investigated accurately by density-functional theory, the dynamical processes in semiconductor heterostructures are successfully described by density matrix theory. In this work, the parameters for density-matrix theory are determined from the results of density-functional calculations. This work is organized in two parts. In Part I, the general fundamentals of the theory are elaborated, covering the fundamentals of canonical quantizations as well as the theory of density-functional and density-matrix theory in 2{sup nd} order Born approximation. While the formalism of density functional theory for structure investigation has been established for a long time and many different codes exist, the requirements for density matrix formalism concerning the geometry and the number of implemented bands exceed the usual possibilities of the existing code in this field. A special attention is therefore attributed to the development of extensions to existing formulations of this theory, where geometrical and fundamental symmetries of the structure and the equations are used. In Part II, the newly developed formalism is applied to a silicon (001)surface in a 2 x 1 reconstruction. As first step, density-functional calculations using the LDA functional are completed, from which the Kohn-Sham-wave functions and eigenvalues are used to calculate interaction matrix elements for the electron-phonon-coupling an the optical excitation. These matrix elements are determined for the optical transitions from valence to conduction bands and for electron-phonon processes inside the
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.
Laird, E; Molloy, A M; McNulty, H; Ward, M; McCarroll, K; Hoey, L; Hughes, C F; Cunningham, C; Strain, J J; Casey, M C
2017-08-01
In this cohort of community dwelling older adults (>60 years), we observed significant positive associations between the frequencies of yogurt intake with measures of bone density, bone biomarkers, and indicators of physical function. Improving yogurt intakes could be a valuable health strategy for maintaining bone health in older adults. The associations of yogurt intakes with bone health and frailty in older adults are not well documented. The aim was to investigate the association of yogurt intakes with bone mineral density (BMD), bone biomarkers, and physical function in 4310 Irish adults from the Trinity, Ulster, Department of Agriculture aging cohort study (TUDA). Bone measures included total hip, femoral neck, and vertebral BMD with bone biochemical markers. Physical function measures included Timed Up and Go (TUG), Instrumental Activities of Daily Living Scale, and Physical Self-Maintenance Scale. Total hip and femoral neck BMD in females were 3.1-3.9% higher among those with the highest yogurt intakes (n = 970) compared to the lowest (n = 1109; P function scores. These results suggest that improving yogurt intakes could be a valuable public health strategy for maintaining bone health in older adults.
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.
Fragment approach to constrained density functional theory calculations using Daubechies wavelets
Energy Technology Data Exchange (ETDEWEB)
Ratcliff, Laura E., E-mail: lratcliff@anl.gov [Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439 (United States); Université de Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry [Université de Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France)
2015-06-21
In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.
Current Issues in Finite-T Density-Functional Theory and Warm-Correlated Matter †
Directory of Open Access Journals (Sweden)
M. W. C. Dharma-wardana
2016-03-01
Full Text Available Finite-temperature density functional theory (DFT has become of topical interest, partly due to the increasing ability to create novel states of warm-correlated matter (WCM.Warm-dense matter (WDM, ultra-fast matter (UFM, and high-energy density matter (HEDM may all be regarded as subclasses of WCM. Strong electron-electron, ion-ion and electron-ion correlation effects and partial degeneracies are found in these systems where the electron temperature Te is comparable to the electron Fermi energy EF. Thus, many electrons are in continuum states which are partially occupied. The ion subsystem may be solid, liquid or plasma, with many states of ionization with ionic charge Zj. Quasi-equilibria with the ion temperature Ti ≠ Te are common. The ion subsystem in WCM can no longer be treated as a passive “external potential”, as is customary in T = 0 DFT dominated by solid-state theory or quantum chemistry. Many basic questions arise in trying to implement DFT for WCM. Hohenberg-Kohn-Mermin theory can be adapted for treating these systems if suitable finite-T exchange-correlation (XC functionals can be constructed. They are functionals of both the one-body electron density ne and the one-body ion densities ρj. Here, j counts many species of nuclei or charge states. A method of approximately but accurately mapping the quantum electrons to a classical Coulomb gas enables one to treat electron-ion systems entirely classically at any temperature and arbitrary spin polarization, using exchange-correlation effects calculated in situ, directly from the pair-distribution functions. This eliminates the need for any XC-functionals. This classical map has been used to calculate the equation of state of WDM systems, and construct a finite-T XC functional that is found to be in close agreement with recent quantum path-integral simulation data. In this review, current developments and concerns in finite-T DFT, especially in the context of non-relativistic warm
Polar-solvation classical density-functional theory for electrolyte aqueous solutions near a wall
Warshavsky, Vadim; Marucho, Marcelo
2016-04-01
A precise description of the structural and dielectric properties of liquid water is critical to understanding the physicochemical properties of solutes in electrolyte solutions. In this article, a mixture of ionic and dipolar hard spheres is considered to account for water crowding and polarization effects on ionic electrical double layers near a uniformly charged hard wall. As a unique feature, solvent hard spheres carrying a dipole at their centers were used to model water molecules at experimentally known concentration, molecule size, and dipolar moment. The equilibrium ionic and dipole density profiles of this electrolyte aqueous model were calculated using a polar-solvation classical density-functional theory (PSCDFT). These profiles were used to calculate the charge density distribution, water polarization, dielectric permittivity function, and mean electric potential profiles as well as differential capacitance, excess adsorptions, and wall-fluid surface tension. These results were compared with those corresponding to the pure dipolar model and unpolar primitive solvent model of electrolyte aqueous solutions to understand the role that water crowding and polarization effects play on the structural and thermodynamic properties of these systems. Overall, PSCDFT predictions are in agreement with available experimental data.
Polar-solvation classical density-functional theory for electrolyte aqueous solutions near a wall.
Warshavsky, Vadim; Marucho, Marcelo
2016-04-01
A precise description of the structural and dielectric properties of liquid water is critical to understanding the physicochemical properties of solutes in electrolyte solutions. In this article, a mixture of ionic and dipolar hard spheres is considered to account for water crowding and polarization effects on ionic electrical double layers near a uniformly charged hard wall. As a unique feature, solvent hard spheres carrying a dipole at their centers were used to model water molecules at experimentally known concentration, molecule size, and dipolar moment. The equilibrium ionic and dipole density profiles of this electrolyte aqueous model were calculated using a polar-solvation classical density-functional theory (PSCDFT). These profiles were used to calculate the charge density distribution, water polarization, dielectric permittivity function, and mean electric potential profiles as well as differential capacitance, excess adsorptions, and wall-fluid surface tension. These results were compared with those corresponding to the pure dipolar model and unpolar primitive solvent model of electrolyte aqueous solutions to understand the role that water crowding and polarization effects play on the structural and thermodynamic properties of these systems. Overall, PSCDFT predictions are in agreement with available experimental data.
The correlation function for density perturbations in an expanding universe. I - Linear theory
Mcclelland, J.; Silk, J.
1977-01-01
The evolution of the two-point correlation function for adiabatic density perturbations in the early universe is studied. Analytical solutions are obtained for the evolution of linearized spherically symmetric adiabatic density perturbations and the two-point correlation function for these perturbations in the radiation-dominated portion of the early universe. The results are then extended to the regime after decoupling. It is found that: (1) adiabatic spherically symmetric perturbations comparable in scale with the maximum Jeans length would survive the radiation-dominated regime; (2) irregular fluctuations are smoothed out up to the scale of the maximum Jeans length in the radiation era, but regular fluctuations might survive on smaller scales; (3) in general, the only surviving structures for irregularly shaped adiabatic density perturbations of arbitrary but finite scale in the radiation regime are the size of or larger than the maximum Jeans length in that regime; (4) infinite plane waves with a wavelength smaller than the maximum Jeans length but larger than the critical dissipative damping scale could survive the radiation regime; and (5) black holes would also survive the radiation regime and might accrete sufficient mass after decoupling to nucleate the formation of galaxies.
Directory of Open Access Journals (Sweden)
Yan Wang
2016-07-01
Full Text Available Objective: To investigate the changes of thyroid function, autoantibodies, bone mineral density and bone metabolism in patients with hyperthyroidism. Methods: A total of 216 cases of hyperthyroidism in our hospital from December 2015 to January 2015 were selected as the case group, 216 cases of healthy people selected the same period in our hospital physical examination center as the control group, detected thyroid function, autoantibodies, bone mineral density and bone metabolism indexes of all the studied subjects and compared with each other. Results: In this study, it was found that diastolic blood pressure, BMI, triglyceride, total cholesterol, HDL-C, VLDL-C, TSH were all significantly lower than the control group (P<0.05, systolic blood pressure, LDL-C, GLU, T3, T4, FT3, FT4, HTG, TG-Ab, TPO-Ab in case group were significantly higher than the control group (P<0.05. Right calcaneal speed of sound (SOS in case group was significantly lower than the control group (P<0.05, BGP, PTH in case group were significantly higher than the control group (P<0.05. Conclusions: Hyperthyroidism can cause thyroid hormone levels abnormal, abnormal increase autoantibodies, decrease bone density, bone metabolism actively, easy to form osteoporosis, clinical treatment of hyperthyroidism in the same time, should actively prevent the occurrence of osteoporosis
Hao, Feng; Armiento, Rickard; Mattsson, Ann E
2014-05-14
We have previously proposed that further improved functionals for density functional theory can be constructed based on the Armiento-Mattsson subsystem functional scheme if, in addition to the uniform electron gas and surface models used in the Armiento-Mattsson 2005 functional, a model for the strongly confined electron gas is also added. However, of central importance for this scheme is an index that identifies regions in space where the correction provided by the confined electron gas should be applied. The electron localization function (ELF) is a well-known indicator of strongly localized electrons. We use a model of a confined electron gas based on the harmonic oscillator to show that regions with high ELF directly coincide with regions where common exchange energy functionals have large errors. This suggests that the harmonic oscillator model together with an index based on the ELF provides the crucial ingredients for future improved semi-local functionals. For a practical illustration of how the proposed scheme is intended to work for a physical system we discuss monoclinic cupric oxide, CuO. A thorough discussion of this system leads us to promote the cell geometry of CuO as a useful benchmark for future semi-local functionals. Very high ELF values are found in a shell around the O ions, and take its maximum value along the Cu-O directions. An estimate of the exchange functional error from the effect of electron confinement in these regions suggests a magnitude and sign that could account for the error in cell geometry.
Doping strategies to control A-centres in silicon: Insights from hybrid density functional theory
Wang, Hao
2014-01-01
Hybrid density functional theory is used to gain insights into the interaction of intrinsic vacancies (V) and oxygen-vacancy pairs (VO, known as A-centres) with the dopants (D) germanium (Ge), tin (Sn), and lead (Pb) in silicon (Si). We determine the structures as well as binding and formation energies of the DVO and DV complexes. The results are discussed in terms of the density of states and in view of the potential of isovalent doping to control A-centres in Si. We argue that doping with Sn is the most efficient isovalent doping strategy to suppress A-centres by the formation of SnVO complexes, as these are charge neutral and strongly bound. © 2014 the Owner Societies.
DENSITY-FUNCTIONAL STUDY OF U-Mo AND U-Zr ALLOYS
Energy Technology Data Exchange (ETDEWEB)
Landa, A; Soderlind, P; Turchi, P A
2010-11-01
Density-functional theory previously used to describe phase equilibria in U-Zr alloys [A. Landa, P. Soederlind, P.E.A. Turchi, J. Alloys Comp. 478 (2009) 103-110] is extended to investigate the ground-state properties of U-Mo solid solutions. We discuss how the heat of formation in both alloys correlates with the charge transfer between the alloy components, and how the specific behavior of the density of states in the vicinity of the Fermi level promotes the stabilization of the U{sub 2}Mo compound. Our calculations prove that, due to the existence of a single {gamma}-phase over the typical fuel operation temperatures, {gamma}-U-Mo alloys should indeed have much lower constituent redistribution than {gamma}-U-Zr alloys for which binodal decomposition causes a high degree of constituent redistribution.
Linear-scaling density functional theory using the projector augmented wave method
Hine, Nicholas D. M.
2017-01-01
Quantum mechanical simulation of realistic models of nanostructured systems, such as nanocrystals and crystalline interfaces, demands computational methods combining high-accuracy with low-order scaling with system size. Blöchl’s projector augmented wave (PAW) approach enables all-electron (AE) calculations with the efficiency and systematic accuracy of plane-wave pseudopotential calculations. Meanwhile, linear-scaling (LS) approaches to density functional theory (DFT) allow for simulation of thousands of atoms in feasible computational effort. This article describes an adaptation of PAW for use in the LS-DFT framework provided by the ONETEP LS-DFT package. ONETEP uses optimisation of the density matrix through in situ-optimised local orbitals rather than the direct calculation of eigenstates as in traditional PAW approaches. The method is shown to be comparably accurate to both PAW and AE approaches and to exhibit improved convergence properties compared to norm-conserving pseudopotential methods.
G-centers in irradiated silicon revisited: A screened hybrid density functional theory approach
Energy Technology Data Exchange (ETDEWEB)
Wang, H.; Schwingenschlögl, U., E-mail: Udo.Schwingenschlogl@kaust.edu.sa [PSE Division, KAUST, Thuwal 23955-6900 (Saudi Arabia); Chroneos, A., E-mail: Alex.Chroneos@open.ac.uk [Engineering and Innovation, The Open University, Milton Keynes MK7 6AA (United Kingdom); Department of Materials, Imperial College, London SW7 2AZ (United Kingdom); Londos, C. A.; Sgourou, E. N. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece)
2014-05-14
Electronic structure calculations employing screened hybrid density functional theory are used to gain fundamental insight into the interaction of carbon interstitial (C{sub i}) and substitutional (C{sub s}) atoms forming the C{sub i}C{sub s} defect known as G-center in silicon (Si). The G-center is one of the most important radiation related defects in Czochralski grown Si. We systematically investigate the density of states and formation energy for different types of C{sub i}C{sub s} defects with respect to the Fermi energy for all possible charge states. Prevalence of the neutral state for the C-type defect is established.
Pure density functional for strong correlations and the thermodynamic limit from machine learning
Li, Li; White, Steven R; Burke, Kieron
2016-01-01
We use density-matrix renormalization group, applied to a one-dimensional model of continuum Hamiltonians, to accurately solve chains of hydrogen atoms of various separations and numbers of atoms. We train and test a machine-learned approximation to $F[n]$, the universal part of the electronic density functional, to within quantum chemical accuracy. Our calculation (a) bypasses the standard Kohn-Sham approach, avoiding the need to find orbitals, (b) includes the strong correlation of highly-stretched bonds without any specific difficulty (unlike all standard DFT approximations) and (c) is so accurate that it can be used to find the energy in the thermodynamic limit to quantum chemical accuracy.
Nuclear parton density functions from jet production in DIS at an EIC
Klasen, M.; Kovařík, K.; Potthoff, J.
2017-05-01
We investigate the potential of inclusive-jet production in deep-inelastic scattering (DIS) at a future electron-ion collider (EIC) to improve our current knowledge of nuclear parton density functions (PDFs). We demonstrate that the kinematic reach is extended similarly to inclusive DIS, but that the uncertainty of the nuclear PDFs, in particular of the gluon density at low Bjorken-x , is considerably reduced, by up to an order of magnitude compared to the present situation. Using an approximate next-to-next-to-leading order (aNNLO) calculation implemented in the program JetViP, we also make predictions for three different EIC designs and for four different light and heavy nuclei.
A Density Functional Theory Study of Doped Tin Monoxide as a Transparent p-type Semiconductor
Bianchi Granato, Danilo
2012-05-01
In the pursuit of enhancing the electronic properties of transparent p-type semiconductors, this work uses density functional theory to study the effects of doping tin monoxide with nitrogen, antimony, yttrium and lanthanum. An overview of the theoretical concepts and a detailed description of the methods employed are given, including a discussion about the correction scheme for charged defects proposed by Freysoldt and others [Freysoldt 2009]. Analysis of the formation energies of the defects points out that nitrogen substitutes an oxygen atom and does not provide charge carriers. On the other hand, antimony, yttrium, and lanthanum substitute a tin atom and donate n-type carriers. Study of the band structure and density of states indicates that yttrium and lanthanum improves the hole mobility. Present results are in good agreement with available experimental works and help to improve the understanding on how to engineer transparent p-type materials with higher hole mobilities.
Density functional theory for non-relativistic fermions in the unitarity limit
Energy Technology Data Exchange (ETDEWEB)
Rupak, Gautam [Department of Physics, North Carolina State University, Raleigh, NC 27695 (United States)], E-mail: grupak@gmail.com; Schaefer, Thomas [Department of Physics, North Carolina State University, Raleigh, NC 27695 (United States)], E-mail: thomas_schaefer@ncsu.edu
2009-01-15
We derive an energy density functional for non-relativistic spin one-half fermions in the limit of a divergent two-body scattering length. Using an epsilon expansion around d=4-{epsilon} spatial dimensions we compute the coefficient of the leading correction beyond the local density approximation (LDA). In the case of N fermionic atoms trapped in a harmonic potential this correction has the form E=E{sub LDA}(1+c{sub s}(3N){sup -2/3}), where E{sub LDA} is the total energy in LDA approximation. At next-to-leading order in the epsilon expansion we find c{sub s}=1.68, which is significantly larger than the result for non-interacting fermions, c{sub s}=0.5.
Density functional study of the stability of various α-Bi2O3 surfaces.
Lei, Yan-Hua; Chen, Zhao-Xu
2013-02-07
Bi(2)O(3) is an important metal oxide in catalysis. In this paper we employed density functional theory and slab model to investigate the surface energies and structures of various α-Bi(2)O(3) surfaces. We first studied ten different terminations along [100] direction which has both polar and nonpolar terminations due to alternating stacking of Bi layers and O layers. Our calculated surface free energies show that the stoichiometric symmetric terminations are most stable at both high and low oxygen pressures, followed by the T(2O)/T(4O) terminations at low/high oxygen pressures. In the low Miller index planes, the (010) plane is the most stable whereas the (110) plane is the least stable. Analyses reveal that relaxation may change the surface structures significantly and there is a nice linear relationship between the surface density of broken short Bi-O bonds and the surface energy before relaxation.
Entropic solvation force between surfaces modified by grafted chains: a density functional approach
Directory of Open Access Journals (Sweden)
O. Pizio
2010-01-01
Full Text Available The behavior of a hard sphere fluid in slit-like pores with walls modified by grafted chain molecules composed of hard sphere segments is studied using density functional theory. The chains are grafted to opposite walls via terminating segments forming pillars. The effects of confinement and of "chemical" modification of pore walls on the entropic solvation force are investigated in detail. We observe that in the absence of adsorbed fluid the solvation force is strongly repulsive for narrow pores and attractive for wide pores. In the presence of adsorbed fluid both parts of the curve of the solvation force may develop oscillatory behavior dependent on the density of pillars, the number of segments and adsorption conditions. Also, the size ratio between adsorbed fluid species and chain segments is of importance for the development of oscillations. The choice of these parameters is crucial for efficient manipulation of the solvation force as desired for pores of different width.
DEFF Research Database (Denmark)
Jensen, Peter Bjerre; Lysgaard, Steen; Quaade, Ulrich J.
2014-01-01
Metal halide ammines have great potential as a future, high-density energy carrier in vehicles. So far known materials, e.g. Mg(NH3)6Cl2 and Sr(NH3)8Cl2, are not suitable for automotive, fuel cell applications, because the release of ammonia is a multi-step reaction, requiring too much heat...... to be supplied, making the total efficiency lower. Here, we apply density functional theory (DFT) calculations to predict new mixed metal halide ammines with improved storage capacities and the ability to release the stored ammonia in one step, at temperatures suitable for system integration with polymer...... electrolyte membrane fuel cells (PEMFC). We use genetic algorithms (GAs) to search for materials containing up to three different metals (alkaline-earth, 3d and 4d) and two different halides (Cl, Br and I) – almost 27000 combinations, and have identified novel mixtures, with significantly improved storage...
Jariwala, P. H.; Gupta, Sanjeev K.; Sonvane, Y. A.; Thakor, P. B.
2017-06-01
We have scrutinized the gold (Au) nanowires with distinct cross-section with 1-10 Au atoms for each unit cell by density-functional approach and performed first-principles computation. Here, we have investigated structural, electronic, transport and mechanical characteristic of Au nanowires. The structural characteristic of cubic bulk and nanowires of Au are very diverse from each other. The electronic density of state (DOS) and band structures of different formations express that all the nanowires are very good conductor in nature. The figure of conduction channels leans on number of atoms for each unit cell, diameter and structure of nanowires. We also inspect that the electronic thermal conductivities dependency on the temperature and we found that all the considered AuNWs have low conductivity than that of the bulk Au. Our results show that AuNWs have potential application in electronic devices like nanoelectro-mechanical systems (NEMS).
Energy Technology Data Exchange (ETDEWEB)
Mao, James X.; Lee, Anita S.; Kitchin, John R.; Nulwala, Hunaid B.; Luebke, David R.; Damodaran, Krishnan
2013-01-25
Density Functional Theory is used to investigate a weakly coordinating room-temperature ionic liquid, 1-ethyl-3-methyl imidazolium tetracyanoborate ([Emim]{sup +}[TCB]{sup -}). Four locally stable conformers of the ion pair were located. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of several hydrogen bonds. Further investigation through the Natural Bond Orbital (NBO) and Natural Energy Decomposition Analysis (NEDA) calculations provided insight into the origin of interactions in the [Emim]{sup +}[TCB]{sup -} ion pair. Strength of molecular interactions in the ionic liquid was correlated with frequency shifts of the characteristic vibrations of the ion pair. Harmonic vibrations of the ion pair were also compared with the experimental Raman and Infrared spectra. Vibrational frequencies were assigned by visualizing displacements of atoms around their equilibrium positions and through Potential Energy Distribution (PED) analysis.
Sjostrom, Travis; Daligault, Jérôme
2015-12-01
We validate the application of our recent orbital-free density functional theory (DFT) approach [Phys. Rev. Lett. 113, 155006 (2014);] for the calculation of ionic and electronic transport properties of dense plasmas. To this end, we calculate the self-diffusion coefficient, the viscosity coefficient, the electrical and thermal conductivities, and the reflectivity coefficient of hydrogen and aluminum plasmas. Very good agreement is found with orbital-based Kohn-Sham DFT calculations at lower temperatures. Because the computational costs of the method do not increase with temperature, we can produce results at much higher temperatures than is accessible by the Kohn-Sham method. Our results for warm dense aluminum at solid density are inconsistent with the recent experimental results reported by Sperling et al. [Phys. Rev. Lett. 115, 115001 (2015)].
Density functional theory study of stoichiometric and nonstoichiometric ZnO grain boundaries
Körner, Wolfgang; Bristowe, Paul D.; Elsässer, Christian
2011-07-01
We present a density functional theory analysis of stoichiometric and nonstoichiometric ZnO tilt grain boundaries (GBs) that reveals under which conditions such extrinsically undoped GBs may become electrically active. In the case of ZnO the self-interaction correction (SIC) scheme used allows a more accurate description of the formation energies as well as the electronic levels than the local density approximation (LDA). The results obtained with the SIC scheme deviate in some crucial ways from the LDA results of recent years. First, stoichiometric and nonstoichiometric ZnO GBs can show occupied deep levels whenever oxygen atoms are undercoordinated. Second, ZnO GBs with an oxygen excess at the boundary plane can exhibit unoccupied deep levels which may account for an experimentally observed weak varistor effect found in undoped polycrystalline ZnO.
Cohesive properties of noble metals by van der Waals-corrected Density Functional Theory
Ambrosetti, Alberto
2016-01-01
The cohesive energy, equilibrium lattice constant, and bulk modulus of noble metals are computed by different van der Waals-corrected Density Functional Theory methods, including vdW-DF, vdW-DF2, vdW-DF-cx, rVV10 and PBE-D. Two specifically-designed methods are also developed in order to effectively include dynamical screening effects: the DFT/vdW-WF2p method, based on the generation of Maximally Localized Wannier Functions, and the RPAp scheme (in two variants), based on a single-oscillator model of the localized electron response. Comparison with results obtained without explicit inclusion of van der Waals effects, such as with the LDA, PBE, PBEsol, or the hybrid PBE0 functional, elucidates the importance of a suitable description of screened van der Waals interactions even in the case of strong metal bonding. Many-body effects are also quantitatively evaluated within the RPAp approach.
Magnetic coupling constants for MnO as calculated using hybrid density functional theory
Logsdail, Andrew J.; Downing, Christopher A.; Catlow, C. Richard A.; Sokol, Alexey A.
2017-12-01
The properties of MnO have been calculated using generalised gradient approximation (GGA-) and hybrid (h-) density functional theory (DFT), specifically variants of the popular PBE and PBESol exchange-correlation functionals. The GGA approaches are shown to be poor at reproducing experimental magnetic coupling constants and rhombohedral structural distortions, with the PBESol functional performing worse than PBE. In contrast, h-DFT results are in reasonable agreement with experiment. Calculation of the Néel temperatures using the mean-field approximation gives overestimates relative to experiment, but the discrepancies are as low as 15 K for the PBE0 approach and, generally, the h-DFT results are significant improvements over previous theoretical studies. For the Curie-Weiss temperature, larger disparities are observed between the theoretical results and previous experimental results.
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.
1999-12-01
A 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. This methodology is based on the extension of the ‘filtered density function’ (FDF) scheme recently proposed by Colucci et al. (1998) for LES of constant-density reacting flows. The FMDF represents the joint probability density function of the subgrid-scale (SGS) scalar quantities and is obtained by solution of its modelled transport equation. In this equation, the effect of chemical reactions appears in a closed form and the influences of SGS mixing and convection are modelled. The stochastic differential equations (SDEs) which yield statistically equivalent results to those of the FMDF transport equation are derived and are solved via a Lagrangian Monte Carlo scheme. The consistency, convergence, and accuracy of the FMDF and the Monte Carlo solution of its equivalent SDEs are assessed. In non-reacting flows, it is shown that the filtered results via the FMDF agree well with those obtained by the ‘conventional’ LES in which the finite difference solution of the transport equations of these filtered quantities is obtained. The advantage of the FMDF is demonstrated in LES of reacting shear flows with non-premixed reactants. The FMDF results are appraised by comparisons with data generated by direct numerical simulation (DNS) and with experimental measurements. In the absence of a closure for the SGS scalar correlations, the results based on the conventional LES are significantly different from those obtained by DNS. The FMDF results show a closer agreement with DNS. These results also agree favourably with laboratory data of exothermic reacting turbulent shear flows, and portray several of the features observed experimentally.
Comparison of the performance of exact-exchange-based density functional methods.
Liu, Fenglai; Proynov, Emil; Yu, Jian-Guo; Furlani, Thomas R; Kong, Jing
2012-09-21
How to describe nondynamic electron correlation is still a major challenge to density functional theory (DFT). Recent models designed particularly for this problem, such as Becke'05 (B05) and Perdew-Staroverov-Tao-Scuseria (PSTS) functionals employ the exact-exchange density, the efficient calculation of which is technically quite challenging. We have recently implemented self-consistently the B05 functional based on an efficient resolution-identity (RI) technique. In this study, we report a self-consistent RI implementation of the PSTS functional. In contrast to its original implementation, our version brings no limitation on the choice of the basis set. We have also implemented the Mori-Sanchez-Cohen-Yang-2 (MCY2) functional, another recent DFT method that includes full exact exchange. The performance of PSTS, B05, and MCY2 is validated on thermochemistry, reaction barriers, and dissociation energy curves, with an emphasis on nondynamic correlation effects in the discussion. All three methods perform rather well in general, B05 and MCY2 being on average somewhat better than PSTS. We include also results with other functionals that represent various aspects of the development in this field in recent years, including B3LYP, M06-HF, M06-2X, ωB97X, and TPSSh. The performance of the heavy-parameterized functionals M06-2X and ωB97X is on average better than that of B05, MCY2, and PSTS for standard thermodynamic properties and reactions, while the latter functionals do better in hydrogen abstraction reactions and dissociation processes. In particular, B05 is found to be the only functional that yields qualitatively correct dissociation curves for two-center symmetric radicals like He(2)(+). Finally, we compare the performance of all these functionals on a strongly correlated exemplary case system, the NO dimer. Only PSTS, B05, and MCY2 describe the system qualitatively correctly. Overall, this new type of functionals show good promise of overcoming some of the
Interaction of boron with graphite: A van der Waals density functional study
Energy Technology Data Exchange (ETDEWEB)
Liu, Juan; Wang, Chen [Beijing Key Lab of Fine Ceramics, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Liang, Tongxiang, E-mail: txliang@tsinghua.edu.cn [State Key Lab of New Ceramic and Fine Processing, Tsinghua University, Beijing 100084 (China); Lai, Wensheng [Advanced Material Laboratory, School of Materials Science & Engineering, Tsinghua University, Beijing, 100084 (China)
2016-08-30
Highlights: • A van der Waals density-functional approach is applied to study the interaction of boron with graphite. • VdW-DF functionals give fair agreement of crystal parameters with experiments. • The π electron approaches boron while adsorbing on graphite surface. • The hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. • PBE cannot describe the interstitial boron in graphite because of the ignoring binding of graphite sheets. - Abstract: Boron doping has been widely investigated to improve oxidation resistance of graphite. In this work the interaction of boron with graphite is investigated by a van der Waals density-functional approach (vdW-DF). The traditional density-functional theory (DFT) is well accounted for the binding in boron-substituted graphite. However, to investigate the boron atom on graphite surface and the interstitial impurities require use of a description of graphite interlayer binding. Traditional DFT cannot describe the vdW physics, for instance, GGA calculations show no relevant binding between graphite sheets. LDA shows some binding, but they fail to provide an accurate account of vdW forces. In this paper, we compare the calculation results of graphite lattice constant and cohesive energy by several functionals, it shows that vdW-DF such as two optimized functionals optB88-vdW and optB86b-vdW give much improved results than traditional DFT. The vdW-DF approach is then applied to study the interaction of boron with graphite. Boron adsorption, substitution, and intercalation are discussed in terms of structural parameters and electronic structures. When adsorbing on graphite surface, boron behaves as π electron acceptor. The π electron approaches boron atom because of more electropositive of boron than carbon. For substitution situation, the hole introduced by boron mainly concentrates on boron and the nearest three carbon atoms. The B-doped graphite system with the hole has less
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.
Dependability of the Exemplary Technical System for Assumed Functions of Defect Density
Directory of Open Access Journals (Sweden)
Stępień Sławomir
2016-12-01
Full Text Available The analysis of structural dependability of technical system, especially determining the change in dependability over time, requires knowledge on density function or the understanding of cumulative distribution function of components belonging to the structure. Based on previously registered data concerning component defect, it is relatively easy to establish the average uptime of component as well as the standard deviation for this time. However, defining distribution shape gives rise to some difficulties. Usually, we do not have the sufficient number of data at our disposal to verify the hypothesis regarding the distribution shape. Due to this fact, it is a common practice, depending on the case under consideration, to apply the function of defect density. However, the question arises: Does the incorrect determination of types of distributions of components leads to the big error of estimation results of dependability and system durability? This article will not respond to this question in whole, but one will conduct a comparison of calculation results for a few cases. The calculations were conducted for the exemplary technical system.
Energy Technology Data Exchange (ETDEWEB)
López-Albarrán, P. [Facultad de Ingeniería en Tecnología de la Madera, Universidad Michoacana de San Nicolás de Hidalgo, Santiago Tapia 403, CP 58000, Morelia, Michoacán (Mexico); Navarro-Santos, P., E-mail: pnavarrosa@conacyt.mx [Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Santiago Tapia 403, CP 58000, Morelia, Michoacán (Mexico); Garcia-Ramirez, M. A. [Research Centre for Innovation in Aeronautical Engineering, Universidad Autónoma de Nuevo León, Ciudad Universitaria, San Nicolás de los Garza, CP 66451 Nuevo León (Mexico); Ricardo-Chávez, J. L. [Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Lomas 4" asección, CP 78216, San Luis Potosí, S. L. P. (Mexico)
2015-06-21
The adsorption of dibenzothiophene (DBT) on bare and boron-doped armchair carbon nanoribbons (ACNRs) is being investigated in the framework of the density functional theory by implementing periodic boundary conditions that include corrections from dispersion interactions. The reactivity of the ACNRs is characterized by using the Fukui functions as well as the electrostatic potential as local descriptors. Non-covalent adsorption mechanism is found when using the local Perdew-Becke-Ernzerhof functional, regardless of the DBT orientation and adsorption location. The dispersion interactions addition is a milestone to describe the adsorption process. The charge defects introduced in small number (i.e., by doping with B atoms), within the ACNRs increases the selectivity towards sulfur mainly due to the charge depletion at B sites. The DBT magnitude in the adsorption energy shows non-covalent interactions. As a consequence, the configurations where the DBT is adsorbed on a BC{sub 3} island increase the adsorption energy compared to random B arrangements. The stability of these configurations can be explained satisfactorily in terms of dipole interactions. Nevertheless, from the charge-density difference analysis and the weak Bader charge-distribution interactions cannot be ruled out completely. This is why the electronic properties of the ribbons are analyzed in order to elucidate the key role played by the B and DBT states in the adsorbed configurations.
Mo, Yirong; Bao, Peng; Gao, Jiali
2011-04-21
An interaction energy decomposition analysis method based on the block-localized wavefunction (BLW-ED) approach is described. The first main feature of the BLW-ED method is that it combines concepts of valence bond and molecular orbital theories such that the intermediate and physically intuitive electron-localized states are variationally optimized by self-consistent field calculations. Furthermore, the block-localization scheme can be used both in wave function theory and in density functional theory, providing a useful tool to gain insights on intermolecular interactions that would otherwise be difficult to obtain using the delocalized Kohn-Sham DFT. These features allow broad applications of the BLW method to energy decomposition (BLW-ED) analysis for intermolecular interactions. In this perspective, we outline theoretical aspects of the BLW-ED method, and illustrate its applications in hydrogen-bonding and π-cation intermolecular interactions as well as metal-carbonyl complexes. Future prospects on the development of a multistate density functional theory (MSDFT) are presented, making use of block-localized electronic states as the basis configurations.
Level densities and gamma-ray strength functions in 170,171,172-Yb
Energy Technology Data Exchange (ETDEWEB)
Agvaanluvsan, U; Schiller, A; Becker, J; Bernstein, L; Garrett, P; Guttormsen, M; Mitchell, G; Rekstad, J; Siem, S; Voinov, A; Younes, W
2004-07-28
Level densities and radiative strength functions in {sup 171}Yb and {sup 170}Yb nuclei have been measured using the {sup 171}Yb({sup 3}He{sup 3}He{gamma}){sup 171}Yb and {sup 171}Yb({sup 3}He,{alpha}{gamma}){sup 170}Yb reactions. New data on {sup 171}Yb are compared to a previous measurement for {sup 171}Yb from the {sup 172}Yb({sup 3}He,{alpha}{gamma}){sup 171}Yb reaction. Systematics of level densities and radiative strength functions in {sup 170,171,172}Yb are established. The entropy excess in {sup 171}Yb relative to the even-even nuclei {sup 170,172}Yb due to the unpaired neutron quasiparticle is found to be approximately 2k{sub B}. Results for the radiative strength function from the two reactions lead to consistent parameters characterizing the ''pygmy'' resonances. Pygmy resonances in the {sup 170,172}Yb populated by the ({sup 3}He,{alpha}) reaction appear to be split into two components for both of which a complete set of resonance parameters are obtained.
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.
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.
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...
Vidya, R.; Ravindran, P; Fjellvåg, H.; Svensson, B. G.; Monakhov, E.; Ganchenkova, M.; Nieminen, Risto M.
2011-01-01
Formation energies of various intrinsic defects and defect complexes in ZnO have been calculated using a density-functional-theory-based pseudopotential all-electron method. The various defects considered are oxygen vacancy (VO), zinc vacancy (VZn), oxygen at an interstitial site (Oi), Zn at an interstitial site (Zni), Zn at VO (ZnO), O at VZn(OZn), and an antisite pair (combination of the preceding two defects). In addition, defect complexes like (VO+Zni) and Zn-vacancy clusters are studied....
Guo, Xinwei; Qu, Zexing; Gao, Jiali
2018-01-01
The multi-state density functional theory (MSDFT) provides a convenient way to estimate electronic coupling of charge transfer processes based on a diabatic representation. Its performance has been benchmarked against the HAB11 database with a mean unsigned error (MUE) of 17 meV between MSDFT and ab initio methods. The small difference may be attributed to different representations, diabatic from MSDFT and adiabatic from ab initio calculations. In this discussion, we conclude that MSDFT provides a general and efficient way to estimate the electronic coupling for charge-transfer rate calculations based on the Marcus-Hush model.
Density functional calculations of elastic properties of portlandite, Ca(OH)(2)
DEFF Research Database (Denmark)
Laugesen, Jakob Lund
2005-01-01
elasticity, applying a least-square method. Young's modulus and bulk modulus are calculated from the stiffness matrix. The results are compared with the Brillouin zone spectroscopy results of F. Holuj et al. [F. Holuj, M. Drozdowski, M. Czajkowski, Brillouin spectrum of Ca(OH)(2), Solid State Commun., 56 (12......The elastic constants of portlandite, Ca(OH)(2), are calculated by use of density functional theory. A lattice optimization of an infinite (periodic boundary conditions) lattice is performed on which strains are applied. The elastic constants are extracted by minimizing Hooke's law of linear...
Spectral discrete probability density function of measured wind turbine noise in the far field
Directory of Open Access Journals (Sweden)
Payam eAshtiani
2015-04-01
Full Text Available Of interest is the spectral character of wind turbine noise at typical residential set-back distances. In this paper a spectral statistical analysis has been applied to immission measurements conducted at three locations. This method provides discrete probability density functions for the Turbine ONLY component of the measured noise. This analysis is completed for 1/3rd Octave sound levels, at integer wind speeds, and is compared to existing metrics for measuring acoustic comfort as well as previous discussions on low frequency noise sources.
Spectral discrete probability density function of measured wind turbine noise in the far field.
Ashtiani, Payam; Denison, Adelaide
2015-01-01
Of interest is the spectral character of wind turbine noise at typical residential set-back distances. In this paper, a spectral statistical analysis has been applied to immission measurements conducted at three locations. This method provides discrete probability density functions for the Turbine ONLY component of the measured noise. This analysis is completed for one-third octave sound levels, at integer wind speeds, and is compared to existing metrics for measuring acoustic comfort as well as previous discussions on low-frequency noise sources.
The electronic structure of TiCl: ligand field versus density functional calculations
Focsa, C.; Bencheikh, M.; Pettersson, L. G. M.
1998-07-01
The electronic structures of titanium chloride and its cation have been analysed by means of both ligand field (LFT) and density functional (DFT) theories. Despite the discrepancy between the DFT and LFT concerning the assignment of the ground state of 0953-4075/31/13/006/img6, an overall agreement is seen for TiCl. The observed 0953-4075/31/13/006/img7 ground state is found to result from our calculated 0953-4075/31/13/006/img8 ground state by a 0953-4075/31/13/006/img9 ionization process with an energy of 0953-4075/31/13/006/img10.
Ethanol reforming on Co(0001) surfaces: a density functional theory study.
Ma, Yuguang; Hernández, Liliana; Guadarrama-Pérez, Carlos; Balbuena, Perla B
2012-02-09
A computational study using density functional theory is carried out to investigate the reaction mechanism of ethanol steam reforming on Co(0001) surfaces. The adsorption properties of the reactant, possible intermediates, and products are carefully examined. The reaction pathway and related transition states are also analyzed. According to our calculations, the reforming mechanism primarily consisting of dehydrogenation steps of ethanol, ethoxy, methanol, methoxy, and formic acid, is feasible on Co(0001) surfaces. It is also found that the reaction of formaldehyde yielding formic acid and hydrogen may not be an elementary reaction. The dehydrogenation of ethoxy possesses the highest barrier and is accordingly identified as the rate-determining step.
Azobenzene-functionalized carbon nanotubes as high-energy density solar thermal fuels.
Kolpak, Alexie M; Grossman, Jeffrey C
2011-08-10
Solar thermal fuels, which reversibly store solar energy in molecular bonds, are a tantalizing prospect for clean, renewable, and transportable energy conversion/storage. However, large-scale adoption requires enhanced energy storage capacity and thermal stability. Here we present a novel solar thermal fuel, composed of azobenzene-functionalized carbon nanotubes, with the volumetric energy density of Li-ion batteries. Our work also demonstrates that the inclusion of nanoscale templates is an effective strategy for design of highly cyclable, thermally stable, and energy-dense solar thermal fuels.
Energy Technology Data Exchange (ETDEWEB)
Saja, D; Joe, I Hubert; Jayakumar, V S [Department of Physics, Mar Ivanios College, Thiruvananthapuram-695015, Kerala (India)
2006-01-01
The NIR-FT Raman, FT-IR spectral analysis of potential NLO material P-Amino Acetanilide is carried out by density functional computations. The optimized geometry shows that NH2 and NHCOCH3 groups substituted in para position of phenyl ring are non-planar which predicts maximum conjugation of molecule with donor and acceptor groups. Vibrational analysis reveals that simultaneous IR and Raman activation of the phenyl ring modes also provide evidence for the charge transfer interaction between the donors and the acceptor can make the molecule highly polarized and the intra molecular charge transfer interaction must be responsible for the NLO properties of PAA.
On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization
Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.
2018-01-01
Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.
Magnetic edge states in MoS2 characterized using density-functional theory
DEFF Research Database (Denmark)
Vojvodic, Aleksandra; Hinnemann, B.; Nørskov, Jens Kehlet
2009-01-01
It is known that the edges of a two-dimensional slab of insulating MoS2 exhibit one-dimensional metallic edge states, the so-called "brim states." Here, we find from density-functional theory calculations that several edge structures, which are relevant for the hydrodesulfurization process......, are magnetic. The magnetism is an edge phenomenon associated with certain metallic edge states. Interestingly, we find that among the two low-index edges, only the S edge displays magnetism under hydrodesulfurization conditions. In addition, the implications of this on the catalytic activity are investigated...
Protein distance constraints predicted by neural networks and probability density functions
DEFF Research Database (Denmark)
Lund, Ole; Frimand, Kenneth; Gorodkin, Jan
1997-01-01
We predict interatomic C-α distances by two independent data driven methods. The first method uses statistically derived probability distributions of the pairwise distance between two amino acids, whilst the latter method consists of a neural network prediction approach equipped with windows taking....... The predictions are based on a data set derived using a new threshold similarity. We show that distances in proteins are predicted more accurately by neural networks than by probability density functions. We show that the accuracy of the predictions can be further increased by using sequence profiles. A threading...
The oxygen reduction reaction mechanism on Pt(111) from density functional theory calculations
DEFF Research Database (Denmark)
Tripkovic, Vladimir; Skulason, Egill; Siahrostami, Samira
2010-01-01
We study the oxygen reduction reaction (ORR) mechanism on a Pt(1 1 1) surface using density functional theory calculations We find that at low overpotentials the surface is covered with a half dissociated water layer We estimate the barrier for proton transfer to this surface and the barrier...... for proton transport parallel to the surface within the half dissociated water network We find both barriers to be small The only potentially dependent step is the proton transfer from water to the half dissociated water layer We find that ORR proceeds via four direct e(-) reductions without significant...