Pourghassem, Hossein
2012-01-01
Material detection is a vital need in dual energy X-ray luggage inspection systems at security of airport and strategic places. In this paper, a novel material detection algorithm based on statistical trainable models using 2-Dimensional power density function (PDF) of three material categories in dual energy X-ray images is proposed. In this algorithm, the PDF of each material category as a statistical model is estimated from transmission measurement values of low and high energy X-ray images by Gaussian Mixture Models (GMM). Material label of each pixel of object is determined based on dependency probability of its transmission measurement values in the low and high energy to PDF of three material categories (metallic, organic and mixed materials). The performance of material detection algorithm is improved by a maximum voting scheme in a neighborhood of image as a post-processing stage. Using two background removing and denoising stages, high and low energy X-ray images are enhanced as a pre-processing procedure. For improving the discrimination capability of the proposed material detection algorithm, the details of the low and high energy X-ray images are added to constructed color image which includes three colors (orange, blue and green) for representing the organic, metallic and mixed materials. The proposed algorithm is evaluated on real images that had been captured from a commercial dual energy X-ray luggage inspection system. The obtained results show that the proposed algorithm is effective and operative in detection of the metallic, organic and mixed materials with acceptable accuracy.
General performance of density functionals.
Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João
2007-10-25
The density functional theory (DFT) foundations date from the 1920s with the work of Thomas and Fermi, but it was after the work of Hohenberg, Kohn, and Sham in the 1960s, and particularly with the appearance of the B3LYP functional in the early 1990s, that the widespread application of DFT has become a reality. DFT is less computationally demanding than other computational methods with a similar accuracy, being able to include electron correlation in the calculations at a fraction of time of post-Hartree-Fock methodologies. In this review we provide a brief outline of the density functional theory and of the historic development of the field, focusing later on the several types of density functionals currently available, and finishing with a detailed analysis of the performance of DFT across a wide range of chemical properties and system types, reviewed from the most recent benchmarking studies, which encompass several well-established density functionals together with the most recent efforts in the field. Globally, an overall picture of the level of performance of the plethora of currently available density functionals for each chemical property is drawn, with particular attention being dedicated to the relative performance of the popular B3LYP density functional.
Partition density functional theory
NASA Astrophysics Data System (ADS)
Nafziger, Jonathan
Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from scratch using real-space grids. It is shown that all three of these programs can exactly reproduce a KS-DFT calculation via fragment calculations. The first of our in-house codes handles non-interacting electrons in arbitrary one-dimensional potentials with any number of fragments. This code is used to explore how the exact partition potential changes for different partitionings of the same system and also to study features which determine which systems yield non-integer PDFT occupations and which systems are locked into integer PDFT occupations. The second in-house code, CADMium, performs real-space calculations of diatomic molecules. Features of the exact partition potential are studied for a variety of cases and an analytical formula determining singularities in the partition potential is derived. We introduce an approximation for the non-additive kinetic energy and show how this quantity can be computed exactly. Finally a PDFT functional is developed to address the issues of static correlation and delocalization errors in approximations within DFT. The functional is applied to the dissociation of H2 + and H2.
Density-dependent covariant energy density functionals
Lalazissis, G. A.
2012-10-20
Relativistic nuclear energy density functionals are applied to the description of a variety of nuclear structure phenomena at and away fromstability line. Isoscalar monopole, isovector dipole and isoscalar quadrupole giant resonances are calculated using fully self-consistent relativistic quasiparticle randomphase approximation, based on the relativistic Hartree-Bogoliubovmodel. The impact of pairing correlations on the fission barriers in heavy and superheavy nuclei is examined. The role of pion in constructing desnity functionals is also investigated.
Density functional theory: Foundations reviewed
NASA Astrophysics Data System (ADS)
Kryachko, Eugene S.; Ludeña, Eduardo V.
2014-11-01
transformation (local-scaling of coordinates proceeds through density transformation) and so, because these functionals are constructed from prototype N-particle wavefunctions, the ensuing density functionals already have built-in N-representability conditions. This theory is presented in great detail with the purpose of illustrating an alternative way to HKS-DFT which could be used to improve the construction of HKS-DFT functionals. Let us clearly indicate, however, that although appealing from a theoretical point of view, the actual application of LS-DFT to large systems has not taken place mostly because of technical difficulties. Thus, our aim in introducing this theory is to foster a better understanding of its foundations with the hope that it may promote a cross-hybridization with the already existing approaches. Also, to complete our previous discussion on symmetry, in particular, spin-symmetry, we discuss this issue from the perspective of LS-DFT. Finally, in Section 6, we discuss dispersion molecular forces emphasizing their relevance to DFT approaches.
Phenomenological Relativistic Energy Density Functionals
Lalazissis, G. A.; Kartzikos, S.; Niksic, T.; Paar, N.; Vretenar, D.; Ring, P.
2009-08-26
The framework of relativistic nuclear energy density functionals is applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of beta-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure is explored using the fully consistent quasiparticle random-phase approximation based on the relativistic Hartree-Bogoliubov model. Recent applications of energy density functionals with explicit density dependence of the meson-nucleon couplings are presented.
Wave-function functionals for the density
Slamet, Marlina; Pan Xiaoyin; Sahni, Viraht
2011-11-15
We extend the idea of the constrained-search variational method for the construction of wave-function functionals {psi}[{chi}] of functions {chi}. The search is constrained to those functions {chi} such that {psi}[{chi}] reproduces the density {rho}(r) while simultaneously leading to an upper bound to the energy. The functionals are thereby normalized and automatically satisfy the electron-nucleus coalescence condition. The functionals {psi}[{chi}] are also constructed to satisfy the electron-electron coalescence condition. The method is applied to the ground state of the helium atom to construct functionals {psi}[{chi}] that reproduce the density as given by the Kinoshita correlated wave function. The expectation of single-particle operators W={Sigma}{sub i}r{sub i}{sup n}, n=-2,-1,1,2, W={Sigma}{sub i}{delta}(r{sub i}) are exact, as must be the case. The expectations of the kinetic energy operator W=-(1/2){Sigma}{sub i}{nabla}{sub i}{sup 2}, the two-particle operators W={Sigma}{sub n}u{sup n}, n=-2,-1,1,2, where u=|r{sub i}-r{sub j}|, and the energy are accurate. We note that the construction of such functionals {psi}[{chi}] is an application of the Levy-Lieb constrained-search definition of density functional theory. It is thereby possible to rigorously determine which functional {psi}[{chi}] is closer to the true wave function.
Density functionals from deep learning
NASA Astrophysics Data System (ADS)
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.
Density functional theory: Foundations reviewed
NASA Astrophysics Data System (ADS)
Kryachko, Eugene S.; Ludeña, Eduardo V.
2014-11-01
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
Gedanken densities and exact constraints in density functional theory
Perdew, John P.; Ruzsinszky, Adrienn; Sun, Jianwei; Burke, Kieron
2014-05-14
Approximations to the exact density functional for the exchange-correlation energy of a many-electron ground state can be constructed by satisfying constraints that are universal, i.e., valid for all electron densities. Gedanken densities are designed for the purpose of this construction, but need not be realistic. The uniform electron gas is an old gedanken density. Here, we propose a spherical two-electron gedanken density in which the dimensionless density gradient can be an arbitrary positive constant wherever the density is non-zero. The Lieb-Oxford lower bound on the exchange energy can be satisfied within a generalized gradient approximation (GGA) by bounding its enhancement factor or simplest GGA exchange-energy density. This enhancement-factor bound is well known to be sufficient, but our gedanken density shows that it is also necessary. The conventional exact exchange-energy density satisfies no such local bound, but energy densities are not unique, and the simplest GGA exchange-energy density is not an approximation to it. We further derive a strongly and optimally tightened bound on the exchange enhancement factor of a two-electron density, which is satisfied by the local density approximation but is violated by all published GGA's or meta-GGA’s. Finally, some consequences of the non-uniform density-scaling behavior for the asymptotics of the exchange enhancement factor of a GGA or meta-GGA are given.
GyPSuM: A Detailed Tomographic Model of Mantle Density and Seismic Wave Speeds
Simmons, N A; Forte, A M; Boschi, L; Grand, S P
2010-03-30
GyPSuM is a tomographic model fo mantle seismic shear wave (S) speeds, compressional wave (P) speeds and detailed density anomalies that drive mantle flow. the model is developed through simultaneous inversion of seismic body wave travel times (P and S) and geodynamic observations while considering realistic mineral physics parameters linking the relative behavior of mantle properties (wave speeds and density). Geodynamic observations include the (up to degree 16) global free-air gravity field, divergence of the tectonic plates, dynamic topography of the free surface, and the flow-induced excess ellipticity of the core-mantle boundary. GyPSuM is built with the philosophy that heterogeneity that most closely resembles thermal variations is the simplest possible solution. Models of the density field from Earth's free oscillations have provided great insight into the density configuration of the mantle; but are limited to very long-wavelength solutions. Alternatively, simply scaling higher resolution seismic images to density anomalies generates density fields that do not satisfy geodynamic observations. The current study provides detailed density structures in the mantle while directly satisfying geodynamic observations through a joint seismic-geodynamic inversion process. Notable density field observations include high-density piles at the base of the superplume structures, supporting the fundamental results of past normal mode studies. However, these features are more localized and lower amplitude than past studies would suggest. When we consider all seismic anomalies in GyPSuM, we find that P and S-wave speeds are strongly correlated throughout the mantle. However, correlations between the high-velocity S zones in the deep mantle ({approx} 2000 km depth) and corresponding P-wave anomalies are very low suggesting a systematic divergence from simplified thermal effects in ancient subducted slab anomalies. Nevertheless, they argue that temperature variations are the
Covariant density functional theory for magnetic rotation
NASA Astrophysics Data System (ADS)
Peng, J.; Meng, J.; Ring, P.; Zhang, S. Q.
2008-08-01
The tilted axis cranking formalism is implemented in relativistic mean field (RMF) theory. It is used for a microscopic description of magnetic rotation in the framework of covariant density functional theory. We assume that the rotational axis is in the xz plane and consider systems with the two symmetries P (space reflection) and PyT (a combination of a reflection in the y direction and time reversal). A computer code based on these symmetries is developed, and first applications are discussed for the nucleus Gd142: the rotational band based on the configuration πh11/22⊗νh11/2-2 is investigated in a fully microscopic and self-consistent way. The results are compared with available data, such as spectra and electromagnetic transition ratios B(M1)/B(E2). The relation between rotational velocity and angular momentum are discussed in detail together with the shears mechanism characteristic of magnetic rotation.
Finding Density Functionals with Machine Learning
NASA Astrophysics Data System (ADS)
Snyder, John C.; Rupp, Matthias; Hansen, Katja; Müller, Klaus-Robert; Burke, Kieron
2012-06-01
Machine learning is used to approximate density functionals. For the model problem of the kinetic energy of noninteracting fermions in 1D, mean absolute errors below 1kcal/mol on test densities similar to the training set are reached with fewer than 100 training densities. A predictor identifies if a test density is within the interpolation region. Via principal component analysis, a projected functional derivative finds highly accurate self-consistent densities. The challenges for application of our method to real electronic structure problems are discussed.
Magnetic fields and density functional theory
Salsbury Jr., Freddie
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.
Density functional theory for carbon dioxide crystal
Chang, Yiwen; Mi, Jianguo Zhong, Chongli
2014-05-28
We present a density functional approach to describe the solid−liquid phase transition, interfacial and crystal structure, and properties of polyatomic CO{sub 2}. Unlike previous phase field crystal model or density functional theory, which are derived from the second order direct correlation function, the present density functional approach is based on the fundamental measure theory for hard-sphere repulsion in solid. More importantly, the contributions of enthalpic interactions due to the dispersive attractions and of entropic interactions arising from the molecular architecture are integrated in the density functional model. Using the theoretical model, the predicted liquid and solid densities of CO{sub 2} at equilibrium triple point are in good agreement with the experimental values. Based on the structure of crystal-liquid interfaces in different planes, the corresponding interfacial tensions are predicted. Their respective accuracies need to be tested.
Accurate density functional thermochemistry for larger molecules.
Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.
1997-06-20
Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).
Maps of current density using density-functional methods
NASA Astrophysics Data System (ADS)
Soncini, A.; Teale, A. M.; Helgaker, T.; de Proft, F.; Tozer, D. J.
2008-08-01
The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O3, CO, PN, and H2CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.
Multicomponent density functional theory embedding formulation
NASA Astrophysics Data System (ADS)
Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.; Hammes-Schiffer, Sharon
2016-07-01
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.
Combining density-functional theory and density-matrix-functional theory
Rohr, Daniel R.; Pernal, Katarzyna; Toulouse, Julien
2010-11-15
We combine density-functional theory with density-matrix-functional theory to draw the best from both worlds. This is achieved by range separation of the electronic interaction which permits one to rigorously combine a short-range density functional with a long-range density-matrix functional. The short-range density functional is approximated by the short-range version of the Perdew-Burke-Ernzerhof functional (srPBE). The long-range density-matrix functional is approximated by the long-range version of the Buijse-Baerends functional (lrBB). The obtained srPBE+lrBB method accurately describes both the static and dynamic electron correlation at a computational cost similar to that of standard density-functional approximations. This is shown for the dissociation curves of the H{sub 2}, LiH, BH, and HF molecules.
Locality of correlation in density functional theory.
Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano
2016-08-01
The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed. PMID:27497544
Locality of correlation in density functional theory
NASA Astrophysics Data System (ADS)
Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano
2016-08-01
The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.
Locality of correlation in density functional theory.
Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano
2016-08-01
The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.
Spectral density response functions for modulated polarimeters.
LaCasse, Charles F; Rodríguez-Herrera, Oscar G; Chipman, Russell A; Tyo, J Scott
2015-11-10
Conventional imaging devices are often compared using their optical transfer functions (OTFs) in space and their impulse responses in time. Modulated polarimeters cannot be directly compared this way, since they are frequency multiplexed. Here we define a spectral density response function that describes how the spectral density matrix of the Stokes parameters for an object transfers through a modulated polarimeter. This response function facilitates the objective comparison of polarimeters in a way that is analogous to the OTF for conventional imaging systems. The spectral density response is used to calculate a Wiener filter for a rotating analyzer polarimeter as an example of filter optimization for modulated polarimetry. PMID:26560776
Density-functional theory of thermoelectric phenomena.
Eich, F G; Di Ventra, M; Vignale, G
2014-05-16
We introduce a nonequilibrium density-functional theory of local temperature and associated local energy density that is suited for the study of thermoelectric phenomena. The theory rests on a local temperature field coupled to the energy-density operator. We identify the excess-energy density, in addition to the particle density, as the basic variable, which is reproduced by an effective noninteracting Kohn-Sham system. A novel Kohn-Sham equation emerges featuring a time-dependent and spatially varying mass which represents local temperature variations. The adiabatic contribution to the Kohn-Sham potentials is related to the entropy viewed as a functional of the particle and energy density. Dissipation can be taken into account by employing linear response theory and the thermoelectric transport coefficients of the electron gas.
Poisson brackets for densities of functionals
NASA Astrophysics Data System (ADS)
Dickey, Leonid A.
In the theory of integrable systems and in other field theories one usually deals with Poisson brackets between functionals. The latter are integrals of densities. Densities are defined up to divergence (boundary) terms. A question arises, is it possible to define a reasonable Poisson bracket for densities themselves? A general theory was suggested by Barnich, Fulp, Lada, Markl and Stasheff which has led them to the notion of a strong homotopy Lie group, (sh Lie). We are giving a few concrete examples.
Nagy, A.
2011-09-15
A link between density and pair density functional theories is presented. Density and pair density scaling are used to derive the Euler equation in both theories. Density scaling provides a constructive way of obtaining approximations for the Pauli potential. The Pauli potential (energy) of the density functional theory is expressed as the difference of the scaled and original exchange-correlation potentials (energies).
Detailed Northern Anatolian Fault Zone crustal structure from receiver functions
NASA Astrophysics Data System (ADS)
Cornwell, D. G.; Kahraman, M.; Thompson, D. A.; Houseman, G. A.; Rost, S.; Turkelli, N.; Teoman, U.; Altuncu Poyraz, S.; Gülen, L.; Utkucu, M.
2013-12-01
We present high resolution images derived from receiver functions of the continental crust in Northern Turkey that is dissected by two fault strands of the Northern Anatolian Fault Zone (NAFZ). The NAFZ is a major continental strike-slip fault system that is comparable in length and slip rate to the San Andreas Fault Zone. Recent large earthquakes occurred towards the western end of the NAFZ in 1999 at Izmit (M7.5) and Düzce (M7.2). As part of the multi-disciplinary Faultlab project, we aim to develop a model of NAFZ crustal structure and locate deformation by constraining variations in seismic properties and anisotropy in the upper and lower crust. The crustal model will be an input to test deformation scenarios in order to match geodetic observations from different phases of the earthquake loading cycle. We calculated receiver functions from teleseismic earthquakes recorded by a rectangular seismometer array spanning the NAFZ with 66 stations at a nominal inter-station spacing of 7 km and 7 additional stations further afield. This Dense Array for North Anatolia (DANA) was deployed from May 2012 until September 2013 and we selected large events (Mw>5.5) from the high quality seismological dataset to analyze further. Receiver functions were calculated for different frequency bands then collected into regional stacks before being inverted for crustal S-wave velocity structure beneath the entire DANA array footprint. In addition, we applied common conversion point (CCP) migration using a regional velocity model to construct a migrated 3D volume of P-to-S converted and multiple energy in order to identify the major crustal features and layer boundaries. We also performed the CCP migration with transverse receiver functions in order to identify regions of anisotropy within the crustal layers. Our preliminary results show a heterogeneous crust above a flat Moho that is typically at a depth of 33 km. We do not observe a prominent step in the Moho beneath the surface
Detailed Numerical Simulation of Liquid Jet In Crossflow Atomization with High Density Ratios
NASA Astrophysics Data System (ADS)
Ghods, Sina
The atomization of a liquid jet by a high speed cross-flowing gas has many applications such as gas turbines and augmentors. The mechanisms by which the liquid jet initially breaks up, however, are not well understood. Experimental studies suggest the dependence of spray properties on operating conditions and nozzle geom- etry. Detailed numerical simulations can offer better understanding of the underlying physical mechanisms that lead to the breakup of the injected liquid jet. In this work, detailed numerical simulation results of turbulent liquid jets injected into turbulent gaseous cross flows for different density ratios is presented. A finite volume, balanced force fractional step flow solver to solve the Navier-Stokes equations is employed and coupled to a Refined Level Set Grid method to follow the phase interface. To enable the simulation of atomization of high density ratio fluids, we ensure discrete consistency between the solution of the conservative momentum equation and the level set based continuity equation by employing the Consistent Rescaled Momentum Transport (CRMT) method. The impact of different inflow jet boundary conditions on different jet properties including jet penetration is analyzed and results are compared to those obtained experimentally by Brown & McDonell(2006). In addition, instability analysis is performed to find the most dominant insta- bility mechanism that causes the liquid jet to breakup. Linear instability analysis is achieved using linear theories for Rayleigh-Taylor and Kelvin- Helmholtz instabilities and non-linear analysis is performed using our flow solver with different inflow jet boundary conditions.
NASA Astrophysics Data System (ADS)
Fortin, W.; Holbrook, W. S.; Mallick, S.; Everson, E. D.; Tobin, H. J.; Keranen, K. M.
2014-12-01
Understanding the geologic composition of the Cascadia Subduction Zone (CSZ) is critically important in assessing seismic hazards in the Pacific Northwest. Despite being a potential earthquake and tsunami threat to millions of people, key details of the structure and fault mechanisms remain poorly understood in the CSZ. In particular, the position and character of the subduction interface remains elusive due to its relative aseismicity and low seismic reflectivity, making imaging difficult for both passive and active source methods. Modern active-source reflection seismic data acquired as part of the COAST project in 2012 provide an opportunity to study the transition from the Cascadia basin, across the deformation front, and into the accretionary prism. Coupled with advances in seismic inversion methods, this new data allow us to produce detailed velocity models of the CSZ and accurate pre-stack depth migrations for studying geologic structure. While still computationally expensive, current computing clusters can perform seismic inversions at resolutions that match that of the seismic image itself. Here we present pre-stack full waveform inversions of the central seismic line of the COAST survey offshore Washington state. The resultant velocity model is produced by inversion at every CMP location, 6.25 m laterally, with vertical resolution of 0.2 times the dominant seismic frequency. We report a good average correlation value above 0.8 across the entire seismic line, determined by comparing synthetic gathers to the real pre-stack gathers. These detailed velocity models, both Vp and Vs, along with the density model, are a necessary step toward a detailed porosity cross section to be used to determine the role of fluids in the CSZ. Additionally, the P-velocity model is used to produce a pre-stack depth migration image of the CSZ.
Particle conservation in dynamical density functional theory
NASA Astrophysics Data System (ADS)
de las Heras, Daniel; Brader, Joseph M.; Fortini, Andrea; Schmidt, Matthias
2016-06-01
We present the exact adiabatic theory for the dynamics of the inhomogeneous density distribution of a classical fluid. Erroneous particle number fluctuations of dynamical density functional theory are absent, both for canonical and grand canonical initial conditions. We obtain the canonical free energy functional, which yields the adiabatic interparticle forces of overdamped Brownian motion. Using an exact and one of the most advanced approximate hard core free energy functionals, we obtain excellent agreement with simulations. The theory applies to finite systems in and out of equilibrium.
Particle conservation in dynamical density functional theory.
de Las Heras, Daniel; Brader, Joseph M; Fortini, Andrea; Schmidt, Matthias
2016-06-22
We present the exact adiabatic theory for the dynamics of the inhomogeneous density distribution of a classical fluid. Erroneous particle number fluctuations of dynamical density functional theory are absent, both for canonical and grand canonical initial conditions. We obtain the canonical free energy functional, which yields the adiabatic interparticle forces of overdamped Brownian motion. Using an exact and one of the most advanced approximate hard core free energy functionals, we obtain excellent agreement with simulations. The theory applies to finite systems in and out of equilibrium.
Nonlocal kinetic-energy-density functionals
Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |
1996-04-01
In this paper we present nonlocal kinetic-energy functionals {ital T}[{ital n}] within the average density approximation (ADA) framework, which do not require any extra input when applied to any electron system and recover the exact kinetic energy and the linear response function of a homogeneous system. In contrast with previous ADA functionals, these present good behavior of the long-range tail of the exact weight function. The averaging procedure for the kinetic functional (averaging the Fermi momentum of the electron gas, instead of averaging the electron density) leads to a functional without numerical difficulties in the calculation of extended systems, and it gives excellent results when applied to atoms and jellium surfaces. {copyright} {ital 1996 The American Physical Society.}
Detailed Shape and Evolutionary Behavior of the X-Ray Luminosity Function of Active Galactic Nuclei
NASA Astrophysics Data System (ADS)
Miyaji, T.; Hasinger, G.; Salvato, M.; Brusa, M.; Cappelluti, N.; Civano, F.; Puccetti, S.; Elvis, M.; Brunner, H.; Fotopoulou, S.; Ueda, Y.; Griffiths, R. E.; Koekemoer, A. M.; Akiyama, M.; Comastri, A.; Gilli, R.; Lanzuisi, G.; Merloni, A.; Vignali, C.
2015-05-01
We construct the rest-frame 2-10 keV intrinsic X-ray luminosity function (XLF) of active galactic nuclei (AGNs) from a combination of X-ray surveys from the all-sky Swift BAT survey to the Chandra Deep Field South. We use ˜3200 AGNs in our analysis, which covers six orders of magnitude in flux. The inclusion of XMM and Chandra COSMOS data has allowed us to investigate the detailed behavior of the XLF and evolution. In deriving our XLF, we take into account realistic AGN spectrum templates, absorption corrections, and probability density distributions in photometric redshift. We present an analytical expression for the overall behavior of the XLF in terms of the luminosity-dependent density evolution, smoothed two-power-law expressions in 11 redshift shells, three-segment power-law expression of the number density evolution in four luminosity classes, and binned XLF. We observe a sudden flattening of the low luminosity end slope of the XLF slope at z ≳0.6. Detailed structures of the AGN downsizing have also been revealed, where the number density curves have two clear breaks at all luminosity classes above log {{L}X}\\gt 43. The two-break structure is suggestive of two-phase AGN evolution, consisting of major merger triggering and secular processes.
Kinetic density functional theory of freezing.
Baskaran, Arvind; Baskaran, Aparna; Lowengrub, John
2014-11-01
A theory of freezing of a dense hard sphere gas is presented. Starting from a revised Enskog theory, hydrodynamic equations that account for non-local variations in the density but local variations in the flow field are derived using a modified Chapman Enskog procedure. These hydrodynamic equations, which retain structural correlations, are shown to be effectively a time dependent density functional theory. The ability of this theory to capture the solid liquid phase transition is established through analysis and numerical simulations.
Periodic subsystem density-functional theory
Genova, Alessandro; Pavanello, Michele; Ceresoli, Davide
2014-11-07
By partitioning the electron density into subsystem contributions, the Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) has recently emerged as a powerful tool for reducing the computational scaling of Kohn–Sham DFT. To date, however, FDE has been employed to molecular systems only. Periodic systems, such as metals, semiconductors, and other crystalline solids have been outside the applicability of FDE, mostly because of the lack of a periodic FDE implementation. To fill this gap, in this work we aim at extending FDE to treat subsystems of molecular and periodic character. This goal is achieved by a dual approach. On one side, the development of a theoretical framework for periodic subsystem DFT. On the other, the realization of the method into a parallel computer code. We find that periodic FDE is capable of reproducing total electron densities and (to a lesser extent) also interaction energies of molecular systems weakly interacting with metallic surfaces. In the pilot calculations considered, we find that FDE fails in those cases where there is appreciable density overlap between the subsystems. Conversely, we find FDE to be in semiquantitative agreement with Kohn–Sham DFT when the inter-subsystem density overlap is low. We also conclude that to make FDE a suitable method for describing molecular adsorption at surfaces, kinetic energy density functionals that go beyond the GGA level must be employed.
Density functional theory for pair correlation functions in polymeric liquids
NASA Astrophysics Data System (ADS)
Yethiraj, Arun; Fynewever, Herb; Shew, Chwen-Yang
2001-03-01
A density functional theory is presented for the pair correlation functions in polymeric liquids. The theory uses the Yethiraj-Woodward free-energy functional for the polymeric liquid, where the ideal gas free-energy functional is treated exactly and the excess free-energy functional is obtained using a weighted density approximation with the simplest choice of the weighting function. Pair correlation functions are obtained using the Percus trick, where the external field is taken to be a single polymer molecule. The minimization of the free energy in the theory requires a two molecule simulation at each iteration. The theory is very accurate for the pair correlation functions in freely jointed tangent-hard-sphere chains and freely rotating fused-hard-sphere chains, especially at low densities and for long chains. In addition, the theory allows the calculation of the virial pressure in these systems and shows a remarkable degree of consistency between the virial and compressibility pressure.
Density Functionals with Broad Applicability in Chemistry
Zhao, Yan; Truhlar, Donald G.
2008-02-01
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by mediumrange correlation energy, such as van der Waals attraction, aromatic-aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree-Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-theboard” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06- 2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic-aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate
Koopmans' condition for density-functional theory
Dabo, Ismaila; Ferretti, Andrea; Poilvert, Nicolas; Marzari, Nicola; Li, Yanli; Cococcioni, Matteo
2010-09-15
In approximate Kohn-Sham density-functional theory, self-interaction manifests itself as the dependence of the energy of an orbital on its fractional occupation. This unphysical behavior translates into qualitative and quantitative errors that pervade many fundamental aspects of density-functional predictions. Here, we first examine self-interaction in terms of the discrepancy between total and partial electron removal energies, and then highlight the importance of imposing the generalized Koopmans' condition - that identifies orbital energies as opposite total electron removal energies - to resolve this discrepancy. In the process, we derive a correction to approximate functionals that, in the frozen-orbital approximation, eliminates the unphysical occupation dependence of orbital energies up to the third order in the single-particle densities. This non-Koopmans correction brings physical meaning to single-particle energies; when applied to common local or semilocal density functionals it provides results that are in excellent agreement with experimental data - with an accuracy comparable to that of GW many-body perturbation theory - while providing an explicit total energy functional that preserves or improves on the description of established structural properties.
Photoelectric scanner makes detailed work function maps of metal surface
NASA Technical Reports Server (NTRS)
Rasor, N. S.
1966-01-01
Photoelectric scanning device maps the work function of a metal surface by scanning it with a light spot and measuring the resulting photocurrent. The device is capable of use over a range of surface temperatures.
Communication: Embedded fragment stochastic density functional theory
Neuhauser, Daniel; Baer, Roi; Rabani, Eran
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.
Communication: Embedded fragment stochastic density functional theory
NASA Astrophysics Data System (ADS)
Neuhauser, Daniel; Baer, Roi; Rabani, Eran
2014-07-01
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.
Density functional theory studies of etoricoxib
NASA Astrophysics Data System (ADS)
Sachdeva, Ritika; Kaur, Prabhjot; Singh, V. P.; Saini, G. S. S.
2016-05-01
Etoricoxib is a COX-2 selective inhibitor drug with molecular formula C18H15ClN2O2S. It is primarily used for the treatment of arthritis(rheumatoid, psoriatic, osteoarthritis), ankylosing spondylitis, gout and chronic low back pain. Theoretical studies of the molecule including geometry optimization and vibrational frequency calculations were carried out with the help of density functional theory calculations using 6-311++ g (d, p) basis set and B3LYP functional.
Density functional theory: Fixing Jacob's ladder
NASA Astrophysics Data System (ADS)
Car, Roberto
2016-09-01
Density functional theory calculations can be carried out with different levels of accuracy, forming a hierarchy that is often represented by the rungs of a ladder. Now a new method has been developed that significantly improves the accuracy of the 'third rung' when calculating the properties of diversely bonded systems.
Towards the Universal Nuclear Energy Density Functional
Stoitsov, Mario; More, J.; Nazarewicz, Witold; Pei, Junchen; Sarich, J.; Schunck, Nicolas F; Staszczak, A.; Wild, S.
2009-01-01
The UNEDF SciDAC project to develop and optimize the energy density functional for atomic nuclei using state-of-the-art computational infrastructure is briefly described. The ultimate goal is to replace current phenomenological models of the nucleus with a well-founded microscopic theory with minimal uncertainties, capable of describing nuclear data and extrapolating to unknown regions.
Basis convergence of range-separated density-functional theory
Franck, Odile Mussard, Bastien; Luppi, Eleonora Toulouse, Julien
2015-02-21
Range-separated density-functional theory (DFT) is an alternative approach to Kohn-Sham density-functional theory. The strategy of range-separated density-functional theory consists in separating the Coulomb electron-electron interaction into long-range and short-range components and treating the long-range part by an explicit many-body wave-function method and the short-range part by a density-functional approximation. Among the advantages of using many-body methods for the long-range part of the electron-electron interaction is that they are much less sensitive to the one-electron atomic basis compared to the case of the standard Coulomb interaction. Here, we provide a detailed study of the basis convergence of range-separated density-functional theory. We study the convergence of the partial-wave expansion of the long-range wave function near the electron-electron coalescence. We show that the rate of convergence is exponential with respect to the maximal angular momentum L for the long-range wave function, whereas it is polynomial for the case of the Coulomb interaction. We also study the convergence of the long-range second-order Møller-Plesset correlation energy of four systems (He, Ne, N{sub 2}, and H{sub 2}O) with cardinal number X of the Dunning basis sets cc − p(C)V XZ and find that the error in the correlation energy is best fitted by an exponential in X. This leads us to propose a three-point complete-basis-set extrapolation scheme for range-separated density-functional theory based on an exponential formula.
Probability density function learning by unsupervised neurons.
Fiori, S
2001-10-01
In a recent work, we introduced the concept of pseudo-polynomial adaptive activation function neuron (FAN) and presented an unsupervised information-theoretic learning theory for such structure. The learning model is based on entropy optimization and provides a way of learning probability distributions from incomplete data. The aim of the present paper is to illustrate some theoretical features of the FAN neuron, to extend its learning theory to asymmetrical density function approximation, and to provide an analytical and numerical comparison with other known density function estimation methods, with special emphasis to the universal approximation ability. The paper also provides a survey of PDF learning from incomplete data, as well as results of several experiments performed on real-world problems and signals. PMID:11709808
NASA Astrophysics Data System (ADS)
Pribram-Jones, Aurora
Warm dense matter (WDM) is a high energy phase between solids and plasmas, with characteristics of both. It is present in the centers of giant planets, within the earth's core, and on the path to ignition of inertial confinement fusion. The high temperatures and pressures of warm dense matter lead to complications in its simulation, as both classical and quantum effects must be included. One of the most successful simulation methods is density functional theory-molecular dynamics (DFT-MD). Despite great success in a diverse array of applications, DFT-MD remains computationally expensive and it neglects the explicit temperature dependence of electron-electron interactions known to exist within exact DFT. Finite-temperature density functional theory (FT DFT) is an extension of the wildly successful ground-state DFT formalism via thermal ensembles, broadening its quantum mechanical treatment of electrons to include systems at non-zero temperatures. Exact mathematical conditions have been used to predict the behavior of approximations in limiting conditions and to connect FT DFT to the ground-state theory. An introduction to FT DFT is given within the context of ensemble DFT and the larger field of DFT is discussed for context. Ensemble DFT is used to describe ensembles of ground-state and excited systems. Exact conditions in ensemble DFT and the performance of approximations depend on ensemble weights. Using an inversion method, exact Kohn-Sham ensemble potentials are found and compared to approximations. The symmetry eigenstate Hartree-exchange approximation is in good agreement with exact calculations because of its inclusion of an ensemble derivative discontinuity. Since ensemble weights in FT DFT are temperature-dependent Fermi weights, this insight may help develop approximations well-suited to both ground-state and FT DFT. A novel, highly efficient approach to free energy calculations, finite-temperature potential functional theory, is derived, which has the
Density functional calculations on model tyrosyl radicals.
Himo, F; Gräslund, A; Eriksson, L A
1997-01-01
A gradient-corrected density functional theory approach (PWP86) has been applied, together with large basis sets (IGLO-III), to investigate the structure and hyperfine properties of model tyrosyl free radicals. In nature, these radicals are observed in, e.g., the charge transfer pathways in photosystem II (PSII) and in ribonucleotide reductases (RNRs). By comparing spin density distributions and proton hyperfine couplings with experimental data, it is confirmed that the tyrosyl radicals present in the proteins are neutral. It is shown that hydrogen bonding to the phenoxyl oxygen atom, when present, causes a reduction in spin density on O and a corresponding increase on C4. Calculated proton hyperfine coupling constants for the beta-protons show that the alpha-carbon is rotated 75-80 degrees out of the plane of the ring in PSII and Salmonella typhimurium RNR, but only 20-30 degrees in, e.g., Escherichia coli, mouse, herpes simplex, and bacteriophage T4-induced RNRs. Furthermore, based on the present calculations, we have revised the empirical parameters used in the experimental determination of the oxygen spin density in the tyrosyl radical in E. coli RNR and of the ring carbon spin densities, from measured hyperfine coupling constants. Images FIGURE 1 FIGURE 5 PMID:9083661
Teaching Density Functional Theory Through Experiential Learning
NASA Astrophysics Data System (ADS)
Narasimhan, Shobhana
2015-09-01
Today, quantum mechanical density functional theory is often the method of choice for performing accurate calculations on atomic, molecular and condensed matter systems. Here, I share some of my experiences in teaching the necessary basics of solid state physics, as well as the theory and practice of density functional theory, in a number of workshops held in developing countries over the past two decades. I discuss the advantages of supplementing the usual mathematically formal teaching methods, characteristic of graduate courses, with the use of visual imagery and analogies. I also describe a successful experiment we carried out, which resulted in a joint publication co-authored by 67 lecturers and students participating in a summer school.
Density functional theory for hard polyhedra.
Marechal, Matthieu; Löwen, Hartmut
2013-03-29
Using the framework of geometry-based fundamental-measure theory, we develop a classical density functional for hard polyhedra and their mixtures and apply it to inhomogeneous fluids of Platonic solids near a hard wall. As revealed by Monte Carlo simulations, the faceted shape of the polyhedra leads to complex layering and orientational ordering near the wall, which is excellently reproduced by our theory. These effects can be verified in real-space experiments on polyhedral colloids.
The problem of the universal density functional and the density matrix functional theory
Bobrov, V. B. Trigger, S. A.
2013-04-15
The analysis in this paper shows that the Hohenberg-Kohn theorem is the constellation of two statements: (i) the mathematically rigorous Hohenberg-Kohn lemma, which demonstrates that the same ground-state density cannot correspond to two different potentials of an external field, and (ii) the hypothesis of the existence of the universal density functional. Based on the obtained explicit expression for the nonrel-ativistic particle energy in a local external field, we prove that the energy of the system of more than two non-interacting electrons cannot be a functional of the inhomogeneous density. This result is generalized to the system of interacting electrons. It means that the Hohenberg-Kohn lemma cannot provide justification of the universal density functional for fermions. At the same time, statements of the density functional theory remain valid when considering any number of noninteracting ground-state bosons due to the Bose condensation effect. In the framework of the density matrix functional theory, the hypothesis of the existence of the universal density matrix functional corresponds to the cases of noninteracting particles and to interaction in the Hartree-Fock approximation.
Unveiling the Detailed Density and Velocity Structures of the Protostellar Core B335
NASA Astrophysics Data System (ADS)
Kurono, Yasutaka; Saito, Masao; Kamazaki, Takeshi; Morita, Koh-Ichiro; Kawabe, Ryohei
2013-03-01
We present an observational study of the protostellar core B335 harboring a low-mass Class 0 source. The observations of the H13CO+(J = 1-0) line emission were carried out using the Nobeyama 45 m telescope and Nobeyama Millimeter Array. Our combined image of the interferometer and single-dish data depicts detailed structures of the dense envelope within the core. We found that the core has a radial density profile of n(r)vpropr -p and a reliable difference in the power-law indices between the outer and inner regions of the core: p ≈ 2 for r >~ 4000 AU and p ≈ 1.5 for r <~ 4000 AU. The dense core shows a slight overall velocity gradient of ~1.0 km s-1 over the scale of 20, 000 AU across the outflow axis. We believe that this velocity gradient represents a solid-body-like rotation of the core. The dense envelope has a quite symmetrical velocity structure with a remarkable line broadening toward the core center, which is especially prominent in the position-velocity diagram across the outflow axis. The model calculations of position-velocity diagrams do a good job of reproducing observational results using the collapse model of an isothermal sphere in which the core has an inner free-fall region and an outer region conserving the conditions at the formation stage of a central stellar object. We derived a central stellar mass of ~0.1 M ⊙, and suggest a small inward velocity, v_{r ≥ r_inf}˜ 0 km s^{-1} in the outer core at >~ 4000 AU. We concluded that our data can be well explained by gravitational collapse with a quasi-static initial condition, such as Shu's model, or by the isothermal collapse of a marginally critical Bonnor-Ebert sphere.
Functional connectivity density alterations in schizophrenia
Zhuo, Chuanjun; Zhu, Jiajia; Qin, Wen; Qu, Hongru; Ma, Xiaolei; Tian, Hongjun; Xu, Qingying; Yu, Chunshui
2014-01-01
Background: Schizophrenia is characterized by altered resting-state functional connectivity. Most previous studies have focused on changes in connectivity strengths; however, the alterations in connectivity density in schizophrenia remain largely unknown. Here, we aimed to investigate changes in resting-state functional connectivity density (rsFCD) in schizophrenia. Methods: A total of 95 schizophrenia patients and 93 sex- and age-matched healthy controls (HCs) underwent resting-state functional MRI examinations. The rsFCD, which reflects the total number of functional connections between a given brain voxel and all other voxels in the entire brain, was calculated for each voxel of each subject. Voxel-based comparisons were performed to identify brain regions with significant rsFCD differences between patients and controls (P < 0.05, corrected). Results: Compared with HCs, patients with schizophrenia showed significantly increased rsFCD in the bilateral striatum and hippocampus and significantly decreased rsFCD in the bilateral sensorimotor cortices and right occipital cortex. However, the rsFCD values of these brain regions were not correlated with antipsychotic dosage, illness duration, or clinical symptom severity. Conclusions: The striatal and hippocampal regions and parietal-occipital regions exhibited completely different changes in rsFCD in schizophrenia, which roughly correspond to dopamine activity in these regions in schizophrenia. These findings support the connectivity disorder hypothesis of schizophrenia and increase our understanding of the neural mechanisms of schizophrenia. PMID:25477799
Molecular Density Functional Theory of Water.
Jeanmairet, Guillaume; Levesque, Maximilien; Vuilleumier, Rodolphe; Borgis, Daniel
2013-02-21
Three-dimensional implementations of liquid-state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short-range. The approach is shown to provide the correct 3-D microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two to three orders of magnitude lower than with explicit simulations. PMID:26281876
Pseudospectral time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Ko, Chaehyuk; Malick, David K.; Braden, Dale A.; Friesner, Richard A.; Martínez, Todd J.
2008-03-01
Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.
Direct propagation of probability density functions in hydrological equations
NASA Astrophysics Data System (ADS)
Kunstmann, Harald; Kastens, Marko
2006-06-01
Sustainable decisions in hydrological risk management require detailed information on the probability density function ( pdf) of the model output. Only then probabilities for the failure of a specific management option or the exceedance of critical thresholds (e.g. of pollutants) can be derived. A new approach of uncertainty propagation in hydrological equations is developed that directly propagates the probability density functions of uncertain model input parameters into the corresponding probability density functions of model output. The basics of the methodology are presented and central applications to different disciplines in hydrology are shown. This work focuses on the following basic hydrological equations: (1) pumping test analysis (Theis-equation, propagation of uncertainties in recharge and transmissivity), (2) 1-dim groundwater contaminant transport equation (Gauss-equation, propagation of uncertainties in decay constant and dispersivity), (3) evapotranspiration estimation (Penman-Monteith-equation, propagation of uncertainty in roughness length). The direct propagation of probability densities is restricted to functions that are monotonically increasing or decreasing or that can be separated in corresponding monotonic branches so that inverse functions can be derived. In case no analytic solutions for inverse functions could be derived, semi-analytical approximations were used. It is shown that the results of direct probability density function propagation are in perfect agreement with results obtained from corresponding Monte Carlo derived frequency distributions. Direct pdf propagation, however, has the advantage that is yields exact solutions for the resulting hydrological pdfs rather than approximating discontinuous frequency distributions. It is additionally shown that the type of the resulting pdf depends on the specific values (order of magnitude, respectively) of the standard deviation of the input pdf. The dependency of skewness and kurtosis
UNVEILING THE DETAILED DENSITY AND VELOCITY STRUCTURES OF THE PROTOSTELLAR CORE B335
Kurono, Yasutaka; Saito, Masao; Kamazaki, Takeshi; Morita, Koh-Ichiro; Kawabe, Ryohei
2013-03-10
We present an observational study of the protostellar core B335 harboring a low-mass Class 0 source. The observations of the H{sup 13}CO{sup +}(J = 1-0) line emission were carried out using the Nobeyama 45 m telescope and Nobeyama Millimeter Array. Our combined image of the interferometer and single-dish data depicts detailed structures of the dense envelope within the core. We found that the core has a radial density profile of n(r){proportional_to}r {sup -p} and a reliable difference in the power-law indices between the outer and inner regions of the core: p Almost-Equal-To 2 for r {approx}> 4000 AU and p Almost-Equal-To 1.5 for r {approx}< 4000 AU. The dense core shows a slight overall velocity gradient of {approx}1.0 km s{sup -1} over the scale of 20, 000 AU across the outflow axis. We believe that this velocity gradient represents a solid-body-like rotation of the core. The dense envelope has a quite symmetrical velocity structure with a remarkable line broadening toward the core center, which is especially prominent in the position-velocity diagram across the outflow axis. The model calculations of position-velocity diagrams do a good job of reproducing observational results using the collapse model of an isothermal sphere in which the core has an inner free-fall region and an outer region conserving the conditions at the formation stage of a central stellar object. We derived a central stellar mass of {approx}0.1 M{sub Sun }, and suggest a small inward velocity, v{sub r{>=}r{sub i{sub n{sub f}}}}{approx}0 km s{sup -1} in the outer core at {approx}> 4000 AU. We concluded that our data can be well explained by gravitational collapse with a quasi-static initial condition, such as Shu's model, or by the isothermal collapse of a marginally critical Bonnor-Ebert sphere.
Density functionals for inorganometallic and organometallic chemistry.
Schultz, Nathan E; Zhao, Yan; Truhlar, Donald G
2005-12-15
We present a database of 21 bond dissociation energies for breaking metal-ligand bonds. The molecules in the metal-ligand bond energy database are AgH, CoH, CoO+, CoOH+, CrCH3+, CuOH2+, FeH, Fe(CO)5, FeO, FeS, LiCl, LiO, MgO, MnCH3NiCH2+, Ni(CO)4, RhC, VCO+, VO, and VS. We have also created databases of metal-ligand bond lengths and atomic ionization potentials. The molecules used for bond lengths are AgH, BeO, CoH, CoO+, FeH, FeO, FeS, LiCl, LiO, MgO, RhC, VO, and VS and the ionization potentials are for the following atoms: C, Co, Cr, Cu, Ni, O, and V. The data were chosen based on their diversity and expected reliability, and they are used along with three previously developed databases (transition metal dimer bond energies and bond lengths and main-group molecular atomization energies) for assessing the accuracy of several kinds of density functionals. In particular, we report tests for 42 previously defined functionals: 2 local spin density approximation (LSDA) functionals, 14 generalized gradient approximation (GGA) methods, 13 hybrid GGA methods, 7 meta GGA methods, and 8 hybrid meta GGA methods. In addition to these functionals, we also examine the effectiveness of scaling the correlation energy by testing 13 functionals with scaled or no gradient-corrected correlation energy, and we find that functionals of this kind are more accurate for metal-metal and metal-ligand bonds than any of the functionals already in the literature. We also present a readjusted GGA and a hybrid GGA with parameters adjusted for metals. When we consider these 57 functionals for metal-ligand and metal-metal bond energies simultaneously with main-group atomization energies, atomic ionization potentials, and bond lengths we find that the most accurate functional is G96LYP, followed closely by MPWLYP1M (new in this article), XLYP, BLYP, and MOHLYP (also new in this article). Four of these five functionals have no Hartree-Fock exchange, and the other has only 5%. As a byproduct of this
Recent progress in density functional theory
NASA Astrophysics Data System (ADS)
Truhlar, Donald
2014-03-01
Ongoing work involves several areas of density functional theory: new methods for computing electronic excitation energies, including a new way to remove spin contamination in the spin-flip Tamm-Dancoff approximation and a configuration-interaction-corrected Tamm-Dancoff Approximation for treating conical intersections; new ways to treat open-shell states, including a reinterpreted broken-symmetry method and multi-configuration Kohn-Sham theory; a new exchange-correlation functional; new tests of density functional theory against databases for electronic transition energies and molecules and solids containing metal atoms; and applications. A selection of results will be presented. I am grateful to the following collaborators for contributions to the ongoing work: Boris Averkiev, Rebecca Carlson, Laura Fernandez, Laura Gagliardi, Chad Hoyer, Francesc Illas, Miho Isegawa, Shaohong Li, Giovanni Li Manni, Sijie Luo, Dongxia Ma, Remi Maurice, Rubén Means-Pañeda, Roberto Peverati, Nora Planas, Prasenjit Seal, Pragya Verma, Bo Wang, Xuefei Xu, Ke R. Yang, Haoyu Yu, Wenjing Zhang, and Jingjing Zheng. Supported in part by the AFOSR and U.S. DOE.
Optimization of constrained density functional theory
NASA Astrophysics Data System (ADS)
O'Regan, David D.; Teobaldi, Gilberto
2016-07-01
Constrained density functional theory (cDFT) is a versatile electronic structure method that enables ground-state calculations to be performed subject to physical constraints. It thereby broadens their applicability and utility. Automated Lagrange multiplier optimization is necessary for multiple constraints to be applied efficiently in cDFT, for it to be used in tandem with geometry optimization, or with molecular dynamics. In order to facilitate this, we comprehensively develop the connection between cDFT energy derivatives and response functions, providing a rigorous assessment of the uniqueness and character of cDFT stationary points while accounting for electronic interactions and screening. In particular, we provide a nonperturbative proof that stable stationary points of linear density constraints occur only at energy maxima with respect to their Lagrange multipliers. We show that multiple solutions, hysteresis, and energy discontinuities may occur in cDFT. Expressions are derived, in terms of convenient by-products of cDFT optimization, for quantities such as the dielectric function and a condition number quantifying ill definition in multiple constraint cDFT.
Modulation Based on Probability Density Functions
NASA Technical Reports Server (NTRS)
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.
Density Functional Study of Perovskite Superconductor MgCNi3
NASA Astrophysics Data System (ADS)
Kumar, Jagdish; Sharma, Devina; Kumar, Ranjan; Awana, V. P. S.; Ahluwalia, P. K.
2011-12-01
We here report the first principle density functional study of MgCNi3 which crystallize in cubic perovskite structure having critical transition temperature of 8 K. The interesting aspect of this compound is that in normal state it is non magnetic in nature despite conduction electrons in it are derived from partially filled Ni d states, which typically lead to ferromagnetism in metallic Ni and many Ni-based binary alloys. To investigate the detailed microscopic origin of the non magnetic nature we have done density functional based calculations on this compound. The lattice constant is calculated using minimum energy criteria from total energy versus lattice constant plot. By taking the calculated values of lattice constant we have done the precise calculations on the compound using Full Potential Linear Augmented Plane Wave (FP-LAPW) method implemented in ELK code. The electronic density of states is found spin degenerate that corresponds to a non-magnetic ground state. The density of states (DOS) at Fermi level, N(EF) is dominated by Ni-d states. The sharp peak observed just below Fermi level corresponds to van Hove singularity (vHs). The projected density of states (PDOS) suggests a strong hybridization of Ni-3d and C-2p states which is responsible for the observed non magnetic nature of MgCNi3.
Density Functional Screening of Metal Hydride Reactions
NASA Astrophysics Data System (ADS)
Johnson, Karl; Alapati, Sudhakar; Dai, Bing; Kim, Ki-Chul; Sholl, David
2008-03-01
The on-board storage of hydrogen is one of the most vexing problems associated with the development of viable fuel cell vehicles. Hydrides of period 2 or 3 metals can store hydrogen at high gravimetric and volumetric densities. However, existing hydrides either have unacceptable thermodynamics or kinetics. New materials for hydrogen storage are therefore needed. We demonstrate how first principles density functional theory (DFT) can be used to screen potential candidate materials for hydrogen storage. We have used DFT calculations in conjunction with a free energy analysis to screen over a million reactions involving 212 known compounds. This approach has identified several interesting reaction schemes that have not yet been explored experimentally. We have computed the phonon density of states and used this information to predict the van't Hoff plots for some of the most promising candidate reactions identified though our modeling. We have also examined the thermodynamics of thin films and nanoparticles for selected metal hydrides by accounting for the surface energies of the films or nanoparticles.
Density functional theory of charged colloidal systems
NASA Astrophysics Data System (ADS)
Chan, Derek Y.
2001-06-01
The phase behavior of charged colloidal systems has been studied recently by the density functional theory formalism (DFT) [R. van Roij, M. Dijkstra, and J. P. Hansen, Phys. Rev. E 59, 2010 (1999)]. A key feature of this approach is the appearance of a density and temperature-dependent effective Hamiltonian between the charged colloids. Under certain approximations, the effective Hamiltonian is made up only of a sum of position-independent one-body or volume terms and two-body colloid-separation dependent terms. In the limit of low colloidal densities, the DFT results do not reduce to the familiar Debye-Hückel limiting law nor do the results agree with previous work based on an identical approach but were developed using traditional statistical-mechanical methods [B. Beresford-Smith, D. Y. C. Chan, and D. J. Mitchell J. Colloid Interface Sci. 105, 216 (1985)]. This paper provides a reconciliation of these differences and comments on the significance of the one-body volume terms in the effective Hamiltonian of a system of charged colloids in determining thermodynamics and phase behavior.
Adiabatic corrections to density functional theory energies and wave functions.
Mohallem, José R; Coura, Thiago de O; Diniz, Leonardo G; de Castro, Gustavo; Assafrão, Denise; Heine, Thomas
2008-09-25
The adiabatic finite-nuclear-mass-correction (FNMC) to the electronic energies and wave functions of atoms and molecules is formulated for density-functional theory and implemented in the deMon code. The approach is tested for a series of local and gradient corrected density functionals, using MP2 results and diagonal-Born-Oppenheimer corrections from the literature for comparison. In the evaluation of absolute energy corrections of nonorganic molecules the LDA PZ81 functional works surprisingly better than the others. For organic molecules the GGA BLYP functional has the best performance. FNMC with GGA functionals, mainly BLYP, show a good performance in the evaluation of relative corrections, except for nonorganic molecules containing H atoms. The PW86 functional stands out with the best evaluation of the barrier of linearity of H2O and the isotopic dipole moment of HDO. In general, DFT functionals display an accuracy superior than the common belief and because the corrections are based on a change of the electronic kinetic energy they are here ranked in a new appropriate way. The approach is applied to obtain the adiabatic correction for full atomization of alcanes C(n)H(2n+2), n = 4-10. The barrier of 1 mHartree is approached for adiabatic corrections, justifying its insertion into DFT. PMID:18537228
Density functional theory study of yttrium monohalides
NASA Astrophysics Data System (ADS)
Ma, Tongmei; Tong, G. S.-M.; Cheung, A. S.-C.
2012-07-01
The molecular properties of the ground state and some low-lying excited states of the yttrium monohalides, YX (X = F, Cl, Br, and I), have been calculated using the B3P86 method of density functional theory (DFT). For each state, the equilibrium bond lengths of re , the harmonic vibrational frequencies of ωe , the dissociation energies of D0 , the term values of Te , the dipole moments of μ, for all the yttrium monohalides were obtained analytically and compared with the experimental and other theoretical values. Compared with the experimental results, the hybrid density functional B3P86 is superior to or comparable with the other theoretical results and predicts well all the spectroscopic parameters such as equilibrium bond lengths and the harmonic vibrational frequencies, but underestimates the term values. By comparing the computed results for B3P86 and CCSD(T), a reasonable explanation has been given for the discrepancy between the computed and experimental term values of YX. In addition, the effect of the halogens on the spectroscopic parameters for the group of YX has been discussed with the help of the molecular orbital diagram.
Band terminations in density functional theory
Afanasjev, A. V.
2008-11-15
The analysis of the terminating bands has been performed in the relativistic mean field framework. It was shown that nuclear magnetism provides an additional binding to the energies of the specific configuration and this additional binding increases with spin and has its maximum exactly at the terminating state. This suggests that the terminating states can be an interesting probe of the time-odd mean fields provided that other effects can be reliably isolated. Unfortunately, a reliable isolation of these effects is not that simple: many terms of the density functional theories contribute into the energies of the terminating states and the deficiencies in the description of those terms affect the result. The recent suggestion [H. Zdunczuk, W. Satula, and R. A. Wyss, Phys. Rev. C 71, 024305 (2005)] that the relative energies of the terminating states in the N{ne}Z,A{approx}44 mass region given by {delta}E provide unique and reliable constraints on time-odd mean fields and the strength of spin-orbit interaction in density functional theories has been reanalyzed. The current investigation shows that the {delta}E value is affected also by the relative placement of the states with different orbital angular momentum l, namely, the placement of the d (l=2) and f (l=3) states. This indicates the dependence of the {delta}E value on the properties of the central potential.
Local spin analyses using density functional theory
NASA Astrophysics Data System (ADS)
Abate, Bayileyegn; Peralta, Juan
Local spin analysis is a valuable technique in computational investigations magnetic interactions on mono- and polynuclear transition metal complexes, which play vital roles in catalysis, molecular magnetism, artificial photosynthesis, and several other commercially important materials. The relative size and complex electronic structure of transition metal complexes often prohibits the use of multi-determinant approaches, and hence, practical calculations are often limited to single-determinant methods. Density functional theory (DFT) has become one of the most successful and widely used computational tools for the electronic structure study of complex chemical systems; transition metal complexes in particular. Within the DFT formalism, a more flexible and complete theoretical modeling of transition metal complexes can be achieved by considering noncollinear spins, in which the spin density is 'allowed to' adopt noncollinear structures in stead of being constrained to align parallel/antiparallel to a universal axis of magnetization. In this meeting, I will present local spin analyses results obtained using different DFT functionals. Local projection operators are used to decompose the expectation value
Chemistry by Way of Density Functional Theory
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Ricca, Alessandra; Partridge, Harry; Langohff, Stephen R.; Arnold, James O. (Technical Monitor)
1996-01-01
In this work we demonstrate that density functional theory (DFT) methods make an important contribution to understanding chemical systems and are an important additional method for the computational chemist. We report calibration calculations obtained with different functionals for the 55 G2 molecules to justify our selection of the B3LYP functional. We show that accurate geometries and vibrational frequencies obtained at the B3LYP level can be combined with traditional methods to simplify the calculation of accurate heats of formation. We illustrate the application of the B3LYP approach to a variety of chemical problems from the vibrational frequencies of polycyclic aromatic hydrocarbons to transition metal systems. We show that the B3LYP method typically performs better than the MP2 method at a significantly lower computational cost. Thus the B3LYP method allows us to extend our studies to much larger systems while maintaining a high degree of accuracy. We show that for transition metal systems, the B3LYP bond energies are typically of sufficient accuracy that they can be used to explain experimental trends and even differentiate between different experimental values. We show that for boron clusters the B3LYP energetics are not as good as for many of the other systems presented, but even in this case the B3LYP approach is able to help understand the experimental trends.
Semiconductor Thermochemistry in Density Functional Calculations
Lany, S.
2008-01-01
The local-density and generalized gradient approximations (LDA and GGA) to density functional theory (DFT) exhibit incomplete error cancellation when energy differences are taken between chemically dissimilar systems. This energy inconsistency is manifested, e.g., in the tendency to underestimate the heat (enthalpy) of formation of semiconducting and insulating compounds in LDA and, even more so, in GGA. Considering a set of 61 compounds that can be formed from 14 elements (cations: Cu, Mg, Ca, Zn, Cd, Al, Ga, and In; anions: N, P, As, O, S, and Se), optimized elemental reference energies are determined by least-squares error minimization of an overdetermined set of linear equations. These elemental energies are 'optimally consistent' with the DFT energies of the semiconductor compounds and imply corrections of up to 1 eV compared to the respective LDA or GGA energies. While these 'corrections' are not to be understood to yield the correct absolute total energies of the elements, they are proposed to give appropriate bounds for the chemical potentials for thermodynamic processes in semiconductors and insulators, such as, e.g., defect formation, surface reconstruction, or catalytic processes. The present model allows to evaluate thermodynamic processes using DFT energy differences taken only between systems that are expected to show good error cancellation.
Effective potential in density matrix functional theory.
Nagy, A; Amovilli, C
2004-10-01
In the previous paper it was shown that in the ground state the diagonal of the spin independent second-order density matrix n can be determined by solving a single auxiliary equation of a two-particle problem. Thus the problem of an arbitrary system with even electrons can be reduced to a two-particle problem. The effective potential of the two-particle equation contains a term v(p) of completely kinetic origin. Virial theorem and hierarchy of equations are derived for v(p) and simple approximations are proposed. A relationship between the effective potential u(p) of the shape function equation and the potential v(p) is established.
Phases of Polonium via Density Functional Theory
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu J.
2010-01-01
The thermodynamical properties of the main phases of metallic polonium are examined using density functional theory. The exceptional nature of the solid-solid phase transition of α to β Po is underlined: it induces a lowering in symmetry, from cubic to rhombohedral, with increasing temperature. This is explained as the result of a delicate balance between bonding and entropic effects. Overall agreement with existing experimental data is good by state-of-the-art standards. The phonons of Po present Kohn anomalies, and it is shown that the effect of spin-orbit interactions is the inverse of that in normal metals: due to the nonspherical nature of the Fermi Surface, spin-orbit effects reduce nesting and harden most phonon frequencies.
Replica density functional theory: an overview
NASA Astrophysics Data System (ADS)
Schmidt, Matthias
2005-11-01
An account is given of density functional theory (DFT) for quenched-annealed fluid mixtures that are used to model fluids adsorbed in random porous matrices. The theory is based on the replica trick and allows the treatment of situations where the quenched random matrix as well as the annealed fluid are inhomogeneous on average. Applications of the framework include investigation of the adsorption properties of hard spheres and model colloid-polymer mixtures in bulk matrices and at matrix surfaces, and the influence of the quenched disorder on phase transitions like fluid demixing, isotropic-nematic ordering, and freezing. Particularly rich wetting behaviour was found for colloid-polymer mixtures adsorbed against a porous wall.
Effective potential in density matrix functional theory.
Nagy, A; Amovilli, C
2004-10-01
In the previous paper it was shown that in the ground state the diagonal of the spin independent second-order density matrix n can be determined by solving a single auxiliary equation of a two-particle problem. Thus the problem of an arbitrary system with even electrons can be reduced to a two-particle problem. The effective potential of the two-particle equation contains a term v(p) of completely kinetic origin. Virial theorem and hierarchy of equations are derived for v(p) and simple approximations are proposed. A relationship between the effective potential u(p) of the shape function equation and the potential v(p) is established. PMID:15473719
Carrier Modulation Via Waveform Probability Density Function
NASA Technical Reports Server (NTRS)
Williams, Glenn L.
2004-01-01
Beyond the classic modes of carrier modulation by varying amplitude (AM), phase (PM), or frequency (FM), we extend the modulation domain of an analog carrier signal to include a class of general modulations which are distinguished by their probability density function histogram. Separate waveform states are easily created by varying the pdf of the transmitted waveform. Individual waveform states are assignable as proxies for digital ONEs or ZEROs. At the receiver, these states are easily detected by accumulating sampled waveform statistics and performing periodic pattern matching, correlation, or statistical filtering. No fundamental natural laws are broken in the detection process. We show how a typical modulation scheme would work in the digital domain and suggest how to build an analog version. We propose that clever variations of the modulating waveform (and thus the histogram) can provide simple steganographic encoding.
Carrier Modulation Via Waveform Probability Density Function
NASA Technical Reports Server (NTRS)
Williams, Glenn L.
2006-01-01
Beyond the classic modes of carrier modulation by varying amplitude (AM), phase (PM), or frequency (FM), we extend the modulation domain of an analog carrier signal to include a class of general modulations which are distinguished by their probability density function histogram. Separate waveform states are easily created by varying the pdf of the transmitted waveform. Individual waveform states are assignable as proxies for digital one's or zero's. At the receiver, these states are easily detected by accumulating sampled waveform statistics and performing periodic pattern matching, correlation, or statistical filtering. No fundamental physical laws are broken in the detection process. We show how a typical modulation scheme would work in the digital domain and suggest how to build an analog version. We propose that clever variations of the modulating waveform (and thus the histogram) can provide simple steganographic encoding.
EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.
Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens
2012-03-01
Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.
Improving Density Functionals with Quantum Harmonic Oscillators
NASA Astrophysics Data System (ADS)
Tkatchenko, Alexandre
2013-03-01
Density functional theory (DFT) is the most widely used and successful approach for electronic structure calculations. However, one of the pressing challenges for DFT is developing efficient functionals that can accurately capture the omnipresent long-range electron correlations, which determine the structure and stability of many molecules and materials. Here we show that, under certain conditions, the problem of computing the long-range correlation energy of interacting electrons can be mapped to a system of coupled quantum harmonic oscillators (QHOs). The proposed model allows us to synergistically combine concepts from DFT, quantum chemistry, and the widely discussed random-phase approximation for the correlation energy. In the dipole limit, the interaction energy for a system of coupled QHOs can be calculated exactly, thereby leading to an efficient and accurate model for the many-body dispersion energy of complex molecules and materials. The studied examples include intermolecular binding energies, the conformational hierarchy of DNA structures, the geometry and stability of molecular crystals, and supramolecular host-guest complexes (A. Tkatchenko, R. A. DiStasio Jr., R. Car, M. Scheffler, Phys. Rev. Lett. 108, 236402 (2012); R. A. DiStasio Jr., A. von Lilienfeld, A. Tkatchenko, PNAS 109, 14791 (2012); A. Tkatchenko, D. Alfe, K. S. Kim, J. Chem. Theory and Comp. (2012), doi: 10.1021/ct300711r; A. Tkatchenko, A. Ambrosetti, R. A. DiStasio Jr., arXiv:1210.8343v1).
A density functional for sparse matter
NASA Astrophysics Data System (ADS)
Langreth, D. C.; Lundqvist, B. I.; Chakarova-Käck, S. D.; Cooper, V. R.; Dion, M.; Hyldgaard, P.; Kelkkanen, A.; Kleis, J.; Kong, Lingzhu; Li, Shen; Moses, P. G.; Murray, E.; Puzder, A.; Rydberg, H.; Schröder, E.; Thonhauser, T.
2009-02-01
Sparse matter is abundant and has both strong local bonds and weak nonbonding forces, in particular nonlocal van der Waals (vdW) forces between atoms separated by empty space. It encompasses a broad spectrum of systems, like soft matter, adsorption systems and biostructures. Density-functional theory (DFT), long since proven successful for dense matter, seems now to have come to a point, where useful extensions to sparse matter are available. In particular, a functional form, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401; Thonhauser et al 2007 Phys. Rev. B 76 125112), has been proposed for the nonlocal correlations between electrons and applied to various relevant molecules and materials, including to those layered systems like graphite, boron nitride and molybdenum sulfide, to dimers of benzene, polycyclic aromatic hydrocarbons (PAHs), doped benzene, cytosine and DNA base pairs, to nonbonding forces in molecules, to adsorbed molecules, like benzene, naphthalene, phenol and adenine on graphite, alumina and metals, to polymer and carbon nanotube (CNT) crystals, and hydrogen storage in graphite and metal-organic frameworks (MOFs), and to the structure of DNA and of DNA with intercalators. Comparison with results from wavefunction calculations for the smaller systems and with experimental data for the extended ones show the vdW-DF path to be promising. This could have great ramifications.
Internal density functional theory of molecular systems
NASA Astrophysics Data System (ADS)
Nalewajski, Roman F.
1984-08-01
A thermodynamiclike theory of internal equilibrium and constrained equilibrium states of individual molecular systems is formulated, based on the Legendre transformed density functional theory (LT DFT). The molecular system (nonrelativistic, field free, Born-Oppenheimer or non-Born-Oppenheimer) is treated as the closed composite thermodynamic system, consisting of very small, rigid (open) subsystems (simple systems) containing a multi-(m)-component charged fluid in the presence of an external field. The generalized Levy constrained search construction of various ``thermodynamic'' potentials of LT DFT is given and the local Maxwell relations are derived. The reduction of various second-order partial functional derivatives (system sensitivities) in terms of few independent, basic kernels is described, using the Jacobian determinants technique. The qualitative implications for the basic kernels of the theory, from the Maxwell relations and stability criteria (generalized Le Châtelier and Le Châtelier-Braun principles) are systematically examined. Finally, possible applications of the general formalism in the thermodynamic analysis of the chemical bond, molecular stability, and chemical reactivity are identified.
Building a Universal Nuclear Energy Density Functional
Carlson, Joe A.; 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.
Flexoelectricity from density-functional perturbation theory
NASA Astrophysics Data System (ADS)
Stengel, Massimiliano
2013-11-01
We derive the complete flexoelectric tensor, including electronic and lattice-mediated effects, of an arbitrary insulator in terms of the microscopic linear response of the crystal to atomic displacements. The basic ingredient, which can be readily calculated from first principles in the framework of density-functional perturbation theory, is the quantum-mechanical probability current response to a long-wavelength acoustic phonon. Its second-order Taylor expansion in the wave vector q around the Γ (q=0) point in the Brillouin zone naturally yields the flexoelectric tensor. At order one in q we recover Martin's theory of piezoelectricity [Martin, Phys. Rev. B 5, 1607 (1972)], thus providing an alternative derivation thereof. To put our derivations on firm theoretical grounds, we perform a thorough analysis of the nonanalytic behavior of the dynamical matrix and other response functions in a vicinity of Γ. Based on this analysis, we find that there is an ambiguity in the specification of the “zero macroscopic field” condition in the flexoelectric case; such arbitrariness can be related to an analytic band-structure term, in close analogy to the theory of deformation potentials. As a by-product, we derive a rigorous generalization of the Cochran-Cowley formula [Cochran and Cowley, J. Phys. Chem. Solids 23, 447 (1962)] to higher orders in q. This can be of great utility in building reliable atomistic models of electromechanical phenomena, as well as for improving the accuracy of the calculation of phonon dispersion curves. Finally, we discuss the physical interpretation of the various contributions to the flexoelectric response, either in the static or dynamic regime, and we relate our findings to earlier theoretical works on the subject.
Dynamical density functional theory for microswimmers.
Menzel, Andreas M; Saha, Arnab; Hoell, Christian; Löwen, Hartmut
2016-01-14
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.
Bone mineral density, adiposity, and cognitive functions.
Sohrabi, Hamid R; Bates, Kristyn A; Weinborn, Michael; Bucks, Romola S; Rainey-Smith, Stephanie R; Rodrigues, Mark A; Bird, Sabine M; Brown, Belinda M; Beilby, John; Howard, Matthew; Criddle, Arthur; Wraith, Megan; Taddei, Kevin; Martins, Georgia; Paton, Athena; Shah, Tejal; Dhaliwal, Satvinder S; Mehta, Pankaj D; Foster, Jonathan K; Martins, Ian J; Lautenschlager, Nicola T; Mastaglia, Francis; Laws, Simon M; Martins, Ralph N
2015-01-01
Cognitive decline and dementia due to Alzheimer's disease (AD) 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 34-87 years old (62.78 ± 9.27), were recruited for this longitudinal study and underwent cognitive and clinical examinations at baseline and after 3 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. PMID:25741279
Dynamical density functional theory for microswimmers
NASA Astrophysics Data System (ADS)
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.
Combining Molecular Dynamics and Density Functional Theory
NASA Astrophysics Data System (ADS)
Kaxiras, Efthimios
2015-03-01
The time evolution of a system consisting of electrons and ions is often treated in the Born-Oppenheimer approximation, with electrons in their instantaneous ground state. This approach cannot capture many interesting processes that involved excitation of electrons and its effects on the coupled electron-ion dynamics. The time scale needed to accurately resolve the evolution of electron dynamics is atto-seconds. This poses a challenge to the simulation of important chemical processes that typically take place on time scales of pico-seconds and beyond, such as reactions at surfaces and charge transport in macromolecules. We will present a methodology based on time-dependent density functional theory for electrons, and classical (Ehrenfest) dynamics for the ions, that successfully captures such processes. We will give a review of key features of the method and several applications. These illustrate how the atomic and electronic structure evolution unravels the elementary steps that constitute a chemical reaction. In collaboration with: G. Kolesov, D. Vinichenko, G. Tritsaris, C.M. Friend, Departments of Physics and of Chemistry and Chemical Biology.
Photostriction in Ferroelectrics from Density Functional Theory.
Paillard, Charles; Xu, Bin; Dkhil, Brahim; Geneste, Grégory; Bellaiche, L
2016-06-17
An ab initio procedure allowing the computation of the deformation of ferroelectric-based materials under light is presented. This numerical scheme consists in structurally relaxing the system under the constraint of a fixed n_{e} concentration of electrons photoexcited into a specific conduction band edge state from a chosen valence band state, via the use of a constrained density functional theory method. The resulting change in lattice constant along a selected crystallographic direction is then calculated for a reasonable estimate of n_{e}. This method is applied to bulk multiferroic BiFeO_{3} and predicts a photostriction effect of the same order of magnitude than the ones recently observed. A strong dependence of photostrictive response on both the reached conduction state and the crystallographic direction (along which this effect is determined) is also revealed. Furthermore, analysis of the results demonstrates that the photostriction mechanism mostly originates from the screening of the spontaneous polarization by the photoexcited electrons in combination with the inverse piezoelectric effect. PMID:27367406
Density functional theory in the solid state
Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.
2014-01-01
Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184
Density functional theory in the solid state.
Hasnip, Philip J; Refson, Keith; Probert, Matt I J; Yates, Jonathan R; Clark, Stewart J; Pickard, Chris J
2014-03-13
Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure-property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program.
Bone mineral density, adiposity, and cognitive functions
Sohrabi, Hamid R.; Bates, Kristyn A.; Weinborn, Michael; Bucks, Romola S.; Rainey-Smith, Stephanie R.; Rodrigues, Mark A.; Bird, Sabine M.; Brown, Belinda M.; Beilby, John; Howard, Matthew; Criddle, Arthur; Wraith, Megan; Taddei, Kevin; Martins, Georgia; Paton, Athena; Shah, Tejal; Dhaliwal, Satvinder S.; Mehta, Pankaj D.; Foster, Jonathan K.; Martins, Ian J.; Lautenschlager, Nicola T.; Mastaglia, Francis; Laws, Simon M.; Martins, Ralph N.
2015-01-01
Cognitive decline and dementia due to Alzheimer's disease (AD) 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 34–87 years old (62.78 ± 9.27), were recruited for this longitudinal study and underwent cognitive and clinical examinations at baseline and after 3 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. PMID:25741279
Level 2 and level 2.5 large deviation functionals for systems with and without detailed balance
NASA Astrophysics Data System (ADS)
Hoppenau, J.; Nickelsen, D.; Engel, A.
2016-08-01
Large deviation functions are an essential tool in the statistics of rare events. Often they can be obtained by contraction from a so-called level 2 or level 2.5 large deviation functional characterizing the empirical density and current of the underlying stochastic process. For Langevin systems obeying detailed balance, the explicit form of the level 2 functional has been known ever since the mathematical work of Donsker and Varadhan. We rederive the Donsker–Varadhan result using stochastic path-integrals. We than generalize the derivation to level 2.5 large deviation functionals for non-equilibrium steady states and elucidate the relation between the large deviation functionals and different notions of entropy production in stochastic thermodynamics. Finally, we discuss some aspects of the contractions to level 1 large deviation functions and illustrate our findings with examples.
Tellgren, E. I. Lange, K. K.; Ekström, U.; Helgaker, T.; Teale, A. M.; Furness, J. W.
2014-01-21
We present a novel implementation of Kohn–Sham density-functional theory utilizing London atomic orbitals as basis functions. External magnetic fields are treated non-perturbatively, which enable the study of both magnetic response properties and the effects of strong fields, using either standard density functionals or current-density functionals—the implementation is the first fully self-consistent implementation of the latter for molecules. Pilot applications are presented for the finite-field calculation of molecular magnetizabilities, hypermagnetizabilities, and nuclear magnetic resonance shielding constants, focusing on the impact of current-density functionals on the accuracy of the results. Existing current-density functionals based on the gauge-invariant vorticity are tested and found to be sensitive to numerical details of their implementation. Furthermore, when appropriately regularized, the resulting magnetic properties show no improvement over standard density-functional results. An advantage of the present implementation is the ability to apply density-functional theory to molecules in very strong magnetic fields, where the perturbative approach breaks down. Comparison with high accuracy full-configuration-interaction results show that the inadequacies of current-density approximations are exacerbated with increasing magnetic field strength. Standard density-functionals remain well behaved but fail to deliver high accuracy. The need for improved current-dependent density-functionals, and how they may be tested using the presented implementation, is discussed in light of our findings.
Xianlong, Gao; Polini, Marco; Tosi, M. P.; Campo, Vivaldo L. Jr.; Capelle, Klaus; Rigol, Marcos
2006-04-15
We present an extensive numerical study of the ground-state properties of confined repulsively interacting fermions in one-dimensional optical lattices. Detailed predictions for the atom-density profiles are obtained from parallel Kohn-Sham density-functional calculations and quantum Monte Carlo simulations. The density-functional calculations employ a Bethe ansatz based local-density approximation for the correlation energy that accounts for Luttinger-liquid and Mott-insulator physics. Semianalytical and fully numerical formulations of this approximation are compared with each other and with a cruder Thomas-Fermi-type local-density approximation for the total energy. Precise quantum Monte Carlo simulations are used to assess the reliability of the various local-density approximations, and in conjunction with these provide a detailed microscopic picture of the consequences of the interplay between particle-particle interactions and confinement in one-dimensional systems of strongly correlated fermions.
A half century of density functional theory
Zangwill, Andrew
2015-07-15
Today’s most popular method for calculating the electronic structure of atoms, molecules, liquids, solids, and plasmas began as a bold hypothesis: The electron density distribution completely characterizes the ground state of a many-electron system.
Ions in solution: Density corrected density functional theory (DC-DFT)
Kim, Min-Cheol; Sim, Eunji; Burke, Kieron
2014-05-14
Standard density functional approximations often give questionable results for odd-electron radical complexes, with the error typically attributed to self-interaction. In density corrected density functional theory (DC-DFT), certain classes of density functional theory calculations are significantly improved by using densities more accurate than the self-consistent densities. We discuss how to identify such cases, and how DC-DFT applies more generally. To illustrate, we calculate potential energy surfaces of HO·Cl{sup −} and HO·H{sub 2}O complexes using various common approximate functionals, with and without this density correction. Commonly used approximations yield wrongly shaped surfaces and/or incorrect minima when calculated self consistently, while yielding almost identical shapes and minima when density corrected. This improvement is retained even in the presence of implicit solvent.
Lithium adsorption on graphite from density functional theory calculations.
Valencia, Felipe; Romero, Aldo H; Ancilotto, Francesco; Silvestrelli, Pier Luigi
2006-08-01
The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes. PMID:16869593
Lithium adsorption on graphite from density functional theory calculations.
Valencia, Felipe; Romero, Aldo H; Ancilotto, Francesco; Silvestrelli, Pier Luigi
2006-08-01
The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes.
Covariant Density Functional Theory--highlights on recent progress and applications
Meng, J.; Li, J.; Zhao, P. W.; Liang, H. Z.; Yao, J. M.
2011-05-06
The density functional theory with a few number of parameters allows a very successful phenomenological description of ground state properties of nuclei all over the nuclear chart. The recent progress on the application of the covariant density functional theory (CDFT) for nuclear structure and astrophysics as well as its extensions by the group in Beijing is summarized. In particular, its application to magnetic moments is discussed in details.
Revealing a Detailed Mass Distribution of a High-density Core MC27/L1521F in Taurus with ALMA
NASA Astrophysics Data System (ADS)
Tokuda, Kazuki; Onishi, Toshikazu; Matsumoto, Tomoaki; Saigo, Kazuya; Kawamura, Akiko; Fukui, Yasuo; Inutsuka, Shu-ichiro; Machida, Masahiro N.; Tomida, Kengo; Tachihara, Kengo; André, Philippe
2016-07-01
We present the results of ALMA observations of dust continuum emission and molecular rotational lines toward a dense core MC27 (aka L1521F) in Taurus, which is considered to be at a very early stage of star formation. The detailed column density distributions on size scales from a few tens to ˜10,000 AU are revealed by combining the ALMA (12 m array + 7 m array) data with the published/unpublished single-dish data. The high angular resolution observations at 0.87 mm with a synthesized beam size of ˜0.″74 × 0.″32 reveal that a protostellar source, MMS-1, is not spatially resolved and lacks associated gas emission, while a starless high-density core, MMS-2, has substructures in both dust and molecular emission. The averaged radial column density distribution of the inner part of MC27/L1521F (r ≲ 3000 AU) is {N}{{{H}}2} ˜ {r}-0.4, clearly flatter than that of the outer part, ˜{r}-1.0. The complex velocity/spatial structure obtained with previous ALMA observations is located inside the inner flatter region, which may reflect the dynamical status of the dense core.
Density-potential mapping in time-dependent density-functional theory
Maitra, N. T.; Todorov, T. N.; Woodward, C.; Burke, K.
2010-04-15
The key questions of uniqueness and existence in time-dependent density-functional theory are usually formulated only for potentials and densities that are analytic in time. Simple examples, standard in quantum mechanics, lead, however, to nonanalyticities. We reformulate these questions in terms of a nonlinear Schroedinger equation with a potential that depends nonlocally on the wave function.
Introduction to Classical Density Functional Theory by a Computational Experiment
ERIC Educational Resources Information Center
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…
NASA Astrophysics Data System (ADS)
Petrenko, Taras; Kossmann, Simone; Neese, Frank
2011-02-01
In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ˜26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ˜27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ˜24 on 30 processors. The
Molecular density functional theory of water including density-polarization coupling
NASA Astrophysics Data System (ADS)
Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel
2016-06-01
We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle’s density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
The Performance of Density Functionals for Sulfate-Water Clusters
Mardirossian, Narbe; Lambrecht, Daniel S.; McCaslin, Laura; Xantheas, Sotiris S.; Head-Gordon, Martin P.
2013-03-12
The performance of 24 density functionals, Hartree-Fock, and MP2 is assessed with respect to the energetics of 49 sulfate-water clusters with between three and six water molecules. Included among the density functionals are GGA, meta-GGA, hybrid GGA, hybrid meta-GGA, and double hybrid density functionals, as well as the LDA. Three types of dispersion corrections (VV10, XDM, and -D) are tested in conjunction with these functionals. The functionals are compared using the relative and binding energies of the sulfatewater clusters as the main criteria. It is discovered that a majority of current density functionals are unable to simultaneously capture the physics necessary to describe both the relative and binding energies of the anionic solvation clusters. The only density functionals that perform acceptably with respect to both measures are XYG3 and XYGJOS, primarily due to their balanced treatment of exchange and correlation. On the other hand, density functionals with exact exchange that lack nonlocal correlation tend to perform well only for the relative energies. However, there is evidence that hybrid density functionals that provide a more comprehensive treatment of local correlation through their dependence on the kinetic energy density and their ability to treat the inhomogeneities in the present system can partially resolve this issue. While dispersion correction functionals cannot replace the accuracy provided by MP2 correlation, it is shown that the proper combination of a hybrid GGA functional with a dispersion correction functional can lead to drastic improvements in the binding energies of the parent functional, while preserving its performance with respect to the relative energies.
Generalized van der Waals density functional theory for nonuniform polymers
Patra, Chandra N.; Yethiraj, Arun
2000-01-15
A density functional theory is presented for the effect of attractions on the structure of polymers at surfaces. The theory treats the ideal gas functional exactly, and uses a weighted density approximation for the hard chain contribution to the excess free energy functional. The attractive interactions are treated using a van der Waals approximation. The theory is in good agreement with computer simulations for the density profiles at surfaces for a wide range of densities and temperatures, except for low polymer densities at low temperatures where it overestimates the depletion of chains from the surface. This deficiency is attributed to the neglect of liquid state correlations in the van der Waals term of the free energy functional. (c) 2000 American Institute of Physics.
Mewes, Stefanie A; Plasser, Felix; Dreuw, Andreas
2015-11-01
Excited-state descriptors based on the one-particle transition density matrix referring to the exciton picture have been implemented for time-dependent density functional theory. State characters such as local, extended ππ(∗), Rydberg, or charge transfer can be intuitively classified by simple comparison of these descriptors. Strong effects of the choice of the exchange-correlation kernel on the physical nature of excited states can be found and decomposed in detail leading to a new perspective on functional performance and the design of new functionals.
NASA Astrophysics Data System (ADS)
Mewes, Stefanie A.; Plasser, Felix; Dreuw, Andreas
2015-11-01
Excited-state descriptors based on the one-particle transition density matrix referring to the exciton picture have been implemented for time-dependent density functional theory. State characters such as local, extended ππ∗, Rydberg, or charge transfer can be intuitively classified by simple comparison of these descriptors. Strong effects of the choice of the exchange-correlation kernel on the physical nature of excited states can be found and decomposed in detail leading to a new perspective on functional performance and the design of new functionals.
Crucial role of detailed function, task, timeline, link and human vulnerability analyses in HRA
Ryan, T.G.; Haney, L.N.; Ostrom, L.T.
1992-10-01
This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.
Exact maps in density functional theory for lattice models
NASA Astrophysics Data System (ADS)
Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel
2016-08-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.
Exact maps in density functional theory for lattice models
NASA Astrophysics Data System (ADS)
Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel
2016-08-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg–Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.
Chemical functionalization of graphene by carbene cycloaddition: A density functional theory study
NASA Astrophysics Data System (ADS)
Zan, Wenyan
2014-08-01
In this work, we have systematically studied the structural, energetic and electronic properties of graphene functionalized with carbene groups by using density functional theory. Introducing a low concentration of CCl2 group in graphene was studied in detail by DFT, and closed cyclopropane-like three-membered ring structure was formed, meanwhile, the potential candidate carbene groups CR2 (R = H, F, CH3, CN, NO2, OCH3, CCH, C6H5) were added to graphene sheet, and CR2 (R = H, NO2, CH3) groups were expected to be good reactive species to covalently modify graphene. The graphene functionalization with carbene groups above can open graphene's band gap. More CCl2 molecules were added to graphene, and different concentrations of CCl2 group can tune graphene's band gap. In addition, the addition of CCl2 group to graphene edges was investigated, and the stronger binding energy was found. Multiple CCl2 molecules preferred to be bound with the same edge of graphene nanoribbon. This work provides an insight into the detailed molecular mechanism of graphene functionalization with carbene groups.
Postfragmentation density function for bacterial aggregates in laminar flow
NASA Astrophysics Data System (ADS)
Byrne, Erin; Bortz, David M.; Dzul, Steve; Solomon, Michael; Younger, John
2011-04-01
The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation.
NBO analysis and vibrational frequencies of tautomers of citrinin by density functional theory
Technology Transfer Automated Retrieval System (TEKTRAN)
Citrinin is a toxic polyketide contaminant of a number of agricultural commodities, notably Monascus-fermented red rice. Detailed structures and electronic properties of three tautomeric forms of citrinin were investigated using density functional theory calculations at various extended basis sets ...
Integration, Continuity and a Connection with Probability Density Functions
ERIC Educational Resources Information Center
Samuels, M.
2006-01-01
This note considers functions of two variables which are continuous on a possibly unbounded closed region in [vertical bar]R[squared], and the functions of one variable obtained by integrating out the other variable over this region. The question of continuity of these functions is investigated, as are connections with joint density and marginal…
Applications and validations of the Minnesota density functionals
NASA Astrophysics Data System (ADS)
Zhao, Yan; Truhlar, Donald G.
2011-01-01
We discuss and review selected recent applications and validations of the Minnesota density functionals, especially the M06 family, emphasizing nanochemistry, organic, inorganic, and biological chemistry, and catalysis and highlighting the broad accuracy of these functionals as compared to previous popular functionals for thermochemistry, kinetics, and noncovalent interactions.
Photoluminescent Organic Molecules from the Perspective of Density Functional Theory
NASA Astrophysics Data System (ADS)
Massaro, Richard Douglas
2011-12-01
I have studied the electronic structure, vibrational modes, and photophysics of methyl salicylate (MS) isomers in detail using density functional theory (DFT) and its time-dependent (TDDFT) companion. I have confirmed that six isomers are stable in their ground states with the ketoB isomer being the global minimum structure. I have performed free energy calculations which show that other isomers may be energetically favorable at higher temperatures. The calculated vibrational modes of ketoB match well with experimental infrared spectra. Using TDDFT, I have confirmed that the ketoB isomer undergoes an energetically favorable excited-state intermolecular proton transfer (ESIPT) to an enol isomer. I found that the ESIPT has a small potential energy barrier when the proton transitions from the ketoB to the enol structure and a ten times larger barrier to accomplish a reverse ESIPT from enol to ketoB. The barrier asymmetry is responsible for the temperature dependent suppression of the far-blue fluorescence. I modeled the emission spectra for gas phase MS using Franck-Condon factors based on the calculated 0-0 transition and vibrational modes for the ground and excited states. The calculated spectra match well to gas phase experimental spectra. Finally, I performed detailed DFT studies on dipicolinic acid (DPA) and determined its stable structures, energetics, and vibrational modes. My calculations predict the existence of six stable isomers of gas phase DPA in the ground state. Three of these isomers are nearly energetically degenerate. I calculated several transition state reaction paths between these isomers. I performed similar calculations on five dimerized formations. By using periodic boundary conditions (PBC) on three dimerized DPA arrays containing hydrogen-bonding DPA monomers, I was able to predict three different crystal structures. I report the band structures of the resulting DPA crystals for the first time. All of them are insulators.
Charge and spin fluctuations in the density functional theory
Gyoerffy, B.L.; Barbieri, A. . H.H. Wills Physics Lab.); Staunton, J.B. . Dept. of Physics); Shelton, W.A.; Stocks, G.M. )
1990-01-01
We introduce a conceptual framework which allow us to treat charge and spin fluctuations about the Local density Approximation (LDA) to the Density Functional Theory (DFT). We illustrate the approach by explicit study of the Disordered Local Moment (DLM) state in Fe above the Curie Temperature {Tc} and the Mott insulating state in MnO. 27 refs., 6 figs.
Local Density Approximation Exchange-correlation Free-energy Functional
NASA Astrophysics Data System (ADS)
Karasiev, Valentin; Sjostrom, Travis; Dufty, James; Trickey, S. B.
2014-03-01
Restricted path integral Monte-Carlo (RPIMC) simulation data for the homogeneous electron gas at finite temperatures are used to fit the exchange-correlation free energy as a function of the density and temperature. Together with a new finite- T spin-polarization interpolation, this provides the local spin density approximation (LSDA) for the exchange-correlation free-energy functional required by finite- T density functional theory. We discuss and compare different methods of fitting to the RPIMC data. The new function reproduces the RPIMC data in the fitting range of Wigner-Seitz radius and temperature, satisfies correct high-density, low- and high- T asymptotic limits and is applicable beyond the range of fitting data. Work supported by U.S. Dept. of Energy, grant DE-SC0002139 and by the DOE Office of Fusion Sciences (FES).
Density and Spin Response Functions in Ultracold Fermionic Atom Gases
Mihaila, Bogdan; Blagoev, Krastan B.; Balatsky, Alexander V.; Smith, Darryl L.; Gaudio, Sergio; Littlewood, Peter B.
2005-08-26
We propose a new method of detecting the onset of superfluidity in a two-component ultracold fermionic gas of atoms governed by an attractive short-range interaction. By studying the two-body correlation functions we find that a measurement of the momentum distribution of the density and spin-response functions allows one to access separately the normal and anomalous densities. The change in sign at low momentum transfer of the normal-ordered part of the density response function signals the transition between a BEC and a BCS regime, characterized by small and large pairs, respectively. This change in sign of the density response function represents an unambiguous signature of the BEC-to-BCS crossover. Spin rotational symmetry breaking due to the magnetic field, if observed, can be used to validate the one-channel model.
Choice of basic variables in current-density-functional theory
NASA Astrophysics Data System (ADS)
Tellgren, Erik I.; Kvaal, Simen; Sagvolden, Espen; Ekström, Ulf; Teale, Andrew M.; Helgaker, Trygve
2012-12-01
The selection of basic variables in current-density-functional theory and formal properties of the resulting formulations are critically examined. Focus is placed on the extent to which the Hohenberg-Kohn theorem, constrained-search approach, and Lieb's formulation (in terms of convex and concave conjugation) of standard density-functional theory can be generalized to provide foundations for current-density-functional theory. For the well-known case with the gauge-dependent paramagnetic current density as a basic variable, we find that the resulting total energy functional is not concave. It is shown that a simple redefinition of the scalar potential restores concavity and enables the application of convex analysis and convex (or concave) conjugation. As a result, the solution sets arising in potential-optimization problems can be given a simple characterization. We also review attempts to establish theories with the physical current density as a basic variable. Despite the appealing physical motivation behind this choice of basic variables, we find that the mathematical foundations of the theories proposed to date are unsatisfactory. Moreover, the analogy to standard density-functional theory is substantially weaker as neither the constrained-search approach nor the convex analysis framework carry over to a theory making use of the physical current density.
Preface: Special Topic on Advances in Density Functional Theory
Yang, Weitao
2014-05-14
This Special Topic Issue on the Advances in Density Functional Theory, published as a celebration of the fifty years of density functional theory, contains a retrospective article, a perspective article, and a collection of original research articles that showcase recent theoretical advances in the field. It provides a timely discussion reflecting a cross section of our understanding, and the theoretical and computational developments, which have significant implications in broad areas of sciences and engineering.
Reflection-Asymmetric Nuclear Deformations within the Density Functional Theory
Olsen, E; Erler, J; Nazarewicz, W.; Stoitsov, M
2012-01-01
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 with Dissipation: Transport through Single Molecules
Kieron Burke
2012-04-30
A huge amount of fundamental research was performed on this grant. Most of it focussed on fundamental issues of electronic structure calculations of transport through single molecules, using density functional theory. Achievements were: (1) First density functional theory with dissipation; (2) Pseudopotential plane wave calculations with master equation; (3) Weak bias limit; (4) Long-chain conductance; and (5) Self-interaction effects in tunneling.
Gutzwiller density functional theory for correlated electron systems
Ho, K. M.; Schmalian, J.; Wang, C. Z.
2008-02-04
We develop a density functional theory (DFT) and formalism for correlated electron systems by taking as reference an interacting electron system that has a ground state wave function which exactly obeys the Gutzwiller approximation for all one-particle operators. The solution of the many-electron problem is mapped onto the self-consistent solution of a set of single-particle Schroedinger equations, analogously to standard DFT-local density approximation calculations.
Wesseling, Mariska; De Groote, Friedl; Bosmans, Lode; Bartels, Ward; Meyer, Christophe; Desloovere, Kaat; Jonkers, Ilse
2016-11-01
This study assessed the relative importance of introducing an increasing level of medical image-based subject-specific detail in bone and muscle geometry in the musculoskeletal model, on calculated hip contact forces during gait. These forces were compared to introducing minimization of hip contact forces in the optimization criterion. With an increasing level of subject-specific detail, specifically MRI-based geometry and wrapping surfaces representing the hip capsule, hip contact forces decreased and were more comparable to contact forces measured using instrumented prostheses (average difference of 0.69 BW at the first peak compared to 1.04 BW for the generic model). Inclusion of subject-specific wrapping surfaces in the model had a greater effect than altering the cost function definition.
Comments on the locality in density-functional theory
Lindgren, Ingvar; Salomonson, Sten
2003-05-01
The 'locality hypothesis' in density-functional theory (DFT), implying that the functional derivative is equivalent to a multiplicative local function, forms the basis of models of Kohn-Sham type. This has been generally accepted by the community since the advent of the model, and has later been formally proved for a large class of functionals. The hypothesis has recently been questioned by Nesbet [Phys. Rev. A 58, R12 (1998) and Phys. Rev. A 65, 010502 (2001)], who claims that it fails for the kinetic-energy functional for a system with more than two noninteracting electrons with a nondegenerate ground state. This conclusion has been questioned by Gal [Phys. Rev. A 62, 044501 (2000)] and by Holas and March [Phys. Rev. A 64, 016501 (2001)]. We claim that the arguments of Nesbet are incorrect, since the orbital functional used for the kinetic energy is not a unique functional of the total density in the domain of unnormalized orbitals. We have demonstrated that with a proper definition of the kinetic energy, which is a unique density functional also in the unnormalized region, the derivative can be represented by a single local multiplicative function for all v-representable densities. Therefore, we consider the controversy connected with the issue raised by Nesbet as resolved. We believe that the proof of the differentiability given here can be extended to larger groups of DFT functionals, and works along these lines are in progress.
Franca, Vivian V.; D'Amico, Irene
2011-04-15
We derive an analytical density functional for the single-site entanglement of the one-dimensional homogeneous Hubbard model by means of an approximation to the linear entropy. We show that this very simple density functional reproduces quantitatively the exact results. We then use this functional as input for a local-density approximation to the single-site entanglement of inhomogeneous systems. We illustrate the power of this approach in a harmonically confined system, which could simulate recent experiments with ultracold atoms in optical lattices as well as in a superlattice and in an impurity system. The impressive quantitative agreement with numerical calculations--which includes reproducing subtle signatures of the particle density stages--shows that our density functional can provide entanglement calculations for actual experiments via density measurements. Next we use our functional to calculate the entanglement in disordered systems. We find that, in contrast with the expectation that disorder destroys the entanglement, there exist regimes for which the entanglement remains almost unaffected by the presence of disordered impurities.
Density functional theory for polymeric systems in 2D
NASA Astrophysics Data System (ADS)
Słyk, Edyta; Roth, Roland; Bryk, Paweł
2016-06-01
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.
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. PMID:27115343
Detailed first-principles studies on surface energy and work function of hexagonal metals
NASA Astrophysics Data System (ADS)
Ji, De-Peng; Zhu, Quanxi; Wang, Shao-Qing
2016-09-01
The surface energies and work functions for ten kinds of Miller-indices surfaces of hexagonal metals, Be, Mg, Tc, Re, Ru, and Os are calculated by means of the density functional theory (DFT) method. The results show that the metals belonging to the same group have a very similar rule in work functions and surface energies. The work functions of (0001), (01 1 - 1)" separators=",, and (10 1 - 0)" separators=", surfaces are generally larger than the work functions of (11 2 - 1)" separators=",, (11 2 - 2)" separators=",, (11 2 - 3)" separators=",, and (31 4 - 0)" separators=", surfaces. In contrast to work functions, there is more regularity in the crystallographic orientation dependence of surface energies. However, for the metals belonging to different groups, there are always some differences in the exact order of orientation dependence. It is also shown that the work functions and surface energies of the main group metals decrease as they go from top to the bottom in the same group of periodic table, while for the transition metals, they do not always obey this rule.
Reactivity of Graphene Investigated by Density-Functional Theory
NASA Astrophysics Data System (ADS)
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.
Global and local curvature in density functional theory
NASA Astrophysics Data System (ADS)
Zhao, Qing; Ioannidis, Efthymios I.; Kulik, Heather J.
2016-08-01
Piecewise linearity of the energy with respect to fractional electron removal or addition is a requirement of an electronic structure method that necessitates the presence of a derivative discontinuity at integer electron occupation. Semi-local exchange-correlation (xc) approximations within density functional theory (DFT) fail to reproduce this behavior, giving rise to deviations from linearity with a convex global curvature that is evidence of many-electron, self-interaction error and electron delocalization. Popular functional tuning strategies focus on reproducing piecewise linearity, especially to improve predictions of optical properties. In a divergent approach, Hubbard U-augmented DFT (i.e., DFT+U) treats self-interaction errors by reducing the local curvature of the energy with respect to electron removal or addition from one localized subshell to the surrounding system. Although it has been suggested that DFT+U should simultaneously alleviate global and local curvature in the atomic limit, no detailed study on real systems has been carried out to probe the validity of this statement. In this work, we show when DFT+U should minimize deviations from linearity and demonstrate that a "+U" correction will never worsen the deviation from linearity of the underlying xc approximation. However, we explain varying degrees of efficiency of the approach over 27 octahedral transition metal complexes with respect to transition metal (Sc-Cu) and ligand strength (CO, NH3, and H2O) and investigate select pathological cases where the delocalization error is invisible to DFT+U within an atomic projection framework. Finally, we demonstrate that the global and local curvatures represent different quantities that show opposing behavior with increasing ligand field strength, and we identify where these two may still coincide.
Range Separation and Local Hybridization in Density Functional Theory†
Henderson, Thomas M.; Janesko, Benjamin G.; Scuseria, Gustavo E.
2016-01-01
Kohn–Sham density functional theory has become a standard method for modeling energetic, spectroscopic, and chemical reactivity properties of large molecules and solids. Density functional theory provides a rigorous theoretical framework for modeling the many-body exchange-correlation effects that dominate the computational cost of traditional wave function approaches. The advent of hybrid exchange-correlation functionals which incorporate a fraction of nonlocal exact exchange has solidified the prominence of density functional theory within computational chemistry. Hybrids provide accurate treatments of properties such as thermochemistry and molecular geometry. But they also exhibit some rather spectacular failures, and often contain multiple empirical parameters. This article reviews our work on developing novel exchange-correlation functionals that build upon the successes of global hybrids. We focus on more flexible functional forms, including local and range-separated hybrid functionals, constructed to obey known exact constraints and (ideally) to incorporate a minimum of empirical parametrization. The article places our work within the context of some other new approximate density functionals and discusses prospects for future work. PMID:19006280
Optimization of an exchange-correlation density functional for water.
Fritz, Michelle; Fernández-Serra, Marivi; Soler, José M
2016-06-14
We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the "correct" parameterization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and on the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems. PMID:27305990
Force Density Function Relationships in 2-D Granular Media
NASA Technical Reports Server (NTRS)
Youngquist, Robert C.; Metzger, Philip T.; Kilts, Kelly N.
2004-01-01
An integral transform relationship is developed to convert between two important probability density functions (distributions) used in the study of contact forces in granular physics. Developing this transform has now made it possible to compare and relate various theoretical approaches with one another and with the experimental data despite the fact that one may predict the Cartesian probability density and another the force magnitude probability density. Also, the transforms identify which functional forms are relevant to describe the probability density observed in nature, and so the modified Bessel function of the second kind has been identified as the relevant form for the Cartesian probability density corresponding to exponential forms in the force magnitude distribution. Furthermore, it is shown that this transform pair supplies a sufficient mathematical framework to describe the evolution of the force magnitude distribution under shearing. Apart from the choice of several coefficients, whose evolution of values must be explained in the physics, this framework successfully reproduces the features of the distribution that are taken to be an indicator of jamming and unjamming in a granular packing. Key words. Granular Physics, Probability Density Functions, Fourier Transforms
Density-functional expansion methods: Generalization of the auxiliary basis
Giese, Timothy J.; York, Darrin M.
2011-01-01
The formulation of density-functional expansion methods is extended to treat the second and higher-order terms involving the response density and spin densities with an arbitrary single-center auxiliary basis. The two-center atomic orbital products are represented by the auxiliary functions centered about those two atoms, and the mapping coefficients are determined from a local constrained variational procedure. This two-center variational procedure allows the mapping coefficients to be pretabulated and splined as a function of internuclear separation for efficient look up. The splines of mapping coefficients have a range no longer than that of the overlap integrals, and the auxiliary density appears as a single point-multipole expansion to all nonoverlapping atoms, thus allowing for the trivial implementation of a linear-scaling algorithm. The method is tested using Gaussian multipole expansions, and the effect of angular and radial completeness is explored. Several auxiliary basis sets are parametrized and compared to an auxiliary basis analogous to that used in the self-consistent-charge density-functional tight-binding model, and the method is demonstrated to greatly improve the representation of the density response with respect to a reference expansion model that does not use an auxiliary basis. PMID:21599040
A real-space stochastic density matrix approach for density functional electronic structure.
Beck, Thomas L
2015-12-21
The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches. PMID:25969148
Kinetic Energy of Hydrocarbons as a Function of Electron Density and Convolutional Neural Networks.
Yao, Kun; Parkhill, John
2016-03-01
We demonstrate a convolutional neural network trained to reproduce the Kohn-Sham kinetic energy of hydrocarbons from an input electron density. The output of the network is used as a nonlocal correction to conventional local and semilocal kinetic functionals. We show that this approximation qualitatively reproduces Kohn-Sham potential energy surfaces when used with conventional exchange correlation functionals. The density which minimizes the total energy given by the functional is examined in detail. We identify several avenues to improve on this exploratory work, by reducing numerical noise and changing the structure of our functional. Finally we examine the features in the density learned by the neural network to anticipate the prospects of generalizing these models.
Density Density Correlation Function for a Bose-Einstein Condensate Analog Black Hole
NASA Astrophysics Data System (ADS)
Anderson, Paul; Balbinot, Roberto; Fabbri, Alessandro; Parentani, Renaud
2013-04-01
The density density correlation function is computed for an analog black hole which consists of a Bose-Einstein condensate with an acoustic horizon. The method used relies only on quantum field theory in curved spacetime techniques. A comparison with the results obtained by ab initio full condensed matter calculations is given, confirming the validity of the approximation used provided the profile of the flow varies smoothly on scales compared to the condensate healing length.
Improved association in a classical density functional theory for water
Krebs, Eric J.; Schulte, Jeff B.; Roundy, David
2014-03-28
We present a modification to our recently published statistical associating fluid theory-based classical density functional theory for water. We have recently developed and tested a functional for the averaged radial distribution function at contact of the hard-sphere fluid that is dramatically more accurate at interfaces than earlier approximations. We now incorporate this improved functional into the association term of our free energy functional for water, improving its description of hydrogen bonding. We examine the effect of this improvement by studying two hard solutes (a hard hydrophobic rod and a hard sphere) and a Lennard-Jones approximation of a krypton atom solute. The improved functional leads to a moderate change in the density profile and a large decrease in the number of hydrogen bonds broken in the vicinity of the hard solutes. We find an improvement of the partial radial distribution for a krypton atom in water when compared with experiment.
Improved association in a classical density functional theory for water.
Krebs, Eric J; Schulte, Jeff B; Roundy, David
2014-03-28
We present a modification to our recently published statistical associating fluid theory-based classical density functional theory for water. We have recently developed and tested a functional for the averaged radial distribution function at contact of the hard-sphere fluid that is dramatically more accurate at interfaces than earlier approximations. We now incorporate this improved functional into the association term of our free energy functional for water, improving its description of hydrogen bonding. We examine the effect of this improvement by studying two hard solutes (a hard hydrophobic rod and a hard sphere) and a Lennard-Jones approximation of a krypton atom solute. The improved functional leads to a moderate change in the density profile and a large decrease in the number of hydrogen bonds broken in the vicinity of the hard solutes. We find an improvement of the partial radial distribution for a krypton atom in water when compared with experiment. PMID:24697459
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 Theory of Crystal Growth: Lennard-Jones Fluids
NASA Astrophysics Data System (ADS)
Shen, Yu Chen; Oxtoby, David
1996-03-01
We employ an extension of density functional theory to the dynamics of phase transitions in order to study the velocities of crystal growth and melting at planar undercooled and superheated crystal-melt interfaces. The free energy functional we use has a square-gradient form, with the parameters for a Lennard-Jones interaction potential determined by a modified weighted density approximation (MWDA) applied locally through the liquid-solid interface. We explore the role of the density change on freezing in crystal and melt growth, and discover a significant asymmetry between freezing and melting both close to and far from the equilibrium freezing point. The behavior of the superheated solid is governed by the close proximity of a spinodal, whereas in the undercooled liquid there is no evidence for a spinodal and the growth at large undercoolings is affected instead by the density deficit that appears in front of the growing interface.
Symmetry groups, density-matrix equations and covariant Wigner functions
NASA Astrophysics Data System (ADS)
Santana, A. E.; Neto, A. Matos; Vianna, J. D. M.; Khanna, F. C.
2000-06-01
A representation theory for Lie groups is developed taking the Hilbert space, say Hw, of the w∗-algebra standard representation as the representation space. In this context the states describing physical systems are amplitude wave functions but closely connected with the notion of the density matrix. Then, based on symmetry properties, a general physical interpretation for the dual variables of thermal theories, in particular the thermofield dynamics (TFD) formalism, is introduced. The kinematic symmetries, Galilei and Poincaré, are studied and (density) amplitude matrix equations are derived for both of these cases. In the same context of group theory, the notion of phase space in quantum theory is analysed. Thus, in the non-relativistic situation, the concept of density amplitude is introduced, and as an example, a spin-half system is algebraically studied; Wigner function representations for the amplitude density matrices are derived and the connection of TFD and the usual Wigner-function methods are analysed. For the Poincaré symmetries the relativistic density matrix equations are studied for the scalar and spinorial fields. The relativistic phase space is built following the lines of the non-relativistic case. So, for the scalar field, the kinetic theory is introduced via the Klein-Gordon density-matrix equation, and a derivation of the Jüttiner distribution is presented as an example, thus making it possible to compare with the standard approaches. The analysis of the phase space for the Dirac field is carried out in connection with the dual spinor structure induced by the Dirac-field density-matrix equation, with the physical content relying on the symmetry groups. Gauge invariance is considered and, as a basic result, it is shown that the Heinz density operator (which has been used to develope a gauge covariant kinetic theory) is a particular solution for the (Klein-Gordon and Dirac) density-matrix equation.
Density functionals that recognize covalent, metallic, and weak bonds.
Sun, Jianwei; Xiao, Bing; Fang, Yuan; Haunschild, Robin; Hao, Pan; Ruzsinszky, Adrienn; Csonka, Gábor I; Scuseria, Gustavo E; Perdew, John P
2013-09-01
Computationally efficient semilocal approximations of density functional theory at the level of the local spin density approximation (LSDA) or generalized gradient approximation (GGA) poorly describe weak interactions. We show improved descriptions for weak bonds (without loss of accuracy for strong ones) from a newly developed semilocal meta-GGA (MGGA), by applying it to molecules, surfaces, and solids. We argue that this improvement comes from using the right MGGA dimensionless ingredient to recognize all types of orbital overlap. PMID:25166685
Surface oxides on Pd(111): STM and density functional calculations
NASA Astrophysics Data System (ADS)
Klikovits, J.; Napetschnig, E.; Schmid, M.; Seriani, N.; Dubay, O.; Kresse, G.; Varga, P.
2007-07-01
The formation of one-layer surface oxides on Pd(111) has been studied by scanning tunneling microscopy (STM) and density functional theory (DFT). Besides the Pd5O4 structure determined previously, structural details of six different surface oxides on Pd(111) will be presented. These oxides are observed for preparation in oxygen-rich conditions, approaching the thermodynamic stability limit of the PdO bulk oxide at an oxygen chemical potential of -0.95to-1.02eV ( 570-605K , 5×10-4mbar O2 ). Sorted by increasing oxygen fraction in the primitive unit cell, the stoichiometry of the surface oxides is Pd5O4 , Pd9O8 , Pd20O18 , Pd23O21 , Pd19O18 , Pd8O8 , and Pd32O32 . All structures are one-layer oxides, in which oxygen atoms form a rectangular lattice, and all structures follow the same rules of favorable alignment of the oxide layer on the Pd(111) substrate. DFT calculations were used to simulate STM images as well as to determine the stability of the surface oxide structures. Simulated and measured STM images are in excellent agreement, indicating that the structural models are correct. Since the newly found surface oxides are clearly less stable than Pd5O4 , we conclude that Pd5O4 is the only thermodynamically stable phase, whereas all newly found structures are only kinetically stabilized. We also discuss possible mechanisms for the formation of these oxide structures.
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.
Perspective: Kohn-Sham density functional theory descending a staircase
NASA Astrophysics Data System (ADS)
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.
Configuration interaction in symmetry-conserving covariant density functional theory
NASA Astrophysics Data System (ADS)
Zhao, P. W.; Ring, P.; Meng, J.
2016-10-01
A new method to calculate spectroscopic properties of deformed nuclei is proposed: configuration interaction on top of projected density functional theory (CI-PDFT). The general concept of this approach is discussed in the framework of covariant density functional theory and its validity is illustrated in an application to the yrast band of the nucleus 54Cr. It is found that the experimentally observed excitation energies for the yrast band in 54Cr can be well reproduced. In contrast to conventional shell-model calculations, there is no core and only a relatively small number of configurations is sufficient for a satisfying description. No new parameters are necessary, because the effective interaction is derived from an universal density functional given in the literature.
Kinetic-energy density functional: Atoms and shell structure
Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E. |
1996-09-01
We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. {copyright} {ital 1996 The American Physical Society.}
Course 4: Density Functional Theory, Methods, Techniques, and Applications
NASA Astrophysics Data System (ADS)
Chrétien, S.; Salahub, D. R.
Contents 1 Introduction 2 Density functional theory 2.1 Hohenberg and Kohn theorems 2.2 Levy's constrained search 2.3 Kohn-Sham method 3 Density matrices and pair correlation functions 4 Adiabatic connection or coupling strength integration 5 Comparing and constrasting KS-DFT and HF-CI 6 Preparing new functionals 7 Approximate exchange and correlation functionals 7.1 The Local Spin Density Approximation (LSDA) 7.2 Gradient Expansion Approximation (GEA) 7.3 Generalized Gradient Approximation (GGA) 7.4 meta-Generalized Gradient Approximation (meta-GGA) 7.5 Hybrid functionals 7.6 The Optimized Effective Potential method (OEP) 7.7 Comparison between various approximate functionals 8 LAP correlation functional 9 Solving the Kohn-Sham equations 9.1 The Kohn-Sham orbitals 9.2 Coulomb potential 9.3 Exchange-correlation potential 9.4 Core potential 9.5 Other choices and sources of error 9.6 Functionality 10 Applications 10.1 Ab initio molecular dynamics for an alanine dipeptide model 10.2 Transition metal clusters: The ecstasy, and the agony... 10.3 The conversion of acetylene to benzene on Fe clusters 11 Conclusions
Lorkova, Lucie; Scigelova, Michaela; Arrey, Tabiwang Ndipanquang; Vit, Ondrej; Pospisilova, Jana; Doktorova, Eliska; Klanova, Magdalena; Alam, Mahmudul; Vockova, Petra; Maswabi, Bokang
2015-01-01
Mantle cell lymphoma (MCL) is a chronically relapsing aggressive type of B-cell non-Hodgkin lymphoma considered incurable by currently used treatment approaches. Fludarabine is a purine analog clinically still widely used in the therapy of relapsed MCL. Molecular mechanisms of fludarabine resistance have not, however, been studied in the setting of MCL so far. We therefore derived fludarabine-resistant MCL cells (Mino/FR) and performed their detailed functional and proteomic characterization compared to the original fludarabine sensitive cells (Mino). We demonstrated that Mino/FR were highly cross-resistant to other antinucleosides (cytarabine, cladribine, gemcitabine) and to an inhibitor of Bruton tyrosine kinase (BTK) ibrutinib. Sensitivity to other types of anti-lymphoma agents was altered only mildly (methotrexate, doxorubicin, bortezomib) or remained unaffacted (cisplatin, bendamustine). The detailed proteomic analysis of Mino/FR compared to Mino cells unveiled over 300 differentially expressed proteins. Mino/FR were characterized by the marked downregulation of deoxycytidine kinase (dCK) and BTK (thus explaining the observed crossresistance to antinucleosides and ibrutinib), but also by the upregulation of several enzymes of de novo nucleotide synthesis, as well as the up-regulation of the numerous proteins of DNA repair and replication. The significant upregulation of the key antiapoptotic protein Bcl-2 in Mino/FR cells was associated with the markedly increased sensitivity of the fludarabine-resistant MCL cells to Bcl-2-specific inhibitor ABT199 compared to fludarabine-sensitive cells. Our data thus demonstrate that a detailed molecular analysis of drug-resistant tumor cells can indeed open a way to personalized therapy of resistant malignancies. PMID:26285204
Bakosi, Jozsef; Ristorcelli, Raymond J
2010-01-01
Probability density function (PDF) methods are extended to variable-density pressure-gradient-driven turbulence. We apply the new method to compute the joint PDF of density and velocity in a non-premixed binary mixture of different-density molecularly mixing fluids under gravity. The full time-evolution of the joint PDF is captured in the highly non-equilibrium flow: starting from a quiescent state, transitioning to fully developed turbulence and finally dissipated by molecular diffusion. High-Atwood-number effects (as distinguished from the Boussinesq case) are accounted for: both hydrodynamic turbulence and material mixing are treated at arbitrary density ratios, with the specific volume, mass flux and all their correlations in closed form. An extension of the generalized Langevin model, originally developed for the Lagrangian fluid particle velocity in constant-density shear-driven turbulence, is constructed for variable-density pressure-gradient-driven flows. The persistent small-scale anisotropy, a fundamentally 'non-Kolmogorovian' feature of flows under external acceleration forces, is captured by a tensorial diffusion term based on the external body force. The material mixing model for the fluid density, an active scalar, is developed based on the beta distribution. The beta-PDF is shown to be capable of capturing the mixing asymmetry and that it can accurately represent the density through transition, in fully developed turbulence and in the decay process. The joint model for hydrodynamics and active material mixing yields a time-accurate evolution of the turbulent kinetic energy and Reynolds stress anisotropy without resorting to gradient diffusion hypotheses, and represents the mixing state by the density PDF itself, eliminating the need for dubious mixing measures. Direct numerical simulations of the homogeneous Rayleigh-Taylor instability are used for model validation.
On the Evolution of the Density Probability Density Function in Strongly Self-gravitating Systems
NASA Astrophysics Data System (ADS)
Girichidis, Philipp; Konstandin, Lukas; Whitworth, Anthony P.; Klessen, Ralf S.
2014-02-01
The time evolution of the probability density function (PDF) of the mass density is formulated and solved for systems in free-fall using a simple approximate function for the collapse of a sphere. We demonstrate that a pressure-free collapse results in a power-law tail on the high-density side of the PDF. The slope quickly asymptotes to the functional form PV (ρ)vpropρ-1.54 for the (volume-weighted) PDF and PM (ρ)vpropρ-0.54 for the corresponding mass-weighted distribution. From the simple approximation of the PDF we derive analytic descriptions for mass accretion, finding that dynamically quiet systems with narrow density PDFs lead to retarded star formation and low star formation rates (SFRs). Conversely, strong turbulent motions that broaden the PDF accelerate the collapse causing a bursting mode of star formation. Finally, we compare our theoretical work with observations. The measured SFRs are consistent with our model during the early phases of the collapse. Comparison of observed column density PDFs with those derived from our model suggests that observed star-forming cores are roughly in free-fall.
On the evolution of the density probability density function in strongly self-gravitating systems
Girichidis, Philipp; Konstandin, Lukas; Klessen, Ralf S.; Whitworth, Anthony P.
2014-02-01
The time evolution of the probability density function (PDF) of the mass density is formulated and solved for systems in free-fall using a simple approximate function for the collapse of a sphere. We demonstrate that a pressure-free collapse results in a power-law tail on the high-density side of the PDF. The slope quickly asymptotes to the functional form P{sub V} (ρ)∝ρ{sup –1.54} for the (volume-weighted) PDF and P{sub M} (ρ)∝ρ{sup –0.54} for the corresponding mass-weighted distribution. From the simple approximation of the PDF we derive analytic descriptions for mass accretion, finding that dynamically quiet systems with narrow density PDFs lead to retarded star formation and low star formation rates (SFRs). Conversely, strong turbulent motions that broaden the PDF accelerate the collapse causing a bursting mode of star formation. Finally, we compare our theoretical work with observations. The measured SFRs are consistent with our model during the early phases of the collapse. Comparison of observed column density PDFs with those derived from our model suggests that observed star-forming cores are roughly in free-fall.
Angular-momentum-dependent orbital-free density functional theory.
Ke, Youqi; Libisch, Florian; Xia, Junchao; Wang, Lin-Wang; Carter, Emily A
2013-08-01
Orbital-free (OF) density functional theory (DFT) directly solves for the electron density rather than the wave function of many electron systems, greatly simplifying and enabling large scale first principles simulations. However, the required approximate noninteracting kinetic energy density functionals and local electron-ion pseudopotentials severely restrict the general applicability of conventional OFDFT. Here, we present a new generation of OFDFT called angular-momentum-dependent (AMD)-OFDFT to harness the accuracy of Kohn-Sham DFT and the simplicity of OFDFT. The angular momenta of electrons are explicitly introduced within atom-centered spheres so that the important ionic core region can be accurately described. In addition to conventional OF total energy functionals, we introduce a crucial nonlocal energy term with a set of AMD energies to correct errors due to the kinetic energy density functional and the local pseudopotential. We find that our AMD-OFDFT formalism offers substantial improvements over conventional OFDFT, as we show for various properties of the transition metal titanium.
"Sloppy" nuclear energy density functionals: Effective model reduction
NASA Astrophysics Data System (ADS)
Nikšić, Tamara; Vretenar, Dario
2016-08-01
Concepts from information geometry are used to analyze parameter sensitivity for a nuclear energy density functional, representative of a class of semiempirical functionals that start from a microscopically motivated ansatz for the density dependence of the energy of a system of protons and neutrons. It is shown that such functionals are "sloppy," namely, characterized by an exponential range of sensitivity to parameter variations. Responsive to only a few stiff parameter combinations, sloppy functionals exhibit an exponential decrease of sensitivity to variations of the remaining soft parameters. By interpreting the space of model predictions as a manifold embedded in the data space, with the parameters of the functional as coordinates on the manifold, it is also shown that the exponential distribution of model manifold widths corresponds to the range of parameter sensitivity. Using the manifold boundary approximation method, we illustrate how to systematically construct effective nuclear density functionals of successively lower dimension in parameter space until sloppiness is eventually eliminated and the resulting functional contains only stiff combinations of parameters.
Density functional theory of crystal growth: Lennard-Jones fluids
NASA Astrophysics Data System (ADS)
Shen, Yu Chen; Oxtoby, David W.
1996-03-01
We employ an extension of density functional theory to the dynamics of phase transitions in order to study the velocities of crystal growth and melting at planar undercooled and superheated crystal-melt interfaces. The free energy functional we use has a square-gradient form, with the parameters for a Lennard-Jones interaction potential determined by a modified weighted density approximation (MWDA) applied locally through the liquid-solid interface. We explore the role of the density change on freezing in crystal and melt growth, and discover a significant asymmetry between freezing and melting both close to and far from the equilibrium freezing point. The behavior of the superheated solid is governed by the close proximity of a spinodal, whereas in the undercooled liquid there is no evidence for a spinodal and the growth at large undercoolings is affected instead by the density deficit that appears in front of the growing interface. Comparisons are made with other density functional approaches and with computer simulations.
Density functionals for the strong-interaction limit
NASA Astrophysics Data System (ADS)
Seidl, Michael; Perdew, John P.; Kurth, Stefan
2000-07-01
The strong-interaction limit of density-functional (DF) theory is simple and provides information required for an accurate resummation of DF perturbation theory. Here we derive the point-charge-plus-continuum (PC) model for that limit, and its gradient expansion. The exchange-correlation (xc) energy Exc[ρ]≡∫10dαWα[ρ] follows from the xc potential energies Wα at different interaction strengths α>=0 [but at fixed density ρ(r)]. For small α~0, the integrand Wα is obtained accurately from perturbation theory, but the perturbation expansion requires resummation for moderate and large α. For that purpose, we present density functionals for the coefficients in the asymptotic expansion Wα-->W∞+W'∞α-1/2 for α-->∞ in the PC model. WPC∞ arises from strict correlation, and W'PC∞ from zero-point vibration of the electrons around their strictly correlated distributions. The PC values for W∞ and W'∞ agree with those from a self-correlation-free meta-generalized gradient approximation, both for atoms and for atomization energies of molecules. We also (i) explain the difference between the PC cell and the exchange-correlation hole, (ii) present a density-functional measure of correlation strength, (iii) describe the electron localization and spin polarization energy in a highly stretched H2 molecule, and (iv) discuss the soft-plasmon instability of the low-density uniform electron gas.
Density functional theory modeling of multilayer "epitaxial" graphene oxide.
Zhou, Si; Bongiorno, Angelo
2014-11-18
CONSPECTUS: Graphene oxide (GO) is a complex material of both fundamental and applied interest. Elucidating the structure of GO is crucial to achieve control over its properties and technological applications. GO is a nonstoichiometric and hygroscopic material with a lamellar structure, and its physical chemical properties depend critically on synthesis procedures and postsynthesis treatments. Numerous efforts are in place to both understand and exploit this versatile layered carbon material. This Account reports on recent density functional theory (DFT) studies of "epitaxial" graphene oxide (hereafter EGO), a type of GO obtained by oxidation of graphene films grown epitaxially on silicon carbide. Here, we rely on selected X-ray photoelectron spectroscopy (XPS), infrared spectroscopy (IR), and X-ray diffraction (XRD) measurements of EGO, and we discuss in great detail how we utilized DFT-based techniques to project out from the experimental data basic atomistic information about the chemistry and structure of these films. This Account provides an example as to how DFT modeling can be used to elucidate complex materials such as GO from a limited set of experimental information. EGO exhibits a uniform layered structure, consisting of a stack of graphene planes hosting predominantly epoxide and hydroxyl groups, and water molecules intercalated between the oxidized carbon layers. Here, we first focus on XPS measurements of EGO, and we use DFT to generate realistic model structures, calculate core-level chemical shifts, and through the comparison with experiment, gain insight on the chemical composition and metastability characteristics of EGO. DFT calculations are then used to devise a simplistic but accurate simulation scheme to study thermodynamic and kinetic stability and to predict the intralayer structure of EGO films aged at room temperature. Our simulations show that aged EGO encompasses layers with nanosized oxidized domains presenting a high concentration of
Fractional spin in reduced density-matrix functional theory.
Helbig, N; Theodorakopoulos, G; Lathiotakis, N N
2011-08-01
We study the behavior of different functionals of the one-body reduced density matrix (1RDM) for systems with fractional z-component of the total spin. We define these systems as ensembles of integer spin states. It is shown that, similarly to density functional theory, the error in the dissociation of diatomic molecules is directly related to the deviation from constancy of the atomic total energies as functions of the fractional spin. However, several functionals of the 1RDM show a size inconsistency which leads to additional errors. We also investigate the difference between a direct evaluation of the energy of an ensemble of integer-spin systems and a direct minimization of the energy of a fractional-spin system.
Conditional probability density function estimation with sigmoidal neural networks.
Sarajedini, A; Hecht-Nielsen, R; Chau, P M
1999-01-01
Real-world problems can often be couched in terms of conditional probability density function estimation. In particular, pattern recognition, signal detection, and financial prediction are among the multitude of applications requiring conditional density estimation. Previous developments in this direction have used neural nets to estimate statistics of the distribution or the marginal or joint distributions of the input-output variables. We have modified the joint distribution estimating sigmoidal neural network to estimate the conditional distribution. Thus, the probability density of the output conditioned on the inputs is estimated using a neural network. We have derived and implemented the learning laws to train the network. We show that this network has computational advantages over a brute force ratio of joint and marginal distributions. We also compare its performance to a kernel conditional density estimator in a larger scale (higher dimensional) problem simulating more realistic conditions.
Applying Density Functional Theory for Atomic Vacancies in Solids
NASA Astrophysics Data System (ADS)
Zhou, Xiaolan; Perdew, John P.
2008-03-01
We use a new generalized gradient approximation of density functional theory -- PBEsol, a revised Perdew-Burke-Ernzerhof GGA, to calculate the vacancy formation energies and other properties of metals and semiconductors: Al, Pt, Pd, GaN [1], etc. By restoring the gradient expansion over a wide range of density gradients, PBEsol [2] yields excellent jellium exchange and correlation surface energies. We expect that this new functional will improve the description of vacancies in real materials, since the vacancy formation energy is essentially the work needed to create an interior surface. [1] Thomas R.Mattsson and Ann E. Mattson. Phys. Rev. B 66, 214410 (2002). [2] John P. Perdew, Adrienn Ruzsinszky, Gabor I. Csonka, Oleg A. Vydrov, Gustavo E. Scuseria, Lucian A. Constantin, Xiaolan Zhou, and Kieron Burke, Restoring the density-gradient expansion for exchange in solids and surfaces, http://arxiv.org/abs/0711.0156
Catalytic activities of platinum nanotubes: a density functional study
NASA Astrophysics Data System (ADS)
Mukherjee, Prajna; Gupta, Bikash C.; Jena, Puru
2015-10-01
In this work we investigate the catalytic properties of platinum nanotubes using density functional theory based calculations. In particular, we study the dissociation of hydrogen and oxygen molecules as well as oxidation of CO molecules. The results indicate that platinum nanotubes have good catalytic properties and can be effectively used in converting CO molecule to CO2.
Implementation Strategies for Orbital-dependent Density Functionals
NASA Astrophysics Data System (ADS)
Bento, Marsal E.; Vieira, Daniel
2016-10-01
The development of density functional theory (DFT) has been focused primarily on two main pillars: (1) the pursuit of more accurate exchange-correlation (XC) density functionals; (2) the feasibility of computational implementation when dealing with many-body systems. In this context, this work is aimed on using one-dimensional quantum systems as theoretical laboratories to investigate the implementation of orbital functionals (OFs) of density. By definition, OFs are those which depend only implicitly on the density, via an explicit formulation in terms of Kohn-Sham orbitals. Typical examples are the XC functionals arising from the Perdew-Zunger self-interaction correction (PZSIC). Formally, via Kohn-Sham equations, the implementation of OFs must be performed by means of the optimized effective potential method (OEP), which is known by requiring an excessive computational effort even when dealing with few electrons systems. Here, we proceed a systematical investigation aiming to simplify or avoid the OEP procedure, taking as reference the implementation of the PZSIC correction applied to one-dimensional Hubbard chains.
Application of nuclear density functionals to lepton number violating weak processes
Rodriguez, Tomas R.; Martinez-Pinedo, Gabriel
2012-10-20
We present an application of energy density functional methods with the Gogny interaction to the calculation of nuclear matrix elements (NME) for neutrinoless double beta decay and double electron capture. Beyond mean field effects have been included by particle number and angular momentum restoration and shape mixing within the generator coordinate method (GCM) framework. We analyze in detail the NME for {sup 116}Cd nucleus which is one of the most promising candidates to detect neutrinoless double beta decay.
Jiao, Y; Stillinger, F H; Torquato, S
2008-03-01
In the first part of this series of two papers, we proposed a theoretical formalism that enables one to model and categorize heterogeneous materials (media) via two-point correlation functions S(2) and introduced an efficient heterogeneous-medium (re)construction algorithm called the "lattice-point" algorithm. Here we discuss the algorithmic details of the lattice-point procedure and an algorithm modification using surface optimization to further speed up the (re)construction process. The importance of the error tolerance, which indicates to what accuracy the media are (re)constructed, is also emphasized and discussed. We apply the algorithm to generate three-dimensional digitized realizations of a Fontainebleau sandstone and a boron-carbide/aluminum composite from the two-dimensional tomographic images of their slices through the materials. To ascertain whether the information contained in S(2) is sufficient to capture the salient structural features, we compute the two-point cluster functions of the media, which are superior signatures of the microstructure because they incorporate topological connectedness information. We also study the reconstruction of a binary laser-speckle pattern in two dimensions, in which the algorithm fails to reproduce the pattern accurately. We conclude that in general reconstructions using S(2) only work well for heterogeneous materials with single-scale structures. However, two-point information via S(2) is not sufficient to accurately model multiscale random media. Moreover, we construct realizations of hypothetical materials with desired structural characteristics obtained by manipulating their two-point correlation functions.
Lima, N A; Silva, M F; Oliveira, L N; Capelle, K
2003-04-11
By shifting the reference system for the local-density approximation (LDA) from the electron gas to other model systems, one obtains a new class of density functionals, which by design account for the correlations present in the chosen reference system. This strategy is illustrated by constructing an explicit LDA for the one-dimensional Hubbard model. While the traditional ab initio LDA is based on a Fermi liquid (the three-dimensional interacting electron gas), this one is based on a Luttinger liquid. First applications to inhomogeneous Hubbard models, including one containing a localized impurity, are reported.
Lima, N A; Silva, M F; Oliveira, L N; Capelle, K
2003-04-11
By shifting the reference system for the local-density approximation (LDA) from the electron gas to other model systems, one obtains a new class of density functionals, which by design account for the correlations present in the chosen reference system. This strategy is illustrated by constructing an explicit LDA for the one-dimensional Hubbard model. While the traditional ab initio LDA is based on a Fermi liquid (the three-dimensional interacting electron gas), this one is based on a Luttinger liquid. First applications to inhomogeneous Hubbard models, including one containing a localized impurity, are reported. PMID:12731934
Density Functional Theory (DFT) simulations of porous tantalum pentoxide
NASA Astrophysics Data System (ADS)
Cochrane, K. R.; Vogler, T. J.; Desjarlais, M. P.; Mattsson, T. R.
2014-05-01
Density Functional Theory (DFT) based molecular dynamics has been established as a method capable of yielding high fidelity results for many materials at a wide range of pressures and temperatures and has recently been applied to complex polymers such as polyethylene, compounds such as ethane or CO2, and oxides such as MgO. We use this method to obtain a Grïneisen Γ and thereby build a Mie-Grüneisen equation of state (EOS) and a Rice-Walsh EOS for tantalum pentoxide (Ta2O5 or tantala) and compare to experimental data. The experimental data have initial densities (ρ00) of approximately 1.13, 3, and 7.4 g/cm3 reduced from a crystalline of 8.36 g/cm3. We found that r becomes constant at higher temperatures and pressure, but is a function of both density and temperature at lower densities and temperatures. Finally, the Mie-Gruneisen EOS is adequate for modeling the slightly distended Hugoniot with an initial density of 7.4 g/cm3 however it is inadequate for the more porous Hugoniot, while the Rice-Walsh EOS combined with a P - λ crush model approximates the experimental data quite well.
Gonis, A.; Zhang, X. G.; Stocks, G. M.; Nicholson, D. M.
2015-10-23
Density functional theory for the case of general, N-representable densities is reformulated in terms of density functional derivatives of expectation values of operators evaluated with wave functions leading to a density, making no reference to the concept of potential. The developments provide a complete solution of the v-representability problem by establishing a mathematical procedure that determines whether a density is v-representable and in the case of an affirmative answer determines the potential (within an additive constant) as a derivative with respect to the density of a constrained search functional. It also establishes the existence of an energy functional of themore » density that, for v-representable densities, assumes its minimum value at the density describing the ground state of an interacting many-particle system. The theorems of Hohenberg and Kohn emerge as special cases of the formalism.« less
Gonis, A.; Zhang, X. G.; Stocks, G. M.; Nicholson, D. M.
2015-10-23
Density functional theory for the case of general, N-representable densities is reformulated in terms of density functional derivatives of expectation values of operators evaluated with wave functions leading to a density, making no reference to the concept of potential. The developments provide a complete solution of the v-representability problem by establishing a mathematical procedure that determines whether a density is v-representable and in the case of an affirmative answer determines the potential (within an additive constant) as a derivative with respect to the density of a constrained search functional. It also establishes the existence of an energy functional of the density that, for v-representable densities, assumes its minimum value at the density describing the ground state of an interacting many-particle system. The theorems of Hohenberg and Kohn emerge as special cases of the formalism.
Relations among several nuclear and electronic density functional reactivity indexes
NASA Astrophysics Data System (ADS)
Torrent-Sucarrat, Miquel; Luis, Josep M.; Duran, Miquel; Toro-Labbé, Alejandro; Solà, Miquel
2003-11-01
An expansion of the energy functional in terms of the total number of electrons and the normal coordinates within the canonical ensemble is presented. A comparison of this expansion with the expansion of the energy in terms of the total number of electrons and the external potential leads to new relations among common density functional reactivity descriptors. The formulas obtained provide explicit links between important quantities related to the chemical reactivity of a system. In particular, the relation between the nuclear and the electronic Fukui functions is recovered. The connection between the derivatives of the electronic energy and the nuclear repulsion energy with respect to the external potential offers a proof for the "Quantum Chemical le Chatelier Principle." Finally, the nuclear linear response function is defined and the relation of this function with the electronic linear response function is given.
Density functional study of bisphenol-A polycarbonate
NASA Astrophysics Data System (ADS)
Montanari, Barbara; Ballone, Pietro; Jones, R. O.
1998-03-01
The optimum structure of a crystalline analog of bisphenol-A polycarbonate (BPA-PC) has been determined using density functional (DF) calculations. We have compared the results given by the local density (LD) approximation for the exchange-correlation energy with those obtained with two different gradient-corrected functionals: the Becke-Perdew (BP) functional and the one due to Perdew, Burke and Ernzerhof (PBE). In all cases the measured geometries are very well reproduced if the unit cell is constrained to have the experimental dimensions, whereas the results for the equilibrium volumes differ. The dynamical properties of two different crystalline modifications have been also investigated using the combination of DF and molecular dynamics (MD) scheme. In particular, we have calculated the energy barriers of the most significant dynamical features measured by NMR: the phenyl ring π-flips and the rotation of the methyl groups.
Ab initio derivation of model energy density functionals
NASA Astrophysics Data System (ADS)
Dobaczewski, Jacek
2016-08-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
Perspective: Fundamental aspects of time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Maitra, Neepa T.
2016-06-01
In the thirty-two years since the birth of the foundational theorems, time-dependent density functional theory has had a tremendous impact on calculations of electronic spectra and dynamics in chemistry, biology, solid-state physics, and materials science. Alongside the wide-ranging applications, there has been much progress in understanding fundamental aspects of the functionals and the theory itself. This Perspective looks back to some of these developments, reports on some recent progress and current challenges for functionals, and speculates on future directions to improve the accuracy of approximations used in this relatively young theory.
A density functional theory of chiral block copolymer melts.
Wang, Shih-Hao; Kawakatsu, Toshihiro; Chen, Peilong; Lu, Chun-Yi David
2013-05-21
A density functional theory is developed for the diblock copolymer melt, where one block contains the segment orientation dependent chiral interaction. In addition to the standard (scalar) pair interaction between the two types of monomers, the chiral block has the additional pairwise interaction, which is linear in the tangent vectors of the segments. We construct a density functional, which contains both the scalar density field and the vector chain alignment field. The quadratic part of the density functional comes from the mean field theory of the microscopic model, whereas the fourth order terms are introduced phenomenologically in the spatially local form. From the stability analysis of this model, we find that the additional chiral interaction shifts the order-disorder transition, which is consistent with the behavior of experimental system. Further numerical calculation reveals a new metastable chiral helical cylinder structure, which is similar to the one found experimentally. Another similar metastable structure but with zigzag modulation is also observed. As the helical and zigzag structures disappear when the chiral interaction is switched off, we understand that the chiral effect is the driving force for the formation of these exotic metastable structures.
Multiphase aluminum equations of state via density functional theory
NASA Astrophysics Data System (ADS)
Sjostrom, Travis; Crockett, Scott; Rudin, Sven
2016-10-01
We have performed density functional theory (DFT) based calculations for aluminum in extreme conditions of both pressure and temperature, up to five times compressed ambient density, and over 1 000 000 K in temperature. In order to cover such a domain, DFT methods including phonon calculations, quantum molecular dynamics, and orbital-free DFT are employed. The results are then used to construct a SESAME equation of state for the aluminum 1100 alloy, encompassing the fcc, hcp, and bcc solid phases as well as the liquid regime. We provide extensive comparison with experiment, and based on this we also provide a slightly modified equation of state for the aluminum 6061 alloy.
Nitroborazines as potential high energy materials: density functional theoretical calculations.
Janning, Jay D; Ball, David W
2010-05-01
As part of a search for new high energy density materials, we used density functional theoretical calculations to determine the thermochemical properties of various nitro-substituted borazine molecules. Optimized geometries, vibrational frequencies and spectra, and enthalpies of formation and combustion were determined for nitroborazine, dinitroborazine, trinitroborazine, and methyltrinitroborazine with substituents on either the boron atoms or the nitrogen atoms of the parent borazine ring. Our results indicate that the specific enthalpy of combustion ranged from 4 to 11 kJ g(-1), with increasing substitution of nitro groups lowering the energy of combustion per unit mass.
Numerical density-to-potential inversions in time-dependent density functional theory.
Jensen, Daniel S; Wasserman, Adam
2016-08-01
We treat the density-to-potential inverse problem of time-dependent density functional theory as an optimization problem with a partial differential equation constraint. The unknown potential is recovered from a target density by applying a multilevel optimization method controlled by error estimates. We employ a classical optimization routine using gradients efficiently computed by the discrete adjoint method. The inverted potential has both a real and imaginary part to reduce reflections at the boundaries and other numerical artifacts. We demonstrate this method on model one-dimensional systems. The method can be straightforwardly extended to a variety of numerical solvers of the time-dependent Kohn-Sham equations and to systems in higher dimensions.
NASA Astrophysics Data System (ADS)
Khan, Shehryar; Kubica-Misztal, Aleksandra; Kruk, Danuta; Kowalewski, Jozef; Odelius, Michael
2015-01-01
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(H2O)-, Gd(III)DTPA(H2O)2-, and Gd(III)(H2O)83+ 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.
SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS
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.
Steady-State Density Functional Theory for Finite Bias Conductances.
Stefanucci, G; Kurth, S
2015-12-01
In the framework of density functional theory, a formalism to describe electronic transport in the steady state is proposed which uses the density on the junction and the steady current as basic variables. We prove that, in a finite window around zero bias, there is a one-to-one map between the basic variables and both local potential on as well as bias across the junction. The resulting Kohn-Sham system features two exchange-correlation (xc) potentials, a local xc potential, and an xc contribution to the bias. For weakly coupled junctions the xc potentials exhibit steps in the density-current plane which are shown to be crucial to describe the Coulomb blockade diamonds. At small currents these steps emerge as the equilibrium xc discontinuity bifurcates. The formalism is applied to a model benzene junction, finding perfect agreement with the orthodox theory of Coulomb blockade. PMID:26571349
Steady-State Density Functional Theory for Finite Bias Conductances.
Stefanucci, G; Kurth, S
2015-12-01
In the framework of density functional theory, a formalism to describe electronic transport in the steady state is proposed which uses the density on the junction and the steady current as basic variables. We prove that, in a finite window around zero bias, there is a one-to-one map between the basic variables and both local potential on as well as bias across the junction. The resulting Kohn-Sham system features two exchange-correlation (xc) potentials, a local xc potential, and an xc contribution to the bias. For weakly coupled junctions the xc potentials exhibit steps in the density-current plane which are shown to be crucial to describe the Coulomb blockade diamonds. At small currents these steps emerge as the equilibrium xc discontinuity bifurcates. The formalism is applied to a model benzene junction, finding perfect agreement with the orthodox theory of Coulomb blockade.
Computational complexity of time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Whitfield, J. D.; Yung, M.-H.; Tempel, D. G.; Boixo, S.; Aspuru-Guzik, A.
2014-08-01
Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. We introduce a V-representability parameter which diverges at the boundary of the existence domain and serves to quantify the numerical difficulty of constructing the Kohn-Sham potential. For bounded values of V-representability, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds.
Ionization potential optimized double-hybrid density functional approximations
NASA Astrophysics Data System (ADS)
Margraf, Johannes T.; Verma, Prakash; Bartlett, Rodney J.
2016-09-01
Double-hybrid density functional approximations (DH-DFAs) provide an accurate description of the electronic structure of molecules by semiempirically mixing density functional and wavefunction theory. In this paper, we investigate the properties of the potential used in such approximations. By using the optimized effective potential approach, the consistent Kohn-Sham (KS) potential for a double-hybrid functional (including the second-order perturbational contribution) can be generated. This potential is shown to provide an improved description of orbital energies as vertical ionization potentials (IPs), relative to the perturbation-free KS potential typically used. Based on this observation, we suggest that DH-DFAs should be constructed in such a way that the potential provides accurate orbital energies. As a proof of principle, the B2-PLYP functional is reparameterized to obtain the IP-optimized B2IP-PLYP functional, using a small set of vertical IPs and atomization energies as reference data. This functional is shown to outperform B2-PLYP in a wide range of benchmarks and is en par with the related B2GP-PLYP. In particular, it is shown to be the most reliable choice in electronically difficult and multireference cases.
Scrutinizing "Invisible" astatine: A challenge for modern density functionals.
Sergentu, Dumitru-Claudiu; David, Grégoire; Montavon, Gilles; Maurice, Rémi; Galland, Nicolas
2016-06-01
The main-group 6p elements did not receive much attention in the development of recent density functionals. In many cases it is still difficult to choose among the modern ones a relevant functional for various applications. Here, we illustrate the case of astatine species (At, Z = 85) and we report the first, and quite complete, benchmark study on several properties concerning such species. Insights on geometries, transition energies and thermodynamic properties of a set of 19 astatine species, for which reference experimental or theoretical data has been reported, are obtained with relativistic (two-component) density functional theory calculations. An extensive set of widely used functionals is employed. The hybrid meta-generalized gradient approximation (meta-GGA) PW6B95 functional is overall the best choice. It is worth noting that the range-separated HSE06 functional as well as the old and very popular B3LYP and PBE0 hybrid-GGAs appear to perform quite well too. Moreover, we found that astatine chemistry in solution can accurately be predicted using implicit solvent models, provided that specific parameters are used to build At cavities. © 2016 Wiley Periodicals, Inc. PMID:27059181
Ionization potential optimized double-hybrid density functional approximations.
Margraf, Johannes T; Verma, Prakash; Bartlett, Rodney J
2016-09-14
Double-hybrid density functional approximations (DH-DFAs) provide an accurate description of the electronic structure of molecules by semiempirically mixing density functional and wavefunction theory. In this paper, we investigate the properties of the potential used in such approximations. By using the optimized effective potential approach, the consistent Kohn-Sham (KS) potential for a double-hybrid functional (including the second-order perturbational contribution) can be generated. This potential is shown to provide an improved description of orbital energies as vertical ionization potentials (IPs), relative to the perturbation-free KS potential typically used. Based on this observation, we suggest that DH-DFAs should be constructed in such a way that the potential provides accurate orbital energies. As a proof of principle, the B2-PLYP functional is reparameterized to obtain the IP-optimized B2IP-PLYP functional, using a small set of vertical IPs and atomization energies as reference data. This functional is shown to outperform B2-PLYP in a wide range of benchmarks and is en par with the related B2GP-PLYP. In particular, it is shown to be the most reliable choice in electronically difficult and multireference cases. PMID:27634250
Scrutinizing "Invisible" astatine: A challenge for modern density functionals.
Sergentu, Dumitru-Claudiu; David, Grégoire; Montavon, Gilles; Maurice, Rémi; Galland, Nicolas
2016-06-01
The main-group 6p elements did not receive much attention in the development of recent density functionals. In many cases it is still difficult to choose among the modern ones a relevant functional for various applications. Here, we illustrate the case of astatine species (At, Z = 85) and we report the first, and quite complete, benchmark study on several properties concerning such species. Insights on geometries, transition energies and thermodynamic properties of a set of 19 astatine species, for which reference experimental or theoretical data has been reported, are obtained with relativistic (two-component) density functional theory calculations. An extensive set of widely used functionals is employed. The hybrid meta-generalized gradient approximation (meta-GGA) PW6B95 functional is overall the best choice. It is worth noting that the range-separated HSE06 functional as well as the old and very popular B3LYP and PBE0 hybrid-GGAs appear to perform quite well too. Moreover, we found that astatine chemistry in solution can accurately be predicted using implicit solvent models, provided that specific parameters are used to build At cavities. © 2016 Wiley Periodicals, Inc.
Precise effective masses from density functional perturbation theory
NASA Astrophysics Data System (ADS)
Laflamme Janssen, J.; Gillet, Y.; Poncé, S.; Martin, A.; Torrent, M.; Gonze, X.
2016-05-01
The knowledge of effective masses is a key ingredient to analyze numerous properties of semiconductors, like carrier mobilities, (magneto)transport properties, or band extrema characteristics yielding carrier densities and density of states. Currently, these masses are usually calculated using finite-difference estimation of density functional theory (DFT) electronic band curvatures. However, finite differences require an additional convergence study and are prone to numerical noise. Moreover, the concept of effective mass breaks down at degenerate band extrema. We assess the former limitation by developing a method that allows to obtain the Hessian of DFT bands directly, using density functional perturbation theory. Then, we solve the latter issue by adapting the concept of "transport equivalent effective mass" to the k .p ̂ framework. The numerical noise inherent to finite-difference methods is thus eliminated, along with the associated convergence study. The resulting method is therefore more general, more robust, and simpler to use, which makes it especially appropriate for high-throughput computing. After validating the developed techniques, we apply them to the study of silicon, graphane, and arsenic. The formalism is implemented into the abinit software and supports the norm-conserving pseudopotential approach, the projector augmented-wave method, and the inclusion of spin-orbit coupling. The derived expressions also apply to the ultrasoft pseudopotential method.
What Density Functional Theory could do for Quantum Information
NASA Astrophysics Data System (ADS)
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.
Density Functional Theory for Steady-State Nonequilibrium Molecular Junctions
Liu, Shuanglong; Nurbawono, Argo; Zhang, Chun
2015-01-01
We present a density functional theory (DFT) for steady-state nonequilibrium quantum systems such as molecular junctions under a finite bias. Based on the steady-state nonequilibrium statistics that maps nonequilibrium to an effective equilibrium, we show that ground-state DFT (GS-DFT) is not applicable in this case and two densities, the total electron density and the density of current-carrying electrons, are needed to uniquely determine the properties of the corresponding nonequilibrium system. A self-consistent mean-field approach based on two densities is then derived. The theory is implemented into SIESTA computational package and applied to study nonequilibrium electronic/transport properties of a realistic carbon-nanotube (CNT)/Benzene junction. Results obtained from our steady-state DFT (SS-DFT) are compared with those of conventional GS-DFT based transport calculations. We show that SS-DFT yields energetically more stable nonequilibrium steady state, predicts significantly lower electric current, and is able to produce correct electronic structures in local equilibrium under a limiting case. PMID:26472080
Excitations and benchmark ensemble density functional theory for two electrons
Pribram-Jones, Aurora; Burke, Kieron; Yang, Zeng-hui; Ullrich, Carsten A.; Trail, John R.; Needs, Richard J.
2014-05-14
A new method for extracting ensemble Kohn-Sham potentials from accurate excited state densities is applied to a variety of two-electron systems, exploring the behavior of exact ensemble density functional theory. The issue of separating the Hartree energy and the choice of degenerate eigenstates is explored. A new approximation, spin eigenstate Hartree-exchange, is derived. Exact conditions that are proven include the signs of the correlation energy components and the asymptotic behavior of the potential for small weights of the excited states. Many energy components are given as a function of the weights for two electrons in a one-dimensional flat box, in a box with a large barrier to create charge transfer excitations, in a three-dimensional harmonic well (Hooke's atom), and for the He atom singlet-triplet ensemble, singlet-triplet-singlet ensemble, and triplet bi-ensemble.
Analyzing the financial crisis using the entropy density function
NASA Astrophysics Data System (ADS)
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.
Semilocal density functional theory with correct surface asymptotics
NASA Astrophysics Data System (ADS)
Constantin, Lucian A.; Fabiano, Eduardo; Pitarke, J. M.; Della Sala, Fabio
2016-03-01
Semilocal density functional theory is the most used computational method for electronic structure calculations in theoretical solid-state physics and quantum chemistry of large systems, providing good accuracy with a very attractive computational cost. Nevertheless, because of the nonlocality of the exchange-correlation hole outside a metal surface, it was always considered inappropriate to describe the correct surface asymptotics. Here, we derive, within the semilocal density functional theory formalism, an exact condition for the imagelike surface asymptotics of both the exchange-correlation energy per particle and potential. We show that this condition can be easily incorporated into a practical computational tool, at the simple meta-generalized-gradient approximation level of theory. Using this tool, we also show that the Airy-gas model exhibits asymptotic properties that are closely related to those at metal surfaces. This result highlights the relevance of the linear effective potential model to the metal surface asymptotics.
Graphyne on metallic surfaces: A density functional theory study
NASA Astrophysics Data System (ADS)
Lazić, P.; Crljen, Ž.
2015-03-01
We show how a structural modification of graphene, which gives the carbon allotrope graphyne, can induce an energy gap at the K point of the Brillouin zone. Upon adsorption on metallic surfaces, the same mechanism is responsible for a further modification of energy bands which occurs via the charge transfer mechanism. We perform the calculation based on the density functional theory with the novel nonlocal van der Waals-density functional correlation of the adsorption of graphyne on Cu(111), Ni(111), and Co(0001) surfaces and show the dependence of the band change on the charge transfer in the system. The binding of graphyne appears to be stronger than that of graphene on the same surfaces.
Neutrinoless double-beta decay in covariant density functional theory
Ring, P.; Yao, J. M.; Song, L. S.; Hagino, K.; Meng, J.
2015-10-15
We use covariant density functional theory beyond mean field in order to describe neutrinoless double-beta decay in a fully relativistic way. The dynamic effects of particle-number and angular-momentum conservations as well as shape fluctuations of quadrupole character are taken into account within the generator coordinate method for both initial and final nuclei. The calculations are based on the full relativistic transition operator. The nuclear matrix elements (NME’s) for a large number of possible transitions are investigated. The results are compared with various non-relativistic calculations, in particular also with the density functional theory based on the Gogny force. We find that the non-relativistic approximation is justified and that the total NME’s can be well approximated by the pure axial-vector coupling term. This corresponds to a considerable reduction of the computational effort.
Covariant density functional theory: The role of the pion
Lalazissis, G. A.; Karatzikos, S.; Serra, M.; Otsuka, T.; Ring, P.
2009-10-15
We investigate the role of the pion in covariant density functional theory. Starting from conventional relativistic mean field (RMF) theory with a nonlinear coupling of the {sigma} meson and without exchange terms we add pions with a pseudovector coupling to the nucleons in relativistic Hartree-Fock approximation. In order to take into account the change of the pion field in the nuclear medium the effective coupling constant of the pion is treated as a free parameter. It is found that the inclusion of the pion to this sort of density functionals does not destroy the overall description of the bulk properties by RMF. On the other hand, the noncentral contribution of the pion (tensor coupling) does have effects on single particle energies and on binding energies of certain nuclei.
NASA Astrophysics Data System (ADS)
Ruggenthaler, Michael; Flick, Johannes; Pellegrini, Camilla; Appel, Heiko; Tokatly, Ilya V.; Rubio, Angel
2014-07-01
In this work, we give a comprehensive derivation of an exact and numerically feasible method to perform ab initio calculations of quantum particles interacting with a quantized electromagnetic field. We present a hierarchy of density-functional-type theories that describe the interaction of charged particles with photons and introduce the appropriate Kohn-Sham schemes. We show how the evolution of a system described by quantum electrodynamics in Coulomb gauge is uniquely determined by its initial state and two reduced quantities. These two fundamental observables, the polarization of the Dirac field and the vector potential of the photon field, can be calculated by solving two coupled, nonlinear evolution equations without the need to explicitly determine the (numerically infeasible) many-body wave function of the coupled quantum system. To find reliable approximations to the implicit functionals, we present the appropriate Kohn-Sham construction. In the nonrelativistic limit, this density-functional-type theory of quantum electrodynamics reduces to the density-functional reformulation of the Pauli-Fierz Hamiltonian, which is based on the current density of the electrons and the vector potential of the photon field. By making further approximations, e.g., restricting the allowed modes of the photon field, we derive further density-functional-type theories of coupled matter-photon systems for the corresponding approximate Hamiltonians. In the limit of only two sites and one mode we deduce the appropriate effective theory for the two-site Hubbard model coupled to one photonic mode. This model system is used to illustrate the basic ideas of a density-functional reformulation in great detail and we present the exact Kohn-Sham potentials for our coupled matter-photon model system.
NASA Astrophysics Data System (ADS)
Sutton, Phil J.; Kusmartsev, Feo V.
2014-04-01
Saturn's rings, reminiscent of an early Solar system present a unique opportunity to investigate experimentally some mechanisms thought to be responsible for planet and planetesimal formation in protoplanetary discs. Here, we extended the comparison of our numerical models of Prometheus encountering the F ring employing non-interacting and interacting particles. Higher resolution analysis revealed that the density increases known to exist at channel edges is more complex and localized than previously thought. Asymmetry between density increases on channel edges revealed that the channel edge facing way from Prometheus to be the most stable but with lowest maximum increases. However, on the channel edge facing Prometheus the interacting model showed large chaotic fluctuations in the maximum density of some clumps, much larger than those of the other channel. The likely cause of this asymmetry is a variance in localized turbulence introduced into the F ring by Prometheus. High-resolution velocity dispersion maps showed that there was a spatial link between the highest densities and the highest velocity dispersions in the interacting model. Thus, suggesting that the high velocity dispersion we see is the reason for the observed inhomogeneous distribution of fans (evidence of embedded moonlets) on some of the channel edges facing Prometheus.
Probability density function modeling for sub-powered interconnects
NASA Astrophysics Data System (ADS)
Pater, Flavius; Amaricǎi, Alexandru
2016-06-01
This paper proposes three mathematical models for reliability probability density function modeling the interconnect supplied at sub-threshold voltages: spline curve approximations, Gaussian models,and sine interpolation. The proposed analysis aims at determining the most appropriate fitting for the switching delay - probability of correct switching for sub-powered interconnects. We compare the three mathematical models with the Monte-Carlo simulations of interconnects for 45 nm CMOS technology supplied at 0.25V.
Autoionization in time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Kapoor, V.
2016-06-01
We compute the exact exchange-correlation potential of the time-dependent density-functional theory (TDDFT) for the correlated process of autoionization. The potential develops barriers which regulate the autoionization rate. TDDFT employing known and practicable exchange-correlation potentials does not capture any autoionization dynamics. Approximate exchange-correlation potentials capturing such dynamics would necessarily require memory effects and are unlikely to be developed, as will be illustrated.
Association between lung function and airway wall density
NASA Astrophysics Data System (ADS)
Leader, J. Ken; Zheng, Bin; Fuhrman, Carl R.; Tedrow, John; Park, Sang C.; Tan, Jun; Pu, Jiantao; Drescher, John M.; Gur, David; Sciurba, Frank C.
2009-02-01
Computed tomography (CT) examination is often used to quantify the relation between lung function and airway remodeling in chronic obstructive pulmonary disease (COPD). In this preliminary study, we examined the association between lung function and airway wall computed attenuation ("density") in 200 COPD screening subjects. Percent predicted FVC (FVC%), percent predicted FEV1 (FEV1%), and the ratio of FEV1 to FVC as a percentage (FEV1/FVC%) were measured post-bronchodilator. The apical bronchus of the right upper lobe was manually selected from CT examinations for evaluation. Total airway area, lumen area, wall area, lumen perimeter and wall area as fraction of the total airway area were computed. Mean HU (meanHU) and maximum HU (maxHU) values were computed across pixels assigned membership in the wall and with a HU value greater than -550. The Pearson correlation coefficients (PCC) between FVC%, FEV1%, and FEV1/FVC% and meanHU were -0.221 (p = 0.002), -0.175 (p = 0.014), and -0.110 (p = 0.123), respectively. The PCCs for maxHU were only significant for FVC%. The correlations between lung function and the airway morphometry parameters were slightly stronger compared to airway wall density. MeanHU was significantly correlated with wall area (PCC = 0.720), airway area (0.498) and wall area percent (0.611). This preliminary work demonstrates that airway wall density is associated with lung function. Although the correlations in our study were weaker than a recent study, airway wall density initially appears to be an important parameter in quantitative CT analysis of COPD.
Finite-size instabilities in nuclear energy density functionals
Hellemans, V.; Heenen, P.-H.; Bender, M.
2012-10-20
The systematic lack of convergence of self-consistent mean-field calculations with certain parameterizations of the Skyrme energy density functional has been attributed to the appearance of finite-size instabilities. In this contribution, we investigate what happens at the instability associated with the C{sub 0}{sup {Delta}s}s{sub 0} Dot-Operator {Delta}s{sub 0} term in a high-spin state of the superdeformed band in {sup 194}Hg.
Probability Density Function Method for Langevin Equations with Colored Noise
Wang, Peng; Tartakovsky, Alexandre M.; Tartakovsky, Daniel M.
2013-04-05
We present a novel method to derive closed-form, computable PDF equations for Langevin systems with colored noise. The derived equations govern the dynamics of joint or marginal probability density functions (PDFs) of state variables, and rely on a so-called Large-Eddy-Diffusivity (LED) closure. We demonstrate the accuracy of the proposed PDF method for linear and nonlinear Langevin equations, describing the classical Brownian displacement and dispersion in porous media.
Density functional theory across chemistry, physics and biology.
van Mourik, Tanja; Bühl, Michael; Gaigeot, Marie-Pierre
2014-03-13
The past decades have seen density functional theory (DFT) evolve from a rising star in computational quantum chemistry to one of its major players. This Theme Issue, which comes half a century after the publication of the Hohenberg-Kohn theorems that laid the foundations of modern DFT, reviews progress and challenges in present-day DFT research. Rather than trying to be comprehensive, this Theme Issue attempts to give a flavour of selected aspects of DFT.
A Wigner Monte Carlo approach to density functional theory
Sellier, J.M. Dimov, I.
2014-08-01
In order to simulate quantum N-body systems, stationary and time-dependent density functional theories rely on the capacity of calculating the single-electron wave-functions of a system from which one obtains the total electron density (Kohn–Sham systems). In this paper, we introduce the use of the Wigner Monte Carlo method in ab-initio calculations. This approach allows time-dependent simulations of chemical systems in the presence of reflective and absorbing boundary conditions. It also enables an intuitive comprehension of chemical systems in terms of the Wigner formalism based on the concept of phase-space. Finally, being based on a Monte Carlo method, it scales very well on parallel machines paving the way towards the time-dependent simulation of very complex molecules. A validation is performed by studying the electron distribution of three different systems, a Lithium atom, a Boron atom and a hydrogenic molecule. For the sake of simplicity, we start from initial conditions not too far from equilibrium and show that the systems reach a stationary regime, as expected (despite no restriction is imposed in the choice of the initial conditions). We also show a good agreement with the standard density functional theory for the hydrogenic molecule. These results demonstrate that the combination of the Wigner Monte Carlo method and Kohn–Sham systems provides a reliable computational tool which could, eventually, be applied to more sophisticated problems.
Thermal Corrections to Density Functional Simulations of Warm Dense Matter
NASA Astrophysics Data System (ADS)
Smith, Justin; Pribram-Jones, Aurora; Burke, Kieron
Present density functional calculations of warm dense matter often use the Mermin-Kohn-Sham (MKS) scheme at finite temperature, but employ ground-state approximations to the exchange-correlation (XC) free energy. In the simplest solvable non-trivial model, an asymmetric Hubbard dimer, we calculate the exact many-body energies, the exact Mermin-Kohn-Sham functionals for this system, and extract the exact XC free energy. For moderate temperatures and weak correlation, we show this approximation is excellent, but fails for stronger correlations. Additionally, we use this system to test various conditions that must be satisfied.
Advances in time-dependent current-density functional theory
NASA Astrophysics Data System (ADS)
Berger, Arjan
In this work we solve the problem of the gauge dependence of molecular magnetic properties (magnetizabilities, circular dichroism) using time-dependent current-density functional theory [1]. We also present a new functional that accurately describes the optical absorption spectra of insulators, semiconductors and metals [2] N. Raimbault, P.L. de Boeij, P. Romaniello, and J.A. Berger Phys. Rev. Lett. 114, 066404 (2015) J.A. Berger, Phys. Rev. Lett. 115, 137402 (2015) This study has been partially supported through the Grant NEXT No. ANR-10-LABX-0037 in the framework of the Programme des Investissements d'Avenir.
Linear Scaling Density Functional Calculations with Gaussian Orbitals
NASA Technical Reports Server (NTRS)
Scuseria, Gustavo E.
1999-01-01
Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.
Atomistic force field for alumina fit to density functional theory
Sarsam, Joanne; Finnis, Michael W.; Tangney, Paul
2013-11-28
We present a force field for bulk alumina (Al{sub 2}O{sub 3}), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.
Conformational Analysis of Thioether Musks Using Density Functional Theory
Setzer, William N.
2009-01-01
A conformational analysis of nine macrocyclic thioether musks has been carried out using molecular mechanics (MMFF), density functional theory (DFT) using both B3LYP and M06 functionals, as well as Hartree-Fock and post-Hartree-Fock (MP2) ab initio methods. 6-Thia-, 10-thia- and 4-methyl-5-thia-14-tetradecananolide, 4-thia-, 7-thia-, 11-thia- and 12-thia-15-pentadecanolide and 6-thia- and 12-thia-16-hexadecanolide were modeled. Unfortunately, there was little agreement between the computational methods at the levels of theory used in this study. PMID:20111690
High-density lipoprotein functionality in coronary artery disease.
Kosmas, Constantine E; Christodoulidis, Georgios; Cheng, Jeh-wei; Vittorio, Timothy J; Lerakis, Stamatios
2014-06-01
The role of high-density lipoprotein (HDL) in cardiovascular atheroprotection is well established. Epidemiological data have clearly demonstrated an inverse relationship between HDL levels and the risk for coronary artery disease, which is independent of the low-density lipoprotein levels. However, more recent data provide evidence that high HDL levels are not always protective and that under certain conditions may even confer an increased risk. Thus, a new concept has arisen, which stresses the importance of HDL functionality, rather than HDL concentration per se, in the assessment of cardiovascular risk. HDL functionality is genetically defined but can also be modified by several environmental and lifestyle factors, such as diet, smoking or certain pharmacologic interventions. Furthermore, HDL is consisted of a heterogeneous group of particles with major differences in their structural, biological and functional properties. Recently, the cholesterol efflux capacity from macrophages was proven to be an excellent metric of HDL functionality, because it was shown to have a strong inverse relationship with the risk of angiographically documented coronary artery disease, independent of the HDL and apolipoprotein A-1 levels, although it may not actually predict the prospective risk for cardiovascular events. Thus, improving the quality of HDL may represent a better therapeutic target than simply raising the HDL level, and assessment of HDL function may prove informative in refining our understanding of HDL-mediated atheroprotection.
Curvature and Frontier Orbital Energies in Density Functional Theory
Stein, Tamar; Autschbach, Jochen; Govind, Niranjan; Kronik, Leeor; Baer, Roi
2012-12-20
Perdew et al. [Phys. Rev. Lett 49, 1691 (1982)] discovered and proved two different properties that exact Kohn-Sham density functional theory (DFT) must obey: (i) The exact total energy versus particle number must be a series of linear segments between integer electron points; (ii) Across an integer number of electrons, the exchange-correlation potential may ``jump’’ by a constant, known as the derivative discontinuity (DD). Here, we show analytically that in both the original and the generalized Kohn-Sham formulation of DFT, the two are in fact two sides of the same coin. Absence of a derivative discontinuity necessitates deviation from piecewise linearity, and the latter can be used to correct for the former, thereby restoring the physical meaning of the orbital energies. Using selected small molecules, we show that this results in a simple correction scheme for any underlying functional, including semi-local and hybrid functionals as well as Hartree-Fock theory, suggesting a practical correction for the infamous gap problem of density functional theory. Moreover, we show that optimally-tuned range-separated hybrid functionals can inherently minimize both DD and curvature, thus requiring no correction, and show that this can be used as a sound theoretical basis for novel tuning strategies.
Density functional theory and chromium: Insights from the dimers
Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael; Walter, Michael
2015-03-28
The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences between functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.
Franco-Pérez, Marco E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Ayers, Paul W. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Gázquez, José L. E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx; Vela, Alberto E-mail: ayers@mcmaster.ca E-mail: avela@cinvestav.mx
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.
Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto
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.
Density functional theory and hydrogen bonds: are we there yet?
Boese, A Daniel
2015-04-01
Density functional theory (DFT) has become more successful at introducing dispersion interactions, and can be thus applied to a wide range of systems. Amongst these are systems that contain hydrogen bonds, which are extremely important for the biological regime. Here, the description of hydrogen-bonded interactions by DFT with and without dispersion corrections is investigated. For small complexes, for which electrostatics are the determining factor in the intermolecular interactions, the inclusion of dispersion with most functionals yields large errors. Only for larger systems, in which van der Waals interactions are more important, do dispersion corrections improve the performance of DFT for hydrogen-bonded systems. None of the studied functionals, including double hybrid functionals (with the exception of DSD-PBEP86 without dispersion corrections), are more accurate than MP2 for the investigated species.
Many-body theory and Energy Density Functionals
NASA Astrophysics Data System (ADS)
Baldo, M.
2016-07-01
In this paper a method is first presented to construct an Energy Density Functional on a microscopic basis. The approach is based on the Kohn-Sham method, where one introduces explicitly the Nuclear Matter Equation of State, which can be obtained by an accurate many-body calculation. In this way it connects the functional to the bare nucleon-nucleon interaction. It is shown that the resulting functional can be performing as the best Gogny force functional. In the second part of the paper it is shown how one can go beyond the mean-field level and the difficulty that can appear. The method is based on the particle-vibration coupling scheme and a formalism is presented that can handle the correct use of the vibrational degrees of freedom within a microscopic approach.
Van der Waals Density Functional Theory with Applications
NASA Astrophysics Data System (ADS)
Langreth, David C.
2004-03-01
We discuss the development of electronic density functionals that are applicable for weakly bound systems where the van der Waals interaction and its ramifications become important. Our current functionals approach the correct asymptotic dependence at large distances and are seamless at small distances. The first form of the functional, appropriate for layered systems, has been recently applied to graphite, boron nitride, and molybdenum sulfide [H. Rydberg et al., Phys. Rev. Lett. 91, 126402 (2003) and D. C. Langreth, Int. J. Quant. Chem. (submitted), see http//:www.physics.rutgers.edu/ ˜langreth/preprints/dft2003.pdf]. The second form of the functional [M. Dion it et al. (to be published)] is appropriate for arbitrary geometries. Recent results on rare gas dimers and the benzene dimer suggest promise for this method as well.
Ultra-nonlocality in density functional theory for photo-emission spectroscopy
Uimonen, A.-M.; Stefanucci, G.; Leeuwen, R. van
2014-05-14
We derive an exact expression for the photocurrent of photo-emission spectroscopy using time-dependent current density functional theory (TDCDFT). This expression is given as an integral over the Kohn-Sham spectral function renormalized by effective potentials that depend on the exchange-correlation kernel of current density functional theory. We analyze in detail the physical content of this expression by making a connection between the density-functional expression and the diagrammatic expansion of the photocurrent within many-body perturbation theory. We further demonstrate that the density functional expression does not provide us with information on the kinetic energy distribution of the photo-electrons. Such information can, in principle, be obtained from TDCDFT by exactly modeling the experiment in which the photocurrent is split into energy contributions by means of an external electromagnetic field outside the sample, as is done in standard detectors. We find, however, that this procedure produces very nonlocal correlations between the exchange-correlation fields in the sample and the detector.
FDE-vdW: A van der Waals inclusive subsystem density-functional theory
Kevorkyants, Ruslan; Pavanello, Michele; Eshuis, Henk
2014-07-28
We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.
Current density partitioning in time-dependent current density functional theory
Mosquera, Martín A.; Wasserman, Adam
2014-05-14
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Density-dependence of functional spiking networks in vitro
Ham, Michael I; Gintautuas, Vadas; Rodriguez, Marko A; Bettencourt, Luis M A; Bennett, Ryan; Santa Maria, Cara L
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.
Generalized Pauli constraints in reduced density matrix functional theory
NASA Astrophysics Data System (ADS)
Theophilou, Iris; Lathiotakis, Nektarios N.; Marques, Miguel A. L.; Helbig, Nicole
2015-04-01
Functionals of the one-body reduced density matrix (1-RDM) are routinely minimized under Coleman's ensemble N-representability conditions. Recently, the topic of pure-state N-representability conditions, also known as generalized Pauli constraints, received increased attention following the discovery of a systematic way to derive them for any number of electrons and any finite dimensionality of the Hilbert space. The target of this work is to assess the potential impact of the enforcement of the pure-state conditions on the results of reduced density-matrix functional theory calculations. In particular, we examine whether the standard minimization of typical 1-RDM functionals under the ensemble N-representability conditions violates the pure-state conditions for prototype 3-electron systems. We also enforce the pure-state conditions, in addition to the ensemble ones, for the same systems and functionals and compare the correlation energies and optimal occupation numbers with those obtained by the enforcement of the ensemble conditions alone.
Generalized Pauli constraints in reduced density matrix functional theory
Theophilou, Iris; Helbig, Nicole; Lathiotakis, Nektarios N.; Marques, Miguel A. L.
2015-04-21
Functionals of the one-body reduced density matrix (1-RDM) are routinely minimized under Coleman’s ensemble N-representability conditions. Recently, the topic of pure-state N-representability conditions, also known as generalized Pauli constraints, received increased attention following the discovery of a systematic way to derive them for any number of electrons and any finite dimensionality of the Hilbert space. The target of this work is to assess the potential impact of the enforcement of the pure-state conditions on the results of reduced density-matrix functional theory calculations. In particular, we examine whether the standard minimization of typical 1-RDM functionals under the ensemble N-representability conditions violates the pure-state conditions for prototype 3-electron systems. We also enforce the pure-state conditions, in addition to the ensemble ones, for the same systems and functionals and compare the correlation energies and optimal occupation numbers with those obtained by the enforcement of the ensemble conditions alone.
Downlink Probability Density Functions for EOS-McMurdo Sound
NASA Technical Reports Server (NTRS)
Christopher, P.; Jackson, A. H.
1996-01-01
The visibility times and communication link dynamics for the Earth Observations Satellite (EOS)-McMurdo Sound direct downlinks have been studied. The 16 day EOS periodicity may be shown with the Goddard Trajectory Determination System (GTDS) and the entire 16 day period should be simulated for representative link statistics. We desire many attributes of the downlink, however, and a faster orbital determination method is desirable. We use the method of osculating elements for speed and accuracy in simulating the EOS orbit. The accuracy of the method of osculating elements is demonstrated by closely reproducing the observed 16 day Landsat periodicity. An autocorrelation function method is used to show the correlation spike at 16 days. The entire 16 day record of passes over McMurdo Sound is then used to generate statistics for innage time, outage time, elevation angle, antenna angle rates, and propagation loss. The levation angle probability density function is compared with 1967 analytic approximation which has been used for medium to high altitude satellites. One practical result of this comparison is seen to be the rare occurrence of zenith passes. The new result is functionally different than the earlier result, with a heavy emphasis on low elevation angles. EOS is one of a large class of sun synchronous satellites which may be downlinked to McMurdo Sound. We examine delay statistics for an entire group of sun synchronous satellites ranging from 400 km to 1000 km altitude. Outage probability density function results are presented three dimensionally.
Stochastic Optimally Tuned Range-Separated Hybrid Density Functional Theory.
Neuhauser, Daniel; Rabani, Eran; Cytter, Yael; Baer, Roi
2016-05-19
We develop a stochastic formulation of the optimally tuned range-separated hybrid density functional theory that enables significant reduction of the computational effort and scaling of the nonlocal exchange operator at the price of introducing a controllable statistical error. Our method is based on stochastic representations of the Coulomb convolution integral and of the generalized Kohn-Sham density matrix. The computational cost of the approach is similar to that of usual Kohn-Sham density functional theory, yet it provides a much more accurate description of the quasiparticle energies for the frontier orbitals. This is illustrated for a series of silicon nanocrystals up to sizes exceeding 3000 electrons. Comparison with the stochastic GW many-body perturbation technique indicates excellent agreement for the fundamental band gap energies, good agreement for the band edge quasiparticle excitations, and very low statistical errors in the total energy for large systems. The present approach has a major advantage over one-shot GW by providing a self-consistent Hamiltonian that is central for additional postprocessing, for example, in the stochastic Bethe-Salpeter approach. PMID:26651840
Density functional theory: Its origins, rise to prominence, and future
NASA Astrophysics Data System (ADS)
Jones, R. O.
2015-07-01
In little more than 20 years, the number of applications of the density functional (DF) formalism in chemistry and materials science has grown in an astonishing fashion. The number of publications alone shows that DF calculations make up a huge success story, and many younger colleagues are surprised to learn that the widespread application of density functional methods, particularly in chemistry, began only after 1990. This is indeed unexpected, because the origins are usually traced to the papers of Hohenberg, Kohn, and Sham more than a quarter of a century earlier. The DF formalism, its applications, and prospects were reviewed for this journal in 1989. About the same time, the combination of DF calculations with molecular dynamics promised to provide an efficient way to study structures and reactions in molecules and extended systems. This paper reviews the development of density-related methods back to the early years of quantum mechanics and follows the breakthrough in their application after 1990. The two examples from biochemistry and materials science are among the many current applications that were simply far beyond expectations in 1990. The reasons why—50 years after its modern formulation and after two decades of rapid expansion—some of the most cited practitioners in the field are concerned about its future are discussed.
Massively parallel density functional calculations for thousands of atoms: KKRnano
NASA Astrophysics Data System (ADS)
Thiess, A.; Zeller, R.; Bolten, M.; Dederichs, P. H.; Blügel, S.
2012-06-01
Applications of existing precise electronic-structure methods based on density functional theory are typically limited to the treatment of about 1000 inequivalent atoms, which leaves unresolved many open questions in material science, e.g., on complex defects, interfaces, dislocations, and nanostructures. KKRnano is a new massively parallel linear scaling all-electron density functional algorithm in the framework of the Korringa-Kohn-Rostoker (KKR) Green's-function method. We conceptualized, developed, and optimized KKRnano for large-scale applications of many thousands of atoms without compromising on the precision of a full-potential all-electron method, i.e., it is a method without any shape approximation of the charge density or potential. A key element of the new method is the iterative solution of the sparse linear Dyson equation, which we parallelized atom by atom, across energy points in the complex plane and for each spin degree of freedom using the message passing interface standard, followed by a lower-level OpenMP parallelization. This hybrid four-level parallelization allows for an efficient use of up to 100000 processors on the latest generation of supercomputers. The iterative solution of the Dyson equation is significantly accelerated, employing preconditioning techniques making use of coarse-graining principles expressed in a block-circulant preconditioner. In this paper, we will describe the important elements of this new algorithm, focusing on the parallelization and preconditioning and showing scaling results for NiPd alloys up to 8192 atoms and 65536 processors. At the end, we present an order-N algorithm for large-scale simulations of metallic systems, making use of the nearsighted principle of the KKR Green's-function approach by introducing a truncation of the electron scattering to a local cluster of atoms, the size of which is determined by the requested accuracy. By exploiting this algorithm, we show linear scaling calculations of more
Applications of large-scale density functional theory in biology.
Cole, Daniel J; Hine, Nicholas D M
2016-10-01
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality. PMID:27494095
Excitation Spectra of Nucleobases with Multiconfigurational Density Functional Theory.
Hubert, Mickaël; Jensen, Hans Jørgen Aa; Hedegård, Erik D
2016-01-14
Range-separated hybrid methods between wave function theory and density functional theory (DFT) can provide high-accuracy results, while correcting some of the inherent flaws of both the underlying wave function theory and DFT. We here assess the accuracy for excitation energies of the nucleobases thymine, uracil, cytosine, and adenine, using a hybrid between complete active space self-consistent field (CASSCF) and DFT methods. The method is based on range separation, thereby avoiding all double-counting of electron correlation and is denoted long-range CASSCF short-range DFT (CAS-srDFT). Using a linear response extension of CAS-srDFT, we compare the first 7-8 excited states of the nucleobases with perturbative multireference approaches as well as coupled cluster based methods. Our results show that the CAS-srDFT method can provide accurate excitation energies in good correspondence with the computationally more expensive methods. PMID:26669578
Applications of large-scale density functional theory in biology.
Cole, Daniel J; Hine, Nicholas D M
2016-10-01
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
Van der Waals Interactions in Density Functional Theory: Intermolecular Complexes
NASA Astrophysics Data System (ADS)
Kannemann, Felix; Becke, Axel
2010-03-01
Conventional density functional theory (GGA and hybrid functionals) fails to account for dispersion interactions and is therefore not applicable to systems where van der Waals interactions play a dominant role, such as intermolecular complexes and biomolecules. The exchange-hole dipole moment (XDM) dispersion model of Becke and Johnson [A. D. Becke and E. R. Johnson, J. Chem. Phys. 127, 154108 (2007)] corrects for this deficiency. We have previously shown that the XDM dispersion model can be combined with standard GGA functionals (PW86 for exchange and PBE for correlation) to give accurate binding energy curves for rare-gas diatomics [F. O. Kannemann and A. D. Becke, J. Chem. Theory Comput. 5, 719 (2009)]. Here we present further tests of the GGA-XDM method using benchmark sets including hydrogen bonding, electrostatic, dispersion and stacking interactions, and systems ranging from rare-gas diatomics to biomolecular complexes.
Applications of large-scale density functional theory in biology
NASA Astrophysics Data System (ADS)
Cole, Daniel J.; Hine, Nicholas D. M.
2016-10-01
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
Sublinear scaling for time-dependent stochastic density functional theory
Gao, Yi; Neuhauser, Daniel; Baer, Roi; Rabani, Eran
2015-01-21
A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (≈16) of such orbitals is enough to obtain meaningful results for absorption spectrum and the RPA correlation energy per electron. We implement the approach for silicon nanocrystals using real-space grids and find that the overall scaling of the algorithm is sublinear with computational time and memory.
Revisiting the Fermi Surface in Density Functional Theory
NASA Astrophysics Data System (ADS)
Das, Mukunda P.; Green, Frederick
2016-06-01
The Fermi surface is an abstract object in the reciprocal space of a crystal lattice, enclosing the set of all those electronic band states that are filled according to the Pauli principle. Its topology is dictated by the underlying lattice structure and its volume is the carrier density in the material. The Fermi surface is central to predictions of thermal, electrical, magnetic, optical and superconducting properties in metallic systems. Density functional theory is a first-principles method used to estimate the occupied-band energies and, in particular, the isoenergetic Fermi surface. In this review we survey several key facts about Fermi surfaces in complex systems, where a proper theoretical understanding is still lacking. We address some critical difficulties.
Relativistic density functional theory for finite nuclei and neutron stars
NASA Astrophysics Data System (ADS)
Piekarewicz, Jorge
In 1939 Oppenheimer and Volkoff demonstrated using Einstein's theory of general relativity that a neutron star supported exclusively by neutron degeneracy pressure will collapse into a black hole if its mass exceeds seven tenths of a solar mass. Seventy five years after such a pioneering prediction the existence of neutron stars with masses as large as two solar masses has been firmly established. This fact alone highlights the critical role that nuclear interactions play in explaining the structure of neutron stars. Indeed, a neutron star is a gold mine for the study of nuclear phenomena that span an enormous range of densities and neutron-proton asymmetries. Physical phenomena over such diverse scales are best described by a formalism based on Relativistic Density Functional Theory. In this contribution I focus on the synergy between theory, experiment, and observation that is needed to elucidate the myriad of exotic states of matter that are believed to exist in a neutron star.
Nuclear chiral and magnetic rotation in covariant density functional theory
NASA Astrophysics Data System (ADS)
Meng, Jie; Zhao, Pengwei
2016-05-01
Excitations of chiral rotation observed in triaxial nuclei and magnetic and/or antimagnetic rotations (AMR) seen in near-spherical nuclei have attracted a lot of attention. Unlike conventional rotation in well-deformed or superdeformed nuclei, here the rotational axis is not necessary coinciding with any principal axis of the nuclear density distribution. Thus, tilted axis cranking (TAC) is mandatory to describe these excitations self-consistently in the framework of covariant density functional theory (CDFT). We will briefly introduce the formalism of TAC-CDFT and its application for magnetic and AMR phenomena. Configuration-fixed CDFT and its predictions for nuclear chiral configurations and for favorable triaxial deformation parameters are also presented, and the discoveries of the multiple chiral doublets in 133Ce and 103Rh are discussed.
Characterizing the Spatial Density Functions of Neural Arbors
NASA Astrophysics Data System (ADS)
Teeter, Corinne Michelle
Recently, it has been proposed that a universal function describes the way in which all arbors (axons and dendrites) spread their branches over space. Data from fish retinal ganglion cells as well as cortical and hippocampal arbors from mouse, rat, cat, monkey and human provide evidence that all arbor density functions (adf) can be described by a Gaussian function truncated at approximately two standard deviations. A Gaussian density function implies that there is a minimal set of parameters needed to describe an adf: two or three standard deviations (depending on the dimensionality of the arbor) and an amplitude. However, the parameters needed to completely describe an adf could be further constrained by a scaling law found between the product of the standard deviations and the amplitude of the function. In the following document, I examine the scaling law relationship in order to determine the minimal set of parameters needed to describe an adf. First, I find that the at, two-dimensional arbors of fish retinal ganglion cells require only two out of the three fundamental parameters to completely describe their density functions. Second, the three-dimensional, volume filling, cortical arbors require four fundamental parameters: three standard deviations and the total length of an arbor (which corresponds to the amplitude of the function). Next, I characterize the shape of arbors in the context of the fundamental parameters. I show that the parameter distributions of the fish retinal ganglion cells are largely homogenous. In general, axons are bigger and less dense than dendrites; however, they are similarly shaped. The parameter distributions of these two arbor types overlap and, therefore, can only be differentiated from one another probabilistically based on their adfs. Despite artifacts in the cortical arbor data, different types of arbors (apical dendrites, non-apical dendrites, and axons) can generally be differentiated based on their adfs. In addition, within
Progress at the interface of wave-function and density-functional theories
Gidopoulos, Nikitas I.
2011-04-15
The Kohn-Sham (KS) potential of density-functional theory (DFT) emerges as the minimizing effective potential in a variational scheme that does not involve fixing the unknown single-electron density. Using Rayleigh Schroedinger (RS) perturbation theory (PT), we construct ab initio approximations for the energy difference, the minimization of which determines the KS potential directly - thereby bypassing DFT's traditional algorithm to search for the density that minimizes the total energy. From second-order RS PT, we obtain variationally stable energy differences to be minimized, solving the severe problem of variational collapse of orbital-dependent exchange-correlation functionals based on second-order RS PT.
SUMO1 Affects Synaptic Function, Spine Density and Memory.
Matsuzaki, Shinsuke; Lee, Linda; Knock, Erin; Srikumar, Tharan; Sakurai, Mikako; Hazrati, Lili-Naz; Katayama, Taiichi; Staniszewski, Agnieszka; Raught, Brian; Arancio, Ottavio; Fraser, Paul E
2015-01-01
Small ubiquitin-like modifier-1 (SUMO1) plays a number of roles in cellular events and recent evidence has given momentum for its contributions to neuronal development and function. Here, we have generated a SUMO1 transgenic mouse model with exclusive overexpression in neurons in an effort to identify in vivo conjugation targets and the functional consequences of their SUMOylation. A high-expressing line was examined which displayed elevated levels of mono-SUMO1 and increased high molecular weight conjugates in all brain regions. Immunoprecipitation of SUMOylated proteins from total brain extract and proteomic analysis revealed ~95 candidate proteins from a variety of functional classes, including a number of synaptic and cytoskeletal proteins. SUMO1 modification of synaptotagmin-1 was found to be elevated as compared to non-transgenic mice. This observation was associated with an age-dependent reduction in basal synaptic transmission and impaired presynaptic function as shown by altered paired pulse facilitation, as well as a decrease in spine density. The changes in neuronal function and morphology were also associated with a specific impairment in learning and memory while other behavioral features remained unchanged. These findings point to a significant contribution of SUMO1 modification on neuronal function which may have implications for mechanisms involved in mental retardation and neurodegeneration. PMID:26022678
Graphene oxide and adsorption of chloroform: A density functional study
NASA Astrophysics Data System (ADS)
Kuisma, Elena; Hansson, C. Fredrik; Lindberg, Th. Benjamin; Gillberg, Christoffer A.; Idh, Sebastian; Schröder, Elsebeth
2016-05-01
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 (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, 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.
Density functional theory study of mercury adsorption on metal surfaces
Steckel, J.A.
2008-01-01
Density functional theory _DFT_ calculations are used to characterize the interaction of mercury with copper, nickel, palladium, platinum, silver, and gold surfaces. Mercury binds relatively strongly to all the metal surfaces studied, with binding energies up to _1 eV for Pt and Pd. DFT calculations underestimate the energy of adsorption with respect to available experimental data. Plane-wave DFT results using the local density approximation and the Perdew-Wang 1991 and Perdew-Burke-Ernzerhof parametrizations of the generalized gradient approximation indicate that binding of mercury at hollow sites is preferred over binding at top orbridge sites. The interaction with mercury in order of increasing reactivity over the six metals studied is Ag_Au_Cu_Ni_Pt_Pd. Binding is stronger on the _001_ faces of the metal surfaces, where mercury issituated in fourfold hollow sites as opposed to the threefold hollow sites on _111_ faces. In general, mercury adsorption leads to decreases in the work function; adsorbate-induced work function changes are particularly dramatic on Pt.
Density functional theory study of mercury adsorption on metal surfaces
Steckel, Janice A.
2008-03-10
Density functional theory (DFT) calculations are used to characterize the interaction of mercury with copper, nickel, palladium, platinum, silver, and gold surfaces. Mercury binds relatively strongly to all the metal surfaces studied, with binding energies up to ~1eV for Pt and Pd. DFT calculations underestimate the energy of adsorption with respect to available experimental data. Plane-wave DFT results using the local density approximation and the Perdew-Wang 1991 and Perdew-Burke-Ernzerhof parametrizations of the generalized gradient approximation indicate that binding of mercury at hollow sites is preferred over binding at top or bridge sites. The interaction with mercury in order of increasing reactivity over the six metals studied is Ag
Dynamic density functional theory with hydrodynamic interactions and fluctuations.
Donev, Aleksandar; Vanden-Eijnden, Eric
2014-06-21
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, "Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps," Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, "A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law," J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
Graphene oxide and adsorption of chloroform: A density functional study.
Kuisma, Elena; Hansson, C Fredrik; Lindberg, Th Benjamin; Gillberg, Christoffer A; Idh, Sebastian; Schröder, Elsebeth
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 (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, 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. PMID:27179497
Dynamic density functional theory with hydrodynamic interactions and fluctuations
Donev, Aleksandar Vanden-Eijnden, Eric
2014-06-21
We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absence of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.
The Physical Content of Eigenvalues from Density Functional Theory (DFT)
NASA Astrophysics Data System (ADS)
Bagayoko, D.; Franklin, L.; Ekuma, C.; Malozovsky, Y.
2013-03-01
The density functional theory (DFT) of Hohenberg and Kohn rests on the energy functional Ev[n] assuming its minimum for the correct density n(r), with the admissible functions restricted by the condition N[n] = ∫ n(r) dr = N , where N is the number of particles in the system under study. We show that, for such a system, there is an infinite number of basis sets (of localized orbitals) for which N is fixed while the density is not necessarily the correct one. Consequently, the eigenvalues obtained with self consistent DFT calculations using a single basis set do not necessarily have any particular physical content. The physical content is ensured only by the search and utilization of the optimal basis set that yields the minima of the occupied energies and physically meaningful values of low laying unoccupied energies. Further, by virtue of the Rayleigh theorem, there exist many basis sets larger than the optimal one [and that contain it] for which some unoccupied energies are lowered on account of a mathematical artifact. We illustrate these points in the cases of ZnO, TiO2, and SrTiO3. The calculated band gaps and other properties of these materials are in excellent agreement with experiment. Work funded by in part by the National Science Foundation, through LASiGMA [NSF AwardEPS-1003897, No. NSF (2010-15)-RII-SUBR, and No. HRD-1002541], LONI [Award No. 2-10915], and the Louisiana Space Consortium (LaSPACE).
Quantification of Uncertainties in Nuclear Density Functional Theory
Schunck, N.; McDonnell, J.D.; Higdon, D.; Sarich, J.; Wild, S.
2015-01-15
Reliable predictions of nuclear properties are needed as much to answer fundamental science questions as in applications such as reactor physics or data evaluation. Nuclear density functional theory is currently the only microscopic, global approach to nuclear structure that is applicable throughout the nuclear chart. In the past few years, a lot of effort has been devoted to setting up a general methodology to assess theoretical uncertainties in nuclear DFT calculations. In this paper, we summarize some of the recent progress in this direction. Most of the new material discussed here will be be published in separate articles.
Density Functional Study of the structural properties in Tamoxifen
NASA Astrophysics Data System (ADS)
de Coss-Martinez, Romeo; Tapia, Jorge A.; Quijano-Quiñones, Ramiro F.; Canto, Gabriel I.
2013-03-01
Using the density functional theory, we have studied the structural properties of Tamoxifen. The calculations were performed with two methodological approaches, which were implemented in SIESTA and Spartan codes. For SIESTA, we considerate a linear combination of atomic orbitals method, using pseudopotentials and the van der Waals approximation for the exchange-correlation potential. Here we analyzed and compared the atomic structure between our results and other theoretical study. We found differences in the bond lengths between the results, that could be attributed to code approaches in each one. This work was supported under Grant FOMIX 2011-09 N: 170297 of Ph.D. A. Tapia.
Hole localization in molecular crystals from hybrid density functional theory.
Sai, Na; Barbara, Paul F; Leung, Kevin
2011-06-01
We use first-principles computational methods to examine hole trapping in organic molecular crystals. We present a computational scheme based on the tuning of the fraction of exact exchange in hybrid density functional theory to eliminate the many-electron self-interaction error. With small organic molecules, we show that this scheme gives accurate descriptions of ionization and dimer dissociation. We demonstrate that the excess hole in perfect molecular crystals forms self-trapped molecular polarons. The predicted absolute ionization potentials of both localized and delocalized holes are consistent with experimental values.
Atomic volumes and polarizabilities in density-functional theory.
Kannemann, Felix O; Becke, Axel D
2012-01-21
Becke and Johnson introduced an ad hoc definition of atomic volume [J. Chem. Phys. 124, 014204 (2006)] in order to obtain atom-in-molecule polarizabilities from free-atom polarizabilities in their nonempirical exchange-hole dipole moment model of dispersion interactions. Here we explore the dependence of Becke-Johnson atomic volumes on basis sets and density-functional approximations and provide reference data for all atoms H-Lr. A persuasive theoretical foundation for the Becke-Johnson definition is also provided.
Density functional theory calculations of Rh-β-diketonato complexes.
Conradie, J
2015-01-28
Density functional theory (DFT) results on the geometry, energies and charges of selected Rh-β-diketonato reactants, products and transition states are discussed. Various DFT techniques are used to increase our understanding of the orientation of ligands coordinated to Rh, to identify the lowest energy geometry of possible geometrical isomers and to get a molecular orbital understanding of ground and transition states. Trends and relationships obtained between DFT calculated energies and charges, experimentally measured values and electronic parameters describing the electron donating power of groups and ligands, enable the design of ligands and complexes of specific reactivity. PMID:25429658
Application of Density Functional Theory to Systems Containing Metal Atoms
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.
2006-01-01
The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+n, MNO+, and MCO+2. The DFT works well for frequencies and geometries, even in case with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of successes as well as failures of DFT will be given.
Density functional theory for strongly-correlated ultracold dipolar gases
NASA Astrophysics Data System (ADS)
Malet Giralt, Francesc; Reimann, Stephanie; Gori-Giorgi, Paola; Lund University Collaboration
2014-03-01
We address quasi-one-dimensional strongly-correlated dipolar ultracold gases by means of density functional theory. We make use of an approximation for the Hartree-exchange-correlation that has been shown to be very accurate for electronic systems with coulombic interactions. We show that this approach allows to treat systems with very large particle numbers at relatively low computational cost. This work has been supported by a VIDI grant of the NWO and a Marie Curie grant within the FP7 programme.
Relativistic Energy Density Functionals: Exotic modes of excitation
Vretenar, D.; Paar, N.; Marketin, T.
2008-11-11
The framework of relativistic energy density functionals has been applied to the description of a variety of nuclear structure phenomena, not only in spherical and deformed nuclei along the valley of {beta}-stability, but also in exotic systems with extreme isospin values and close to the particle drip-lines. Dynamical aspects of exotic nuclear structure have been investigated with the relativistic quasiparticle random-phase approximation. We present results for the evolution of low-lying dipole (pygmy) strength in neutron-rich nuclei, and charged-current neutrino-nucleus cross sections.
Nuclear clustering in the energy density functional approach
Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.
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.
Momentum distribution function of the electron gas at metallic densities
NASA Astrophysics Data System (ADS)
Takada, Yasutami; Yasuhara, H.
1991-10-01
The momentum distribution function n(k) of the electron gas is calculated in the effective-potential-expansion method at metallic densities. The recently established self-consistency relation between n(k) and the correlation energy [Y. Takada and T. Kita, J. Phys. Soc. Jpn. 60, 25 (1991)] is employed to check the accuracy of our results. This check shows that the effective-potential-expansion method provides probably the exact and at least more accurate results of n(k) than all the other methods that have given n(k) thus far.
DENSITY-FUNCTIONAL STUDY OF Zr-BASED ACTINIDE ALLOYS
Landa, A; Soderlind, P; Turchi, P; Vitos, L; Ruban, A
2008-06-26
Density-functional formalism is applied to study the phase equilibria in the U-Zr system. The obtained ground-state properties of the {gamma} (bcc) and {delta} (C32) phases are in good agreement with experimental data. The decomposition curve for the {gamma}-based U-Zr solutions is calculated. We argue that stabilization of the {delta}-UZr{sub 2} phase relative to the {alpha}-Zr (hcp) structure is due to an increase of the Zr d-band occupancy that occurs when U is alloyed with Zr.
Adsorption of Te on Ge(001): Density-functional calculations
NASA Astrophysics Data System (ADS)
Çakmak, M.; Srivastava, G. P.; Ellialtıoğlu, Ş.
2003-05-01
We present ab initio density-functional calculations for the adsorption of Te on the Ge(001) surface. Various possible adsorption geometries for the 0.5-, 0.8-, 1-, and 2-ML (monolayer) coverages of Te have been investigated. Our results for sub-monolayer coverages confirm earlier results as well as provide some new insight into the adsorption of Te. Furthermore, our results for the 2-ML coverage of Te suggest that the bonding between the overlayer and the substrate has changed significantly. This may provide useful information on possible desorption of Te in the form of strongly bonded Te2 units.
NASA Astrophysics Data System (ADS)
Slamet, Marlina; Sahni, Viraht
2006-03-01
In the QDFT mapping from a ground or excited state of the interacting system to one of noninteracting fermions in a particular excited state with equivalent density, there is an arbitrariness in the wave function of the model system. For example, in the case of a two-electron atom, the mapping to the excited singlet 2^1S state of the model system, there are three wave functions that lead to the same density: two single Slater determinants of the orbitals that are eigen functions of only Sz, and a linear combination of Slater determinants of these orbitals that is an eigen function of both Sz and S^2. Neither of the wave functions is more appropriate than the other, since all three wave functions deliver the same density. However, based on the choice of wave function, the structure of the corresponding Fermi and Coulomb holes, and therefore the values of the resulting Pauli and Coulomb correlation energies, will differ. Their sum, the Fermi-Coulomb holes, and the Pauli-Coulomb energy, remains unchanged. The wave function arbitrariness will be demonstrated via the Hooke's atom.1 Quantal Density Functional Theory, V. Sahni (Springer-Verlag, 2004).
A tight-binding/density functional search for the structures of Ge clusters
NASA Astrophysics Data System (ADS)
Ghosh, Nandini; Jackson, Koblar; Hajnal, Zoltan; Frauenheim, Thomas
2001-03-01
We have used a combined tight-binding/density functional theory approach to search for the optimal structures of small and intermediate-sized Gen clusters, with n <= 30. The approach uses a computationally fast tight-binding method to survey the cluster energy surface for candidate structures. The search employs a novel single-parent genetic algorithm (SPGA) that successfully located the global minima for Si clusters in the same size range (Rata et al., Phys. Rev. Lett. 85, 546 (2000)). Gradient-corrected density functional theory (DFT) calculations are then performed to study the candidate structures in more detail. We show that our tight-binding model and the DFT yield consistent global minima for clusters up to n=10. The initial results of the SPGA searches for larger clusters show that prolate Gen clusters remain more stable than compact structures beyond n=26, the size at which Si clusters are known to undergo a prolate to compact transition.
Density Functional Study of Perovskite Superconductor MgCNi{sub 3}
Kumar, Jagdish; Sharma, Devina; Kumar, Ranjan; Awana, V. P. S.; Ahluwalia, P. K.
2011-12-12
We here report the first principle density functional study of MgCNi{sub 3} which crystallize in cubic perovskite structure having critical transition temperature of 8 K. The interesting aspect of this compound is that in normal state it is non magnetic in nature despite conduction electrons in it are derived from partially filled Ni d states, which typically lead to ferromagnetism in metallic Ni and many Ni-based binary alloys. To investigate the detailed microscopic origin of the non magnetic nature we have done density functional based calculations on this compound. The lattice constant is calculated using minimum energy criteria from total energy versus lattice constant plot. By taking the calculated values of lattice constant we have done the precise calculations on the compound using Full Potential Linear Augmented Plane Wave (FP-LAPW) method implemented in ELK code. The electronic density of states is found spin degenerate that corresponds to a non-magnetic ground state. The density of states (DOS) at Fermi level, N(E{sub F}) is dominated by Ni-d states. The sharp peak observed just below Fermi level corresponds to van Hove singularity (vHs). The projected density of states (PDOS) suggests a strong hybridization of Ni-3d and C-2p states which is responsible for the observed non magnetic nature of MgCNi{sub 3}.
Garcia-Aldea, David; Alvarellos, J. E.
2008-02-15
We propose a kinetic energy density functional scheme with nonlocal terms based on the von Weizsaecker functional, instead of the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional. The proposed functionals recover the exact kinetic energy and reproduce the linear response function of homogeneous electron systems. In order to assess their quality, we have tested the total kinetic energies as well as the kinetic energy density for atoms. The results show that these nonlocal functionals give as good results as the most sophisticated functionals in the literature. The proposed scheme for constructing the functionals means a step ahead in the field of fully nonlocal kinetic energy functionals, because they are capable of giving better local behavior than the semilocal functionals, yielding at the same time accurate results for total kinetic energies. Moreover, the functionals enjoy the possibility of being evaluated as a single integral in momentum space if an adequate reference density is defined, and then quasilinear scaling for the computational cost can be achieved.
Antisites in III-V semiconductors: Density functional theory calculations
NASA Astrophysics Data System (ADS)
Chroneos, A.; Tahini, H. A.; Schwingenschlögl, U.; Grimes, R. W.
2014-07-01
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.
Uncertainty Quantification and Propagation in Nuclear Density Functional Theory
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.
Electronic properties of graphene nanoribbons: A density functional investigation
Kumar, Sandeep Sharma, Hitesh
2015-05-15
Density functional theory calculations have been performed on graphene nano ribbons (GNRs) to investigate the electronic properties as a function of chirality, size and hydrogenation on the edges. The calculations were performed on GNRs with armchair and zigzag configurations with 28, 34, 36, 40, 50, 56, 62, 66 carbon atoms. The structural stability of AGNR and ZGNR increases with the size of nanoribbon where as hydrogenation of GNR tends to lowers their structural stability. All GNRs considered have shown semiconducting behavior with HOMO-LUMO gap decreasing with the increase in the GNR size. The hydrogenation of GNR decreases its HOMO-LUMO gap significantly. The results are in agreement with the available experimental and theoretical results.
Towards the island of stability with relativistic energy density functionals
Prassa, V.; Niksic, T.; Lalazissis, G. A.; Vretenar, D.
2012-10-20
Relativistic energy density functionals (REDF) provide a complete and accurate, global description of nuclear structure phenomena. Modern semi-empirical functionals, adjusted to the nuclear matter equation of state and to empirical masses of deformed nuclei, are applied to studies of shapes of superheavy nuclei. The theoretical framework is tested in a comparison to empirical masses, quadrupole deformations, and energy barriers of actinide nuclei. The model is used in a self-consistent mean-field calculation of spherical, axial and triaxial shapes of superheavy nuclei, alpha-decay energies and lifetimes. The effect of explicit treatment of collective correlations is analyzed in calculations that consistently use a collective Hamiltonian model based on REDFs.
BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)
Nazarewicz, Witold
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.
Lutsker, V; Aradi, B; Niehaus, T A
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. PMID:26567646
Lutsker, V.; Niehaus, T. A.; Aradi, B.
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.
NASA Astrophysics Data System (ADS)
Lutsker, V.; Aradi, B.; Niehaus, T. A.
2015-11-01
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.
Direct Neutron Capture Calculations with Covariant Density Functional Theory Inputs
NASA Astrophysics Data System (ADS)
Zhang, Shi-Sheng; Peng, Jin-Peng; Smith, Michael S.; Arbanas, Goran; Kozub, Ray L.
2014-09-01
Predictions of direct neutron capture are of vital importance for simulations of nucleosynthesis in supernovae, merging neutron stars, and other astrophysical environments. We calculate the direct capture cross sections for E1 transitions using nuclear structure information from a covariant density functional theory as input for the FRESCO coupled-channels reaction code. We find good agreement of our predictions with experimental cross section data on the double closed-shell targets 16O, 48Ca, and 90Zr, and the exotic nucleus 36S. Extensions of the technique for unstable nuclei and for large-scale calculations will be discussed. Predictions of direct neutron capture are of vital importance for simulations of nucleosynthesis in supernovae, merging neutron stars, and other astrophysical environments. We calculate the direct capture cross sections for E1 transitions using nuclear structure information from a covariant density functional theory as input for the FRESCO coupled-channels reaction code. We find good agreement of our predictions with experimental cross section data on the double closed-shell targets 16O, 48Ca, and 90Zr, and the exotic nucleus 36S. Extensions of the technique for unstable nuclei and for large-scale calculations will be discussed. Supported by the U.S. Dept. of Energy, Office of Nuclear Physics.
NASA Astrophysics Data System (ADS)
Mattsson, Thomas R.
2007-06-01
Atomistic simulations employing Density Functional Theory (DFT) have recently emerged as a powerful way of increasing our understanding of materials and processes in high energy density physics. Knowledge of the properties of water (equation of state, electrical conductivity, diffusion, low-energy opacity) is essential for correctly describing the physics of giant planets as well as shock waves in water. Although a qualitative picture of water electrical conductivity has emerged, the necessary quantitative information is scarce over a wide range of temperature and density. Since experiments can only access certain areas of phase space, and often require modeling as a part of the analysis, Quantum Molecular Dynamics simulations play a vital role. Using finite-temperature density functional theory (FT-DFT), we have investigated the structure and electronic conductivity of water across three phase transitions (molecular liquid/ ionic liquid/ superionic/ electronic liquid). The ionic contribution to the conduction is calculated from proton diffusion and the electronic contribution is calculated using the Kubo-Greenwood formula. The calculations are performed with VASP, a plane-wave pseudo-potential code. There is a rapid transition to ionic conduction at 2000 K and 2 g/cm^3, whereas electronic conduction dominates at temperatures at and above 6000 K&[tilde;1]. Contrary to earlier results using the Car-Parrinello method&[tilde;2], we predict that the fluid bordering the superionic phase is conducting above 4000 K and 100 GPa. Our comprehensive use of FT-DFT explains the new findings. The calculated conductivity is compared to experimental data. I gratefully acknowledge Mike Desjarlais, my collaborator in this effort. The LDRD office at Sandia supported this work. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL
NASA Astrophysics Data System (ADS)
Bruno, Ezio; Mammano, Francesco; Fiorino, Antonino; Morabito, Emanuela V.
2008-04-01
The class of the generalized coherent-potential approximations (GCPAs) to the density functional theory (DFT) is introduced within the multiple scattering theory formalism with the aim of dealing with ordered or disordered metallic alloys. All GCPA theories are based on a common ansatz for the kinetic part of the Hohenberg-Kohn functional and each theory of the class is specified by an external model concerning the potential reconstruction. Most existing DFT implementations of CPA-based theories belong to the GCPA class. The analysis of the formal properties of the density functional defined by GCPA theories shows that it consists of marginally coupled local contributions. Furthermore, it is shown that the GCPA functional does not depend on the details of the charge density and that it can be exactly rewritten as a function of the appropriate charge multipole moments to be associated with each lattice site. A general procedure based on the integration of the qV laws is described that allows for the explicit construction of the same function. The coarse-grained nature of the GCPA density functional implies a great deal of computational advantages and is connected with the O(N) scalability of GCPA algorithms. Moreover, it is shown that a convenient truncated series expansion of the GCPA functional leads to the charge-excess functional (CEF) theory [E. Bruno , Phys. Rev. Lett. 91, 166401 (2003)], which here is offered in a generalized version that includes multipolar interactions. CEF and the GCPA numerical results are compared with status of art linearized augmented plane wave (LAPW) full-potential density functional calculations for 62 bcc- and fcc-based ordered CuZn alloys, in all the range of concentrations. Two facts clearly emerge from these extensive tests. In the first place, the discrepancies between GCPA and CEF results are always within the numerical accuracy of the calculations, both for the site charges and the total energies. In the second place, the
Daubechies wavelets for linear scaling density functional theory.
Mohr, Stephan; Ratcliff, Laura E; Boulanger, Paul; Genovese, Luigi; Caliste, Damien; Deutsch, Thierry; Goedecker, Stefan
2014-05-28
We demonstrate that Daubechies wavelets can be used to construct a minimal set of optimized localized adaptively contracted basis functions in which the Kohn-Sham orbitals can be represented with an arbitrarily high, controllable precision. Ground state energies and the forces acting on the ions can be calculated in this basis with the same accuracy as if they were calculated directly in a Daubechies wavelets basis, provided that the amplitude of these adaptively contracted basis functions is sufficiently small on the surface of the localization region, which is guaranteed by the optimization procedure described in this work. This approach reduces the computational costs of density functional theory calculations, and can be combined with sparse matrix algebra to obtain linear scaling with respect to the number of electrons in the system. Calculations on systems of 10,000 atoms or more thus become feasible in a systematic basis set with moderate computational resources. Further computational savings can be achieved by exploiting the similarity of the adaptively contracted basis functions for closely related environments, e.g., in geometry optimizations or combined calculations of neutral and charged systems. PMID:24880269
Daubechies wavelets for linear scaling density functional theory
Mohr, Stephan; Ratcliff, Laura E.; Genovese, Luigi; Caliste, Damien; Deutsch, Thierry; Boulanger, Paul; Goedecker, Stefan
2014-05-28
We demonstrate that Daubechies wavelets can be used to construct a minimal set of optimized localized adaptively contracted basis functions in which the Kohn-Sham orbitals can be represented with an arbitrarily high, controllable precision. Ground state energies and the forces acting on the ions can be calculated in this basis with the same accuracy as if they were calculated directly in a Daubechies wavelets basis, provided that the amplitude of these adaptively contracted basis functions is sufficiently small on the surface of the localization region, which is guaranteed by the optimization procedure described in this work. This approach reduces the computational costs of density functional theory calculations, and can be combined with sparse matrix algebra to obtain linear scaling with respect to the number of electrons in the system. Calculations on systems of 10 000 atoms or more thus become feasible in a systematic basis set with moderate computational resources. Further computational savings can be achieved by exploiting the similarity of the adaptively contracted basis functions for closely related environments, e.g., in geometry optimizations or combined calculations of neutral and charged systems.
Medium density polyethylene composites with functionalized carbon nanotubes.
Pulikkathara, Merlyn X; Kuznetsov, Oleksandr V; Peralta, Ivana R G; Wei, Xin; Khabashesku, Valery N
2009-05-13
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- C(11)H(23) derivative. The latter was refluorinated to yield a new perfluorinated derivative, F-SWNT- C(11)F(x)H(y). 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- C(11)F(x)H(y), 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.
The probability density function (PDF) of Lagrangian Turbulence
NASA Astrophysics Data System (ADS)
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
Ab initio phonon dispersion in crystalline naphthalene using van der Waals density functionals
NASA Astrophysics Data System (ADS)
Brown-Altvater, Florian; Rangel, Tonatiuh; Neaton, Jeffrey B.
2016-05-01
Acene molecular crystals are of current interest in organic optoelectronics, both as active materials and for exploring and understanding new phenomena. Phonon scattering can be an important facilitator and dissipation mechanism in charge separation and carrier transport processes. Here, we carry out density functional theory (DFT) calculations of the structure and the full phonon dispersion of crystalline naphthalene, a well-characterized acene crystal for which detailed neutron-diffraction measurements, as well as infrared and Raman spectroscopy, are available. We evaluate the performance, relative to experiments, of DFT within the local density approximation (LDA); the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE); and a recent van der Waals-corrected nonlocal correlation (vdW-DF-cx) functional. We find that the vdW-DF-cx functional accurately predicts lattice parameters of naphthalene within 1%. Intermolecular and intramolecular phonon frequencies across the Brillouin zone are reproduced within 7.8% and 1%, respectively. As expected, LDA (PBE) underestimates (overestimates) the lattice parameters and overestimates (underestimates) phonon frequencies, demonstrating their shortcomings for predictive calculations of weakly bound materials. If the unit cell is fixed to the experimental lattice parameters, PBE is shown to lead to improved phonon frequencies. Our study provides a detailed understanding of the phonon spectrum of naphthalene, and highlights the importance of including van der Waals dispersion interactions in predictive calculations of lattice parameters and phonon frequencies of molecular crystals and related organic materials.
Density functional theory based generalized effective fragment potential method
Nguyen, Kiet A. E-mail: ruth.pachter@wpafb.af.mil; Pachter, Ruth E-mail: ruth.pachter@wpafb.af.mil; Day, Paul N.
2014-06-28
We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.
Density functional theory based generalized effective fragment potential method
NASA Astrophysics Data System (ADS)
Nguyen, Kiet A.; Pachter, Ruth; Day, Paul N.
2014-06-01
We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.
Density functional theory for comprehensive orbital energy calculations.
Nakata, Ayako; Tsuneda, Takao
2013-08-14
This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.
Building A Universal Nuclear Energy Density Functional (UNEDF)
Joe Carlson; Dick Furnstahl; Mihai Horoi; Rusty Lusk; Witek Nazarewicz; Esmond Ng; Ian Thompson; James Vary
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.
Density-functional theory: time to move up?
NASA Astrophysics Data System (ADS)
Marzari, Nicola
2013-03-01
Materials' simulations based on density-functional theory (DFT) have become an extremely powerful and widely used tool for scientific discovery and technological advancement. Still, in the current approximations, they remain an imperfect tool for predicting materials' properties, with open and urgent challenges in the quest towards qualitative and quantitative accuracy. Several of these challenges stem from the remnants of self-interaction in the electronic-structure framework, leading to qualitative failures in describing some of the fundamental processes involved e.g. in energy applications - from charge-transfer excitations to photoemission spectra to the structure and reactivity of transition-metal complexes. I'll discuss these challenges in realistic case studies, and present a brief overview of some of our suggestions for possible solutions - including constrained DFT, DFT + onsite and intersite Hubbard terms, and Koopmans' compliant energy functionals. In particular, I'll highlight how Koopmans' compliant functionals point to a beyond-DFT formulation where both total energies and spectroscopic properties can be accounted for. Such framework will be illustrated with applications to real systems and with simplified models that can be solved exactly. Work done in collaboration with Patrick H-L Sit, Heather Kulik, Damian Scherlis, Matteo Cococcioni, Ismaila Dabo, Andrea Ferretti, Nicolas Poilvert, Cheol-Hwan Park, Giovanni Borghi, and Linh Nguyen.
Probability Density Functions of Observed Rainfall in Montana
NASA Technical Reports Server (NTRS)
Larsen, Scott D.; Johnson, L. Ronald; Smith, Paul L.
1995-01-01
The question of whether a rain rate probability density function (PDF) can vary uniformly between precipitation events is examined. Image analysis on large samples of radar echoes is possible because of advances in technology. The data provided by such an analysis easily allow development of radar reflectivity factors (and by extension rain rate) distribution. Finding a PDF becomes a matter of finding a function that describes the curve approximating the resulting distributions. Ideally, one PDF would exist for all cases; or many PDF's that have the same functional form with only systematic variations in parameters (such as size or shape) exist. Satisfying either of theses cases will, validate the theoretical basis of the Area Time Integral (ATI). Using the method of moments and Elderton's curve selection criteria, the Pearson Type 1 equation was identified as a potential fit for 89 percent of the observed distributions. Further analysis indicates that the Type 1 curve does approximate the shape of the distributions but quantitatively does not produce a great fit. Using the method of moments and Elderton's curve selection criteria, the Pearson Type 1 equation was identified as a potential fit for 89% of the observed distributions. Further analysis indicates that the Type 1 curve does approximate the shape of the distributions but quantitatively does not produce a great fit.
Density functional theory predictions of isotropic hyperfine coupling constants.
Hermosilla, L; Calle, P; García de la Vega, J M; Sieiro, C
2005-02-17
The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.
Electrical conductivity of shocked water from Density Functional Theory
NASA Astrophysics Data System (ADS)
Mattsson, Thomas R.
2005-07-01
We present Density Functional Theory (DFT) calculations of water in a region of phase space of interest in shock experiments. The onset of electrical conductivity in shocked water is determined by ionic conductivity, with the electron contribution dominating at higher pressures. The ionic contribution to the conduction is calculated from proton diffusion (Green-Kubo formula) and the electronic contribution is calculated using the Kubo-Greenwood formula [1]. The calculations are performed with VASP, a plane-wave pseudopotential code. At 2000K and a density of 2.3 g/cc, we find a significant dissociation of water into H, OH, and H3O, not only intermittent formation of OH - H3O pairs as suggested earlier for 2000 K and 1.95 g/cc [2]. The calculated conductivity is compared to experimental data [3]. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Safety Administration under contract DE-AC04-94AL85000. This project was supported by the Sandia LDRD office. [1] M. P. Desjarlais, J. D. Kress, and L. A. Collins; Phys. Rev. B 66, 025401 (2002). [2] E. Schwegler, et al. Phys. Rev. Lett. 87, 265501 (2001). [3] P.M. Celliers, et. al. Physics of Plasmas 11, L41 (2004).
Electrical conductivity of shocked water from density functional theory.
Desjarlais, Michael Paul; Mattsson, Thomas Kjell Rene
2005-07-01
We present Density Functional Theory (DFT) calculations of water in a region of phase space of interest in shock experiments. The onset of electrical conductivity in shocked water is determined by ionic conductivity, with the electron contribution dominating at higher pressures. The ionic contribution to the conduction is calculated from proton diffusion (Green-Kubo formula) and the electronic contribution is calculated using the Kubo-Greenwood formula [1]. The calculations are performed with VASP, a plane-wave pseudopotential code. At 2000K and a density of 2.3 g/cc, we find a significant dissociation of water into H, OH, and H3O, not only intermittent formation of OH - H3O pairs as suggested earlier for 2000 K and 1.95 g/cc [2]. The calculated conductivity is compared to experimental data [3]. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Safety Administration under contract DE-AC04-94AL85000. This project was supported by the Sandia LDRD office. [1] M. P. Desjarlais, J. D. Kress, and L. A. Collins; Phys. Rev. B 66, 025401 (2002). [2] E. Schwegler, et al. Phys. Rev. Lett. 87, 265501 (2001). [3] P.M. Celliers, et. al. Physics of Plasmas 11, L41 (2004).
Atomic structures of 13-atom clusters by density functional theory
NASA Astrophysics Data System (ADS)
Chen, Hsin-Yi; Wei, Ching-Ming
2007-03-01
The 13-atom cluster structures of the alkaline metals, alkaline earth metals, boron group, 3d, 4d, and 5d transition metals in the periodic table, and Pb are investigated by density functional theory with three kinds of exchange correlation approximation: i) LDA (Local Density Approximation), ii) GGA (Generalized Gradient Approximation) [1], and iii) PBE (Perdew-Burke-Ernzerhof) [2]. The results mainly focus on five 3-D structures: icosahedral, cuboctahedral, hexagonal-closed packed, body-center cubic, decahedral, and the other two layer structures: buckled biplanar (bbp) and garrison-cap biplanar (gbp) structures. Limited by accuracy of exchange correlation approximation, two interesting results are found. The ground states of Ca13, Sr13, Ba13, Sc13, Y13, La13, Ti13, Zr13, and Hf13 are icosahedral structures. The clusters of Ir13, Pt13, Cu13, Ag13, and Au13 are more favorable for layer structures (i.e. bbp and gbp) than the other five 3-D structures. [1] J. P. Perdew et al., Phys. Rev. B 46, 6671 (1992). [2] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).
Density functional theory and phytochemical study of 8-hydroxyisodiospyrin
NASA Astrophysics Data System (ADS)
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.
A Density Functional Study on the Torsional Conformation of Polyethylene
NASA Astrophysics Data System (ADS)
Miao, M.; Mintmire, J. W.; Ladik, J. J.; van Camp, P. E.; van Doren, V. E.
1996-03-01
Two different local density approximations - X_α and Perdew-Zunger (PZ)- of the density functional method have been used to calculate structural properties of polyethylene systems with several different dihedral angles. The planar zigzag conformation values for the CC bond length (l) of 1.534ÅX_α) and 1.515ÅPZ), the CCC angle(θ) of 112.97^circ (X_α) and 112.98^circ (PZ), the HCH angle(φ) of 109.99^circ (X_α) and 109.66^circ (PZ) are in good agreement with the experiment values (S. Kavesh and J.M. Schultz, J.Polym.Sci. A2), 243 (1970). (l = 2.89 a.u., θ= 112.0^circ , φ= 107.0^circ ) and HF results (A. Imamura, J. Chem. Phys. 52), 3168(1970). (l = 2.87 a.u., θ= 112.4^circ , φ = 107^circ ).All the parameters appear to be strongly coupled with torsional freedom and change with dihedral angles parallel to the variation of the total energy.The total energy has an absolute minimum for the planar zigzag conformation but a distinct local minimum for the quasistable helical conformation at 57.45 ^circ for X_α and 57.32 ^circ for PZ.
Accurate ionization potential of semiconductors from efficient density functional calculations
NASA Astrophysics Data System (ADS)
Ye, Lin-Hui
2016-07-01
Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.
Reproducibility in density functional theory calculations of solids.
Lejaeghere, Kurt; Bihlmayer, Gustav; Björkman, Torbjörn; Blaha, Peter; Blügel, Stefan; Blum, Volker; Caliste, Damien; Castelli, Ivano E; Clark, Stewart J; Dal Corso, Andrea; de Gironcoli, Stefano; Deutsch, Thierry; Dewhurst, John Kay; Di Marco, Igor; Draxl, Claudia; Dułak, Marcin; Eriksson, Olle; Flores-Livas, José A; Garrity, Kevin F; Genovese, Luigi; Giannozzi, Paolo; Giantomassi, Matteo; Goedecker, Stefan; Gonze, Xavier; Grånäs, Oscar; Gross, E K U; Gulans, Andris; Gygi, François; Hamann, D R; Hasnip, Phil J; Holzwarth, N A W; Iuşan, Diana; Jochym, Dominik B; Jollet, François; Jones, Daniel; Kresse, Georg; Koepernik, Klaus; Küçükbenli, Emine; Kvashnin, Yaroslav O; Locht, Inka L M; Lubeck, Sven; Marsman, Martijn; Marzari, Nicola; Nitzsche, Ulrike; Nordström, Lars; Ozaki, Taisuke; Paulatto, Lorenzo; Pickard, Chris J; Poelmans, Ward; Probert, Matt I J; Refson, Keith; Richter, Manuel; Rignanese, Gian-Marco; Saha, Santanu; Scheffler, Matthias; Schlipf, Martin; Schwarz, Karlheinz; Sharma, Sangeeta; Tavazza, Francesca; Thunström, Patrik; Tkatchenko, Alexandre; Torrent, Marc; Vanderbilt, David; van Setten, Michiel J; Van Speybroeck, Veronique; Wills, John M; Yates, Jonathan R; Zhang, Guo-Xu; Cottenier, Stefaan
2016-03-25
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 report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
Density functional theory studies of HCOOH decomposition on Pd(111)
NASA Astrophysics Data System (ADS)
Scaranto, Jessica; Mavrikakis, Manos
2016-08-01
The investigation of formic acid (HCOOH) decomposition on transition metal surfaces is important to derive useful insights for vapor phase catalysis involving HCOOH and for the development of direct HCOOH fuel cells (DFAFC). Here we present the results obtained from periodic, self-consistent, density functional theory (DFT-GGA) calculations for the elementary steps involved in the gas-phase decomposition of HCOOH on Pd(111). Accordingly, we analyzed the minimum energy paths for HCOOH dehydrogenation to CO2 + H2 and dehydration to CO + H2O through the carboxyl (COOH) and formate (HCOO) intermediates. Our results suggest that HCOO formation is easier than COOH formation, but HCOO decomposition is more difficult than COOH decomposition, in particular in the presence of co-adsorbed O and OH species. Therefore, both paths may contribute to HCOOH decomposition. CO formation goes mainly through COOH decomposition.
Nitrotyrosine adsorption on defective graphene: A density functional theory study
NASA Astrophysics Data System (ADS)
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.
Kernel polynomial approximations for densities of states and spectral functions
Silver, R.N.; Voter, A.F.; Kress, J.D.; Roeder, H.
1996-03-01
Chebyshev polynomial approximations are an efficient and numerically stable way to calculate properties of the very large Hamiltonians important in computational condensed matter physics. The present paper derives an optimal kernal polynomial which enforces positivity of density of states and spectral estimates, achieves the best energy resolution, and preserves normalization. This kernel polynomial method (KPM) is demonstrated for electronic structure and dynamic magnetic susceptibility calculations. For tight binding Hamiltonians of Si, we show how to achieve high precision and rapid convergence of the cohesive energy and vacancy formation energy by careful attention to the order of approximation. For disordered XXZ-magnets, we show that the KPM provides a simpler and more reliable procedure for calculating spectral functions than Lanczos recursion methods. Polynomial approximations to Fermi projection operators are also proposed. 26 refs., 10 figs.
The photochemistry of transition metal complexes using density functional theory.
Garino, Claudio; Salassa, Luca
2013-07-28
The use of density functional theory (DFT) and time-dependent DFT (TD-DFT) to study the photochemistry of metal complexes is becoming increasingly important among chemists. Computational methods provide unique information on the electronic nature of excited states and their atomic structure, integrating spectroscopy observations on transient species and excited-state dynamics. In this contribution, we present an overview on photochemically active transition metal complexes investigated by DFT. In particular, we discuss a representative range of systems studied up to now, which include CO- and NO-releasing inorganic and organometallic complexes, haem and haem-like complexes dissociating small diatomic molecules, photoactive anti-cancer Pt and Ru complexes, Ru polypyridyls and diphosphino Pt derivatives.
Self-consistent polarization density functional theory: Application to Argon
Maerzke, Katie A.; Murdachaew, Garold; Mundy, Christopher J.; Schenter, Gregory K.; Siepmann, J. I.
2009-03-12
We present a comprehensive set of results for argon, a case study in weak interactions, using the selfconsistent polarization density functional theory (SCP-DFT). With minimal parameterization, SCPDFT is found is give excellent results for the dimer interaction energy, the second virial coefficient, the liquid structure, and the lattice constant and cohesion energy of the face-centered cubic (fcc) crystal compared to both accurate theoretical and experimental benchmarks. Thus, SCP-DFT holds promise as a fast, efficient, and accurate method for performing ab initio dynamics that include additional polarization and dispersion interactions for large, complex systems involving solvation and bond breaking. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.
Reproducibility in density functional theory calculations of solids.
Lejaeghere, Kurt; Bihlmayer, Gustav; Björkman, Torbjörn; Blaha, Peter; Blügel, Stefan; Blum, Volker; Caliste, Damien; Castelli, Ivano E; Clark, Stewart J; Dal Corso, Andrea; de Gironcoli, Stefano; Deutsch, Thierry; Dewhurst, John Kay; Di Marco, Igor; Draxl, Claudia; Dułak, Marcin; Eriksson, Olle; Flores-Livas, José A; Garrity, Kevin F; Genovese, Luigi; Giannozzi, Paolo; Giantomassi, Matteo; Goedecker, Stefan; Gonze, Xavier; Grånäs, Oscar; Gross, E K U; Gulans, Andris; Gygi, François; Hamann, D R; Hasnip, Phil J; Holzwarth, N A W; Iuşan, Diana; Jochym, Dominik B; Jollet, François; Jones, Daniel; Kresse, Georg; Koepernik, Klaus; Küçükbenli, Emine; Kvashnin, Yaroslav O; Locht, Inka L M; Lubeck, Sven; Marsman, Martijn; Marzari, Nicola; Nitzsche, Ulrike; Nordström, Lars; Ozaki, Taisuke; Paulatto, Lorenzo; Pickard, Chris J; Poelmans, Ward; Probert, Matt I J; Refson, Keith; Richter, Manuel; Rignanese, Gian-Marco; Saha, Santanu; Scheffler, Matthias; Schlipf, Martin; Schwarz, Karlheinz; Sharma, Sangeeta; Tavazza, Francesca; Thunström, Patrik; Tkatchenko, Alexandre; Torrent, Marc; Vanderbilt, David; van Setten, Michiel J; Van Speybroeck, Veronique; Wills, John M; Yates, Jonathan R; Zhang, Guo-Xu; Cottenier, Stefaan
2016-03-25
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 report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements. PMID:27013736
DX centers in CdTe: a density functional study
Du, Mao-Hua
2008-01-01
DX centers induced by both group-III and group-VII donors in CdTe are studied using density functional calculations. The results show that, for group-VII donors, the DX centers with a cation-cation bond ({alpha}- and {beta}-CCB-DX centers) are more stable than the previously proposed broken-bond DX (BB-DX) center and the {beta}-CCB-DX center is the most stable. The stability trend found for the CCB-DX centers for different donors in CdTe is consistent with that for GaAs and GaSb, which suggests a general rule that the CCB-DX centers are favored for small donor atoms on anion site especially for semiconductors with large anion size.
Density Functional Plus Dynamical Mean Field Theory of Correlated Oxides
NASA Astrophysics Data System (ADS)
Millis, Andrew
2015-03-01
The density functional plus dynamical mean field method is outlined and a few recent successes including applications to spin crossover molecules, oxide superlattices and metal-insulator transitions in bulk transition metals are outlined. Insights from the method into the essential role played by lattice distortions (both rotations and bond length changes) in determining the phase diagrams of correlated materials are presented. The key theoretical issue of the double counting correction is outlined, different approaches are compared, and a connection to the energy level differences between strongly and weakly correlated orbitals is presented. Charge transfer across oxide interfaces shown to depend crucially on the double counting correction, suggesting that experiments on oxide superlattices may provide insights into this important problem. Future directions are discussed. This work is performed in collaboration with Jia Chen, Hung Dang, Hyowon Park and Chris Marianetti. This research supported by the DOE Office of Science, Grant ER 046169.
Plutonium: The density-functional-theory point of view
Soderlind, P; Landa, A
2008-10-30
Density-functional theory (DFT) is a remarkably successful tool for describing many metals throughout the Periodic Table. Here we present the results of this theory when applied to plutonium metal, the perhaps most complex and difficult-to-model metal of all. The fundamental product of DFT is the ground-state total energy. In the case of Pu, we show that DFT produces total energies that can predict the complex phase diagram accurately. Focusing on the {delta} phase, we show that DFT electronic structure is consistent with measured photoemission spectra. The observed non-magnetic state of {delta}-Pu could possibly be explained in DFT by spin moments, likely disordered, that are magnetically neutralized by anti-parallel aligned orbital moments. As an alternative to this non-magnetic model an extension of DFT with enhanced orbital polarization is presented in which magnetism can be suppressed.
Vibrational spectroscopy and density functional theory study of ninhydrin
NASA Astrophysics Data System (ADS)
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.
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. PMID:25459727
Descriptions of carbon isotopes within the energy density functional theory
Ismail, Atef; Cheong, Lee Yen; Yahya, Noorhana; Tammam, M.
2014-10-24
Within the energy density functional (EDF) theory, the structure properties of Carbon isotopes are systematically studied. The shell model calculations are done for both even-A and odd-A nuclei, to study the structure of rich-neutron Carbon isotopes. The EDF theory indicates the single-neutron halo structures in {sup 15}C, {sup 17}C and {sup 19}C, and the two-neutron halo structures in {sup 16}C and {sup 22}C nuclei. It is also found that close to the neutron drip-line, there exist amazing increase in the neutron radii and decrease on the binding energies BE, which are tightly related with the blocking effect and correspondingly the blocking effect plays a significant role in the shell model configurations.
Simulation of sprays using a Lagrangian filtered density function approach
NASA Astrophysics Data System (ADS)
Liu, Wanjiao; Garrick, Sean
2013-11-01
Sprays and atomization have wide applications in industry, including combustion/engines, pharmaceutics and agricultural spraying. Due to the complexity of the underlying processes, much of the underlying phenomena are not fully understood. Numerical simulation may provide ways to investigate atomization and spray dynamics. Large eddy simulation (LES) is a practical approach to flow simulation as it resolves only the large-scale structures while modeling the sub-grid scale (SGS) effects. We combine a filtered density function (FDF) based approach with a Lagrangian volume-of-fluid method to perform LES. This resulting methodology is advantageous in that it has no diffusive or dissipative numerical errors, and the highly non-linear surface tension force appears in closed form thus the modeling of the SGS surface tension is not needed when simulating turbulent, multiphase flows. We present the methodology and some results for the simulation of multiphase jets.
Detecting landmines using weighted density distribution function features
NASA Astrophysics Data System (ADS)
Stanley, Ronald J.; Theera-Umpon, Nipon; Gader, Paul D.; Somanchi, Satish; Ho, Dominic K.
2001-08-01
Land mine detection using metal detector (MD) and ground penetrating radar (GPR) sensors in hand-held units is a difficult problem. Detection difficulties arise due to: 1) the varying composition and type of metal in land mines, 2) the time-varying nature of background and 3) the variation in height and velocity of the hand-held unit in data measurement. This research introduces new spatially distributed MD features for differentiating land mine signatures from background. The spatially distributed features involve correlating sequences of MD energy values with six weighted density distribution functions. These features are evaluated using a standard back propagation neural network on real data sets containing more than 2,300 mine encounters of different size, shape, content and metal composition that are measured under different soil conditions.
Native defects in Tl6SI4: Density functional calculations
NASA Astrophysics Data System (ADS)
Shi, Hongliang; Du, Mao-Hua
2015-05-01
Tl6SI4 is a promising room-temperature semiconductor radiation detection material. Here, we report density functional calculations of native defects and dielectric properties of Tl6SI4. Formation energies and defect levels of native point defects and defect complexes are calculated. Donor-acceptor defect complexes are shown to be abundant in Tl6SI4. High resistivity can be obtained by Fermi level pinning by native donor and acceptor defects. Deep donors that are detrimental to electron transport are identified and methods to mitigate such problem are discussed. Furthermore, we show that mixed ionic-covalent character of Tl6SI4 gives rise to enhanced Born effective charges and large static dielectric constant, which provides effective screening of charged defects and impurities.
Density functional calculations of Hubbard parameter in actinide series
Puri, A.; Sen, K.D.
1993-05-01
The calculations of Hubbard parameter, U, which defines the polar state formation energy of the reaction 2(5f{sup n} 6d{sup 1} 7d{sup 2}) {yields} 5f{sup n-1} 6d{sup 2}7s{sup 2} + 5f{sup n+1} 7s{sup 2} for the actinide atoms, Th-No, have been carried out using the self-interaction-corrected (SIC) quasi-relativistic local spin density (LSD) functional due to Perdew and Zunger. Based on the available bandwidth calculations for the 5f metals and its monotonically decreasing trend with increasing nuclear charge it is predicted that the 5f state is iterent in Th-Np beyond which it becomes localized. These calculations agree with the conclusions drawn earlier by Johansson using the semiempirical data.
Fundamental gap of molecular crystals via constrained density functional theory
NASA Astrophysics Data System (ADS)
Droghetti, Andrea; Rungger, Ivan; Das Pemmaraju, Chaitanya; Sanvito, Stefano
2016-05-01
The energy gap of a molecular crystal is one of the most important properties since it determines the crystal charge transport when the material is utilized in electronic devices. This is, however, a quantity difficult to calculate and standard theoretical approaches based on density functional theory (DFT) have proven unable to provide accurate estimates. In fact, besides the well-known band-gap problem, DFT completely fails in capturing the fundamental gap reduction occurring when molecules are packed in a crystal structures. The failure has to be associated with the inability of describing the electronic polarization and the real space localization of the charged states. Here we describe a scheme based on constrained DFT, which can improve upon the shortcomings of standard DFT. The method is applied to the benzene crystal, where we show that accurate results can be achieved for both the band gap and also the energy level alignment.
β -decay study within multireference density functional theory and beyond
NASA Astrophysics Data System (ADS)
Konieczka, M.; Bączyk, P.; Satuła, W.
2016-04-01
A pioneering study of Gamow-Teller (GT) and Fermi matrix elements (MEs) using no-core-configuration-interaction formalism rooted in multireference density functional theory is presented. After a successful test performed for 6He→6Liβ decay, the model is applied to compute MEs in the s d - and p f -shell T =1 /2 mirror nuclei. The calculated GT MEs and the isospin-symmetry-breaking corrections to the Fermi branch are found to be in very good agreement with shell-model predictions in spite of fundamental differences between these models concerning model space, treatment of correlations, or inclusion of a core. This result indirectly supports the two-body-current-based scenarios behind the quenching of the axial-vector coupling constant.
Native defects in Tl6SI4: Density functional calculations
Shi, Hongliang; Du, Mao -Hua
2015-05-05
In this study, Tl6SI4 is a promising room-temperature semiconductor radiation detection material. Here, we report density functional calculations of native defects and dielectric properties of Tl6SI4. Formation energies and defect levels of native point defects and defect complexes are calculated. Donor-acceptor defect complexes are shown to be abundant in Tl6SI4. High resistivity can be obtained by Fermi level pinning by native donor and acceptor defects. Deep donors that are detrimental to electron transport are identified and methods to mitigate such problem are discussed. Furthermore, we show that mixed ionic-covalent character of Tl6SI4 gives rise to enhanced Born effective charges andmore » large static dielectric constant, which provides effective screening of charged defects and impurities.« less
Density Functional Exploration of C4H3N Isomers.
Custer, Thomas; Szczepaniak, Urszula; Gronowski, Marcin; Fabisiewicz, Emilia; Couturier-Tamburelli, Isabelle; Kołos, Robert
2016-07-28
Molecules having C4H3N stoichiometry are of astrophysical interest. Two of these, methylcyanoacetylene (CH3C3N) and its structural isomer allenyl cyanide (H2CCCHN), have been observed in interstellar space, while several more have been examined in laboratories. Here we describe, for a broad range of C4H3N isomers, density functional calculations (B3LYP/aug-cc-pVTZ) of molecular parameters including the energetics, geometries, rotational constants, electric dipole moments, polarizabilities, vibrational IR frequencies, IR absorption intensities, and Raman activities. Singlet-triplet splittings as well as singlet vertical electronic excitation energies are given for selected species. The identification of less stable C4H3N molecules, generated in ongoing spectroscopic experiments, relies heavily on these quantum chemical predictions. PMID:27341606
Band Anticrossing in Dilute Germanium Carbides Using Hybrid Density Functionals
NASA Astrophysics Data System (ADS)
Stephenson, Chad A.; O'brien, William A.; Qi, Meng; Penninger, Michael; Schneider, William F.; Wistey, Mark A.
2016-04-01
Dilute germanium carbides (Ge1- x C x ) offer a direct bandgap for compact silicon photonics, but widely varying properties have been reported. This work reports improved band structure calculations for Ge1- x C x using ab initio simulations that employ the HSE06 exchange-correlation density functional. Contrary to Vegard's law, the conduction band minimum at Γ is consistently found to decrease with increasing C content, while L and X valleys change much more slowly. The calculated Ge bandgap is within 11% of experimental values. A decrease in energy at the Γ conduction band valley of (170 meV ± 50)/%C is predicted, leading to a direct bandgap for x > 0.008. These results indicate a promising material for Group IV lasers.
Measuring response saturation in human MT and MST as a function of motion density.
Durant, Szonya; Furlan, Michele
2014-01-01
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. PMID:25057944
NASA Astrophysics Data System (ADS)
Rong, Yang; Bin, Tang; Tao, Gao; BingYun, Ao
2016-06-01
Hybrid density functional theory is employed to systematically investigate the structural, magnetic, vibrational, thermodynamic properties of plutonium monocarbide (PuC and PuC0.75). For comparison, the results obtained by DFT, DFT + U are also given. For PuC and PuC0.75, Fock-0.25 hybrid functional gives the best lattice constants and predicts the correct ground states of antiferromagnetic (AFM) structure. The calculated phonon spectra suggest that PuC and PuC0.75 are dynamically stable. Values of the Helmholtz free energy ΔF, internal energy ΔE, entropy S, and constant-volume specific heat C v of PuC and PuC0.75 are given. The results are in good agreement with available experimental or theoretical data. As for the chemical bonding nature, the difference charge densities, the partial densities of states and the Bader charge analysis suggest that the Pu-C bonds of PuC and PuC0.75 have a mixture of covalent character and ionic character. The effect of carbon vacancy on the chemical bonding is also discussed in detail. We expect that our study can provide some useful reference for further experimental research on the phonon density of states, thermodynamic properties of the plutonium monocarbide. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160 and 21401173).
Origin of anomeric effect: A density functional steric analysis
Huang, Ying; Zhong, Ai-Guo; Yang, Qinsong; Liu, Shubin
2011-01-01
The anomeric effect (the tendency of heteroatomic substituents adjacent to a heteroatom within the cyclohexane ring to prefer the axial orientation instead of the sterically less hindered equatorial position) is traditionally explained through either the dipole moment repulsion or the hyperconjugation effect. In this work, by employing our recent work in density functional steric analysis, we provide a novel two-component explanation, which is consistent with the common belief in chemistry that the effect has a stereoelectronic origin. With α-D-glucopyranose as the prototype, we systematically explore its conformational space and generate 32 isomers, leading to a total of 80 axial–equatorial conformation pairs. The energy difference analysis of these pairs shows that while statistically speaking the tendency is valid, the anomeric effect is not always true and can be violated. Three energy components, exchange–correlation, classical electrostatic, and density functional steric, are found to be directly proportional to the total energy difference between axial and equatorial isomers. We also found that the total dipole moment change, not the hyperconjugation effect, is a reasonable indicator of the total energy difference. However, all these correlations alone are not strong enough to provide a compellingly convincing explanation for the general validity of the effect. With the help of strong correlations between energy components, an explanation with two energy components, steric and electrostatic, was proposed in this work. We show that the axial–equatorial energy difference in general, with the anomeric effect as a special case, is dictated by two factors of the stereoelectronic origin, steric hindrance and classical electrostaticinteractions, synchronously working together. Another explanation in terms of exchange–correlation and electrostaticinteractions has also been obtained in this work.
Beyond Vmax and Km: How details of enzyme function influence geochemical cycles
NASA Astrophysics Data System (ADS)
Steen, A. D.
2015-12-01
Enzymes catalyze the vast majority of chemical reactions relevant to geomicrobiology. Studies of the activities of enzymes in environmental systems often report Vmax (the maximum possible rate of reaction; often proportional to the concentration of enzymes in the system) and sometimes Km (a measure of the affinity between enzymes and their substrates). However, enzyme studies - particularly those related to enzymes involved in organic carbon oxidation - are often limited to only those parameters, and a relatively limited and mixed set of enzymes. Here I will discuss some novel methods to assay and characterize the specific sets of enzymes that may be important to the carbon cycle in aquatic environments. First, kinetic experiments revealed the collective properties of the complex mixtures of extracellular peptidases that occur where microbial communities are diverse. Crystal structures combined with biochemical characterization of specific enzymes can yield more detailed information about key steps in organic carbon transformations. These new techniques have the potential to provide mechanistic grounding to geomicrobiological models.
Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.
Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M
2015-09-01
We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations.
Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.
Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M
2015-09-01
We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations. PMID:26575912
A density functional for core-valence correlation energy.
Ranasinghe, Duminda S; Frisch, Michael J; Petersson, George A
2015-12-01
A density functional, εCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of εLY P (corr)(ρc), εV WN5 (corr)(ρc, ρv), εPBE (corr)(ρc, ρv), εSlater (ex)(ρc, ρv), εHCTH (ex)(ρc, ρv), εHF (ex)(ρc, ρv), and FCV-DFTNi,Zi, a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from εCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the εCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory. PMID:26646873
Reduced density-matrix functional theory: Correlation and spectroscopy
Di Sabatino, S.; Romaniello, P.; Berger, J. A.; Reining, L.
2015-07-14
In this work, we explore the performance of approximations to electron correlation in reduced density-matrix functional theory (RDMFT) and of approximations to the observables calculated within this theory. Our analysis focuses on the calculation of total energies, occupation numbers, removal/addition energies, and spectral functions. We use the exactly solvable Hubbard dimer at 1/4 and 1/2 fillings as test systems. This allows us to analyze the underlying physics and to elucidate the origin of the observed trends. For comparison, we also report the results of the GW approximation, where the self-energy functional is approximated, but no further hypothesis is made concerning the approximations of the observables. In particular, we focus on the atomic limit, where the two sites of the dimer are pulled apart and electrons localize on either site with equal probability, unless a small perturbation is present: this is the regime of strong electron correlation. In this limit, using the Hubbard dimer at 1/2 filling with or without a spin-symmetry-broken ground state allows us to explore how degeneracies and spin-symmetry breaking are treated in RDMFT. We find that, within the used approximations, neither in RDMFT nor in GW, the signature of strong correlation is present, when looking at the removal/addition energies and spectral function from the spin-singlet ground state, whereas both give the exact result for the spin-symmetry broken case. Moreover, we show how the spectroscopic properties change from one spin structure to the other.
Thyroid function and bone mineral density among Indian subjects
Marwaha, Raman K.; Garg, M. K.; Tandon, Nikhil; Kanwar, Ratnesh; Narang, Aparna; Sastry, Archna; Bhadra, Kuntal
2012-01-01
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(OH)D, 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(OH)D 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. PMID:22837919
A density functional for core-valence correlation energy
NASA Astrophysics Data System (ADS)
Ranasinghe, Duminda S.; Frisch, Michael J.; Petersson, George A.
2015-12-01
A density functional, ɛCV-DFT(ρc, ρv), describing the core-valence correlation energy has been constructed as a linear combination of ɛLY Pcorr(ρc), ɛV WN5corr(ρc, ρv), ɛPBEcorr(ρc, ρv), ɛSlaterex(ρc, ρv), ɛHCTHex(ρc, ρv), ɛHFex(ρc, ρv), and F CV -DFT (" separators=" N i , Z i ) , a function of the nuclear charges. This functional, with 6 adjustable parameters, reproduces (±0.27 kcal/mol rms error) a benchmark set of 194 chemical energy changes including 9 electron affinities, 18 ionization potentials, and 167 total atomization energies covering the first- and second-rows of the periodic table. This is almost twice the rms error (±0.16 kcal/mol) obtained with CCSD(T)/MTsmall calculations, but less than half the rms error (±0.65 kcal/mol) obtained with MP2/GTlargeXP calculations, and somewhat smaller than the rms error (±0.39 kcal/mol) obtained with CCSD/MTsmall calculations. The largest positive and negative errors from ɛCV-DFT(ρc, ρv) were 0.88 and -0.75 kcal/mol with the set of 194 core-valence energy changes ranging from +3.76 kcal/mol for the total atomization energy of propyne to -9.05 kcal/mol for the double ionization of Mg. Evaluation of the ɛCV-DFT(ρc, ρv) functional requires less time than a single SCF iteration, and the accuracy is adequate for any model chemistry based on the CCSD(T) level of theory.
Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G
2015-11-01
Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively.
Hoyer, Chad E; Gagliardi, Laura; Truhlar, Donald G
2015-11-01
Time-dependent Kohn-Sham density functional theory (TD-KS-DFT) is useful for calculating electronic excitation spectra of large systems, but the low-energy spectra are often complicated by artificially lowered higher-energy states. This affects even the lowest energy excited states. Here, by calculating the lowest energy spin-conserving excited state for atoms from H to K and for formaldehyde, we show that this problem does not occur in multiconfiguration pair-density functional theory (MC-PDFT). We use the tPBE on-top density functional, which is a translation of the PBE exchange-correlation functional. We compare to a robust multireference method, namely, complete active space second-order perturbation theory (CASPT2), and to TD-KS-DFT with two popular exchange-correlation functionals, PBE and PBE0. We find for atoms that the mean unsigned error (MUE) of MC-PDFT with the tPBE functional improves from 0.42 to 0.40 eV with a double set of diffuse functions, whereas the MUEs for PBE and PBE0 drastically increase from 0.74 to 2.49 eV and from 0.45 to 1.47 eV, respectively. PMID:26722961
Corsini, Niccolò R. C. Greco, Andrea; Haynes, Peter D.; Hine, Nicholas D. M.; Molteni, Carla
2013-08-28
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 simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.
NASA Astrophysics Data System (ADS)
Kolincio, Kamil; Pérez, Olivier; Hébert, Sylvie; Fertey, Pierre; Pautrat, Alain
2016-06-01
Detailed structural and magnetotransport properties of monophosphate tungsten bronze Kx(PO2)4(WO3)8 single crystals are reported. Both galvanomagnetic and thermal properties are shown to be consistent with a charge density wave electronic transition due to hidden nesting of the quasi-1D portion of the Fermi surface. We also observe the enhancement of electronic anisotropy due to reconstruction of the Fermi surface at the Peierls transition. The resistivity presents a thermal hysteresis suggesting a first-order nature characteristic of a strong-coupling scenario. However, other measurements such as the change of carrier density demonstrate a second-order Peierls scenario with weak-coupling features. We suggest that the structural transition driven by the residual strain in the K-P-O environment is responsible for the resistivity hysteresis and modifies the Fermi surface which then helps the rise to the second-order Peierls instability.
NASA Astrophysics Data System (ADS)
Sinnott, Susan Buthaina
In the research presented here, various theoretical electronic structure techniques are utilized to analyze widely different systems from silicon clusters to transition metal solids and surfaces. For the silicon clusters, first principles density functional methods are used to investigate Si_{rm N} for N = 2-8. The goal is to understand the different types of bonding that can occur in such small clusters where the coordination of the atoms differs substantially from that of the stable bulk tetrahedral bonding. Such uncoordinated structures can provide a good test of more approximate theories that can be used eventually to model silicon surfaces, of obvious technological importance. For the transition metal systems, non-self-consistent electronic structure methods are used to provide an understanding of the driving force for surface relaxations. An in-depth analysis of the results is presented and the physical basis of surface relaxation within the theory is discussed. In addition, the limitations inherent in calculations of metal surface relaxation are addressed. Finally, in an effort to increase understanding of approximate methods, a novel non-self-consistent density functional electronic structure method is developed that is ~1000 times faster computationally than more sophisticated methods. This new method is tested for a variety of systems including diatomics, mixed clusters, surfaces and bulk lattices. The strengths and weaknesses of the new theory are discussed in detail, leading to greater understanding of non-self-consistent density functional theories as a whole.
The QTP family of consistent functionals and potentials in Kohn-Sham density functional theory
NASA Astrophysics Data System (ADS)
Jin, Yifan; Bartlett, Rodney J.
2016-07-01
This manuscript presents the second, consistent density functional in the QTP (Quantum Theory Project) family, that is, the CAM-QTP(01). It is a new range-separated exchange-correlation functional in which the non-local exchange contribution is 100% at large separation. It follows the same basic principles of this family that the Kohn-Sham eigenvalues of the occupied orbitals approximately equal the vertical ionization energies, which is not fulfilled by most of the traditional density functional methods. This new CAM-QTP(01) functional significantly improves the accuracy of the vertical excitation energies especially for the Rydberg states in the test set. It also reproduces many other properties such as geometries, reaction barrier heights, and atomization energies.
Extracting electron transfer coupling elements from constrained density functional theory
NASA Astrophysics Data System (ADS)
Wu, Qin; Van Voorhis, Troy
2006-10-01
Constrained density functional theory (DFT) is a useful tool for studying electron transfer (ET) reactions. It can straightforwardly construct the charge-localized diabatic states and give a direct measure of the inner-sphere reorganization energy. In this work, a method is presented for calculating the electronic coupling matrix element (Hab) based on constrained DFT. This method completely avoids the use of ground-state DFT energies because they are known to irrationally predict fractional electron transfer in many cases. Instead it makes use of the constrained DFT energies and the Kohn-Sham wave functions for the diabatic states in a careful way. Test calculations on the Zn2+ and the benzene-Cl atom systems show that the new prescription yields reasonable agreement with the standard generalized Mulliken-Hush method. We then proceed to produce the diabatic and adiabatic potential energy curves along the reaction pathway for intervalence ET in the tetrathiafulvalene-diquinone (Q-TTF-Q) anion. While the unconstrained DFT curve has no reaction barrier and gives Hab≈17kcal /mol, which qualitatively disagrees with experimental results, the Hab calculated from constrained DFT is about 3kcal /mol and the generated ground state has a barrier height of 1.70kcal/mol, successfully predicting (Q-TTF-Q)- to be a class II mixed-valence compound.
Can density cumulant functional theory describe static correlation effects?
Mullinax, J Wayne; Sokolov, Alexander Yu; Schaefer, Henry F
2015-06-01
We evaluate the performance of density cumulant functional theory (DCT) for capturing static correlation effects. In particular, we examine systems with significant multideterminant character of the electronic wave function, such as the beryllium dimer, diatomic carbon, m-benzyne, 2,6-pyridyne, twisted ethylene, as well as the barrier for double-bond migration in cyclobutadiene. We compute molecular properties of these systems using the ODC-12 and DC-12 variants of DCT and compare these results to multireference configuration interaction and multireference coupled-cluster theories, as well as single-reference coupled-cluster theory with single, double (CCSD), and perturbative triple excitations [CCSD(T)]. For all systems the DCT methods show intermediate performance between that of CCSD and CCSD(T), with significant improvement over the former method. In particular, for the beryllium dimer, m-benzyne, and 2,6-pyridyne, the ODC-12 method along with CCSD(T) correctly predict the global minimum structures, while CCSD predictions fail qualitatively, underestimating the multireference effects. Our results suggest that the DC-12 and ODC-12 methods are capable of describing emerging static correlation effects but should be used cautiously when highly accurate results are required. Conveniently, the appearance of multireference effects in DCT can be diagnosed by analyzing the DCT natural orbital occupations, which are readily available at the end of the energy computation.
Metallophilic interactions from dispersion-corrected density-functional theory.
Otero-de-la-Roza, Alberto; Mallory, Joel D; Johnson, Erin R
2014-05-14
In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Møller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH3)4](+) cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.
Metallophilic interactions from dispersion-corrected density-functional theory
NASA Astrophysics Data System (ADS)
Otero-de-la-Roza, Alberto; Mallory, Joel D.; Johnson, Erin R.
2014-05-01
In this article, we present the first comprehensive study of metallophilic (aurophilic) interactions using dispersion-corrected density-functional theory. Dispersion interactions (an essential component of metallophilicity) are treated using the exchange-hole dipole moment (XDM) model. By comparing against coupled-cluster benchmark calculations on simple dimers, we show that LC-ωPBE-XDM is a viable functional to study interactions between closed-shell transition metals and that it performs uniformly better than second-order Møller-Plesset theory, the basic computational technique used in previous works. We apply LC-ωPBE-XDM to address several open questions regarding metallophilicity, such as the interplay between dispersion and relativistic effects, the interaction strength along group 11, the additivity of homo- and hetero-metallophilic effects, the stability of [E(AuPH3)4]+ cations (E = N, P, As, Sb), and the role of metallophilic effects in crystal packing. We find that relativistic effects explain the prevalence of aurophilicity not by stabilizing metal-metal contacts, but by preventing gold from forming ionic structures involving bridge anions (which are otherwise common for Ag and Cu) as a result of the increased electron affinity of the metal. Dispersion effects are less important than previously assumed and their stabilization contribution is relatively independent of the metal.
Solvation of complex surfaces via molecular density functional theory.
Levesque, Maximilien; Marry, Virginie; Rotenberg, Benjamin; Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel
2012-12-14
We show that classical molecular density functional theory, here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational, and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular Clay Force Field (CLAYFF). Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.
Acrolein impairs the cholesterol transport functions of high density lipoproteins.
Chadwick, Alexandra C; Holme, Rebecca L; Chen, Yiliang; Thomas, Michael J; Sorci-Thomas, Mary G; Silverstein, Roy L; Pritchard, Kirkwood A; Sahoo, Daisy
2015-01-01
High density lipoproteins (HDL) are considered athero-protective, primarily due to their role in reverse cholesterol transport, where they transport cholesterol from peripheral tissues to the liver for excretion. The current study was designed to determine the impact of HDL modification by acrolein, a highly reactive aldehyde found in high abundance in cigarette smoke, on the cholesterol transport functions of HDL. HDL was chemically-modified with acrolein and immunoblot and mass spectrometry analyses confirmed apolipoprotein crosslinking, as well as acrolein adducts on apolipoproteins A-I and A-II. The ability of acrolein-modified HDL (acro-HDL) to serve as an acceptor of free cholesterol (FC) from COS-7 cells transiently expressing SR-BI was significantly decreased. Further, in contrast to native HDL, acro-HDL promotes higher neutral lipid accumulation in murine macrophages as judged by Oil Red O staining. The ability of acro-HDL to mediate efficient selective uptake of HDL-cholesteryl esters (CE) into SR-BI-expressing cells was reduced compared to native HDL. Together, the findings from our studies suggest that acrolein modification of HDL produces a dysfunctional particle that may ultimately promote atherogenesis by impairing functions that are critical in the reverse cholesterol transport pathway.
Self-interaction corrections in density functional theory
Tsuneda, Takao; Hirao, Kimihiko
2014-05-14
Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds.
Self-interaction corrections in density functional theory
NASA Astrophysics Data System (ADS)
Tsuneda, Takao; Hirao, Kimihiko
2014-05-01
Self-interaction corrections for Kohn-Sham density functional theory are reviewed for their physical meanings, formulations, and applications. The self-interaction corrections get rid of the self-interaction error, which is the sum of the Coulomb and exchange self-interactions that remains because of the use of an approximate exchange functional. The most frequently used self-interaction correction is the Perdew-Zunger correction. However, this correction leads to instabilities in the electronic state calculations of molecules. To avoid these instabilities, several self-interaction corrections have been developed on the basis of the characteristic behaviors of self-interacting electrons, which have no two-electron interactions. These include the von Weizsäcker kinetic energy and long-range (far-from-nucleus) asymptotic correction. Applications of self-interaction corrections have shown that the self-interaction error has a serious effect on the states of core electrons, but it has a smaller than expected effect on valence electrons. This finding is supported by the fact that the distribution of self-interacting electrons indicates that they are near atomic nuclei rather than in chemical bonds.
Effects of Methylation on Zebularine Studied by Density Functional Theory
NASA Astrophysics Data System (ADS)
Selvam, Lalitha; Vasilyev, Vladislav; Wang, Feng; Vasilyev, Vladislav
2009-06-01
1-(β -D-ribofuranosyl)-2-pyrimidone (zebularine or zeb) and 1-(β -D-ribofuranosyl)-5-methyl-2-pyrimidinone (d5) are effective inhibitors of cytidine deaminases (CDA). Methyl modification of zeb at the C(5) position in the base moiety produces d5. A density functional theory (DFT) study reveals the impact of the methyl group on the electronic structures and spectra of the nucleoside pair. It is found that the addition of methyl group has little effect on the geometry of the nucleosides as well as their sugar puckering, but affects anisotropic properties such as dihedral angles, condensed Fukui functions and charge distribution can be seen in their molecular electrostatic potentials (MEPs). Electron spectra serve as the fingerprint for the methyl group. The valence spectra clearly indicate that the molecular pair is related in the inner valence space of IP > 20 eV, whereas the outer valence space reveals the methyl associated electronic structural modifications of the molecular pair. In the present study, the molecular orbitals (MO) such as MO8, MO18 and MO37 (HOMO as MO1) are identified as the fingerprint MOs for methyl, whereas other MOs marked in the figure are secondary methyl related MOs. Chemical shift in the inner shell and their spectra are also calculated. It reveals the similarities and differences of methyl effect to large nucleosides and small amino acids such as L-alanine.
Can density cumulant functional theory describe static correlation effects?
Mullinax, J Wayne; Sokolov, Alexander Yu; Schaefer, Henry F
2015-06-01
We evaluate the performance of density cumulant functional theory (DCT) for capturing static correlation effects. In particular, we examine systems with significant multideterminant character of the electronic wave function, such as the beryllium dimer, diatomic carbon, m-benzyne, 2,6-pyridyne, twisted ethylene, as well as the barrier for double-bond migration in cyclobutadiene. We compute molecular properties of these systems using the ODC-12 and DC-12 variants of DCT and compare these results to multireference configuration interaction and multireference coupled-cluster theories, as well as single-reference coupled-cluster theory with single, double (CCSD), and perturbative triple excitations [CCSD(T)]. For all systems the DCT methods show intermediate performance between that of CCSD and CCSD(T), with significant improvement over the former method. In particular, for the beryllium dimer, m-benzyne, and 2,6-pyridyne, the ODC-12 method along with CCSD(T) correctly predict the global minimum structures, while CCSD predictions fail qualitatively, underestimating the multireference effects. Our results suggest that the DC-12 and ODC-12 methods are capable of describing emerging static correlation effects but should be used cautiously when highly accurate results are required. Conveniently, the appearance of multireference effects in DCT can be diagnosed by analyzing the DCT natural orbital occupations, which are readily available at the end of the energy computation. PMID:26575548
Antisites in III-V semiconductors: Density functional theory calculations
Chroneos, A.; Tahini, H. A.; Schwingenschlögl, U.; Grimes, R. W.
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.
Augmented Lagrangian formulation of orbital-free density functional theory
Suryanarayana, Phanish Phanish, Deepa
2014-10-15
We present an Augmented Lagrangian formulation and its real-space implementation for non-periodic Orbital-Free Density Functional Theory (OF-DFT) calculations. In particular, we rewrite the constrained minimization problem of OF-DFT as a sequence of minimization problems without any constraint, thereby making it amenable to powerful unconstrained optimization algorithms. Further, we develop a parallel implementation of this approach for the Thomas–Fermi–von Weizsacker (TFW) kinetic energy functional in the framework of higher-order finite-differences and the conjugate gradient method. With this implementation, we establish that the Augmented Lagrangian approach is highly competitive compared to the penalty and Lagrange multiplier methods. Additionally, we show that higher-order finite-differences represent a computationally efficient discretization for performing OF-DFT simulations. Overall, we demonstrate that the proposed formulation and implementation are both efficient and robust by studying selected examples, including systems consisting of thousands of atoms. We validate the accuracy of the computed energies and forces by comparing them with those obtained by existing plane-wave methods.
NASA Astrophysics Data System (ADS)
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.
Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas; Papadopoulos, Georgios E
2015-12-01
The spread of microwave technology and new microwave applications in medicine have revitalized interest in the dielectric behavior of biological systems. In this work, the Fröhlich-Kirkwood approach and the linear response theory have been applied in conjunction with molecular dynamics simulations to study the dielectric response of a lysozyme solution as a model. The overall experimental dielectric behavior of a 9.88 mM lysozyme solution has been reproduced in a quantitative manner by employing a method based on the decomposition of the hydration shells close to the solute. Detailed analysis of the calculated spectra identified two δ-processes located at 200 MHz (δ1) and about 1 GHz (δ2), respectively. δ1 is associated mainly with the first hydration shell, while δ2 mainly with bulk water and the second hydration shell. Moreover, indications for the existence of an even faster relaxation in the 10(11)-Hz frequency range were found for the first time. Finally, the static dielectric constants of lysozyme and its first and second hydration shells were calculated based on the Fröhlich-Kirkwood and the linear response theory approaches.
Understanding density functional theory (DFT) and completing it in practice
Bagayoko, Diola
2014-12-15
We review some salient points in the derivation of density functional theory (DFT) and of the local density approximation (LDA) of it. We then articulate an understanding of DFT and LDA that seems to be ignored in the literature. We note the well-established failures of many DFT and LDA calculations to reproduce the measured energy gaps of finite systems and band gaps of semiconductors and insulators. We then illustrate significant differences between the results from self consistent calculations using single trial basis sets and those from computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Unlike the former, the latter calculations verifiably attain the absolute minima of the occupied energies, as required by DFT. These minima are one of the reasons for the agreement between their results and corresponding, experimental ones for the band gap and a host of other properties. Further, we note predictions of DFT BZW-EF calculations that have been confirmed by experiment. Our subsequent description of the BZW-EF method ends with the application of the Rayleigh theorem in the selection, among the several calculations the method requires, of the one whose results have a full, physics content ascribed to DFT. This application of the Rayleigh theorem adds to or completes DFT, in practice, to preserve the physical content of unoccupied, low energy levels. Discussions, including implications of the method, and a short conclusion follow the description of the method. The successive augmentation of the basis set in the BZW-EF method, needed for the application of the Rayleigh theorem, is also necessary in the search for the absolute minima of the occupied energies, in practice.
A detailed study of nucleon structure function in nuclei in the valence quark region
Bianchi, N.
1994-04-01
The so called {open_quotes}EMC effect{close_quotes} discovered during the 1980`s, has caused a big controversy in the community of nuclear and high energy physicists; during the last ten years, five experiments have been performed in different laboratories and several hundreds of papers about the possible interpretation of the modification of the nucleon structure function inside nuclei have been published. However, from the experimental point of view, the main goal of four experiments (EMC, BCDMS, NMC, FNAL) has been to emphasize the region of low x{sub b}, where shadowing effects appear. In the region of valence quarks and nuclear effects (x{sub b} > 0.1 - 0.2) the most reliable data presently available are from the SLAC E139 experiment performed in 1983 with only 80 hours of beam time. New precise data in the valence quark region are necessary to measure separate structure functions F{sub 2}(x{sub b}, Q{sup 2}) and R{sup lt}(x{sub b},Q{sup 2}) = {sigma}{sub l}/{sigma}{sub t}, and to investigate the real A-dependence of the ratio between bound and free-nucleon structure functions which is not completely defined by the SLAC data. Moreover, from the nuclear physics point of view, a measurement on some unexplored nuclei, like {sup 3}He and {sup 48}Ca, would be of great interest. The intermediate scaling region (0.1 < x{sub b} < 0.7) would be accessible at CEBAF if the machine energy will reach 6-8 GeV, as suggested by all the tests performed on the RF cavities. This physics program has been already presented in two letter of intents.
Filtered density function approach for reactive transport in groundwater
NASA Astrophysics Data System (ADS)
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
Angular momentum dependent orbital-free density functional theory: Formulation and implementation
NASA Astrophysics Data System (ADS)
Ke, Youqi; Libisch, Florian; Xia, Junchao; Carter, Emily A.
2014-04-01
Orbital-free density functional theory (OFDFT) directly solves for the ground-state electron density. It scales linearly with respect to system size, providing a promising tool for large-scale material simulations. Removal of the orbitals requires use of approximate noninteracting kinetic energy density functionals. If replacing ionic cores with pseudopotentials, removal of the orbitals also requires these pseudopotentials to be local. These are two severe challenges to the capabilities of conventional OFDFT. While main group elements are often well described within conventional OFDFT, transition metals remain intractable due to their localized d electrons. To advance the accuracy and general applicability of OFDFT, we have recently reported a general angular momentum dependent formulation as a next-generation OFDFT. In this formalism, we incorporate the angular momenta of electrons by devising a hybrid scheme based on a muffin tin geometry: inside spheres centered at the ionic cores, the electron density is expanded in a set of atom-centered basis functions combined with an onsite density matrix. The explicit treatment of the angular momenta of electrons provides an important basis for accurately describing the important ionic core region, which is not possible in conventional OFDFT. In addition to the conventional OFDFT total energy functional, we introduce a nonlocal energy term containing a set of angular momentum dependent energies to correct the errors due to the approximate kinetic energy density functional and local pseudopotentials. Our approach greatly increases the accuracy of OFDFT while largely preserving its numerical simplicity. Here, we provide details of the theoretical formulation and practical implementation, including the hybrid scheme, the derivation of the nonlocal energy term, the choice of basis functions, the direct minimization of the total energy, the procedure to determine the angular momentum dependent energies, the force formula with
NASA Astrophysics Data System (ADS)
Pham, Thinh H.; Ramprasad, Rampi; Nguyen, Huy-Viet
2016-06-01
Due to the lack of treatment of long-range dispersion energies, density functional theory with local and semilocal approximations of exchange-correlation energy is known to fail in describing van der Waals complexes, including polymer crystals. This limitation can be overcome by using a different class of functionals, called van der Waals density functional (vdW-DF), originally developed by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. In this work, we performed a systematic study of structural properties of polymeric crystals using the original vdW-DF functional by Dion et al. and its variants and refinements. Our study shows that this class of functional outperforms the conventional LDA or PBE functionals and gives results with similar accuracy to that of empirical dispersion-corrected schemes such as DFT-D. This study suggests the use of vdW-DF2 functional — a revised version of vdW-DF functional — to obtain a high-fidelity prediction of structural and other properties of polymeric materials.
Pham, Thinh H; Ramprasad, Rampi; Nguyen, Huy-Viet
2016-06-01
Due to the lack of treatment of long-range dispersion energies, density functional theory with local and semilocal approximations of exchange-correlation energy is known to fail in describing van der Waals complexes, including polymer crystals. This limitation can be overcome by using a different class of functionals, called van der Waals density functional (vdW-DF), originally developed by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. In this work, we performed a systematic study of structural properties of polymeric crystals using the original vdW-DF functional by Dion et al. and its variants and refinements. Our study shows that this class of functional outperforms the conventional LDA or PBE functionals and gives results with similar accuracy to that of empirical dispersion-corrected schemes such as DFT-D. This study suggests the use of vdW-DF2 functional - a revised version of vdW-DF functional - to obtain a high-fidelity prediction of structural and other properties of polymeric materials. PMID:27276968
Pham, Thinh H; Ramprasad, Rampi; Nguyen, Huy-Viet
2016-06-01
Due to the lack of treatment of long-range dispersion energies, density functional theory with local and semilocal approximations of exchange-correlation energy is known to fail in describing van der Waals complexes, including polymer crystals. This limitation can be overcome by using a different class of functionals, called van der Waals density functional (vdW-DF), originally developed by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. In this work, we performed a systematic study of structural properties of polymeric crystals using the original vdW-DF functional by Dion et al. and its variants and refinements. Our study shows that this class of functional outperforms the conventional LDA or PBE functionals and gives results with similar accuracy to that of empirical dispersion-corrected schemes such as DFT-D. This study suggests the use of vdW-DF2 functional - a revised version of vdW-DF functional - to obtain a high-fidelity prediction of structural and other properties of polymeric materials.
NASA Astrophysics Data System (ADS)
Sousa, Fernanda; Mandal, Subhra; Garrovo, Chiara; Astolfo, Alberto; Bonifacio, Alois; Latawiec, Diane; Menk, Ralf Hendrik; Arfelli, Fulvia; Huewel, Sabine; Legname, Giuseppe; Galla, Hans-Joachim; Krol, Silke
2010-12-01
In the present study, the in vivo distribution of polyelectrolyte multilayer coated gold nanoparticles is shown, starting from the living animal down to cellular level. The coating was designed with functional moieties to serve as a potential nano drug for prion disease. With near infrared time-domain imaging we followed the biodistribution in mice up to 7 days after intravenous injection of the nanoparticles. The peak concentration in the head of mice was detected between 19 and 24 h. The precise particle distribution in the brain was studied ex vivo by X-ray microtomography, confocal laser and fluorescence microscopy. We found that the particles mainly accumulate in the hippocampus, thalamus, hypothalamus, and the cerebral cortex.In the present study, the in vivo distribution of polyelectrolyte multilayer coated gold nanoparticles is shown, starting from the living animal down to cellular level. The coating was designed with functional moieties to serve as a potential nano drug for prion disease. With near infrared time-domain imaging we followed the biodistribution in mice up to 7 days after intravenous injection of the nanoparticles. The peak concentration in the head of mice was detected between 19 and 24 h. The precise particle distribution in the brain was studied ex vivo by X-ray microtomography, confocal laser and fluorescence microscopy. We found that the particles mainly accumulate in the hippocampus, thalamus, hypothalamus, and the cerebral cortex. Electronic supplementary information (ESI) available: Fig. S1-S6. See DOI: 10.1039/c0nr00345j
Ryan, T.G.; Haney, L.N.; Ostrom, L.T.
1992-01-01
This paper addresses one major cause for large uncertainties in human reliability analysis (HRA) results, that is, an absence of detailed function, task, timeline, link and human vulnerability analyses. All too often this crucial step in the HRA process is done in a cursory fashion using word of mouth or written procedures which themselves may incompletely or inaccurately represent the human action sequences and human error vulnerabilities being analyzed. The paper examines the potential contributions these detailed analyses can make in achieving quantitative and qualitative HRA results which are: (1) creditable, that is, minimize uncertainty, (2) auditable, that is, systematically linking quantitative results and qualitative information from which the results are derived, (3) capable of supporting root cause analyses on human reliability factors determined to be major contributors to risk, and (4) capable of repeated measures and being combined with similar results from other analyses to examine HRA issues transcending individual systems and facilities. Based on experience analyzing test and commercial nuclear reactors, and medical applications of nuclear technology, an iterative process is suggested for doing detailed function, task, timeline, link and human vulnerability analyses using documentation reviews, open-ended and structured interviews, direct observations, and group techniques. Finally, the paper concludes that detailed analyses done in this manner by knowledgeable human factors practitioners, can contribute significantly to the credibility, auditability, causal factor analysis, and combining goals of the HRA.
Mode-detailed analysis of transmission based directly on Green's functions
NASA Astrophysics Data System (ADS)
Jin, Cailong; Lan, Jin; Zhao, Xuean; Sui, Wenquan
2016-08-01
Fisher-Lee relation bm{t= {i}bmΓ_L1/2bm{G}bmΓ1/2_R} is a well-established tool to decode the mode information from Green's function and coupling parameters. Using the Bloch eigen-modes of the leads, we show that the bm{Γ1/2L/R}term can be expressed by the Bloch eigen-mode vectors and the wave velocities which give unambiguous algorithm of bm{Γ1/2L/R}in the Fish-Lee relation. Using this approach, we present an accurate and convenient technique to analyze all transport modes and also the dominant channels of an electronic transport system in tight-binding model. We study graphene nanoribbon structures to demonstrate the typical application of our technique.
Mode-detailed analysis of transmission based directly on Green's functions
NASA Astrophysics Data System (ADS)
Jin, Cailong; Lan, Jin; Zhao, Xuean; Sui, Wenquan
2016-09-01
Fisher-Lee relation {bm{t}= {i}bm{Γ}_L^{1/2}bm{G}bm{Γ}^{1/2}_R} t = i Γ L 1 / 2 G Γ R 1 / 2 is a well-established tool to decode the mode information from Green's function and coupling parameters. Using the Bloch eigen-modes of the leads, we show that the {bm{Γ}^{1/2}_{L/R}} Γ L / R 1 / 2 term can be expressed by the Bloch eigen-mode vectors and the wave velocities which give unambiguous algorithm of {bm{Γ}^{1/2}_{L/R}} Γ L / R 1 / 2 in the Fish-Lee relation. Using this approach, we present an accurate and convenient technique to analyze all transport modes and also the dominant channels of an electronic transport system in tight-binding model. We study graphene nanoribbon structures to demonstrate the typical application of our technique.
Khan, Shehryar Odelius, Michael; Kubica-Misztal, Aleksandra; Kruk, Danuta; Kowalewski, Jozef
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.
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.
Density functional investigation of epitaxial silicene on semiconducting substrates
NASA Astrophysics Data System (ADS)
Das, G. P.; Bhattacharya, A.; Bhattacharya, S.
2013-03-01
In spite of the uniqueness of carbon to form pristine fullerene, nanotube and graphene, there have been attempts to replicate these nanostructures with silicon. Most recently, the free-standing quasi-2D honeycomb structure of silicene has been predicted to be stable with linear band dispersion and Dirac cone feature similar to graphene. Epitaxial silicene on Ag(110) and on ZrB2(0001) substrates have already been reported. We have carried out first principles density functional investigation of the structural and electronic properties of silicene monolayer on various wurzite structured III-V and II-VI semiconducting substrates, with metal terminated (MT) as well as non-metal terminated (NMT) top surface. The binding energies of silicene on MT semiconductors are in the range 0.5 - 0.7 eV/atom and their behavior can be metallic, semi-metallic or even magnetic, depending on the choice of substrates. The silicene overlayer undergoes n-/p-type doping on MT/NMT semiconductor surface, depending upon the direction of the charge transfer.
Numerical methods for high-dimensional probability density function equations
NASA Astrophysics Data System (ADS)
Cho, H.; Venturi, D.; Karniadakis, G. E.
2016-01-01
In this paper we address the problem of computing the numerical solution to kinetic partial differential equations involving many phase variables. These types of equations arise naturally in many different areas of mathematical physics, e.g., in particle systems (Liouville and Boltzmann equations), stochastic dynamical systems (Fokker-Planck and Dostupov-Pugachev equations), random wave theory (Malakhov-Saichev equations) and coarse-grained stochastic systems (Mori-Zwanzig equations). We propose three different classes of new algorithms addressing high-dimensionality: The first one is based on separated series expansions resulting in a sequence of low-dimensional problems that can be solved recursively and in parallel by using alternating direction methods. The second class of algorithms relies on truncation of interaction in low-orders that resembles the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) framework of kinetic gas theory and it yields a hierarchy of coupled probability density function equations. The third class of algorithms is based on high-dimensional model representations, e.g., the ANOVA method and probabilistic collocation methods. A common feature of all these approaches is that they are reducible to the problem of computing the solution to high-dimensional equations via a sequence of low-dimensional problems. The effectiveness of the new algorithms is demonstrated in numerical examples involving nonlinear stochastic dynamical systems and partial differential equations, with up to 120 variables.
Density functional theory for plasmon-assisted superconductivity
NASA Astrophysics Data System (ADS)
Akashi, Ryosuke; Arita, Ryotaro
2014-03-01
The predictive calculation of superconducting transition temperatures (Tc) is a fascinating but extremely difficult problem in the field of superconductivity. For a conventional phonon-induced superconducting mechanism, an accurate predictive scheme to calculate Tc is established by the recent progress in the density functional theory for superconductors (SCDFT) [Lueders et al., PRB 72, 024545 (2005); Marques et al., PRB 72, 024546 (2005)]; the current SCDFT-based scheme systematically reproduces Tc observed by experiments in the conventional systems such as niobium and MgB2, with discrepancies no more than a few kelvin. However, further extensions including other mechanisms are essential to treat more general materials. Recently, we extended the SCDFT-based scheme to include a plasmon mechanism of superconductivity [Akashi and Arita, PRL 111, 057006 (2013)]. The plasmon mechanism, which has been considered solely in rather dilute electron systems, is also expected to be relevant in a wider range of materials because it can cooperate with the conventional phonon mechanism. Our extended scheme enables us to evaluate the effects on Tc of the plasmon and phonon mechanisms on equal footing. In the talk, we present recent applications to elemental metals.
Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory
Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.
2015-04-02
The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO22+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K1 values are significantly overestimated. Accurate predictions of the absolute log K1 values (root mean square deviation from experiment < 1.0 for log K1 values ranging from 0more » to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less
Density functional theory study of oxygen migration in molten carbonate
NASA Astrophysics Data System (ADS)
Lei, Xueling; Haines, Kahla; Huang, Kevin; Qin, Changyong
2016-02-01
The process of oxygen migration in alkali molten carbonate salts has been examined using density functional theory method. All geometries were optimized at the B3LYP/6-31G(d) level, while single point energy corrections were performed using MP4 and CCSD(T). At TS, a O-O-O linkage is formed and O-O bond forming and breaking is concerted. A cooperative "cogwheel" mechanism as described in the equation of CO42- + CO32- → CO32- ⋯O ⋯ CO32- → CO32- + CO42- is involved. The energy barrier is calculated to be 103.0, 136.3 and 127.9 kJ/mol through an intra-carbonate pathway in lithium, sodium and potassium carbonate, respectively. The reliability and accuracy of B3LYP/6-31G(d) were confirmed by CCSD(T). The calculated low values of activation energy indicate that the oxygen transfer in molten carbonate salts is fairly easy. In addition, it is found that lithium carbonate is not only a favorable molten carbonate salt for better cathode kinetics, but also it is widely used for reducing the melting point of Li/Na and Li/K eutectic MC mixtures. The current results imply that the process of oxygen reduction in MC modified cathodes is facilitated by the presence of MC, resulting in an enhancement of cell performance at low operating temperatures.
Density Functional Study for Homodendrimers and Amphiphilic Dendrimers.
Chen, Cangyi; Tang, Ping; Qiu, Feng; Shi, An-Chang
2016-06-23
The conformation of homodendrimers and amphiphilic dendrimers in various solvents is studied using classical density functional theory (DFT), in which the excluded-volume effects are treated explicitly. For homodendrimers in an athermal solvent, DFT results predict a remarkable fold-back behavior for the outer generation of segments, supporting the dense-core model. A coil-to-globule transition is observed for homodendrimers in a poor solvent. The size of the dendrimers, characterized by the radius of gyration, ⟨Rg⟩, is found to follow the scaling relationship, ⟨Rg⟩ ∼ N(ν), where N is the total number of segments of the dendrimers. For amphiphilic dendrimers, DFT results show that chemical modification in the outermost generation is an effective method to drive the ends toward the periphery of the dendrimers. In particular, a conformation with a hollow interior structure could be formed for amphiphilic dendrimers with longer end spacers in a selective solvent. The resulting unimolecular micelles with a hollow core and dense shell could serve as a unique candidate for encapsulation applications, such as sustained-drug-release nanocontainers.
Parameterizing deep convection using the assumed probability density function method
Storer, R. L.; Griffin, B. M.; Höft, J.; Weber, J. K.; Raut, E.; Larson, V. E.; Wang, M.; Rasch, P. J.
2014-06-11
Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method. The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing ismore » weak. The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less
Parameterizing deep convection using the assumed probability density function method
Storer, R. L.; Griffin, B. M.; Hoft, Jan; Weber, J. K.; Raut, E.; Larson, Vincent E.; Wang, Minghuai; Rasch, Philip J.
2015-01-06
Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method.The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection.These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing is weak. The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.
Parameterizing deep convection using the assumed probability density function method
Storer, R. L.; Griffin, B. M.; Höft, J.; Weber, J. K.; Raut, E.; Larson, V. E.; Wang, M.; Rasch, P. J.
2015-01-06
Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method. The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and midlatitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing ismore » weak. The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less
Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory
Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.
2015-04-02
The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K_{1 }values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO_{2}^{2+} complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K_{1} values are significantly overestimated. Accurate predictions of the absolute log K_{1} values (root mean square deviation from experiment < 1.0 for log K_{1} values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.
Density functional and neutron diffraction studies of lithium polymer electrolytes.
Baboul, A. G.
1998-06-26
The structure of PEO doped with lithium perchlorate has been determined using neutron diffraction on protonated and deuterated samples. The experiments were done in the liquid state. Preliminary analysis indicates the Li-O distance is about 2.0 {angstrom}. The geometries of a series of gas phase lithium salts [LiCF{sub 3}SO{sub 3}, Li(CF{sub 3}SO{sub 2}){sub 2}N, Li(CF{sub 3}SO{sub 2}){sub 2}CH, LiClO{sub 4}, LiPF{sub 6}, LiAsF{sub 6}] used in polymer electrolytes have been optimized at B3LYP/6-31G(d) density functional level of theory. All local minima have been identified. For the triflate, imide, methanide, and perchlorate anions, the lithium cation is coordinated to two oxygens and have binding energies of ca 141 kcal/mol at the B3LYP/6-311+G(3df,2p)/B3LYP/6-31G* level of theory. For the hexafluoroarsenate and hexafluorophosphate the lithium cation is coordinated to three oxygens and have binding energies of ca. 136 kcal/mol.
Efficiency issues related to probability density function comparison
Kelly, P.M.; Cannon, M.; Barros, J.E.
1996-03-01
The CANDID project (Comparison Algorithm for Navigating Digital Image Databases) employs probability density functions (PDFs) of localized feature information to represent the content of an image for search and retrieval purposes. A similarity measure between PDFs is used to identify database images that are similar to a user-provided query image. Unfortunately, signature comparison involving PDFs is a very time-consuming operation. In this paper, we look into some efficiency considerations when working with PDFS. Since PDFs can take on many forms, we look into tradeoffs between accurate representation and efficiency of manipulation for several data sets. In particular, we typically represent each PDF as a Gaussian mixture (e.g. as a weighted sum of Gaussian kernels) in the feature space. We find that by constraining all Gaussian kernels to have principal axes that are aligned to the natural axes of the feature space, computations involving these PDFs are simplified. We can also constrain the Gaussian kernels to be hyperspherical rather than hyperellipsoidal, simplifying computations even further, and yielding an order of magnitude speedup in signature comparison. This paper illustrates the tradeoffs encountered when using these constraints.
DENSITY-FUNCTIONAL STUDY OF THE U-ZR SYSTEM
Landa, A; Soderlind, P; Turchi, P
2008-06-25
Density-functional formalism is applied to study the phase equilibria in the U-Zr system. The obtained ground-state properties of the {gamma} (bcc) and {delta} (C32) phases are in good agreement with experimental data. The decomposition curve for the {gamma}-based U-Zr solutions is calculated. Our calculations confirm that experimentally observed 'partial' ordering of the alloy components in the {delta}-UZr{sub 2} (AlB{sub 2}) phase, in which Zr atoms occupy the 'Al' position and the two 'B' sites are randomly shared by the U and Zr atoms, is the most energetically favorable within the C32 structure. We argue that stabilization of the {delta}-UZr{sub 2} phase relative to the {alpha}-Zr (hcp) structure is due to an increase of the Zr d-band occupancy that occurs when U is alloyed with Zr. A comparison with stabilization of the {omega}-phase (also C32) in Zr under compression is made.
Efficiency issues related to probability density function comparison
NASA Astrophysics Data System (ADS)
Kelly, Patrick M.; Cannon, T. Michael; Barros, Julio E.
1996-03-01
The CANDID project (comparison algorithm for navigating digital image databases) employs probability density functions (PDFs) of localized feature information to represent the content of an image for search and retrieval purposes. A similarity measure between PDFs is used to identify database images that are similar to a user-provided query image. Unfortunately, signature comparison involving PDFs is a very time-consuming operation. In this paper, we look into some efficiency considerations when working with PDFs. Since PDFs can take on many forms, we look into tradeoffs between accurate representation and efficiency of manipulation for several data sets. In particular, we typically represent each PDF as a Gaussian mixture (e.g. as a weighted sum of Gaussian kernels) in the feature space. We find that by constraining all Gaussian kernels to have principal axes that are aligned to the natural axes of the feature space, computations involving these PDFs are simplified. We can also constrain the Gaussian kernels to be hyperspherical rather than hyperellipsoidal, simplifying computations even further, and yielding an order of magnitude speedup in signature comparison. This paper illustrates the tradeoffs encountered when using these constraints.
Structure and dynamics in liquid bismuth and Bi(n) clusters: a density functional study.
Akola, J; Atodiresei, N; Kalikka, J; Larrucea, J; Jones, R O
2014-11-21
Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristic in both liquid and clusters, the number of large voids and the total cavity volume is much larger in the liquid at 1023 K, with larger local concentration variations. The inclusion of spin-orbit coupling results in a lowering of the cohesive energies in Bin clusters of 0.3-0.5 eV/atom.
Mixtures of ions and amphiphilic molecules in slit-like pores: A density functional approach
Pizio, O.; Rżysko, W. Sokołowski, S.; Sokołowska, Z.
2015-04-28
We investigate microscopic structure and thermodynamic properties of a mixture that contains amphiphilic molecules and charged hard spheres confined in slit-like pores with uncharged hard walls. The model and the density functional approach are the same as described in details in our previous work [Pizio et al., J. Chem. Phys. 140, 174706 (2014)]. Our principal focus is in exploring the effects brought by the presence of ions on the structure of confined amphiphilic particles. We have found that for some cases of anisotropic interactions, the change of the structure of confined fluids occurs via the first-order transitions. Moreover, if anions and cations are attracted by different hemispheres of amphiphiles, a charge at the walls appears at the zero value of the wall electrostatic potential. For a given thermodynamic state, this charge is an oscillating function of the pore width.
Structure and dynamics in liquid bismuth and Bi{sub n} clusters: A density functional study
Akola, J.; Atodiresei, N.; Kalikka, J.; Larrucea, J.; Jones, R. O.
2014-11-21
Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristic in both liquid and clusters, the number of large voids and the total cavity volume is much larger in the liquid at 1023 K, with larger local concentration variations. The inclusion of spin-orbit coupling results in a lowering of the cohesive energies in Bi{sub n} clusters of 0.3–0.5 eV/atom.
Swint-Kruse, Liskin; Zhan, Hongli; Matthews, Kathleen Shive
2005-08-23
Protein structural change underlies many signal transduction processes. Although end-state structures are known for various allosteric proteins, intermediates are difficult to observe. Recently, targeted molecular dynamics simulation (TMD) was used to examine the conformational transition and predict relevant intermediates for wild-type lactose repressor (LacI). A catalog of involved residues suggests that the transition of this homodimer is asymmetric and that K84 is a prominent participant in the dynamic N-subdomain interface. Previous experiments indicated that hydrophobic substitutions at position 84 engender slowed, biphasic inducer binding kinetics, which might reflect the same phenomena observed in TMD. Here, we report biochemical confirmation that DNA and inducer binding remain allosterically linked in K84A and K84L, albeit with a differential smaller than that found in wild-type LacI. Other features of these mutant proteins are consistent with an allosteric conformational shift that approximates that of the wild type. As a consequence, these repressors can be utilized to explore an unanswered question about LacI function: How many inducers (one or two per dimer) are required to diminish operator affinity? The biphasic natures of the K84L and K84A inducer association rates allow direct correlation between the two distinct inducer binding events and operator release. Indeed, the kinetics of operator release for the K84A and K84L closely parallel those for the second inducer binding event. Together with implications from previous equilibrium results for wild-type and mutant proteins, these kinetic data demonstrate that binding of two inducers per dimeric DNA binding unit is required to release the operator in these variant LacI proteins. PMID:16101304
Quantum Drude friction for time-dependent density functional theory.
Neuhauser, Daniel; Lopata, Kenneth
2008-10-01
sophisticated description of the coupling, and to memory functionals. Our results open the way to very simple finite grid description of scattering and multistage conductance using time-dependent density functional theory away from the linear regime, just as absorbing potentials and self-energies are useful for noninteracting systems and leads. PMID:19045077
Nonlocal density-functional description constructed from a correlated many-body wave function
NASA Astrophysics Data System (ADS)
Umezawa, Naoto; Tsuneyuki, Shinji
2004-03-01
We suggest a new approach to the nonlocal density-functional theory. In our method, the nonlocal correlation functional is derived from a correlated many-body wave function using the transcorrelated similarity transformation [1,2]. Our formalism is rigorous in principle if the v-representable density is assumed. In practice, Jastrow-Slater-type wave function is adopted and the correlation functional consists of many-body interactions originated from the Jastrow factor. Instead of struggling with these higher order interactions, we retain only 2-body interactions multiplying an adjusting parameter so that it can reproduce the exact correlation energy for the homogeneous electron gas. Therefore, the computational cost is comparable to the exact exchange method. Moreover, parameters in the Jastrow factor are determined by the two conditions: the cusp conditions and the random-phase approximation without empirical fitting. We found that our correlation functional gives fairly good results for small atoms and ions (He, Li^+, Be^2+, Li, and Be). [1]S. F. Boys and N. C. Handy, Proc. Roy. Soc. A, 309, 209; 310, 43; 310, 63; 311, 309. [2] N. Umezawa and S. Tsuneyuki, J. Chem. Phys. 119, 10015 (2003).
NASA Astrophysics Data System (ADS)
Karpenko, Alexander; Espinosa Leal, Leonardo; Caro, Miguel; Lehtomaki, Jouko; Lopez-Acevedo, Olga
Because of issues with accuracy and transferability of existing orbital-free (OF) density functionals, OF functional development remains an active research area. Due to numerical difficulties, all-electron self-consistent assessment of OF functionals is limited. Using the projector augmented wave method we compute OFDFT all-electron values and we evaluate the performance of a parametrized OF functional for atoms and molecules. We combine the parametrized Thomas-Fermi-Weizsäcker (TF-W) kinetic model λ and γ for the fractions of Weizsäcker and TF functionals, respectively, with LDA for atoms. We found that one-to-one relation between λ and γ values defines a region in parameter space that allows the atomic energies and eigenvalues to be approximated with a small average error with respect to the Kohn-Sham values. The optimum values is however different for every property and for every atom. Recently, these results have been combined to test parameter transferability from atoms to molecules and we expect will help for further systematic improvement of OF density functionals. Karpenko et al., in preparation.
Density functional theory study of the organic functionalization of hydrogenated silicene.
Rubio-Pereda, Pamela; Takeuchi, Noboru
2013-05-21
Silicene, the silicon analogous of graphene, is a newly synthesized two-dimensional nanomaterial, with unique features and promising potential applications. In this paper we present density functional theory calculations of the organic functionalization of hydrogenated silicene with acetylene, ethylene, and styrene. The results are compared with previous works of the adsorption on H-Si[111]. For styrene, binding energies for the intermediate and final states as well as the energy barrier for hydrogen abstraction are rather similar for the two systems. On the other hand, results for acetylene and ethylene are surprisingly different in H-silicene: the abstraction barrier is much smaller in H-silicene than in H-Si[111]. These differences can be understood by the different electrostatic potentials due to the presence of the H atoms at the bottom of the silicene bilayer that allows the delocalization of the spin density at the reaction intermediate state.
Symmetry Energy as a Function of Density and Mass
Danielewicz, Pawel; Lee, Jenny
2007-10-26
Energy in nuclear matter is, in practice, completely characterized at different densities and asymmetries, when the density dependencies of symmetry energy and of energy of symmetric matter are specified. The density dependence of the symmetry energy at subnormal densities produces mass dependence of nuclear symmetry coefficient and, thus, can be constrained by that latter dependence. We deduce values of the mass dependent symmetry coefficients, by using excitation energies to isobaric analog states. The coefficient systematic, for intermediate and high masses, is well described in terms of the symmetry coefficient values of a{sub a}{sup V} = (31.5-33.5) MeV for the volume coefficient and a{sub a}{sup S} = (9-12) MeV for the surface coefficient. These two further correspond to the parameter values describing density dependence of symmetry energy, of L{approx}95 MeV and K{sub sym}{approx}25 MeV.
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.
DGDFT: A massively parallel method for large scale density functional theory calculations
Hu, Wei Yang, Chao; Lin, Lin
2015-09-28
We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.
Wang, Deming; Yang, Zhengyi
2008-03-01
The use of polynomial functions for modeling geometric distortion in magnetic resonance imaging (MRI) that arises from scanner's hardware imperfection is studied in detail. In this work, the geometric distortion data from four representative MRI systems were used. Modeling of these data using polynomial functions of the fourth, fifth, sixth, and seventh orders was carried out. In order to investigate how this modeling performed for different size and shape of the volume of interest, the modeling was carried out for three different volumes of interest (VOI): a cube, a cylinder, and a sphere. The modeling's goodness was assessed using both the maximum and mean absolute errors. The modeling results showed that (i) for the cube VOI there appears to be an optimal polynomial function that gives the least modeling errors and the sixth order polynomial was found to be the optimal polynomial function for the size of the cubic VOI considered in the present work; (ii) for the cylinder VOI, all four polynomials performed approximately equally well but a trend of a slight decrease in the mean absolute error with the increasing order of the polynomial was noted; and (iii) for the sphere VOI, the maximum absolute error showed some variations with the order of the polynomial, with the fourth order polynomial producing the smallest maximum absolute errors. It is further noted that extrapolation could lead to very large errors so any extrapolation needs to be avoided. A detailed analysis on the modeling errors is presented.
NASA Astrophysics Data System (ADS)
Putaja, A.; Eich, F. G.; Baldsiefen, T.; Räsänen, E.
2016-03-01
Physically valid and numerically efficient approximations for the exchange and correlation energy are critical for reduced-density-matrix-functional theory to become a widely used method in electronic structure calculations. Here we examine the physical limits of power functionals of the form f (n ,n') =(nn')α for the scaling function in the exchange-correlation energy. To this end we obtain numerically the minimizing momentum distributions for the three- and two-dimensional homogeneous electron gas, respectively. In particular, we examine the limiting values for the power α to yield physically sound solutions that satisfy the Lieb-Oxford lower bound for the exchange-correlation energy and exclude pinned states with the condition n (k )<1 for all wave vectors k . The results refine the constraints previously obtained from trial momentum distributions. We also compute the values for α that yield the exact correlation energy and its kinetic part for both the three- and two-dimensional electron gas. In both systems, narrow regimes of validity and accuracy are found at α ≳0.6 and at rs≳10 for the density parameter, corresponding to relatively low densities.
Advanced Density Functional Theory Methods for Materials Science
NASA Astrophysics Data System (ADS)
Demers, Steven
In this work we chiefly deal with two broad classes of problems in computational materials science, determining the doping mechanism in a semiconductor and developing an extreme condition equation of state. While solving certain aspects of these questions is well-trodden ground, both require extending the reach of existing methods to fully answer them. Here we choose to build upon the framework of density functional theory (DFT) which provides an efficient means to investigate a system from a quantum mechanics description. Zinc Phosphide (Zn3P2) could be the basis for cheap and highly efficient solar cells. Its use in this regard is limited by the difficulty in n-type doping the material. In an effort to understand the mechanism behind this, the energetics and electronic structure of intrinsic point defects in zinc phosphide are studied using generalized Kohn-Sham theory and utilizing the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional for exchange and correlation. Novel 'perturbation extrapolation' is utilized to extend the use of the computationally expensive HSE functional to this large-scale defect system. According to calculations, the formation energy of charged phosphorus interstitial defects are very low in n-type Zn3P2 and act as 'electron sinks', nullifying the desired doping and lowering the fermi-level back towards the p-type regime. Going forward, this insight provides clues to fabricating useful zinc phosphide based devices. In addition, the methodology developed for this work can be applied to further doping studies in other systems. Accurate determination of high pressure and temperature equations of state is fundamental in a variety of fields. However, it is often very difficult to cover a wide range of temperatures and pressures in an laboratory setting. Here we develop methods to determine a multi-phase equation of state for Ta through computation. The typical means of investigating thermodynamic properties is via 'classical' molecular
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.
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. PMID:25570426
Density functional study on the functionalization of BN nanotubes with nitramide
NASA Astrophysics Data System (ADS)
Kakemam, Jamal; Noei, M.
2014-10-01
Chemical functionalization of a boron nitride nanotube (BNNT) with nitramide molecule (H2NNO2) has been investigated using density functional theory. It was found that the molecule prefers to be adsorbed and dissociated on a diagonal B-N bond of the tube surface so that the -NH2 and -NO2 groups are attached on B and N atoms, releasing energy of 0.50 eV. The results show that the functionalized BNNT is more soluble than the pristine one which may render the chemical modification process to be an effective way for purification of the BNNTs. Depending on the cleavage behavior of nitramide on the tube, HOMO/LUMO gap of the system can be either decreased or increased while the chemically modified BNNT is still a semiconductor. Furthermore, the chemical functionalization results in hindered field emission in the tube by raising the potential barrier of the electron emission.
NASA Astrophysics Data System (ADS)
Mattsson, Ann E.; Wills, John M.
2013-03-01
The inability to computationally describe the physics governing the properties of actinides and their alloys is the poster child of failure of existing Density Functional Theory exchange-correlation functionals. The intricate competition between localization and delocalization of the electrons, present in these materials, exposes the limitations of functionals only designed to properly describe one or the other situation. We will discuss the manifestation of this competition in real materials and propositions on how to construct a functional able to accurately describe properties of these materials. I addition we will discuss both the importance of using the Dirac equation to describe the relativistic effects in these materials, and the connection to the physics of transition metal oxides. 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.
Nishimoto, Yoshio
2015-09-01
We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well. PMID:26342360
Nishimoto, Yoshio
2015-09-07
We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.
Baczewski, Andrew David; Shulenburger, Luke; Desjarlais, Michael Paul; Magyar, Rudolph J.
2014-02-01
In recent years, DFT-MD has been shown to be a useful computational tool for exploring the properties of WDM. These calculations achieve excellent agreement with shock compression experiments, which probe the thermodynamic parameters of the Hugoniot state. New X-ray Thomson Scattering diagnostics promise to deliver independent measurements of electronic density and temperature, as well as structural information in shocked systems. However, they require the development of new levels of theory for computing the associated observables within a DFT framework. The experimentally observable x-ray scattering cross section is related to the electronic density-density response function, which is obtainable using TDDFT - a formally exact extension of conventional DFT that describes electron dynamics and excited states. In order to develop a capability for modeling XRTS data and, more generally, to establish a predictive capability for rst principles simulations of matter in extreme conditions, real-time TDDFT with Ehrenfest dynamics has been implemented in an existing PAW code for DFT-MD calculations. The purpose of this report is to record implementation details and benchmarks as the project advances from software development to delivering novel scienti c results. Results range from tests that establish the accuracy, e ciency, and scalability of our implementation, to calculations that are veri ed against accepted results in the literature. Aside from the primary XRTS goal, we identify other more general areas where this new capability will be useful, including stopping power calculations and electron-ion equilibration.
Exact density functional and wave function embedding schemes based on orbital localization
NASA Astrophysics Data System (ADS)
Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály
2016-08-01
Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.
Zinc surface complexes on birnessite: A density functional theory study
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.
Density Functional Theory Calculations of Mass Transport in UO2
Andersson, Anders D.; Dorado, Boris; Uberuaga, Blas P.; Stanek, Christopher R.
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
Density functional theory study of the oligomerization of carboxylic acids.
Di Tommaso, Devis; Watson, Ken L
2014-11-20
We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of
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.
Ronca, Enrico; Angeli, Celestino; Belpassi, Leonardo; De Angelis, Filippo; Tarantelli, Francesco; Pastore, Mariachiara
2014-09-01
Making use of the recently developed excited state charge displacement analysis [E. Ronca et al., J. Chem. Phys. 140, 054110 (2014)], suited to quantitatively characterize the charge fluxes coming along an electronic excitation, we investigate the role of the density relaxation effects in the overall description of electronically excited states of different nature, namely, valence, ionic, and charge transfer (CT), considering a large set of prototypical small and medium-sized molecular systems. By comparing the response densities provided by time-dependent density functional theory (TDDFT) and the corresponding relaxed densities obtained by applying the Z-vector postlinear-response approach [N. C. Handy and H. F. Schaefer, J. Chem. Phys. 81, 5031 (1984)] with those obtained by highly correlated state-of-the-art wave function calculations, we show that the inclusion of the relaxation effects is imperative to get an accurate description of the considered excited states. We also examine what happens at the quality of the response function when an increasing amount of Hartree-Fock (HF) exchange is included in the functional, showing that the usually improved excitation energies in the case of CT states are not always the consequence of an improved description of their overall properties. Remarkably, we find that the relaxation of the response densities is always able to reproduce, independently of the extent of HF exchange in the functional, the benchmark wave function densities. Finally, we propose a novel and computationally convenient strategy, based on the use of the natural orbitals derived from the relaxed TDDFT density to build zero-order wave function for multireference perturbation theory calculations. For a significant set of different excited states, the proposed approach provided accurate excitation energies, comparable to those obtained by computationally demanding ab initio calculations.
Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors
The interaction between density dependence (DD) and environmental stressors can result in a compensatory or synergistic response in population growth, and population models that use density-independent demographic rates or generic DD functions may be introducing bias into managem...
Sundararajan, Mahesh; Sinha, Vivek; Bandyopadhyay, Tusar; Ghosh, Swapan K
2012-05-01
The feasibility of using cucurbituril host molecule as a probable actinyl cation binders candidate is investigated through density functional theory based calculations. Various possible binding sites of the cucurbit[5]uril host molecule to uranyl are analyzed and based on the binding energy evaluations, μ(5)-binding is predicted to be favored. For this coordination, the structure, vibrational spectra, and binding energies are evaluated for the binding of three actinyls in hexa-valent and penta-valent oxidation states with functionalized cucurbiturils. Functionalizing cucurbituril with methyl and cyclohexyl groups increases the binding affinities of actinyls, whereas fluorination decreases the binding affinities as compared to the native host molecule. Surprisingly hydroxylation of the host molecule does not distinguish the oxidation state of the three actinyls.
NASA Astrophysics Data System (ADS)
Tachikawa, Hiroto; Iyama, Tetsuji; Kawabata, Hiroshi
2016-05-01
Electronic structures and formation mechanism of hydrogen functionalized carbon nanotube (CNT) have been investigated by means of density functional theory (DFT) method. The mechanism of hydrogen addition reaction to the CNT surface was also investigated. Pure and boron-nitrogen (BN) substituted CNT (denoted by CNT and BN-CNT, respectively) were examined as the carbon nanotubes. It was found that the additions of hydrogen atom to B (boron atom) and C (carbon atom) sites of BN-CNT proceed without activation barrier, whereas the hydrogenation of N (nitrogen atom) site needs the activation energy. The electronic states of hydrogen functionalized CNT and BN-CNT were discussed on the basis of theoretical results.
Sundararajan, Mahesh; Sinha, Vivek; Bandyopadhyay, Tusar; Ghosh, Swapan K
2012-05-01
The feasibility of using cucurbituril host molecule as a probable actinyl cation binders candidate is investigated through density functional theory based calculations. Various possible binding sites of the cucurbit[5]uril host molecule to uranyl are analyzed and based on the binding energy evaluations, μ(5)-binding is predicted to be favored. For this coordination, the structure, vibrational spectra, and binding energies are evaluated for the binding of three actinyls in hexa-valent and penta-valent oxidation states with functionalized cucurbiturils. Functionalizing cucurbituril with methyl and cyclohexyl groups increases the binding affinities of actinyls, whereas fluorination decreases the binding affinities as compared to the native host molecule. Surprisingly hydroxylation of the host molecule does not distinguish the oxidation state of the three actinyls. PMID:22471316
Gas-phase reactions of pd with acetone: A theoretical investigation using density functional theory
NASA Astrophysics Data System (ADS)
Dai, Guo-Liang; Wang, Chuan-Feng
2012-12-01
The gas-phase reaction of palladium atom with acetone is investigated using density functional theory. Geometries and energies of the reactants, intermediates, and products involved are calculated. Both ground and excited state potential energy surfaces are investigated in detail. The present results show that the title reaction start with the formation of an η2-CH3COCH3-metal complex, followed by C-O, C-H, and C-C activation. These reactions can lead to four different products (PdO + C3H6, PdCH2COCH3 + H, PdCH2 + CH3CHO, and PdCOCH2 + CH4). The present results may be helpful in understanding the mechanism of the title reaction and further experimental investigation of the reaction.
Nonlocal orbital-free density functional theory for warm dense matter
NASA Astrophysics Data System (ADS)
Sjostrom, Travis
2014-03-01
Accurate simulations of warm dense matter remain challenging in current research, while being motivated further as recent experiments probe more accurately into this regime. While the de facto standard is quantum molecular dynamics using Kohn-Sham DFT, this methods scales significantly with temperature due to the orbital dependence. From the other side, the orbital-free Thomas-Fermi approximation works well for hot dense systems, but loses accuracy at lower temperatures. Recently developed nonlocal orbital-free functionals for the noninteracting free energy [Phys. Rev. B 88, 195103], which show near Kohn-Sham accuracy for broad ranges of temperature and density are presented. The application of which are detailed in regards to pseudopotentials and molecular dynamics for various systems. Comparisons with local orbital-free methods as well as orbital-dependent Kohn-Sham calculations, including accuracy and computational cost are made. This research has been supported by the DOE Office of Fusion Sciences (FES).
Density-functional study of small interstitial clusters in Si: Comparison with experiments
Carvalho, A.; Coutinho, J.; Jones, R.; Briddon, P.R.
2005-10-15
Local density functional calculations are carried out on models of tri- and tetra-self-interstitial clusters in Si. Electrical levels and local vibrational modes (LVMs) of the defects are found. The latter are compared with recent experiments detailing the isotopic shifts of LVM frequencies associated with phonon replicas of the W- and X-photoluminescence lines, attributed to I{sub 3} ad I{sub 4}, respectively. While the ground state I{sub 4} structure accounts well for the measured optical and electrical data, the most stable I{sub 3} aggregates either show no gap states, or the lack for LVMs that could be linked with the W-line. Instead, this optical center can be linked to a metastable form of I{sub 3}.
Solving the self-interaction problem in Kohn-Sham density functional theory: Application to atoms
NASA Astrophysics Data System (ADS)
Däne, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.
2015-04-01
In previous work, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn-Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In this paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. We present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.
Solving the Self-Interaction Problem in Kohn-Sham Density Functional Theory. Application to Atoms
Daene, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.
2014-10-14
Previously, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn–Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In our paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We also prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. We present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.
Solving the Self-Interaction Problem in Kohn-Sham Density Functional Theory. Application to Atoms
Daene, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.
2014-10-14
Previously, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn–Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In our paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We also prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. Wemore » present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.« less
Self-consistent van der Waals density functional study of benzene adsorption on Si(100)
NASA Astrophysics Data System (ADS)
Hamamoto, Yuji; Hamada, Ikutaro; Inagaki, Kouji; Morikawa, Yoshitada
2016-06-01
The adsorption of benzene on the Si(100) surface is studied theoretically using the self-consistent van der Waals density functional (vdW-DF) method. The adsorption energies of two competing adsorption structures, butterfly (BF) and tight-bridge (TB) structures, are calculated with several vdW-DFs at saturation coverage. Our results show that recently proposed vdW-DFs with high accuracy all prefer TB to BF, in accord with more accurate calculations based on exact exchange and correlation within the random-phase approximation. Detailed analyses reveal the important roles played by the molecule-surface interaction and molecular deformation upon adsorption, and we suggest that their precise description is a prerequisite for accurate prediction of the most stable adsorption structure of organic molecules on semiconductor surfaces.
Kinetic theory of correlated fluids: from dynamic density functional to Lattice Boltzmann methods.
Marconi, Umberto Marini Bettolo; Melchionna, Simone
2009-07-01
Using methods of kinetic theory and liquid state theory we propose a description of the nonequilibrium behavior of molecular fluids, which takes into account their microscopic structure and thermodynamic properties. The present work represents an alternative to the recent dynamic density functional theory, which can only deal with colloidal fluids and is not apt to describe the hydrodynamic behavior of a molecular fluid. The method is based on a suitable modification of the Boltzmann transport equation for the phase space distribution and provides a detailed description of the local structure of the fluid and its transport coefficients. Finally, we propose a practical scheme to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the Lattice Boltzmann method.
NASA Astrophysics Data System (ADS)
Xiao, Ling-Ping; Zeng, Zhi; Chen, Xiao-Jia
2016-06-01
The pressure effect on the geometrical and electronic structures of crystalline naphthalene is calculated up to 30 GPa by performing density functional calculations. The lattice parameters a, b, and c, decrease by 1.77 Å (-20.4%), 0.85 Å (-14.1%), and 0.91 Å (-8.2%), respectively, while the monoclinic angle β increases by 3.95° in this pressure region. At the highest pressure of 30 GPa the unit cell volume decreases by 62.7%. The detailed analysis of the molecular arrangement within crystal structure reveals that the molecular motion becomes more and more localized, and hints towards the evolution of intermolecular interaction with pressure. Moreover, the electronic structure of naphthalene under high pressure is also discussed. A pressure induced decrease of the band gap is observed.
A relativistic time-dependent density functional study of the excited states of the mercury dimer.
Kullie, Ossama
2014-01-14
In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s(2) + 6s6p), (6s(2) + 6s7s), and (6s(2) + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2.
A relativistic time-dependent density functional study of the excited states of the mercury dimer
NASA Astrophysics Data System (ADS)
Kullie, Ossama
2014-01-01
In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s2 + 6s6p), (6s2 + 6s7s), and (6s2 + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2.
The computational foundations of time dependent density functional theory
NASA Astrophysics Data System (ADS)
Whitfield, James
2014-03-01
The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. Since a quantum computer can efficiently produce such time-dependent densities, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds. Further, we find that systems do not immediately become non-representable but rather become ill-representable as one approaches this boundary. A representability parameter is defined in our work which quantifies the distance to the boundary of representability and the computational difficulty of finding the Kohn-Sham system.
NASA Technical Reports Server (NTRS)
1974-01-01
The capabilities for preflight feeding of flight personnel and the supply and control of the space shuttle flight food system were investigated to determine ground support requirements; and the functional details of an onboard food system galley are shown in photographic mockups. The elements which were identified as necessary to the efficient accomplishment of ground support functions include the following: (1) administration; (2) dietetics; (3) analytical laboratories; (4) flight food warehouse; (5) stowage module assembly area; (6) launch site module storage area; (7) alert crew restaurant and disperse crew galleys; (8) ground food warehouse; (9) manufacturing facilities; (10) transport; and (11) computer support. Each element is discussed according to the design criteria of minimum cost, maximum flexibility, reliability, and efficiency consistent with space shuttle requirements. The galley mockup overview illustrates the initial operation configuration, food stowage locations, meal assembly and serving trays, meal preparation configuration, serving, trash management, and the logistics of handling and cleanup equipment.
Kohn-Sham density-functional theory and renormalization of many-body perturbation expansions
NASA Astrophysics Data System (ADS)
Valiev, Marat
1998-03-01
Numerous practical applications provide strong evidence that despite its simplicity and crude approximations, density-functional theory leads to a rather accurate description of ground state properties of various condensed matter systems. Although well documented numerically, to our knowledge a theoretical explanation of the accuracy of density-functional theory has not been given. This issue is clarified in this work by demonstrating that density-functional theory represents a particular renormalization procedure of a many-body perturbation expansion. In other words, it is shown that density-functional theory is a many-body perturbation theory whose convergence properties have been optimized. The realization of this fact brings new meaning into density-functional theory and explains the success of density-functional based calculations. For more information go to http://alchemy.ucsd.edu/marat/ .
Tensorial density functional theory for non-spherical hard-body fluids.
Hansen-Goos, Hendrik; Mecke, Klaus
2010-09-15
In a recent publication (Hansen-Goos and Mecke 2009 Phys. Rev. Lett. 102 018302) we constructed a free energy functional for the inhomogeneous hard-body fluid, which reduces to Rosenfeld's fundamental measure theory (Rosenfeld 1989 Phys. Rev. Lett. 63 980) when applied to hard spheres. The new functional is able to yield the isotropic-nematic transition for the hard-spherocylinder fluid in contrast to Rosenfeld's fundamental measure theory for non-spherical particles (Rosenfeld 1994 Phys. Rev. E 50 R3318). The description of inhomogeneous isotropic fluids is also improved when compared with data from Monte Carlo simulations for hard spherocylinders in contact with a planar hard wall. However, the new functional for the inhomogeneous fluid in general does not comply with the exact second order virial expansion. We introduced the ζ correction in order to minimize the deviation from Onsager's exact result in the isotropic bulk fluid. In this article we give a detailed account of the construction of the new functional. An extension of the ζ correction makes the latter better suited for non-isotropic particle distributions. The extended ζ correction is shown to improve the description of the isotropic-nematic bulk phase diagram while it has little effect on the results for the isotropic but inhomogeneous hard-spherocylinder fluid. We argue that the gain from using higher order tensorial weighted densities in the theory is likely to be inferior to the associated increase in complexity. PMID:21386523
Patching the Exchange-Correlation Potential in Density Functional Theory.
Huang, Chen
2016-05-10
A method for directly patching exchange-correlation (XC) potentials in materials is derived. The electron density of a system is partitioned into subsystem densities by dividing its Kohn-Sham (KS) potential among the subsystems. Inside each subsystem, its projected KS potential is required to become the total system's KS potential. This requirement, together with the nearsightedness principle of electronic matters, ensures that the electronic structures inside subsystems can be good approximations to the total system's electronic structure. The nearsightedness principle also ensures that subsystem densities could be well localized in their regions, making it possible to use high-level methods to invert the XC potentials for subsystem densities. Two XC patching methods are developed. In the local XC patching method, the total system's XC potential is improved in the cluster region. We show that the coupling between a cluster and its environment is important for achieving a fast convergence of the electronic structure in the cluster region. In the global XC patching method, we discuss how to patch the subsystem XC potentials to construct the XC potential in the total system, aiming to scale up high-level quantum mechanics simulations of materials. Proof-of-principle examples are given.
Stretched hydrogen molecule from a constrained-search density-functional perspective
Valone, Steven M; Levy, Mel
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.
Systematic construction of density functionals based on matrix product state computations
NASA Astrophysics Data System (ADS)
Lubasch, Michael; Fuks, Johanna I.; Appel, Heiko; Rubio, Angel; Cirac, J. Ignacio; Bañuls, Mari-Carmen
2016-08-01
We propose a systematic procedure for the approximation of density functionals in density functional theory that consists of two parts. First, for the efficient approximation of a general density functional, we introduce an efficient ansatz whose non-locality can be increased systematically. Second, we present a fitting strategy that is based on systematically increasing a reasonably chosen set of training densities. We investigate our procedure in the context of strongly correlated fermions on a one-dimensional lattice in which we compute accurate training densities with the help of matrix product states. Focusing on the exchange-correlation energy, we demonstrate how an efficient approximation can be found that includes and systematically improves beyond the local density approximation. Importantly, this systematic improvement is shown for target densities that are quite different from the training densities.
Electronic states of alkyl-radical-functionalized C20 fullerene using density functional theory
NASA Astrophysics Data System (ADS)
Abe, Shigeaki; Kawano, Shimpei; Toida, Yu; Nakamura, Mariko; Inoue, Satoshi; Sano, Hidehiko; Yoshida, Yasuhiro; Kawabata, Hiroshi; Tachikawa, Hiroto
2016-03-01
The structures and electronic states of alkyl-radical-functionalized C20 fullerenes (denoted by C20-R) have been investigated using density functional theory (DFT). The different alkyl radicals investigated were methyl, ethyl, propyl, and butyl radicals. The DFT calculation indicated that the alkyl radical binds to the carbon atom of C20 in the on-top site, thus forming a strong C-C single bond. The binding energies of the alkyl radicals to C20 were calculated to be 83.9-86.6 kcal/mol at the CAM-B3LYP/6-311G(d,p) level. The electronic states of the C20-R complex are discussed on the basis of the theoretical results.
Fixed-sample optimization using a probability density function
Barnett, R.N.; Sun, Zhiwei; Lester, W.A. Jr. |
1997-12-31
We consider the problem of optimizing parameters in a trial function that is to be used in fixed-node diffusion Monte Carlo calculations. We employ a trial function with a Boys-Handy correlation function and a one-particle basis set of high quality. By employing sample points picked from a positive definite distribution, parameters that determine the nodes of the trial function can be varied without introducing singularities into the optimization. For CH as a test system, we find that a trial function of high quality is obtained and that this trial function yields an improved fixed-node energy. This result sheds light on the important question of how to improve the nodal structure and, thereby, the accuracy of diffusion Monte Carlo.
Local thermodynamic mapping for effective liquid density-functional theory
NASA Technical Reports Server (NTRS)
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.
Chittenden, L M; Schertz, K F; Lin, Y R; Wing, R A; Paterson, A H
1994-03-01
The first "complete" genetic linkage map of Sorghum section Sorghum is described, comprised of ten linkage groups putatively corresponding to the ten gametic chromosomes of S. bicolor and S. propinquum. The map includes 276 RFLP loci, predominately detected by PstI-digested S. bicolor genomic probes, segregating in 56 F2 progeny of a cross between S. bicolor and S. propinquum. Although prior cytological evidence suggests that the genomes of these species are largely homosequential, a high level of molecular divergence is evidenced by the abundant RFLP and RAPD polymorphisms, the marked deviations from Mendelian segregation in many regions of the genome, and several species-specific DNA probes. The remarkable level of DNA polymorphism between these species will facilitate development of a high-density genetic map. Further, the high level of DNA polymorphism permitted mapping of multiple loci for 21 (8.2%) DNA probes. Linkage relationships among eight (38%) of these probes suggest ancestral duplication of three genomic regions. Mapping of 13 maize genomic clones in this cross was consistent with prior results. Mapping of heterologous cDNAs from rice and oat suggests that it may be feasible to extend comparative mapping to these distantly-related species, and to ultimately generate a detailed description of chromosome rearrangements among cultivated Gramineae. Limited investigation of a small number of RFLPs showed several alleles common to S. bicolor and S. Halepense ("johnson-grass"), but few alleles common to S. propinquum and S. halepense, raising questions about the origin of S. halepense.
Constrained Parmeterization of Reduced Density Approximation of Kinetic Energy Functionals
NASA Astrophysics Data System (ADS)
Chakraborty, Debajit; Trickey, Samuel; Karasiev, Valentin
2014-03-01
Evaluation of forces in ab initio MD is greatly accelerated by orbital-free DFT, especially at finite temperature. The recent achievement of a fully non-empirical constraint-based generalized gradient (GGA) functional for the Kohn-Sham KE Ts [ n ] brings to light the inherent limitations of GGAs. This motivates inclusion of higher-order derivatives in the form of reduced derivative approximation (RDA) functionals. That, in turn, requires new functional forms and design criteria. RDA functionals are constrained further to produce a positive-definite, non-singular Pauli potential. We focus on designing a non-empirical constraint-based meta-GGA functional with certain combinations of higher-order derivatives which avoid nuclear-site singularities to a specified order of gradient expansion. Here we report progress on this agenda. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.
Electronic states of aryl radical functionalized graphenes: Density functional theory study
NASA Astrophysics Data System (ADS)
Tachikawa, Hiroto; Kawabata, Hiroshi
2016-06-01
Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1-4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR-(Bz) n (n = 1-4) showed that the aryl radical binds to the carbon atom of GR, and a C-C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol-1. The electronic states of GR-(Bz) n were examined on the basis of theoretical results.
Electronic states of aryl radical functionalized graphenes: Density functional theory study
NASA Astrophysics Data System (ADS)
Tachikawa, Hiroto; Kawabata, Hiroshi
2016-06-01
Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1–4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR–(Bz) n (n = 1–4) showed that the aryl radical binds to the carbon atom of GR, and a C–C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol‑1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol‑1. The electronic states of GR–(Bz) n were examined on the basis of theoretical results.
Fine, Leon G
2003-01-01
Charles Edward Isaacs (1811-1860), an anatomist working in New York, undertook a series of studies which attempted to define the microscopic structure of the nephrons in a variety of species. Given that he published his findings 15 years after William Bowman's seminal paper on the subject, he was able to add only a few of the finer details to the picture. He observed the continuity of the epithelium of the glomerular capsule with that of the proximal tubule and he demonstrated that the glomerular tuft is covered by a layer of epithelial cells. In a series of studies on human renal function he erroneously concluded that the glomerulus must have an excretory function in addition to its filtration function and that diuretics act primarily on the glomerlus. The latter conclusion was based upon observations of substances not currently categorized as being diuretic agents. The absence of a major conceptual advance in the writings of Isaacs probably accounts for that fact that his contribution has been largely forgotten.
Element orbitals for Kohn-Sham density functional theory
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.
McKechnie, Scott; Booth, George H.; Cohen, Aron J.; Cole, Jacqueline M.
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.
McKechnie, Scott; Booth, George H; Cohen, Aron J; Cole, Jacqueline M
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.
Standardized Pearson type 3 density function area tables
NASA Technical Reports Server (NTRS)
Cohen, A. C.; Helm, F. R.; Sugg, M.
1971-01-01
Tables constituting extension of similar tables published in 1936 are presented in report form. Single and triple parameter gamma functions are discussed. Report tables should interest persons concerned with development and use of numerical analysis and evaluation methods.
Krykunov, Mykhaylo; Seth, Mike; Ziegler, Tom
2014-05-14
We have applied the relaxed and self-consistent extension of constricted variational density functional theory (RSCF-CV-DFT) for the calculation of the lowest charge transfer transitions in the molecular complex X-TCNE between X = benzene and TCNE = tetracyanoethylene. Use was made of functionals with a fixed fraction (α) of Hartree-Fock exchange ranging from α = 0 to α = 0.5 as well as functionals with a long range correction (LC) that introduces Hartree-Fock exchange for longer inter-electronic distances. A detailed comparison and analysis is given for each functional between the performance of RSCF-CV-DFT and adiabatic time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation. It is shown that in this particular case, all functionals afford the same reasonable agreement with experiment for RSCF-CV-DFT whereas only the LC-functionals afford a fair agreement with experiment using TDDFT. We have in addition calculated the CT transition energy for X-TCNE with X = toluene, o-xylene, and naphthalene employing the same functionals as for X = benzene. It is shown that the calculated charge transfer excitation energies are in as good agreement with experiment as those obtained from highly optimized LC-functionals using adiabatic TDDFT. We finally discuss the relation between the optimization of length separation parameters and orbital relaxation in the RSCF-CV-DFT scheme.
Density Functional Theory (dft) Simulations of Shocked Liquid Xenon
NASA Astrophysics Data System (ADS)
Mattsson, Thomas R.; Magyar, Rudolph J.
2009-12-01
Xenon is not only a technologically important element used in laser technologies and jet propulsion, but it is also one of the most accessible materials in which to study the metal-insulator transition with increasing pressure. Because of its closed shell electronic configuration, xenon is often assumed to be chemically inert, interacting almost entirely through the van der Waals interaction, and at liquid density, is typically modeled well using Leonard-Jones potentials. However, such modeling has a limited range of validity as xenon is known to form compounds under normal conditions and likely exhibits considerably more chemistry at higher densities when hybridization of occupied orbitals becomes significant. We present DFT-MD simulations of shocked liquid xenon with the goal of developing an improved equation of state. The calculated Hugoniot to 2 MPa compares well with available experimental shock data. Sandia is a mul-tiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Density Functional Theory (DFT) Simulations of Shocked Liquid Xenon
NASA Astrophysics Data System (ADS)
Mattsson, Thomas R.; Magyar, Rudolph J.
2009-06-01
Xenon is not only a technologically important element used in laser technologies and jet propulsion, but it is also one of the most accessible materials in which to study the metal-insulator transition with increasing pressure. Because of its closed shell electronic configuration, Xenon is often assumed to be chemically inert, interacting almost entirely through the van der Waals interaction, and at liquid density, is typically modeled well using Leonard-Jones potentials. However, such modeling has a limited range of validity as Xenon is known to form compounds at normal conditions and likely exhibits considerably more chemistry at higher densities when hybridization of occupied orbitals becomes significant. In this talk, we present DFT-MD simulations of shocked liquid Xenon with the goal of developing an improved equation of state. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
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.
Solovyeva, Alisa; Pavanello, Michele; Neugebauer, Johannes
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.
From dilute matter to the equilibrium point in the energy-density-functional theory
NASA Astrophysics Data System (ADS)
Yang, C. J.; Grasso, M.; Lacroix, D.
2016-09-01
Due to the large value of the scattering length in nuclear systems, standard density-functional theories based on effective interactions usually fail to reproduce the nuclear Fermi-liquid behavior both at very low densities and close to equilibrium. Guided on one side by the success of the Skyrme density functional and, on the other side, by resummation techniques used in effective field theories for systems with large scattering lengths, a new energy-density functional is proposed. This functional, adjusted on microscopic calculations, reproduces the nuclear equations of state of neutron and symmetric matter at various densities. Furthermore, it provides reasonable saturation properties as well as an appropriate density dependence for the symmetry energy.
A Variational Framework for Spectral Approximations of Kohn-Sham Density Functional Theory
NASA Astrophysics Data System (ADS)
Wang, Xin-Cindy; Blesgen, Thomas; Bhattacharya, Kaushik; Ortiz, Michael
2016-08-01
We reformulate the Kohn-Sham density functional theory (KSDFT) as a nested variational problem in the one-particle density operator, the electrostatic potential and a field dual to the electron density. The corresponding functional is linear in the density operator and thus amenable to spectral representation. Based on this reformulation, we introduce a new approximation scheme, termed spectral binning, which does not require smoothing of the occupancy function and thus applies at arbitrarily low temperatures. We prove convergence of the approximate solutions with respect to spectral binning and with respect to an additional spatial discretization of the domain.
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.
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. PMID:27295451
NASA Astrophysics Data System (ADS)
Mathews, Grant J.; Meixner, Matthew; Olson, J. Pocahontas; Lan, Nguyen Q.; Dalhed, Holister E.
2013-10-01
We present an updated and improved equation of state (which we call the NDL EoS) for use in neutron-star structure and core-collapse supernova simulations. This EoS is begins with a framework originally developed by Bowers & Wilson, but there are numerous changes. Among them are: (1) a reformulation in the context of density functional theory; (2) the possibility of the formation of material with a net proton excess (Ye > 0 . 5); (3) an improved treatment of the nuclear statistical equilibrium and the transition to heavy nuclei as the density approaches nuclear matter density; (4) an improved treatment of the effects of pions in the regime above nuclear matter density including the incorporation of all the known mesonic and baryonic states at high temperature; (5) the effects of 3-body nuclear forces at high densities; and (6) the possibility of a first-order or crossover transition to a QCD chiral symmetry restoration and deconfinement phase at densities above nuclear matter density. This paper details the physics of, and constraints on, this new EoS and describes its implementation in numerical simulations. We show comparisons of this EoS with other equations of state commonly used in supernova collapse simulations. Work at the University of Notre Dame is supported by the U.S. Department of Energy under Nuclear Theory Grant DE-FG02-95-ER40934.
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.
Afanasjev, A. V.
2015-10-15
The assessment of the global performance of the state-of-the-art covariant energy density functionals and related theoretical uncertainties in the description of ground state observables has recently been performed. Based on these results, the correlations between global description of binding energies and nuclear matter properties of covariant energy density functionals have been studied in this contribution.
Harbola, Upendra; Mukamel, Shaul
2004-11-01
Electrostatic and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge-density response functions of the isolated molecules, which in turn are expanded using the collective electronic oscillator (CEO) eigenmodes of linearized time-dependent density-functional theory. Closed expressions for the intermolecular energy are derived to sixth order in charge fluctuation amplitudes.
Density functional theory with spatial-symmetry breaking and configuration mixing
NASA Astrophysics Data System (ADS)
Lesinski, Thomas
2014-04-01
This article generalizes the notion of the local density of a many-body system to introduce collective coordinates as explicit degrees of freedom. It is shown that the energy of the system can be expressed as a functional of this object. The latter can in turn be factorized as the product of the square modulus of a collective wave function and a normalized collective-coordinate-dependent density. Energy minimization translates into a set of coupled equations, i.e., a local Schrödinger equation for the collective wave function and a set of Kohn-Sham equations for optimizing the normalized density at each point in the collective space. These equations reformulate the many-body problem exactly provided one is able to determine density- and collective-wave-function-dependent terms of the collective mass and potential which play a similar role to the exchange-correlation term in electronic Kohn-Sham density functional theory.
Application of the response probability density function technique to biodynamic models.
Hershey, R L; Higgins, T H
1978-01-01
A method has been developed, which we call the "response probability density function technique," which has applications in predicting the probability of injury in a wide range of biodynamic situations. The method, which was developed in connection with sonic boom damage prediction, utilized the probability density function of the excitation force and the probability density function of the sensitivity of the material being acted upon. The method is especially simple to use when both these probability density functions are lognormal. Studies thus far have shown that the stresses from sonic booms, as well as the strengths of glass and mortars, are distributed lognormally. Some biodynamic processes also have lognormal distributions and are, therefore, amenable to modeling by this technique. In particular, this paper discusses the application of the response probability density function technique to the analysis of the thoracic response to air blast and the prediction of skull fracture from head impact. PMID:623590
Wave-function inspired density functional applied to the H2/{{\\rm{H}}}_{2}^{+} challenge
NASA Astrophysics Data System (ADS)
Zhang, Igor Ying; Rinke, Patrick; Scheffler, Matthias
2016-07-01
We start from the Bethe–Goldstone equation (BGE) to derive a simple orbital-dependent correlation functional—BGE2—which terminates the BGE expansion at the second-order, but retains the self-consistent coupling of electron-pair correlations. We demonstrate that BGE2 is size consistent and one-electron ‘self-correlation’ free. The electron-pair correlation coupling ensures the correct H2 dissociation limit and gives a finite correlation energy for any system even if it has a no energy gap. BGE2 provides a good description of both H2 and {{{H}}}2+ dissociation, which is regarded as a great challenge in density functional theory (DFT). We illustrate the behavior of BGE2 analytically by considering H2 in a minimal basis. Our analysis shows that BGE2 captures essential features of the adiabatic connection path that current state-of-the-art DFT approximations do not.
Helbig, N.; Fuks, J. I.; Verstraete, M. J.; Marques, M. A. L.; Tokatly, I. V.; Rubio, A.
2011-03-15
We present a local density approximation (LDA) for one-dimensional (1D) systems interacting via the soft-Coulomb interaction based on quantum Monte Carlo calculations. Results for the ground-state energies and ionization potentials of finite 1D systems show excellent agreement with exact calculations obtained by exploiting the mapping of an N-electron system in d dimensions onto a single electron in Nxd dimensions, properly symmetrized by the Young diagrams. We conclude that 1D LDA is of the same quality as its three-dimensional (3D) counterpart, and we infer conclusions about 3D LDA. The linear and nonlinear time-dependent responses of 1D model systems using LDA, exact exchange, and the exact solution are investigated and show very good agreement in both cases, except for the well-known problem of missing double excitations. Consequently, the 3D LDA is expected to be of good quality beyond the linear response. In addition, the 1D LDA should prove useful in modeling the interaction of atoms with strong laser fields, where this specific 1D model is often used.
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.
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.
Predicting Infrared Spectra of Nerve Agents Using Density Functional Theory
NASA Astrophysics Data System (ADS)
Zhang, Y.-P.; Wang, H.-T.; Zheng, W.-P.; Sun, C.; Bai, Y.; Guo, X.-D.; Sun, H.
2016-09-01
Vibration frequencies of four nerve agents and two simulators are calculated using B3LYP coupled with ten basis sets. To evaluate the accuracy of calculated spectra, root mean square error (RMSE) and weighted cross-correlation average (WCCA) are considered. The evaluation shows that B3LYP/6-311+g(d,p) performs best in predicting infrared spectra, and polarization functions are found to be more important than diffusion functions in spectra simulation. Moreover, B3LYP calculation underestimates frequencies related to the P atom. The WCCA metric derives 1.008 as a unique scaling factor for calculated frequencies. The results indicate that the WCCA metric can identify six agents based on calculated spectra.
Density functional theory for systems with mesoscopic inhomogeneities
NASA Astrophysics Data System (ADS)
Ciach, A.; Gozdz, W. T.
2016-06-01
We study the effects of fluctuations on the mesoscopic length scale on systems with mesoscopic inhomogeneities. Equations for the correlation function and for the average volume fraction are derived in the self-consistent Gaussian approximation. The equations are further simplified by postulating the expression for the structure factor consistent with scattering experiments for self-assembling systems. Predictions of the approximate theory are verified by a comparison with the exact results obtained earlier for the one-dimensional lattice model with first-neighbor attraction and third-neighbor repulsion. We find qualitative agreement for the correlation function, the equation of state and the dependence of the chemical potential μ on the volume fraction ζ. Our results confirm also that strong inhomogeneities in the disordered phase are found only in the case of strong repulsion. The inhomogeneities are reflected in an oscillatory decay of the correlation function with a very large correlation length, three inflection points in the μ ≤ft(\\zeta \\right) curve and a compressibility that for increasing ζ takes very large, very small and again very large values.
Time-Dependent Density Functional Theory for Extreme Environments
NASA Astrophysics Data System (ADS)
Baczewski, Andrew; Magyar, Rudolph; Shulenburger, Luke
2013-10-01
In recent years, DFT-MD has been shown to be a powerful tool for calculating the equation of state and constitutive properties of warm dense matter (WDM). These studies are validated through a number of experiments, including recently developed X-Ray Thomson Scattering (XRTS) techniques. Here, electronic temperatures and densities of WDM are accessible through x-ray scattering data, which is related to the system's dynamic structure factor (DSF)-a quantity that is accessible through DFT-MD calculations. Previous studies predict the DSF within the Born-Oppenheimer approximation, with the electronic state computed using Mermin DFT. A capability for including more general coupled electron-ion dynamics is desirable, to study both the effect on XRTS observables and the broader problem of electron-ion energy transfer in extreme WDM conditions. Progress towards such a capability will be presented, in the form of an Ehrenfest MD framework using TDDFT. Computational challenges and open theoretical questions will be discussed. 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 Security Administration under contract DE-AC04-94AL85000.
NASA Astrophysics Data System (ADS)
Liang, Wenkel; Isborn, Christine M.; Li, Xiaosong
2009-11-01
The calculation of doubly excited states is one of the major problems plaguing the modern day excited state workhorse methodology of linear response time dependent Hartree-Fock (TDHF) and density function theory (TDDFT). We have previously shown that the use of a resonantly tuned field within real-time TDHF and TDDFT is able to simultaneously excite both the α and β electrons to achieve the two-electron excited states of minimal basis H2 and HeH+ [C. M. Isborn and X. Li, J. Chem. Phys. 129, 204107 (2008)]. We now extend this method to many electron systems with the use of our Car-Parrinello density matrix search (CP-DMS) with a first-principles fictitious mass method for wave function optimization [X. Li, C. L. Moss, W. Liang, and Y. Feng, J. Chem. Phys. 130, 234115 (2009)]. Real-time TDHF/TDDFT is used during the application of the laser field perturbation, driving the electron density toward the doubly excited state. The CP-DMS method then converges the density to the nearest stationary state. We present these stationary state doubly excited state energies and properties at the HF and DFT levels for H2, HeH+, lithium hydride, ethylene, and butadiene.
A density functional theory study of the zero-field splitting in high-spin nitrenes.
Misochko, Eugenii Ya; Korchagin, Denis V; Bozhenko, Konstantin V; Chapyshev, Sergei V; Aldoshin, Sergei M
2010-08-14
This work presents a detailed evaluation of the performance of density functional theory (DFT) for the prediction of zero-field splittings (ZFSs) in high-spin nitrenes. A number of well experimentally characterized triplet mononitrenes, quartet nitrenoradicals, quintet dinitrenes, and septet trinitrenes have been considered. Several DFT-based approaches for the prediction of ZFSs have been compared. It is shown that the unrestricted Kohn-Sham and the Pederson-Khanna approaches are the most successful for the estimation of the direct spin-spin (SS) interaction and the spin-orbit coupling (SOC) parts, respectively, to the final ZFS parameters. The most accurate theoretical predictions (within 10%) are achieved by using the PBE density functional in combination with the DZ, EPR-II, and TZV basis sets. For high-spin nitrenes constituted from light atoms, the contribution of the SOC part to ZFS parameters is quite small (7%-12%). By contrast, for chlorine-substituted septet trinitrenes, the contribution of the SOC part is small only to D value but, in the case of E value, it is as large as the SS part and has opposite sign. Due to this partial cancellation of two different contributions, SS and SOC, the resulting values of E in heavy molecules are almost two times smaller than those predicted by analysis of the widely used semiempirical one-center spin-spin interaction model. The decomposition of D(SS) into n-center (n=1-4) interactions shows that the major contribution to D(SS) results from the one-center spin-spin interactions. This fact indicates that the semiempirical SS interaction model accurately predicts the ZFS parameters for all types of high-spin nitrenes with total spin S=2 and 3, if their molecules are constructed from the first-row atoms.
NASA Astrophysics Data System (ADS)
Thompson, D. R.; Gotwols, B. L.
1994-05-01
Data ranging from L to Ka band were collected from radars mounted on the Forschungsplatform Nordsee during the Synthetic Aperture Radar and X Band Ocean Nonlinearities experiment in November 1990. In this paper we examine, for each of these radars, the total amplitude probability density function (pdf) of the field backscattered from the ocean surface. These pdfs are compared with predictions from a simulation based on our time-dependent scattering model. We find that for lower incidence angles (˜20°), the agreement between the measured and computed pdfs is generally quite good. At these small incidence angles the behavior of the pdfs is determined by the local tilting of the long-wave surface. No modulation of the shortwave spectral density over the long-wave phase is needed to obtain good agreement. For larger incidence angles (˜45°) the agreement between the measured and predicted pdfs is not so good; the major discrepancy is that the tails of the predicted pdfs are somewhat too short. In this study we have attempted to account for the hydrodynamic modulation of the short-scale waves using an approximate procedure based on the assumption that the hydrodynamic modulation is due to the interaction of the short-scale waves with the orbital velocity of the long waves. With this procedure we are able to obtain agreement between the measured and computed pdfs at 45° incidence, although the strength of the hydrodynamic modulation needs to be adjusted. Our simulation procedure will be discussed in some detail. Also, we will show how our results are related to more conventional measurements of so-called modulation transfer functions and give some arguments as to why in many cases the correlation between the backscattered power and the long-wave surface velocity can be rather low.
A relativistic time-dependent density functional study of the excited states of the mercury dimer
Kullie, Ossama E-mail: ossama.kullie@unistra.fr
2014-01-14
In previous works on Zn{sub 2} and Cd{sub 2} dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s{sup 2} + 6s6p), (6s{sup 2} + 6s7s), and (6s{sup 2} + 6s7p) atomic asymptotes for the mercury dimer Hg{sub 2}. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg{sub 2} including a comparative analysis with the lighter dimers of the group 12, Cd{sub 2}, and Zn{sub 2}, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg{sub 2}.
Penta-BxNy sheet: a density functional theory study of two-dimensional material.
Li, Jiao; Fan, Xinyu; Wei, Yanpei; Chen, Gang
2016-01-01
By using density functional theory with generalized gradient approximation, we have carried out detailed investigations of two-dimensional BxNy nanomaterials in the Cairo pentagonal tiling geometry fully composed of pentagons (penta-BxNy). Only penta-BN and BN2 planar structures are dynamically stable without imaginary modes in their phonon spectra. Their stabilities have been further evaluated by formation energy analysis, first-principles molecular dynamics simulation, and mechanical stability analysis. Penta-BN2 is superior to penta-BN in structural stability. Its stability analysis against oxidization and functional group adsorption as well as its synthesizing reaction path analysis show possibilities in fabricating penta-BN2 on experiment. Furthermore, the penta-BN2 could be transferred from metallic to semiconducting by ionizing or covalently binding an electron per dinitrogen. Also, it has been found to have superior mechanical properties, such as the negative Poisson's ratio and the comparable stiffness as that of hexagonal h-BN sheet. These studies on the stabilities, electronic properties, and mechanical properties suggest penta-BN2 as an attractive material to call for further studies on both theory and experiment. PMID:27539445
NASA Astrophysics Data System (ADS)
Wang, Mengen; Zhong, Jianqiang; Boscoboinik, Jorge Anibal; Lu, Deyu
Zeolites are important industrial catalysts with porous three-dimensional structures. The catalytically active sites are located inside the pores, thus rendering them inaccessible for surface science measurements. We synthesized a two-dimensional (2D) zeolite model system, consisting of an (alumino)silicate bilayer weakly bound to a Ru (0001) surface. The 2D zeolite is suitable for surface science studies; it allows a detailed characterization of the atomic structure of the active site and interrogation of the model system during the catalytic reaction. As an initial step, we use Ar adsorption to obtain a better understanding of the atomic structure of the 2D zeolite. In addition, atomic level studies of rare gas adsorption and separation by zeolite are important for its potential application in nuclear waste sequestration. Experimental studies found that Ar atoms can be trapped inside the 2D-zeolite, raising an interesting question on whether Ar atoms are trapped inside the hexagonal prism nano-cages or at the interface between the (alumino)silicate bilayer and Ru(0001), or both. DFT calculations using van der Waals density functionals were carried out to determine the preferred Ar adsorption sites and the corresponding adsorption energies. This research used resources of the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.
Penta-BxNy sheet: a density functional theory study of two-dimensional material
NASA Astrophysics Data System (ADS)
Li, Jiao; Fan, Xinyu; Wei, Yanpei; Chen, Gang
2016-08-01
By using density functional theory with generalized gradient approximation, we have carried out detailed investigations of two-dimensional BxNy nanomaterials in the Cairo pentagonal tiling geometry fully composed of pentagons (penta-BxNy). Only penta-BN and BN2 planar structures are dynamically stable without imaginary modes in their phonon spectra. Their stabilities have been further evaluated by formation energy analysis, first-principles molecular dynamics simulation, and mechanical stability analysis. Penta-BN2 is superior to penta-BN in structural stability. Its stability analysis against oxidization and functional group adsorption as well as its synthesizing reaction path analysis show possibilities in fabricating penta-BN2 on experiment. Furthermore, the penta-BN2 could be transferred from metallic to semiconducting by ionizing or covalently binding an electron per dinitrogen. Also, it has been found to have superior mechanical properties, such as the negative Poisson’s ratio and the comparable stiffness as that of hexagonal h-BN sheet. These studies on the stabilities, electronic properties, and mechanical properties suggest penta-BN2 as an attractive material to call for further studies on both theory and experiment.
A mixed basis density functional approach for one-dimensional systems with B-splines
NASA Astrophysics Data System (ADS)
Ren, Chung-Yuan; Chang, Yia-Chung; Hsue, Chen-Shiung
2016-05-01
A mixed basis approach based on density functional theory is extended to one-dimensional (1D) systems. The basis functions here are taken to be the localized B-splines for the two finite non-periodic dimensions and the plane waves for the third periodic direction. This approach will significantly reduce the number of the basis and therefore is computationally efficient for the diagonalization of the Kohn-Sham Hamiltonian. For 1D systems, B-spline polynomials are particularly useful and efficient in two-dimensional spatial integrations involved in the calculations because of their absolute localization. Moreover, B-splines are not associated with atomic positions when the geometry structure is optimized, making the geometry optimization easy to implement. With such a basis set we can directly calculate the total energy of the isolated system instead of using the conventional supercell model with artificial vacuum regions among the replicas along the two non-periodic directions. The spurious Coulomb interaction between the charged defect and its repeated images by the supercell approach for charged systems can also be avoided. A rigorous formalism for the long-range Coulomb potential of both neutral and charged 1D systems under the mixed basis scheme will be derived. To test the present method, we apply it to study the infinite carbon-dimer chain, graphene nanoribbon, carbon nanotube and positively-charged carbon-dimer chain. The resulting electronic structures are presented and discussed in detail.
Penta-BxNy sheet: a density functional theory study of two-dimensional material
Li, Jiao; Fan, Xinyu; Wei, Yanpei; Chen, Gang
2016-01-01
By using density functional theory with generalized gradient approximation, we have carried out detailed investigations of two-dimensional BxNy nanomaterials in the Cairo pentagonal tiling geometry fully composed of pentagons (penta-BxNy). Only penta-BN and BN2 planar structures are dynamically stable without imaginary modes in their phonon spectra. Their stabilities have been further evaluated by formation energy analysis, first-principles molecular dynamics simulation, and mechanical stability analysis. Penta-BN2 is superior to penta-BN in structural stability. Its stability analysis against oxidization and functional group adsorption as well as its synthesizing reaction path analysis show possibilities in fabricating penta-BN2 on experiment. Furthermore, the penta-BN2 could be transferred from metallic to semiconducting by ionizing or covalently binding an electron per dinitrogen. Also, it has been found to have superior mechanical properties, such as the negative Poisson’s ratio and the comparable stiffness as that of hexagonal h-BN sheet. These studies on the stabilities, electronic properties, and mechanical properties suggest penta-BN2 as an attractive material to call for further studies on both theory and experiment. PMID:27539445
NASA Astrophysics Data System (ADS)
Haataja, Mikko; Gránásy, László; Löwen, Hartmut
2010-08-01
, about a half of which are related to the theoretical materials science community and the other half came from the soft-matter community. We begin by discussing papers related to PFC. Diverse subjects related to the phase-field crystal model include exciting topics such as predicting/controlling the equilibrium phase behavior [19, 18, 17] and kinetics of epitaxial island formation on nano-membranes [20]. Moreover, phase-field crystal modeling has proved to be very successful in simulating homogeneous and heterogeneous crystal nucleation and growth, and several aspects of these phenomena are discussed in this issue [18, 21]. Finally, it is shown how to incorporate additional orientational degrees of freedom within the PFC approach to model liquid crystals [22]. On the DFT side, the other papers in this special issue deal with problems associated with advanced DFT techniques and applications. The existence of a structural instability in sub-critical crystalline fluctuations in a supercooled liquid within a square-gradient theory is discussed in [23]. Fundamental measure theory for hard-body systems is improved by discussing a correction term in detail, as discussed in [24]. A mean-field-like density functional for charges is applied to the effective interaction between charged colloids obtained within a cell model [25]. The remaining articles provide fundamental insight into how to supplement DDFT-type methods with hydrodynamics [26, 27], highlight the role of the projection operator technique in deriving dynamical density functional theories [28], and demonstrate how perturbation methods can be employed to compute the properties of solid-liquid interfaces [29]. This particular collection of papers demonstrates rather convincingly the significant potential that classical density functional techniques possess in modeling complex systems built of either soft or hard matter (or combinations thereof). While the PFC approach offers a simple and appealing means to simulate
van der Waals forces in density functional theory: a review of the vdW-DF method.
Berland, Kristian; Cooper, Valentino R; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T; Hyldgaard, Per; Lundqvist, Bengt I
2015-06-01
A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.
van der Waals forces in density functional theory: a review of the vdW-DF method
Berland, Kristian; Cooper, Valentino R.; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T.; Hyldgaard, Per; Lundqvist, Bengt I.
2015-05-15
We review a density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology. The insights that led to the construction of the Rutgers–Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only formore » dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.« less
van der Waals forces in density functional theory: a review of the vdW-DF method
Berland, Kristian; Cooper, Valentino R.; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T.; Hyldgaard, Per; Lundqvist, Bengt I.
2015-05-15
We review a density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology. The insights that led to the construction of the Rutgers–Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.
Communication: Self-interaction correction with unitary invariance in density functional theory
Pederson, Mark R.; Ruzsinszky, Adrienn; Perdew, John P.
2014-03-28
Standard spin-density functionals for the exchange-correlation energy of a many-electron ground state make serious self-interaction errors which can be corrected by the Perdew-Zunger self-interaction correction (SIC). We propose a size-extensive construction of SIC orbitals which, unlike earlier constructions, makes SIC computationally efficient, and a true spin-density functional. The SIC orbitals are constructed from a unitary transformation that is explicitly dependent on the non-interacting one-particle density matrix. When this SIC is applied to the local spin-density approximation, improvements are found for the atomization energies of molecules.
CURRO,JOHN G.; HOOPER,JUSTIN B.; MCCOY,JOHN D.; PILEGGI, MORGAN T.; WEINHOLD,JEFFREY D.
1999-10-28
Simple tangent, hard site chains near a hard wall are modeled with a Density Functional (DF) theory that uses the direct correlation function, c(r), as its ''input''. Two aspects of this DF theory are focused upon: (1) the consequences of variations in c(r)'s detailed form; and (2) the correct way to introduce c(r) into the DF formalism. The most important aspect of c(r) is found to be its integrated value, {cflx c}(0). Indeed, it appears that, for fixed {cflx c}(0), all reasonable guesses of the detailed shape of c(r) result in surprisingly similar density distributions, {rho}(r). Of course, the more accurate the c(r), the better the {rho}(r). As long as the length scale introduced by c(r) is roughly the hard site diameter and as long as the solution remains liquid-like, the {rho}(r) is found to be in good agreement with simulation results. The c(r) is used in DF theory to calculate the medium-induced-potential, U{sub M}(r) from the density distribution, {rho}(r). The form of U{sub M}(r) can be chosen to be one of a number of different forms. It is found that the forms for U{sub M}(r), which yield the most accurate results for the wall problem, are also those which were suggested as accurate in previous, related studies.
Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura
2016-02-01
A correct description of electronically excited states is critical to the interpretation of visible-ultraviolet spectra, photochemical reactions, and excited-state charge-transfer processes in chemical systems. 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 and a new kind of density functional called an on-top density functional. Here, we show that MC-PDFT with a first-generation on-top density functional performs as well as CASPT2 for an organic chemistry database including valence, Rydberg, and charge-transfer excitations. The results are very encouraging for practical applications. PMID:26794241
Towards a Microscopic Reaction Description Based on Energy Density Functionals
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.
Dane, Markus; Gonis, Antonios
2016-07-05
Based on a computational procedure for determining the functional derivative with respect to the density of any antisymmetric N-particle wave function for a non-interacting system that leads to the density, we devise a test as to whether or not a wave function known to lead to a given density corresponds to a solution of a Schrödinger equation for some potential. We examine explicitly the case of non-interacting systems described by Slater determinants. Here, numerical examples for the cases of a one-dimensional square-well potential with infinite walls and the harmonic oscillator potential illustrate the formalism.
Bartel, J.; Bencheikh, K.; Meyer, J.
2008-02-15
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.
Analysis of the segmented contraction of basis functions using density matrix theory.
Custodio, Rogério; Gomes, André Severo Pereira; Sensato, Fabrício Ronil; Trevas, Júlio Murilo Dos Santos
2006-11-30
A particular formulation based on density matrix (DM) theory at the Hartree-Fock level of theory and the description of the atomic orbitals as integral transforms is introduced. This formulation leads to a continuous representation of the density matrices as functions of a generator coordinate and to the possibility of plotting either the continuous or discrete density matrices as functions of the exponents of primitive Gaussian basis functions. The analysis of these diagrams provides useful information allowing: (a) the determination of the most important primitives for a given orbital, (b) the core-valence separation, and (c) support for the development of contracted basis sets by the segmented method.
Weijtens, M E; Hart, E H; Bolhuis, R L
2000-01-01
Genetically engineered expression of tumor-specific single chain antibody chimeric receptors (ch-Rec) on human T lymphocytes endow these cells with the parental monoclonal antibody (mAb) dictated tumor specificity and may be useful for clinical immuno-genetherapy. Therefore it was of importance to assess how the densities of tumor-specific receptors and tumor associated antigens (TAA), respectively, affect primary human T lymphocyte functions in relation to target cell susceptibilities to lysis. We therefore studied the functional balance between ch-Rec densities on human T lymphocytes and TAA on tumor cells. The gene construct encoding a ch-Rec derived from (1) a renal carcinoma cell (RCC) specific mouse mAb (G250), and (2) the human signal transducing Fc(epsilon)RI gamma-chain was used. To obtain ch-RecHIGH-POS and ch-RecLOW-POS T lymphocytes, two distinct retroviral vectors were used to introduce the gene constructs into primary human T lymphocytes. Levels of ch-Rec-redirected T lymphocyte mediated tumor cell lysis, as well as lymphokine production were determined using RCC lines as target/stimulator cells, which express either no or increasing densities of the TAA. A functional and dynamic balance between ch-Rec densities on cytotoxic T lymphocytes (CTLs) on the one hand and TAA densities on RCCs on the other, was found. In short, ch-RecHIGH-POS CTLs are triggered by TAAHIGH-POS as well as TAALOW-POS RCCs to lyse tumor cells and produce (IFN-gamma and TNF-alpha) lymphokine. In contrast, ch-RecLOW-POS T lymphocytes are only triggered for cytolysis and lymphokine production by relatively TAAHIGH-POS RCCs. In conclusion, (1) the activation of T lymphocyte responses is co-determined by the expression levels of the ch-Rec on T lymphocytes and the TAA on tumor cells and (2) at relatively high T lymphocyte ch-Rec expression levels the CTLs lyse tumor cells with a wide range of TAA densities. Gene Therapy (2000) 7, 35-42. PMID:10680014
Ensemble density variational methods with self- and ghost-interaction-corrected functionals
Pastorczak, Ewa; Pernal, Katarzyna
2014-05-14
Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.
Robust location and spread measures for nonparametric probability density function estimation.
López-Rubio, Ezequiel
2009-10-01
Robustness against outliers is a desirable property of any unsupervised learning scheme. In particular, probability density estimators benefit from incorporating this feature. A possible strategy to achieve this goal is to substitute the sample mean and the sample covariance matrix by more robust location and spread estimators. Here we use the L1-median to develop a nonparametric probability density function (PDF) estimator. We prove its most relevant properties, and we show its performance in density estimation and classification applications.
Calle-Vallejo, Federico; Martínez, José Ignacio; Rossmeisl, Jan
2011-09-14
Low-temperature fuel cells are appealing alternatives to the conventional internal combustion engines for transportation applications. However, in order for them to be commercially viable, effective, stable and low-cost electrocatalysts are needed for the Oxygen Reduction Reaction (ORR) at the cathode. In this contribution, on the basis of Density Functional Theory (DFT) calculations, we show that graphitic materials with active sites composed of 4 nitrogen atoms and transition metal atoms belonging to groups 7 to 9 in the periodic table are active towards ORR, and also towards Oxygen Evolution Reaction (OER). Spin analyses suggest that the oxidation state of those elements in the active sites should in general be +2. Moreover, our results verify that the adsorption behavior of transition metals is not intrinsic, since it can be severely altered by changes in the local geometry of the active site, the chemical nature of the nearest neighbors, and the oxidation states. Nonetheless, we find that these catalysts trend-wise behave as oxides and that their catalytic activity is limited by exactly the same universal scaling relations. PMID:21796295
Vibrational spectroscopy: Can density functional theory cope with highly electronegative atoms?
NASA Astrophysics Data System (ADS)
Petković, Milena
2010-12-01
Vibrational properties of molecules composed solely of highly electronegative atoms are studied by means of density functional methods. Performance of different combinations of exchange and correlation functionals is tested. It is demonstrated that certain functionals can successfully simulate infrared spectra of systems containing only fluorine, oxygen and nitrogen.
Introduction to Density Functional Theory: Calculations by Hand on the Helium Atom
ERIC Educational Resources Information Center
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…
Half-metallic ferromagnetism of RbSe and CsTe compounds: A density functional theory study
NASA Astrophysics Data System (ADS)
Xie, Huan-Huan; Ma, Run-Yu; Gao, Qiang; Li, Lei; Deng, Jian-Bo
2016-09-01
We investigate the electronic structures and magnetic properties of RbSe and CsTe compounds in CsCl, RS and ZB structures by using density functional theory calculation. It is shown that these two compounds exhibit half-metallic ferromagnetism with an integer magnetic moment of 1.00 μB per formula unit in all the three structures. Total energy calculations indicate the CsCl phase is more stable than the other two phases. We investigate these two compounds with CsCl structure in detail. The ferromagnetism results mainly from the spin-polarization of p states of anion Se (Te) for the two compounds.
Lykissa, Iliana; Li, Shu-Yi; Granqvist, Claes G.; Niklasson, Gunnar A.; Ramzan, Muhammad; Chakraborty, Sudip; Ahuja, Rajeev
2014-05-14
Thin films of V{sub 2}O{sub 5} were prepared by sputter deposition onto transparent and electrically conducting substrates and were found to be X-ray amorphous. Their electrochemical density of states was determined by chronopotentiometry and displayed a pronounced low-energy peak followed by an almost featureless contribution at higher energies. These results were compared with density functional theory calculations for amorphous V{sub 2}O{sub 5}. Significant similarities were found between measured data and computations; specifically, the experimental low-energy peak corresponds to a split-off part of the conduction band apparent in the computations. Furthermore, the calculations approximately reproduce the experimental band gap observed in optical measurements.
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.
Putz, Mihai V.
2009-01-01
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. PMID:20087467
Screened-exchange density functionals with broad accuracy for chemistry and solid-state physics.
Peverati, Roberto; Truhlar, Donald G
2012-12-21
We present two new exchange-correlation functionals for hybrid Kohn-Sham electronic structure calculations based on the nonseparable functional form introduced recently in the N12 and MN12-L functionals but now with the addition of screened Hartree-Fock exchange. The first functional depends on the density and the density gradient and is called N12-SX; the second functional depends on the density, the density gradient, and the kinetic energy density and is called MN12-SX. Both new functionals include a portion of the Hartree-Fock exchange at short-range, but Hartree-Fock exchange is screened at long range. The accuracies of the two new functionals are compared to those of the recent N12 and MN12-L local functionals to show the effect of adding screened exchange, are compared to the previously best available screened exchange functional, HSE06, and are compared to the best available global-hybrid generalized gradient approximation (GGA) and to a high-performance long-range-corrected meta-GGA.
Patabendige, Adjanie; Skinner, Robert A; Morgan, Louise; Abbott, N Joan
2013-07-12
The blood-brain barrier (BBB) is formed by the endothelial cells of cerebral microvessels and forms the critical interface regulating molecular flux between blood and brain. It contributes to homoeostasis of the microenvironment of the central nervous system and protection from pathogens and toxins. Key features of the BBB phenotype are presence of complex intercellular tight junctions giving a high transendothelial electrical resistance (TEER), and strongly polarised (apical:basal) localisation of transporters and receptors. In vitro BBB models have been developed from primary culture of brain endothelial cells of several mammalian species, but most require exposure to astrocytic factors to maintain the BBB phenotype. Other limitations include complicated procedures for isolation, poor yield and batch-to-batch variability. Some immortalised brain endothelial cell models have proved useful for transport studies but most lack certain BBB features and have low TEER. We have developed an in vitro BBB model using primary cultured porcine brain endothelial cells (PBECs) which is relatively simple to prepare, robust, and reliably gives high TEER (mean~800 Ω cm(2)); it also shows good functional expression of key tight junction proteins, transporters, receptors and enzymes. The model can be used either in monoculture, for studies of molecular flux including permeability screening, or in co-culture with astrocytes when certain specialised features (e.g. receptor-mediated transcytosis) need to be maximally expressed. It is also suitable for a range of studies of cell:cell interaction in normal physiology and in pathology. The method for isolating and growing the PBECs is given in detail to facilitate adoption of the model. This article is part of a Special Issue entitled Companion Paper. PMID:23603406
Degenerate ground states and nonunique potentials: Breakdown and restoration of density functionals
Capelle, K.; Ullrich, C. A.; Vignale, G.
2007-07-15
The Hohenberg-Kohn (HK) theorem is one of the most fundamental theorems of quantum mechanics, and constitutes the basis for the very successful density-functional approach to inhomogeneous interacting many-particle systems. Here we show that in formulations of density-functional theory (DFT) that employ more than one density variable, applied to systems with a degenerate ground state, there is a subtle loophole in the HK theorem, as all mappings between densities, wave functions, and potentials can break down. Two weaker theorems which we prove here, the joint-degeneracy theorem and the internal-energy theorem, restore the internal, total, and exchange-correlation energy functionals to the extent needed in applications of DFT to atoms, molecules, and solids. The joint-degeneracy theorem constrains the nature of possible degeneracies in general many-body systems.
QSAR and density functional approaches to evaluate trichothecene toxicity and detection
Technology Transfer Automated Retrieval System (TEKTRAN)
Occasionally, agricultural commodities are contaminated with molds capable of producing structurally related trichothecene metabolites at levels associated with food safety risks. A comprehensive study on 34 trichothecene mycotoxins and biosynthetic precursors was conducted using density functional ...
Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry
NASA Astrophysics Data System (ADS)
Tao, Jianmin; Mo, Yuxiang
2016-08-01
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.
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.
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. PMID:27563956
Bigelow, Robin T; Semenov, Yevgeniy R; Anson, Eric; du Lac, Sascha; Ferrucci, Luigi; Agrawal, Yuri
2016-10-01
Animal studies have demonstrated that experimentally induced vestibular ablation leads to a decrease in bone mineral density, through mechanisms mediated by the sympathetic nervous system. Loss of bone mineral density is a common and potentially morbid condition that occurs with aging, and we sought to investigate whether vestibular loss is associated with low bone mineral density in older adults. We evaluated this question in a cross-sectional analysis of data from the Baltimore Longitudinal Study of Aging (BLSA), a large, prospective cohort study managed by the National Institute on Aging (N = 389). Vestibular function was assessed with cervical vestibular evoked myogenic potentials (cVEMPs), a measure of saccular function. Bone mineral density was assessed using dual-energy X-ray absorptiometry (DEXA). In two-way t test analysis, we observed that individuals with reduced vestibular physiologic function had significantly lower bone mineral density. In adjusted multivariate linear regression analyses, we observed that older individuals with reduced vestibular physiologic function had significantly lower bone mineral density, specifically in weight-bearing hip and lower extremity bones. These results suggest that the vestibular system may contribute to bone homeostasis in older adults, notably of the weight-bearing hip bones at greatest risk of osteoporotic fracture. Further longitudinal analysis of vestibular function and bone mineral density in humans is needed to characterize this relationship and investigate the potential confounding effect of physical activity.
Extensions of time density functional theory to QED: QED-Chemistry
NASA Astrophysics Data System (ADS)
Rubio, Angel
n this talk we will review the recent advances within density-functional and many-body based schemes to describe spectroscopic properties of complex systems with special emphasis to modelling time and spatially resolved electron spectroscopies We will discuss the theoretical approaches developed in the group for the characterisation of matter out of equilibrium, the control material processes at the electronic level and tailor material properties, and master energy and information on the nanoscale to propose new devices with capabilities. We will focus on examples linked to the efficient conversion of light into electricity or chemical fuels (''artificial photosynthesis'') and the design on new nanostructured based optoelectronic devices based on inorganic nanotubes, among others. The goal is to provide a detailed, efficient, and at the same time accurate microscopic approach for the ab-initio description and control of the dynamics of decoherence and dissipation in quantum many-body systems. With the help of quantum optimal control (QOC) theory and the mastery over spectroscopy we could direct the movement of electrons, selectively trigger chemical reactions and processes, and create new materials
Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory.
Frink, Laura J Douglas; Frischknecht, Amalie L; Heroux, Michael A; Parks, Michael L; Salinger, Andrew G
2012-04-10
We describe methods to determine optimal coarse-grained models of lipid bilayers for use in fluids density functional theory (fluids-DFT) calculations. Both coarse-grained lipid architecture and optimal parametrizations of the models based on experimental measures are discussed in the context of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in water. The calculations are based on a combination of the modified-iSAFT theory for bonded systems and an accurate fundamental measures theory (FMT) for hard sphere reference fluids. We furthermore discuss a novel approach for pressure control in the fluids-DFT calculations that facilitates both partitioning studies and zero tension control for the bilayer studies. A detailed discussion of the numerical implementations for both solvers and pressure control capabilities are provided. We show that it is possible to develop a coarse-grained lipid bilayer model that is consistent with experimental properties (thickness and area per lipid) of DPPC provided that the coarse-graining is not too extreme. As a final test of the model, we find that the predicted area compressibility moduli and lateral pressure profiles of the optimized models are in reasonable agreement with prior results.
Time-odd mean fields in covariant density functional theory: Rotating systems
Afanasjev, A. V.; Abusara, H.
2010-09-15
Time-odd mean fields (nuclear magnetism) and their impact on physical observables in rotating nuclei are studied in the framework of covariant density functional theory (CDFT). It is shown that they have profound effect on the dynamic and kinematic moments of inertia. Particle number, configuration, and rotational frequency dependencies of their impact on the moments of inertia have been analyzed in a systematic way. Nuclear magnetism can also considerably modify the band crossing features such as crossing frequencies and the properties of the kinematic and dynamic moments of inertia in the band crossing region. The impact of time-odd mean fields on the moments of inertia in the regions away from band crossing only weakly depends on the relativistic mean-field parametrization, reflecting good localization of the properties of time-odd mean fields in CDFT. The moments of inertia of normal-deformed nuclei considerably deviate from the rigid-body value. On the contrary, superdeformed and hyperdeformed nuclei have the moments of inertia which are close to rigid-body value. The structure of the currents in rotating frame, their microscopic origin, and the relations to the moments of inertia have been systematically analyzed. The phenomenon of signature separation in odd-odd nuclei, induced by time-odd mean fields, has been analyzed in detail.
Qin, Wu; Li, Xin; Bian, Wen-Wen; Fan, Xiu-Juan; Qi, Jing-Yao
2010-02-01
There is increasing attention in the unique biological and medical properties of graphene, and it is expected that biomaterials incorporating graphene will be developed for the graphene-based drug delivery systems and biomedical devices. Despite the importance of biomolecules-graphene interactions, a detailed understanding of the adsorption mechanism and features of biomolecules onto the surfaces of graphene is lacking. To address this, we have performed density functional theory (DFT) and molecular dynamics (MD) methods exploring the adsorption geometries, adsorption energies, electronic band structures, adsorption isotherms, and adsorption dynamics of l-leucine (model biomolecule)/graphene composite system. DFT calculations confirmed the energetic stability of adsorption model and revealed that electronic structure of graphene can be controlled by the adsorption direction of l-leucine. MD simulations further investigate the potential energy and van der Waals energy for the interaction processes of l-leucine/graphene system at different temperatures and pressures. We find that the van der Waals interaction between the l-leucine and the graphene play a dominant role in the adsorption process under a certain range of temperature and pressure, and the l-leucine molecule could be adsorbed onto graphene spontaneously in aqueous solution. PMID:19880174
2-Chlorophenol adsorption on Cu(1 0 0): First-principles density functional study
NASA Astrophysics Data System (ADS)
Altarawneh, Mohammednoor; Radny, Marian W.; Smith, Phillip V.; Mackie, John C.; Kennedy, Eric M.; Dlugogorski, Bogdan Z.
2008-04-01
Interactions between a 2-chlorophenol molecule and the Cu(1 0 0) surface have been analyzed using a first-principles density functional theory (DFT) plane-wave method as the first step in gaining a detailed understanding at the molecular level of the copper catalyzed formation of PCDD/F's (dioxin compounds). While the 2-chlorophenol molecule is found to be only very weakly bound to the Cu(1 0 0) surface in a number of vertical and flat-lying configurations, its dissociation into either 2-hydroxyl-phenyl (C 6H 4OH) or benzyne (C 6H 4) results in chemisorption on the surface. The dissociative reaction (2-chlorophenol + Cu surface → 2-chlorophenoxy + H-Cu surface), which is an initial and key step in the catalytic process, is also found to be exothermic on two considered sites. The 2-chlorophenoxy radical on the Cu(1 0 0) surface transforms into a mono chloro-phenolate and is more stable than the gas-phase species by about 1.74 eV. The most stable configurations occur when the benzyne moiety, hydroxyl group and chlorine atom are all separately chemisorbed on the surface with an overall stability of 0.97 eV.
Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics.
Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel
2009-10-21
The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies. PMID:20568869