Propositional idea density in older men's written language: findings from the HIMS study using computerised analysis.

PubMed

Spencer, Elizabeth; Ferguson, Alison; Craig, Hugh; Colyvas, Kim; Hankey, Graeme J; Flicker, Leon

2015-02-01

Decline in linguistic function has been associated with decline in cognitive function in previous research. This research investigated the informativeness of written language samples of Australian men from the Health in Men's Study (HIMS) aged from 76 to 93 years using the Computerised Propositional Idea Density Rater (CPIDR 5.1). In total, 60,255 words in 1147 comments were analysed using a linear-mixed model for statistical analysis. Results indicated no relationship with education level (p = 0.79). Participants for whom English was not their first learnt language showed Propositional Idea Density (PD) scores slightly lower (0.018 per 1 word). Mean PD per 1 word for those for whom English was their first language for comments below 60 words was 0.494 and above 60 words 0.526. Text length was found to have an effect (p = <0.0001). The mean PD was higher than previously reported for men and lower than previously reported for a similar cohort for Australian women.

Density-functional theory of spherical electric double layers and zeta potentials of colloidal particles in restricted-primitive-model electrolyte solutions.

PubMed

Yu, Yang-Xin; Wu, Jianzhong; Gao, Guang-Hua

2004-04-15

A density-functional theory is proposed to describe the density profiles of small ions around an isolated colloidal particle in the framework of the restricted primitive model where the small ions have uniform size and the solvent is represented by a dielectric continuum. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for the hard-sphere repulsion and a quadratic functional Taylor expansion for the electrostatic interactions. The theoretical predictions are in good agreement with the results from Monte Carlo simulations and from previous investigations using integral-equation theory for the ionic density profiles and the zeta potentials of spherical particles at a variety of solution conditions. Like the integral-equation approaches, the density-functional theory is able to capture the oscillatory density profiles of small ions and the charge inversion (overcharging) phenomena for particles with elevated charge density. In particular, our density-functional theory predicts the formation of a second counterion layer near the surface of highly charged spherical particle. Conversely, the nonlinear Poisson-Boltzmann theory and its variations are unable to represent the oscillatory behavior of small ion distributions and charge inversion. Finally, our density-functional theory predicts charge inversion even in a 1:1 electrolyte solution as long as the salt concentration is sufficiently high. (c) 2004 American Institute of Physics.

Metal-ligand delocalization and spin density in the CuCl2 and [CuCl4](2-) molecules: Some insights from wave function theory.

PubMed

Giner, Emmanuel; Angeli, Celestino

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl2 and [CuCl4](2-) systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that each valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.

Melting slope of MgO from molecular dynamics and density functional theory

NASA Astrophysics Data System (ADS)

Tangney, Paul; Scandolo, Sandro

2009-09-01

We combine density functional theory (DFT) with molecular dynamics simulations based on an accurate atomistic force field to calculate the pressure derivative of the melting temperature of magnesium oxide at ambient pressure—a quantity for which a serious disagreement between theory and experiment has existed for almost 15 years. We find reasonable agreement with previous DFT results and with a very recent experimental determination of the slope. We pay particular attention to areas of possible weakness in theoretical calculations and conclude that the long-standing discrepancy with experiment could only be explained by a dramatic failure of existing density functionals or by flaws in the original experiment.

Speed-of-light limitations in passive linear media

NASA Astrophysics Data System (ADS)

Welters, Aaron; Avniel, Yehuda; Johnson, Steven G.

2014-08-01

We prove that well-known speed-of-light restrictions on electromagnetic energy velocity can be extended to a new level of generality, encompassing even nonlocal chiral media in periodic geometries, while at the same time weakening the underlying assumptions to only passivity and linearity of the medium (either with a transparency window or with dissipation). As was also shown by other authors under more limiting assumptions, passivity alone is sufficient to guarantee causality and positivity of the energy density (with no thermodynamic assumptions). Our proof is general enough to include a very broad range of material properties, including anisotropy, bianisotropy (chirality), nonlocality, dispersion, periodicity, and even delta functions or similar generalized functions. We also show that the "dynamical energy density" used by some previous authors in dissipative media reduces to the standard Brillouin formula for dispersive energy density in a transparency window. The results in this paper are proved by exploiting deep results from linear-response theory, harmonic analysis, and functional analysis that had previously not been brought together in the context of electrodynamics.

On the derivation of selection functions from redshift survey data

NASA Technical Reports Server (NTRS)

Strauss, Michael A.; Yahil, Amos; Davis, Marc

1991-01-01

A previously unrecognized effect is described in the derivation of luminosity functions and selection functions from existing redshift survey data, due to binning of quoted magnitudes and diameters. Corrections are made for this effect in the Center for Astrophysics (CfA) and Southern Sky (SSRS) Redshift Surveys. The correction makes subtle but systematic changes in the derived density fields of the CfA survey, especially within 2000 km/s of the Local Group. The effect on the density field of the SSRS survey is negligible.

On extending Kohn-Sham density functionals to systems with fractional number of electrons.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2017-06-07

We analyze four ways of formulating the Kohn-Sham (KS) density functionals with a fractional number of electrons, through extending the constrained search space from the Kohn-Sham and the generalized Kohn-Sham (GKS) non-interacting v-representable density domain for integer systems to four different sets of densities for fractional systems. In particular, these density sets are (I) ensemble interacting N-representable densities, (II) ensemble non-interacting N-representable densities, (III) non-interacting densities by the Janak construction, and (IV) non-interacting densities whose composing orbitals satisfy the Aufbau occupation principle. By proving the equivalence of the underlying first order reduced density matrices associated with these densities, we show that sets (I), (II), and (III) are equivalent, and all reduce to the Janak construction. Moreover, for functionals with the ensemble v-representable assumption at the minimizer, (III) reduces to (IV) and thus justifies the previous use of the Aufbau protocol within the (G)KS framework in the study of the ground state of fractional electron systems, as defined in the grand canonical ensemble at zero temperature. By further analyzing the Aufbau solution for different density functional approximations (DFAs) in the (G)KS scheme, we rigorously prove that there can be one and only one fractional occupation for the Hartree Fock functional, while there can be multiple fractional occupations for general DFAs in the presence of degeneracy. This has been confirmed by numerical calculations using the local density approximation as a representative of general DFAs. This work thus clarifies important issues on density functional theory calculations for fractional electron systems.

Metabolites related to renal function, immune activation, and carbamylation are associated with muscle composition in older adults.

PubMed

Lustgarten, Michael S; Fielding, Roger A

2017-12-15

Reduced skeletal muscle density in older adults is associated with insulin resistance, decreased physical function, and an increased all-cause mortality risk. To elucidate mechanisms that may underlie the maintenance of skeletal muscle density, we conducted a secondary analysis of previously published muscle composition and serum metabolomic data in 73 older adults (average age, 78y). Multivariable-adjusted linear regression was used to examine associations between 321 metabolites with muscle composition, defined as the ratio between normal density (NDM) with low density (LDM) thigh muscle cross sectional area (NDM/LDM). Sixty metabolites were significantly (p≤0.05 and q<0.30) associated with NDM/LDM. Decreased renal function and the immune response have been previously linked with reduced muscle density, but the mechanisms underlying these connections are less clear. Metabolites that were significantly associated with muscle composition were then tested for their association with circulating markers of renal function (blood urea nitrogen, creatinine, uric acid), and with the immune response (neutrophils/lymphocytes) and activation (kynurenine/tryptophan). 43 significant NDM/LDM metabolites (including urea) were co-associated with at least 1 marker of renal function; 23 of these metabolites have been previously identified as uremic solutes. The neutrophil/lymphocyte ratio was significantly associated with NDM/LDM (β±SE: -0.3±0.1, p=0.01, q=0.04). 35 significant NDM/LDM metabolites were co-associated with immune activation. Carbamylation (defined as homocitrulline/lysine) was identified as a pathway that may link renal function and immune activation with muscle composition, as 29 significant NDM/LDM metabolites were co-associated with homocitrulline/lysine, with at least 2 markers of renal function, and with kynurenine/tryptophan. When considering that elevated urea and uremic metabolites have been linked with an increased systemic microbial burden, that antimicrobial defense can be reduced in the presence of carbamylation, and that adipocytes can promote host defense, we propose the novel hypothesis that the age-related increase in adipogenesis within muscle may be a compensatory antimicrobial response to protect against an elevated microbial burden. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative atmosphere structure experiment

NASA Technical Reports Server (NTRS)

Sommer, S.

1974-01-01

Atmospheric structure of outer planets as determined by pressure, temperature, and accelerometers is reviewed and results obtained from the PAET earth entry are given. In order to describe atmospheric structure, entry is divided into two regimes, high and low speed. Acceleration is then measured: from these measurements density is determined as a function of time. The equations of motion are integrated to determine velocity, flight path angle, and altitude as a function of time. Density is then determined as a function of altitude from the previous determinations of density and altitude as a function of time. Hydrostatic equilibrium was assumed to determine pressure as a function of altitude. Finally the equation of space applied to determine temperature as a function of altitude, if the mean molecular weight is known. The mean molecular weight is obtained independently from either the low speed experiment or from the composition experiments.

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

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

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Characterizing bonding patterns in diradicals and triradicals by density-based wave function analysis: A uniform approach

DOE PAGES

Orms, Natalie; Rehn, Dirk; Dreuw, Andreas; ...

2017-12-21

Density-based wave function analysis enables unambiguous comparisons of electronic structure computed by different methods and removes ambiguity of orbital choices. Here, we use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such asmore » polyradicals. We also show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of bonding pattern.« less

Density functional theory and an experimentally-designed energy functional of electron density.

PubMed

Miranda, David A; Bueno, Paulo R

2016-09-21

We herein demonstrate that capacitance spectroscopy (CS) experimentally allows access to the energy associated with the quantum mechanical ground state of many-electron systems. Priorly, electrochemical capacitance, C [small mu, Greek, macron] [ρ], was previously understood from conceptual and computational density functional theory (DFT) calculations. Thus, we herein propose a quantum mechanical experiment-based variational method for electron charging processes based on an experimentally-designed functional of the ground state electron density. In this methodology, the electron state density, ρ, and an energy functional of the electron density, E [small mu, Greek, macron] [ρ], can be obtained from CS data. CS allows the derivative of the electrochemical potential with respect to the electron density, (δ[small mu, Greek, macron][ρ]/δρ), to be obtained as a unique functional of the energetically minimised system, i.e., β/C [small mu, Greek, macron] [ρ], where β is a constant (associated with the size of the system) and C [small mu, Greek, macron] [ρ] is an experimentally observable quantity. Thus the ground state energy (at a given fixed external potential) can be obtained simply as E [small mu, Greek, macron] [ρ], from the experimental measurement of C [small mu, Greek, macron] [ρ]. An experimental data-set was interpreted to demonstrate the potential of this quantum mechanical experiment-based variational principle.

Exchange Energy Density Functionals that reproduce the Linear Response Function of the Free Electron Gas

NASA Astrophysics Data System (ADS)

García-Aldea, David; Alvarellos, J. E.

2009-03-01

We present several nonlocal exchange energy density functionals that reproduce the linear response function of the free electron gas. These nonlocal functionals are constructed following a similar procedure used previously for nonlocal kinetic energy density functionals by Chac'on-Alvarellos-Tarazona, Garc'ia-Gonz'alez et al., Wang-Govind-Carter and Garc'ia-Aldea-Alvarellos. The exchange response function is not known but we have used the approximate response function developed by Utsumi and Ichimaru, even we must remark that the same ansatz can be used to reproduce any other response function with the same scaling properties. We have developed two families of new nonlocal functionals: one is constructed with a mathematical structure based on the LDA approximation -- the Dirac functional for the exchange - and for the second one the structure of the second order gradient expansion approximation is took as a model. The functionals are constructed is such a way that they can be used in localized systems (using real space calculations) and in extended systems (using the momentum space, and achieving a quasilinear scaling with the system size if a constant reference electron density is defined).

Lattice density functional theory for confined Ising fluids: comparison between different functional approximations in slit pore

NASA Astrophysics Data System (ADS)

Chen, Xueqian; Feng, Wei; Liu, Honglai; Hu, Ying

2016-09-01

In this paper, Lafuente and Cuesta's cluster density functional theory (CDFT) and lattice mean field approximation (LMFA) are formulated and compared within the framework of lattice density functional theory (LDFT). As a comparison, an LDFT based on our previous work on nonrandom correction to LMFA is also developed, where local density approximation is adopted on the correction. The numerical results of density distributions of an Ising fluid confined in a slit pore obtained from Monte Carlo simulation are used to check these functional approximations. Due to rational treatment on the coupling between site-excluding entropic effect and contact-attracting enthalpic effect by CDFT with Bethe-Peierls approximation (named as BPA-CDFT for short), the improvement of BPA-CDFT beyond LMFA is checked as expected. And it is interesting that our LDFT has a comparative accuracy with BPA-CDFT. Apparent differences between the profiles such as solvation force, excess adsorption quantity and interfacial tension from LMFA and non-LMFAs are found in our calculations. We also discuss some possible theoretical extensions of BPA-CDFT.

Metal-ligand delocalization and spin density in the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} molecules: Some insights from wave function theory

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

Giner, Emmanuel, E-mail: gnrmnl@unife.it; Angeli, Celestino, E-mail: anc@unife.it

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that eachmore » valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.« less

On the feasibility of p-type Ga2O3

NASA Astrophysics Data System (ADS)

Kyrtsos, Alexandros; Matsubara, Masahiko; Bellotti, Enrico

2018-01-01

We investigate the various cation substitutional dopants in Ga2O3 for the possibility of p-type conductivity using density functional theory. Our calculations include both standard density functional theory and hybrid functional calculations. We demonstrate that all the investigated dopants result in deep acceptor levels, not able to contribute to the p-type conductivity of Ga2O3. In light of these results, we compare our findings with other wide bandgap oxides and reexamine previous experiments on zinc doping in Ga2O3.

Bluegill growth as modified by plant density: an exploration of underlying mechanisms

USGS Publications Warehouse

Savino, Jacqueline F.; Marschall, Elizabeth A.; Stein, Roy A.

1992-01-01

Bluegill (Lepomis macrochira) growth varies inconsistently with plant density. In laboratory and field experiments, we explored mechanisms underlying bluegill growth as a function of plant and invertebrate density. In the laboratory, bluegills captured more chironomids (Chironomus riparius) than damselflies (Enallagma spp. and Ischnura spp.), but energy intake per time spent searching did not differ between damselfly and chironomid treatments. From laboratory data, we described prey encounter rates as functions of plant and invertebrate density. In Clark Lake, Ohio, we created 0.05-ha mesocosms of inshore vegetation to generate macrophyte densities of 125, 270, and 385 stems/m2 of Potamogeton and Ceratophyllum and added 46-mm bluegill (1/m2). In these mesocosms, invertebrate density increased as a function of macrophyte density. Combining this function with encounter rate functions derived from laboratory data, we predicted that bluegill growth should peak at a high macrophyte density, greater than 1000 stems/m2, even though growth should change only slightly beyond 100 stems/m2. Consistent with our predictions, bluegills did not grow differentially, nor did their use of different prey taxa differ, across macrophyte densities in the field. Bluegills preferred chironomid pupae, which were relatively few in numbers but vulnerable to predation, whereas more cryptic, chironomid larvae, which were associated with vegetation but were relatively abundant, were eaten as encountered. Bluegill avoided physid snails. Contrary to previous work, vegetation did not influence growth or diet of bluegill beyond relatively low densities owing to the interaction between capture probabilities and macroinvertebrate densities.

Linear stability analysis of the Vlasov-Poisson equations in high density plasmas in the presence of crossed fields and density gradients

NASA Technical Reports Server (NTRS)

Kaup, D. J.; Hansen, P. J.; Choudhury, S. Roy; Thomas, Gary E.

1986-01-01

The equations for the single-particle orbits in a nonneutral high density plasma in the presence of inhomogeneous crossed fields are obtained. Using these orbits, the linearized Vlasov equation is solved as an expansion in the orbital radii in the presence of inhomogeneities and density gradients. A model distribution function is introduced whose cold-fluid limit is exactly the same as that used in many previous studies of the cold-fluid equations. This model function is used to reduce the linearized Vlasov-Poisson equations to a second-order ordinary differential equation for the linearized electrostatic potential whose eigenvalue is the perturbation frequency.

Comment on "Nonuniqueness of algebraic first-order density-matrix functionals"

NASA Astrophysics Data System (ADS)

Gritsenko, O. V.

2018-02-01

Wang and Knowles (WK) [Phys. Rev. A 92, 012520 (2015), 10.1103/PhysRevA.92.012520] have given a counterexample to the conventional in reduced density-matrix functional theory representation of the second-order reduced density matrix (2RDM) Γi j ,k l in the basis of the natural orbitals as a function Γi j ,k l(n ) of the orbital occupation numbers (ONs) ni. The observed nonuniqueness of Γi j ,k l for prototype systems of different symmetry has been interpreted as the inherent inability of ON functions to reproduce the 2RDM, due to the insufficient information contained in the 1RDM spectrum. In this Comment, it is argued that, rather than totally invalidating Γi j ,k l(n ) , the WK example exposes its symmetry dependence which, as well as the previously established analogous dependence in density functional theory, is demonstrated with a general formulation based on the Levy constrained search.

Simulation of Mach Probes in Non-Uniform Magnetized Plasmas: the Influence of a Background Density Gradient

NASA Astrophysics Data System (ADS)

Haakonsen, Christian Bernt; Hutchinson, Ian H.

2013-10-01

Mach probes can be used to measure transverse flow in magnetized plasmas, but what they actually measure in strongly non-uniform plasmas has not been definitively established. A fluid treatment in previous work has suggested that the diamagnetic drifts associated with background density and temperature gradients affect transverse flow measurements, but detailed computational study is required to validate and elaborate on those results; it is really a kinetic problem, since the probe deforms and introduces voids in the ion and electron distribution functions. A new code, the Plasma-Object Simulator with Iterated Trajectories (POSIT) has been developed to self-consistently compute the steady-state six-dimensional ion and electron distribution functions in the perturbed plasma. Particle trajectories are integrated backwards in time to the domain boundary, where arbitrary background distribution functions can be specified. This allows POSIT to compute the ion and electron density at each node of its unstructured mesh, update the potential based on those densities, and then iterate until convergence. POSIT is used to study the impact of a background density gradient on transverse Mach probe measurements, and the results compared to the previous fluid theory. C.B. Haakonsen was supported in part by NSF/DOE Grant No. DE-FG02-06ER54512, and in part by an SCGF award administered by ORISE under DOE Contract No. DE-AC05-06OR23100.

Internal wave energy flux from density perturbations in nonlinear stratifications

NASA Astrophysics Data System (ADS)

Lee, Frank M.; Allshouse, Michael R.; Swinney, Harry L.; Morrison, P. J.

2017-11-01

Tidal flow over the topography at the bottom of the ocean, whose density varies with depth, generates internal gravity waves that have a significant impact on the energy budget of the ocean. Thus, understanding the energy flux (J = p v) is important, but it is difficult to measure simultaneously the pressure and velocity perturbation fields, p and v . In a previous work, a Green's-function-based method was developed to calculate the instantaneous p, v , and thus J , given a density perturbation field for a constant buoyancy frequency N. Here we extend the previous analytic Green's function work to include nonuniform N profiles, namely the tanh-shaped and linear cases, because background density stratifications that occur in the ocean and some experiments are nonlinear. In addition, we present a finite-difference method for the general case where N has an arbitrary profile. Each method is validated against numerical simulations. The methods we present can be applied to measured density perturbation data by using our MATLAB graphical user interface EnergyFlux. PJM was supported by the U.S. Department of Energy Contract DE-FG05-80ET-53088. HLS and MRA were supported by ONR Grant No. N000141110701.

mBEEF-vdW: Robust fitting of error estimation density functionals

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

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less

mBEEF-vdW: Robust fitting of error estimation density functionals

DOE PAGES

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes; ...

2016-06-15

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less

Theory of time-resolved photoelectron imaging. Comparison of a density functional with a time-dependent density functional approach

NASA Astrophysics Data System (ADS)

Suzuki, Yoshi-ichi; Seideman, Tamar; Stener, Mauro

2004-01-01

Time-resolved photoelectron differential cross sections are computed within a quantum dynamical theory that combines a formally exact solution of the nuclear dynamics with density functional theory (DFT)-based approximations of the electronic dynamics. Various observables of time-resolved photoelectron imaging techniques are computed at the Kohn-Sham and at the time-dependent DFT levels. Comparison of the results serves to assess the reliability of the former method and hence its usefulness as an economic approach for time-domain photoelectron cross section calculations, that is applicable to complex polyatomic systems. Analysis of the matrix elements that contain the electronic dynamics provides insight into a previously unexplored aspect of femtosecond-resolved photoelectron imaging.

Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals.

PubMed

Viñes, Francesc; Illas, Francesc

2017-03-30

The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0.25 eV smaller than equivalent nonrelativistic all electron PBE0 calculations indicating possible sources of error in nonrelativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ∼0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ∼450 atoms using a numeric atomic-centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.

PubMed

Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M

2015-09-08

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.

Brownian systems with spatially inhomogeneous activity

NASA Astrophysics Data System (ADS)

Sharma, A.; Brader, J. M.

2017-09-01

We generalize the Green-Kubo approach, previously applied to bulk systems of spherically symmetric active particles [J. Chem. Phys. 145, 161101 (2016), 10.1063/1.4966153], to include spatially inhomogeneous activity. The method is applied to predict the spatial dependence of the average orientation per particle and the density. The average orientation is given by an integral over the self part of the Van Hove function and a simple Gaussian approximation to this quantity yields an accurate analytical expression. Taking this analytical result as input to a dynamic density functional theory approximates the spatial dependence of the density in good agreement with simulation data. All theoretical predictions are validated using Brownian dynamics simulations.

Evolution of HI from Z=5 to the present

NASA Technical Reports Server (NTRS)

Storrie-Lombardi, L. J.

2002-01-01

Studies of damped Lya systems provide us with a good measure of the evolution of the HI column density distribution function and the contribution to the comoving mass density in neutral gas out to redshifts of z = 5 . The column density distribution function at high redshift steepens for the highest column density HI absorbers, though the contribution to the comoving mass density of neutral gas remains fiat from 2 < z < 5 . Results from studies at z < 2 are finding substantial numbers of damped absorbers identified from MgII absorption, compared to previous blind surveys. These results indicate that the contribution to the comoving mass density in neutral gas may be constant from z 0 to z 5. Details of recent work in the redshift range z < 2 work is covered elsewhere in this volume (see D. Nestor). We review here recent results for the redshift range 2 < z < 5.

Cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride and assignment using solid-state density functional theory.

PubMed

Hakey, Patrick M; Allis, Damian G; Ouellette, Wayne; Korter, Timothy M

2009-04-30

The cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride from 10.0 to 100.0 cm(-1) is presented, as is the complete structural analysis and vibrational assignment of the compound using solid-state density functional theory. This cryogenic investigation reveals multiple spectral features that were not previously reported in room-temperature terahertz studies of the title compound. Modeling of the compound employed eight density functionals utilizing both solid-state and isolated-molecule methods. The results clearly indicate the necessity of solid-state simulations for the accurate assignment of solid-state THz spectra. Assignment of the observed spectral features to specific atomic motions is based on the BP density functional, which provided the best-fit solid-state simulation of the experimental spectrum. The seven experimental spectral features are the result of thirteen infrared-active vibrational modes predicted at a BP/DNP level of theory with more than 90% of the total spectral intensity associated with external crystal vibrations.

Structural, Electronic and Dynamical Properties of Curium Monopnictides: Density Functional Calculations

NASA Astrophysics Data System (ADS)

Roondhe, Basant; Upadhyay, Deepak; Som, Narayan; Pillai, Sharad B.; Shinde, Satyam; Jha, Prafulla K.

2017-03-01

The structural, electronic, dynamical and thermodynamical properties of CmX (X = N, P, As, Sb, and Bi) compounds are studied using first principles calculations within density functional theory. The Perdew-Burke-Ernzerhof spin polarized generalized gradient approximation and Perdew-Wang (PW) spin polarized local density approximation as the exchange correlational functionals are used in these calculations. There is a good agreement between the present and previously reported data. The calculated electronic density of states suggests that the curium monopnictides are metallic in nature, which is consistent with earlier studies. The significant values of magnetic moment suggest their magnetic nature. The phonon dispersion curves and phonon density of states are also calculated, which depict the dynamical stability of these compounds. There is a significant separation between the optical and acoustical phonon branches. The temperature dependence of the thermodynamical functions are also calculated and discussed. Internal energy and vibrational contribution to the Helmholtz free energy increases and decreases, respectively, with temperature. The entropy increases with temperature. The specific heat at constant volume and Debye temperature obey Debye theory. The temperature variation of the considered thermodynamical functions is in line with those of other crystalline solids.

The exact solution of the monoenergetic transport equation for critical cylinders

NASA Technical Reports Server (NTRS)

Westfall, R. M.; Metcalf, D. R.

1972-01-01

An analytic solution for the critical, monoenergetic, bare, infinite cylinder is presented. The solution is obtained by modifying a previous development based on a neutron density transform and Case's singular eigenfunction method. Numerical results for critical radii and the neutron density as a function of position are included and compared with the results of other methods.

Exact and Approximate Statistical Inference for Nonlinear Regression and the Estimating Equation Approach.

PubMed

Demidenko, Eugene

2017-09-01

The exact density distribution of the nonlinear least squares estimator in the one-parameter regression model is derived in closed form and expressed through the cumulative distribution function of the standard normal variable. Several proposals to generalize this result are discussed. The exact density is extended to the estimating equation (EE) approach and the nonlinear regression with an arbitrary number of linear parameters and one intrinsically nonlinear parameter. For a very special nonlinear regression model, the derived density coincides with the distribution of the ratio of two normally distributed random variables previously obtained by Fieller (1932), unlike other approximations previously suggested by other authors. Approximations to the density of the EE estimators are discussed in the multivariate case. Numerical complications associated with the nonlinear least squares are illustrated, such as nonexistence and/or multiple solutions, as major factors contributing to poor density approximation. The nonlinear Markov-Gauss theorem is formulated based on the near exact EE density approximation.

Superconductivity in 2D and nearly 2D: A Conserving Description

NASA Astrophysics Data System (ADS)

Deisz, John; Hess, Daryl; Serene, Joe

1998-03-01

In a previous work,(J.J. Deisz, D.W. Hess, and J.W. Serene, Phys. Rev. Lett., to appear.) we used a 2D Hubbard model with an attractive interaction to explicitly show that a superconducting state in the fluctuation exchange approximation (FEA) could be detected from self-consistent calculations of the internal energy and free energy as a function of a threaded flux. The FEA is a conserving approximation beyond mean field theory that includes the exchange of Cooper pair, density, and spin fluctuations. Here, we present extensions of our previous calculations and show a phase diagram as a function of interaction strength and density. We discuss the nature of the FEA phase transition in 2D and focus on how it changes with increasing coupling between planes.

Bulk dynamics of Brownian hard disks: Dynamical density functional theory versus experiments on two-dimensional colloidal hard spheres

NASA Astrophysics Data System (ADS)

Stopper, Daniel; Thorneywork, Alice L.; Dullens, Roel P. A.; Roth, Roland

2018-03-01

Using dynamical density functional theory (DDFT), we theoretically study Brownian self-diffusion and structural relaxation of hard disks and compare to experimental results on quasi two-dimensional colloidal hard spheres. To this end, we calculate the self-van Hove correlation function and distinct van Hove correlation function by extending a recently proposed DDFT-approach for three-dimensional systems to two dimensions. We find that the theoretical results for both self-part and distinct part of the van Hove function are in very good quantitative agreement with the experiments up to relatively high fluid packing fractions of roughly 0.60. However, at even higher densities, deviations between the experiment and the theoretical approach become clearly visible. Upon increasing packing fraction, in experiments, the short-time self-diffusive behavior is strongly affected by hydrodynamic effects and leads to a significant decrease in the respective mean-squared displacement. By contrast, and in accordance with previous simulation studies, the present DDFT, which neglects hydrodynamic effects, shows no dependence on the particle density for this quantity.

Conjugate-gradient optimization method for orbital-free density functional calculations.

PubMed

Jiang, Hong; Yang, Weitao

2004-08-01

Orbital-free density functional theory as an extension of traditional Thomas-Fermi theory has attracted a lot of interest in the past decade because of developments in both more accurate kinetic energy functionals and highly efficient numerical methodology. In this paper, we developed a conjugate-gradient method for the numerical solution of spin-dependent extended Thomas-Fermi equation by incorporating techniques previously used in Kohn-Sham calculations. The key ingredient of the method is an approximate line-search scheme and a collective treatment of two spin densities in the case of spin-dependent extended Thomas-Fermi problem. Test calculations for a quartic two-dimensional quantum dot system and a three-dimensional sodium cluster Na216 with a local pseudopotential demonstrate that the method is accurate and efficient. (c) 2004 American Institute of Physics.

mBEEF-vdW: Robust fitting of error estimation density functionals

NASA Astrophysics Data System (ADS)

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes; Jacobsen, Karsten W.; Bligaard, Thomas

2016-06-01

We propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework [J. Wellendorff et al., Phys. Rev. B 85, 235149 (2012), 10.1103/PhysRevB.85.235149; J. Wellendorff et al., J. Chem. Phys. 140, 144107 (2014), 10.1063/1.4870397]. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator over the training datasets. Using this estimator, we show that the robust loss function leads to a 10 % improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.

π-π stacking tackled with density functional theory

PubMed Central

Swart, Marcel; van der Wijst, Tushar; Fonseca Guerra, Célia

2007-01-01

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface. Figure Additivity approximation for the π-π interaction between two stacked Watson–Crick base pairs in terms of pairwise interactions between individual bases Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0239-y) contains supplementary material, which is available to authorized users. PMID:17874150

Compton profiles of NiO and TiO2 obtained from first principles GWA spectral function

NASA Astrophysics Data System (ADS)

S, M. Khidzir; M, F. M. Halid; W, A. T. Wan Abdullah

2016-06-01

In this work, we first use momentum density studies to understand strongly correlated electron behavior, which is typically seen in transition metal oxides. We observe that correlated electron behavior as seen in bulk NiO is due to the Fermi break located in the middle of overlapping spectral functions obtained from a GW (G is Green’s function and W is the screened Coulomb interaction) approximation (GWA) calculation while in the case of TiO2 we can see that the origin of the constant momentum distribution in lower momenta is due to a pile up of spectra before the Fermi energy. These observations are then used to compare our calculated Compton profiles with previous experimental studies of Fukamachi and Limandri. Our calculations for NiO are observed to follow the same trend as the experimental profile but it is seen to have a wide difference in the case of TiO2before the Fermi break. The ground state momentum densities differ significantly from the quasiparticle momentum density, thus stressing the importance of the quasiparticle wave function as the input for the study of charge density and the electron localization function. Finally we perform a calculation of the quasiparticle renormalization function, giving a quantitative description of the discontinuity of the GWA momentum density.

Bypassing the malfunction junction in warm dense matter simulations

NASA Astrophysics Data System (ADS)

Cangi, Attila; Pribram-Jones, Aurora

2015-03-01

Simulation of warm dense matter requires computational methods that capture both quantum and classical behavior efficiently under high-temperature and high-density conditions. The state-of-the-art approach to model electrons and ions under those conditions is density functional theory molecular dynamics, but this method's computational cost skyrockets as temperatures and densities increase. We propose finite-temperature potential functional theory as an in-principle-exact alternative that suffers no such drawback. In analogy to the zero-temperature theory developed previously, we derive an orbital-free free energy approximation through a coupling-constant formalism. Our density approximation and its associated free energy approximation demonstrate the method's accuracy and efficiency. A.C. has been partially supported by NSF Grant CHE-1112442. A.P.J. is supported by DOE Grant DE-FG02-97ER25308.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

PubMed

Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

2016-10-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

PubMed Central

Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

2016-01-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

Trajectory Software With Upper Atmosphere Model

NASA Technical Reports Server (NTRS)

Barrett, Charles

2012-01-01

The Trajectory Software Applications 6.0 for the Dec Alpha platform has an implementation of the Jacchia-Lineberry Upper Atmosphere Density Model used in the Mission Control Center for International Space Station support. Previous trajectory software required an upper atmosphere to support atmosphere drag calculations in the Mission Control Center. The Functional operation will differ depending on the end-use of the module. In general, the calling routine will use function-calling arguments to specify input to the processor. The atmosphere model will then compute and return atmospheric density at the time of interest.

Spectral Discrete Probability Density Function of Measured Wind Turbine Noise in the Far Field

PubMed Central

Ashtiani, Payam; Denison, Adelaide

2015-01-01

Of interest is the spectral character of wind turbine noise at typical residential set-back distances. In this paper, a spectral statistical analysis has been applied to immission measurements conducted at three locations. This method provides discrete probability density functions for the Turbine ONLY component of the measured noise. This analysis is completed for one-third octave sound levels, at integer wind speeds, and is compared to existing metrics for measuring acoustic comfort as well as previous discussions on low-frequency noise sources. PMID:25905097

The gluon density of the proton at low x from a QCD analysis of F2

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lohmander, H.; Lomas, J.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Migliori, A.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, Y.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Stolze, K.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

We present a QCD analysis of the proton structure function F2 measured by the H1 experiment at HERA, combined with data from previous fixed target experiments. The gluon density is extracted from the scaling violations of F2 in the range 2 · 10 -4 < x < 3 · 10 -2 and compared with an approximate solution of the QCD evolution equations. The gluon density is found to rise steeply with decreasing x.

Equation of state and electron localisation in fcc lithium

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

Frost, Mungo; Levitan, Abraham L.; Sun, Peihao

We present an improved equation of state for the high-pressure fcc phase of lithium with ambient temperature experimental data, extending the pressure range of previous studies to 36 GPa. Accompanying density functional theory calculations, which reproduce the experimental equation of state, show that with increasing density the phase diverges from a nearly free electron metal. At the high pressure limit of its stability fcc lithium exhibits enhanced electron density on the octahedral interstices with a high degree of localisation.

Equation of state and electron localisation in fcc lithium

DOE PAGES

Frost, Mungo; Levitan, Abraham L.; Sun, Peihao; ...

2018-02-14

We present an improved equation of state for the high-pressure fcc phase of lithium with ambient temperature experimental data, extending the pressure range of previous studies to 36 GPa. Accompanying density functional theory calculations, which reproduce the experimental equation of state, show that with increasing density the phase diverges from a nearly free electron metal. At the high pressure limit of its stability fcc lithium exhibits enhanced electron density on the octahedral interstices with a high degree of localisation.

Statistical properties of Pu 243 , and Pu 242 ( n , γ ) cross section calculation

DOE PAGES

Laplace, T. A.; Zeiser, F.; Guttormsen, M.; ...

2016-01-29

The level density and γ-ray strength function (γSF) of 243Pu have been measured in the quasicontinuum using the Oslo method. Excited states in 243Pu were populated using the 242Pu(d,p) reaction. The level density closely follows the constant-temperature level density formula for excitation energies above the pairing gap. The γSF displays a double-humped resonance at low energy as also seen in previous investigations of actinide isotopes. The structure is interpreted as the scissors resonance and has a centroid of ω SR = 2.42(5) MeV and a total strength of B SR = 10.1(15) μ 2 N, which is in excellent agreementmore » with sum-rule estimates. Lastly, the measured level density and γSF were used to calculate the 242Pu(n,γ) cross section in a neutron energy range for which there were previously no measured data.« less

Inelastic neutron scattering spectrum of cyclotrimethylenetrinitramine: a comparison with solid-state electronic structure calculations.

PubMed

Ciezak, Jennifer A; Trevino, S F

2006-04-20

Solid-state geometry optimizations and corresponding normal-mode analysis of the widely used energetic material cyclotrimethylenetrinitramine (RDX) were performed using density functional theory with both the generalized gradient approximation (BLYP and BP functionals) and the local density approximation (PWC and VWN functionals). The structural results were found to be in good agreement with experimental neutron diffraction data and previously reported calculations based on the isolated-molecule approximation. The vibrational inelastic neutron scattering (INS) spectrum of polycrystalline RDX was measured and compared with simulated INS constructed from the solid-state calculations. The vibrational frequencies calculated from the solid-state methods had average deviations of 10 cm(-1) or less, whereas previously published frequencies based on an isolated-molecule approximation had deviations of 65 cm(-1) or less, illustrating the importance of including crystalline forces. On the basis of the calculations and analysis, it was possible to assign the normal modes and symmetries, which agree well with previous assignments. Four possible "doorway modes" were found in the energy range defined by the lattice modes, which were all found to contain fundamental contributions from rotation of the nitro groups.

Application of SEAWAT to select variable-density and viscosity problems

USGS Publications Warehouse

Dausman, Alyssa M.; Langevin, Christian D.; Thorne, Danny T.; Sukop, Michael C.

2010-01-01

SEAWAT is a combined version of MODFLOW and MT3DMS, designed to simulate three-dimensional, variable-density, saturated groundwater flow. The most recent version of the SEAWAT program, SEAWAT Version 4 (or SEAWAT_V4), supports equations of state for fluid density and viscosity. In SEAWAT_V4, fluid density can be calculated as a function of one or more MT3DMS species, and optionally, fluid pressure. Fluid viscosity is calculated as a function of one or more MT3DMS species, and the program also includes additional functions for representing the dependence of fluid viscosity on temperature. This report documents testing of and experimentation with SEAWAT_V4 with six previously published problems that include various combinations of density-dependent flow due to temperature variations and/or concentration variations of one or more species. Some of the problems also include variations in viscosity that result from temperature differences in water and oil. Comparisons between the results of SEAWAT_V4 and other published results are generally consistent with one another, with minor differences considered acceptable.

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Electronic structure of the organic semiconductor Alq3 (aluminum tris-8-hydroxyquinoline) from soft x-ray spectroscopies and density functional theory calculations.

PubMed

DeMasi, A; Piper, L F J; Zhang, Y; Reid, I; Wang, S; Smith, K E; Downes, J E; Peltekis, N; McGuinness, C; Matsuura, A

2008-12-14

The element-specific electronic structure of the organic semiconductor aluminum tris-8-hydroxyquinoline (Alq(3)) has been studied using a combination of resonant x-ray emission spectroscopy, x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory (DFT) calculations. Resonant and nonresonant x-ray emission spectroscopy were used to measure directly the carbon, nitrogen and oxygen 2p partial densities of states in Alq(3), and good agreement was found with the results of DFT calculations. Furthermore, resonant x-ray emission at the carbon K-edge is shown to be able to measure the partial density of states associated with individual C sites. Finally, comparison of previous x-ray emission studies and the present data reveal the presence of clear photon-induced damage in the former.

Towards time-dependent current-density-functional theory in the non-linear regime

NASA Astrophysics Data System (ADS)

Escartín, J. M.; Vincendon, M.; Romaniello, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

2015-02-01

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Towards time-dependent current-density-functional theory in the non-linear regime.

PubMed

Escartín, J M; Vincendon, M; Romaniello, P; Dinh, P M; Reinhard, P-G; Suraud, E

2015-02-28

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.

Semilocal density functional obeying a strongly tightened bound for exchange

PubMed Central

Sun, Jianwei; Perdew, John P.; Ruzsinszky, Adrienn

2015-01-01

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb–Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic “meta-GGA made very simple” (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew–Burke–Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules. PMID:25561554

Semilocal density functional obeying a strongly tightened bound for exchange.

PubMed

Sun, Jianwei; Perdew, John P; Ruzsinszky, Adrienn

2015-01-20

Because of its useful accuracy and efficiency, density functional theory (DFT) is one of the most widely used electronic structure theories in physics, materials science, and chemistry. Only the exchange-correlation energy is unknown, and needs to be approximated in practice. Exact constraints provide useful information about this functional. The local spin-density approximation (LSDA) was the first constraint-based density functional. The Lieb-Oxford lower bound on the exchange-correlation energy for any density is another constraint that plays an important role in the development of generalized gradient approximations (GGAs) and meta-GGAs. Recently, a strongly and optimally tightened lower bound on the exchange energy was proved for one- and two-electron densities, and conjectured for all densities. In this article, we present a realistic "meta-GGA made very simple" (MGGA-MVS) for exchange that respects this optimal bound, which no previous beyond-LSDA approximation satisfies. This constraint might have been expected to worsen predicted thermochemical properties, but in fact they are improved over those of the Perdew-Burke-Ernzerhof GGA, which has nearly the same correlation part. MVS exchange is however radically different from that of other GGAs and meta-GGAs. Its exchange enhancement factor has a very strong dependence upon the orbital kinetic energy density, which permits accurate energies even with the drastically tightened bound. When this nonempirical MVS meta-GGA is hybridized with 25% of exact exchange, the resulting global hybrid gives excellent predictions for atomization energies, reaction barriers, and weak interactions of molecules.

Finite Temperature Densities via the S-Function Method with Application to Electron Screening in Plasmas

NASA Astrophysics Data System (ADS)

Watrous, Mitchell James

1997-12-01

A new approach to the Green's-function method for the calculation of equilibrium densities within the finite temperature, Kohn-Sham formulation of density functional theory is presented, which extends the method to all temperatures. The contour of integration in the complex energy plane is chosen such that the density is given by a sum of Green's function differences evaluated at the Matsubara frequencies, rather than by the calculation and summation of Kohn-Sham single-particle wave functions. The Green's functions are written in terms of their spectral representation and are calculated as the solutions of their defining differential equations. These differential equations are boundary value problems as opposed to the standard eigenvalue problems. For large values of the complex energy, the differential equations are further simplified from second to first-order by writing the Green's functions in terms of logarithmic derivatives. An asymptotic expression for the Green's functions is derived, which allows the sum over Matsubara poles to be approximated. The method is applied to the screening of nuclei by electrons in finite temperature plasmas. To demonstrate the method's utility, and to illustrate its advantages, the results of previous wave function type calculations for protons and neon nuclei are reproduced. The method is also used to formulate a new screening model for fusion reactions in the solar core, and the predicted reaction rate enhancements factors are compared with existing models.

Immigration Rates during Population Density Reduction in a Coral Reef Fish

PubMed Central

Turgeon, Katrine; Kramer, Donald L.

2016-01-01

Although the importance of density-dependent dispersal has been recognized in theory, few empirical studies have examined how immigration changes over a wide range of densities. In a replicated experiment using a novel approach allowing within-site comparison, we examined changes in immigration rate following the gradual removal of territorial damselfish from a limited area within a much larger patch of continuous habitat. In all sites, immigration occurred at intermediate densities but did not occur before the start of removals and only rarely as density approached zero. In the combined data and in 5 of 7 sites, the number of immigrants was a hump-shaped function of density. This is the first experimental evidence for hump-shaped, density-dependent immigration. This pattern may be more widespread than previously recognized because studies over more limited density ranges have identified positive density dependence at low densities and negative density dependence at high densities. Positive density dependence at low density can arise from limits to the number of potential immigrants and from behavioral preferences for settling near conspecifics. Negative density dependence at high density can arise from competition for resources, especially high quality territories. The potential for non-linear effects of local density on immigration needs to be recognized for robust predictions of conservation reserve function, harvest impacts, pest control, and the dynamics of fragmented populations. PMID:27271081

Experimental investigation of alternative transmission functions: Quantitative evidence for the importance of nonlinear transmission dynamics in host-parasite systems.

PubMed

Orlofske, Sarah A; Flaxman, Samuel M; Joseph, Maxwell B; Fenton, Andy; Melbourne, Brett A; Johnson, Pieter T J

2018-05-01

Understanding pathogen transmission is crucial for predicting and managing disease. Nonetheless, experimental comparisons of alternative functional forms of transmission remain rare, and those experiments that are conducted are often not designed to test the full range of possible forms. To differentiate among 10 candidate transmission functions, we used a novel experimental design in which we independently varied four factors-duration of exposure, numbers of parasites, numbers of hosts and parasite density-in laboratory infection experiments. We used interactions between amphibian hosts and trematode parasites as a model system and all candidate models incorporated parasite depletion. An additional manipulation involving anaesthesia addressed the effects of host behaviour on transmission form. Across all experiments, nonlinear transmission forms involving either a power law or a negative binomial function were the best-fitting models and consistently outperformed the linear density-dependent and density-independent functions. By testing previously published data for two other host-macroparasite systems, we also found support for the same nonlinear transmission forms. Although manipulations of parasite density are common in transmission studies, the comprehensive set of variables tested in our experiments revealed that variation in density alone was least likely to differentiate among competing transmission functions. Across host-pathogen systems, nonlinear functions may often more accurately represent transmission dynamics and thus provide more realistic predictions for infection. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Time-dependent density functional theory description of total photoabsorption cross sections

NASA Astrophysics Data System (ADS)

Tenorio, Bruno Nunes Cabral; Nascimento, Marco Antonio Chaer; Rocha, Alexandre Braga

2018-02-01

The time-dependent version of the density functional theory (TDDFT) has been used to calculate the total photoabsorption cross section of a number of molecules, namely, benzene, pyridine, furan, pyrrole, thiophene, phenol, naphthalene, and anthracene. The discrete electronic pseudo-spectra, obtained in a L2 basis set calculation were used in an analytic continuation procedure to obtain the photoabsorption cross sections. The ammonia molecule was chosen as a model system to compare the results obtained with TDDFT to those obtained with the linear response coupled cluster approach in order to make a link with our previous work and establish benchmarks.

Investigation of thermoelectricity in KScSn half-Heusler compound

NASA Astrophysics Data System (ADS)

Shrivastava, Deepika; Acharya, Nikita; Sanyal, Sankar P.

2018-05-01

The electronic and transport properties of KScSn half-Heusler (HH) compound have been investigated using first-principles density functional theory and semi classical Boltzmann transport theory. The electronic band structure and density of states (total and partial) show semiconducting nature of KScSn with band gap 0.48 eV which agree well with previously reported results. The transport coefficient such as electrical conductivity, Seebeck coefficient, electronic thermal conductivity and power factor as a function of chemical potential are evaluated. KScSn has high power factor for p-type doping and is a potential candidate for thermoelectric applications.

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

PubMed

Yu, Yang; Li, Chen; Yin, Bing; Li, Jian-Li; Huang, Yuan-He; Wen, Zhen-Yi; Jiang, Zhen-Yi

2013-08-07

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Multivariate Epi-splines and Evolving Function Identification Problems

DTIC Science & Technology

2015-04-15

such extrinsic information as well as observed function and subgradient values often evolve in applications, we establish conditions under which the...previous study [30] dealt with compact intervals of IR. Splines are intimately tied to optimization problems through their variational theory pioneered...approxima- tion. Motivated by applications in curve fitting, regression, probability density estimation, variogram computation, financial curve construction

The large-scale gravitational bias from the quasi-linear regime.

NASA Astrophysics Data System (ADS)

Bernardeau, F.

1996-08-01

It is known that in gravitational instability scenarios the nonlinear dynamics induces non-Gaussian features in cosmological density fields that can be investigated with perturbation theory. Here, I derive the expression of the joint moments of cosmological density fields taken at two different locations. The results are valid when the density fields are filtered with a top-hat filter window function, and when the distance between the two cells is large compared to the smoothing length. In particular I show that it is possible to get the generating function of the coefficients C_p,q_ defined by <δ^p^({vec}(x)_1_)δ^q^({vec}(x)_2_)>_c_=C_p,q_ <δ^2^({vec}(x))>^p+q-2^ <δ({vec}(x)_1_)δ({vec}(x)_2_)> where δ({vec}(x)) is the local smoothed density field. It is then possible to reconstruct the joint density probability distribution function (PDF), generalizing for two points what has been obtained previously for the one-point density PDF. I discuss the validity of the large separation approximation in an explicit numerical Monte Carlo integration of the C_2,1_ parameter as a function of |{vec}(x)_1_-{vec}(x)_2_|. A straightforward application is the calculation of the large-scale ``bias'' properties of the over-dense (or under-dense) regions. The properties and the shape of the bias function are presented in details and successfully compared with numerical results obtained in an N-body simulation with CDM initial conditions.

Density-based Energy Decomposition Analysis for Intermolecular Interactions with Variationally Determined Intermediate State Energies

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

Wu, Q.; Ayers, P.W.; Zhang, Y.

2009-10-28

The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented with the Wu-Yang algorithm [Q. Wu and W. Yang, J. Chem. Phys. 118, 2498 (2003) ]. This variational process dispenses with the Heitler-London antisymmetrization of wave functions used in most previous methods and calculates the electrostatic and Pauli repulsion energies together without any distortion of the frozen density, an important fact that enables a clean separation of these twomore » terms from the relaxation (i.e., polarization and charge transfer) terms. The new EDA also employs the constrained density functional theory approach [Q. Wu and T. Van Voorhis, Phys. Rev. A 72, 24502 (2005)] to separate out charge transfer effects. Because the charge transfer energy is based on the density flow in real space, it has a small basis set dependence. Applications of this decomposition to hydrogen bonding in the water dimer and the formamide dimer show that the frozen density energy dominates the binding in these systems, consistent with the noncovalent nature of the interactions. A more detailed examination reveals how the interplay of electrostatics and the Pauli repulsion determines the distance and angular dependence of these hydrogen bonds.« less

Effect of heroin-conditioned auditory stimuli on cerebral functional activity in rats

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

Trusk, T.C.; Stein, E.A.

1988-08-01

Cerebral functional activity was measured as changes in distribution of the free fatty acid (1-14C)octanoate in autoradiograms obtained from rats during brief presentation of a tone previously paired to infusions of heroin or saline. Rats were trained in groups of three consisting of one heroin self-administering animal and two animals receiving yoked infusions of heroin or saline. Behavioral experiments in separate groups of rats demonstrated that these training parameters imparts secondary reinforcing properties to the tone for animals self-administering heroin while the tone remains behaviorally neutral in yoked-infusion animals. The optical densities of thirty-seven brain regions were normalized to amore » relative index for comparisons between groups. Previous pairing of the tone to heroin infusions irrespective of behavior (yoked-heroin vs. yoked-saline groups) produced functional activity changes in fifteen brain areas. In addition, nineteen regional differences in octanoate labeling density were evident when comparison was made between animals previously trained to self-administer heroin to those receiving yoked-heroin infusions, while twelve differences were noted when comparisons were made between the yoked vehicle and self administration group. These functional activity changes are presumed related to the secondary reinforcing capacity of the tone acquired by association with heroin, and may identify neural substrates involved in auditory signalled conditioning of positive reinforcement to opiates.« less

Electronic Structure of the Organic Semiconductor Alq3 (aluminum tris-8-hydroxyquinoline) from Soft X-ray Spectroscopies and Density Functional Theory Calculations

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

DeMasi, A.; Piper, L; Zhang, Y

2008-01-01

The element-specific electronic structure of the organic semiconductor aluminum tris-8-hydroxyquinoline (Alq3) has been studied using a combination of resonant x-ray emission spectroscopy, x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory (DFT) calculations. Resonant and nonresonant x-ray emission spectroscopy were used to measure directly the carbon, nitrogen and oxygen 2p partial densities of states in Alq3, and good agreement was found with the results of DFT calculations. Furthermore, resonant x-ray emission at the carbon K-edge is shown to be able to measure the partial density of states associated with individual C sites. Finally, comparison of previous x-ray emission studiesmore » and the present data reveal the presence of clear photon-induced damage in the former.« less

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

Escartín, J. M.; CNRS, UMR5152, F-31062 Toulouse Cedex; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT.more » This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na{sub 2}. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.« less

Robust control algorithms for Mars aerobraking

NASA Technical Reports Server (NTRS)

Shipley, Buford W., Jr.; Ward, Donald T.

1992-01-01

Four atmospheric guidance concepts have been adapted to control an interplanetary vehicle aerobraking in the Martian atmosphere. The first two offer improvements to the Analytic Predictor Corrector (APC) to increase its robustness to density variations. The second two are variations of a new Liapunov tracking exit phase algorithm, developed to guide the vehicle along a reference trajectory. These four new controllers are tested using a six degree of freedom computer simulation to evaluate their robustness. MARSGRAM is used to develop realistic atmospheres for the study. When square wave density pulses perturb the atmosphere all four controllers are successful. The algorithms are tested against atmospheres where the inbound and outbound density functions are different. Square wave density pulses are again used, but only for the outbound leg of the trajectory. Additionally, sine waves are used to perturb the density function. The new algorithms are found to be more robust than any previously tested and a Liapunov controller is selected as the most robust control algorithm overall examined.

A Gaussian theory for fluctuations in simple liquids.

PubMed

Krüger, Matthias; Dean, David S

2017-04-07

Assuming an effective quadratic Hamiltonian, we derive an approximate, linear stochastic equation of motion for the density-fluctuations in liquids, composed of overdamped Brownian particles. From this approach, time dependent two point correlation functions (such as the intermediate scattering function) are derived. We show that this correlation function is exact at short times, for any interaction and, in particular, for arbitrary external potentials so that it applies to confined systems. Furthermore, we discuss the relation of this approach to previous ones, such as dynamical density functional theory as well as the formally exact treatment. This approach, inspired by the well known Landau-Ginzburg Hamiltonians, and the corresponding "Model B" equation of motion, may be seen as its microscopic version, containing information about the details on the particle level.

A Gaussian theory for fluctuations in simple liquids

NASA Astrophysics Data System (ADS)

Krüger, Matthias; Dean, David S.

2017-04-01

Assuming an effective quadratic Hamiltonian, we derive an approximate, linear stochastic equation of motion for the density-fluctuations in liquids, composed of overdamped Brownian particles. From this approach, time dependent two point correlation functions (such as the intermediate scattering function) are derived. We show that this correlation function is exact at short times, for any interaction and, in particular, for arbitrary external potentials so that it applies to confined systems. Furthermore, we discuss the relation of this approach to previous ones, such as dynamical density functional theory as well as the formally exact treatment. This approach, inspired by the well known Landau-Ginzburg Hamiltonians, and the corresponding "Model B" equation of motion, may be seen as its microscopic version, containing information about the details on the particle level.

Extending density functional embedding theory for covalently bonded systems.

PubMed

Yu, Kuang; Carter, Emily A

2017-12-19

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

The trust-region self-consistent field method in Kohn-Sham density-functional theory.

PubMed

Thøgersen, Lea; Olsen, Jeppe; Köhn, Andreas; Jørgensen, Poul; Sałek, Paweł; Helgaker, Trygve

2005-08-15

The trust-region self-consistent field (TRSCF) method is extended to the optimization of the Kohn-Sham energy. In the TRSCF method, both the Roothaan-Hall step and the density-subspace minimization step are replaced by trust-region optimizations of local approximations to the Kohn-Sham energy, leading to a controlled, monotonic convergence towards the optimized energy. Previously the TRSCF method has been developed for optimization of the Hartree-Fock energy, which is a simple quadratic function in the density matrix. However, since the Kohn-Sham energy is a nonquadratic function of the density matrix, the local energy functions must be generalized for use with the Kohn-Sham model. Such a generalization, which contains the Hartree-Fock model as a special case, is presented here. For comparison, a rederivation of the popular direct inversion in the iterative subspace (DIIS) algorithm is performed, demonstrating that the DIIS method may be viewed as a quasi-Newton method, explaining its fast local convergence. In the global region the convergence behavior of DIIS is less predictable. The related energy DIIS technique is also discussed and shown to be inappropriate for the optimization of the Kohn-Sham energy.

Statistical properties of swarms of self-propelled particles with repulsions across the order-disorder transition

NASA Astrophysics Data System (ADS)

Romenskyy, Maksym; Lobaskin, Vladimir

2013-03-01

We study dynamic self-organisation and order-disorder transitions in a two-dimensional system of self-propelled particles. Our model is a variation of the Vicsek model, where particles align the motion to their neighbours but repel each other at short distances. We use computer simulations to measure the orientational order parameter for particle velocities as a function of intensity of internal noise or particle density. We show that in addition to the transition to an ordered state on increasing the particle density, as reported previously, there exists a transition into a disordered phase at the higher densities, which can be attributed to the destructive action of the repulsions. We demonstrate that the transition into the ordered phase is accompanied by the onset of algebraic behaviour of the two-point velocity correlation function and by a non-monotonous variation of the velocity relaxation time. The critical exponent for the decay of the velocity correlation function in the ordered phase depends on particle concentration at low densities but assumes a universal value in more dense systems.

Density functional theory study of structural, electronic, and thermal properties of Pt, Pd, Rh, Ir, Os and PtPd X (X = Ir, Os, and Rh) alloys

NASA Astrophysics Data System (ADS)

Shabbir, Ahmed; Muhammad, Zafar; M, Shakil; M, A. Choudhary

2016-03-01

The structural, electronic, mechanical, and thermal properties of Pt, Pd, Rh, Ir, Os metals and their alloys PtPdX (X = Ir, Os and Rh) are studied systematically using ab initio density functional theory. The groundstate properties such as lattice constant and bulk modulus are calculated to find the equilibrium atomic position for stable alloys. The electronic band structure and density of states are calculated to study the electronic behavior of metals on making their alloys. The electronic properties substantiate the metallic behavior for all studied materials. The firstprinciples density functional perturbation theory as implemented in quasi-harmonic approximation is used for the calculations of thermal properties. We have calculated the thermal properties such as the Debye temperature, vibrational energy, entropy and constant-volume specific heat. The calculated properties are compared with the previously reported experimental and theoretical data for metals and are found to be in good agreement. Calculated results for alloys could not be compared because there is no data available in the literature with such alloy composition.

Dynamical density functional theory for arbitrary-shape colloidal fluids including inertia and hydrodynamic interactions

NASA Astrophysics Data System (ADS)

Duran-Olivencia, Miguel A.; Goddard, Ben; Kalliadasis, Serafim

2015-11-01

Over the last few decades the classical density-functional theory (DFT) and its dynamic extensions (DDFTs) have become a remarkably powerful tool in the study of colloidal fluids. Recently there has been extensive research to generalise all previous DDFTs finally yielding a general DDFT equation (for spherical particles) which takes into account both inertia and hydrodynamic interactions (HI) which strongly influence non-equilibrium properties. The present work will be devoted to a further generalisation of such a framework to systems of anisotropic particles. To this end, the kinetic equation for the Brownian particle distribution function is derived starting from the Liouville equation and making use of Zwanzig's projection-operator techniques. By averaging over all but one particle, a DDFT equation is finally obtained with some similarities to that for spherical colloids. However, there is now an inevitable translational-rotational coupling which affects the diffusivity of asymmetric particles. Lastly, in the overdamped (high friction) limit the theory is notably simplified leading to a DDFT equation which agrees with previous derivations. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

How Well Can Modern Density Functionals Predict Internuclear Distances at Transition States?

PubMed

Xu, Xuefei; Alecu, I M; Truhlar, Donald G

2011-06-14

We introduce a new database called TSG48 containing 48 transition state geometrical data (in particular, internuclear distances in transition state structures) for 16 main group reactions. The 16 reactions are the 12 reactions in the previously published DBH24 database (which includes hydrogen transfer reactions, heavy-atom transfer reactions, nucleophilic substitution reactions, and association reactions plus one unimolecular isomerization) plus four H-transfer reactions in which a hydrogen atom is abstracted by the methyl or hydroperoxyl radical from the two different positions in methanol. The data in TSG48 include data for four reactions that have previously been treated at a very high level in the literature. These data are used to test and validate methods that are affordable for the entire test suite, and the most accurate of these methods is found to be the multilevel BMC-CCSD method. The data that constitute the TSG48 database are therefore taken to consist of these very high level calculations for the four reactions where they are available and BMC-CCSD calculations for the other 12 reactions. The TSG48 database is used to assess the performance of the eight Minnesota density functionals from the M05-M08 families and 26 other high-performance and popular density functionals for locating transition state geometries. For comparison, the MP2 and QCISD wave function methods have also been tested for transition state geometries. The MC3BB and MC3MPW doubly hybrid functionals and the M08-HX and M06-2X hybrid meta-GGAs are found to have the best performance of all of the density functionals tested. M08-HX is the most highly recommended functional due to the excellent performance for all five subsets of TSG48, as well as having a lower cost when compared to doubly hybrid functionals. The mean absolute errors in transition state internuclear distances associated with breaking and forming bonds as calculated by the B2PLYP, MP2, and B3LYP methods are respectively about 2, 3, and 5 times larger than those calculated by MC3BB and M08-HX.

Universal calculational recipe for solvent-mediated potential: based on a combination of integral equation theory and density functional theory

NASA Astrophysics Data System (ADS)

Zhou, Shiqi

2004-07-01

A universal formalism, which enables calculation of solvent-mediated potential (SMP) between two equal or non-equal solute particles with any shape immersed in solvent reservior consisting of atomic particle and/or polymer chain or their mixture, is proposed by importing a density functional theory externally into OZ equation systems. Only if size asymmetry of the solvent bath components is moderate, the present formalism can calculate the SMP in any complex fluids at the present development stage of statistical mechanics, and therefore avoids all of limitations of previous approaches for SMP. Preliminary calculation indicates the reliability of the present formalism.

Estimation of the four-wave mixing noise probability-density function by the multicanonical Monte Carlo method.

PubMed

Neokosmidis, Ioannis; Kamalakis, Thomas; Chipouras, Aristides; Sphicopoulos, Thomas

2005-01-01

The performance of high-powered wavelength-division multiplexed (WDM) optical networks can be severely degraded by four-wave-mixing- (FWM-) induced distortion. The multicanonical Monte Carlo method (MCMC) is used to calculate the probability-density function (PDF) of the decision variable of a receiver, limited by FWM noise. Compared with the conventional Monte Carlo method previously used to estimate this PDF, the MCMC method is much faster and can accurately estimate smaller error probabilities. The method takes into account the correlation between the components of the FWM noise, unlike the Gaussian model, which is shown not to provide accurate results.

Time-dependent spin-density-functional-theory description of He+-He collisions

NASA Astrophysics Data System (ADS)

Baxter, Matthew; Kirchner, Tom; Engel, Eberhard

2017-09-01

Theoretical total cross-section results for all ionization and capture processes in the He+-He collision system are presented in the approximate impact energy range of 10-1000 keV/amu. Calculations were performed within the framework of time-dependent spin-density functional theory. The Krieger-Li-Iafrate approximation was used to determine an accurate exchange-correlation potential in the exchange-only limit. The results of two models, one where electron translation factors in the orbitals used to calculate the potential are ignored and another where partial electron translation factors are included, are compared with available experimental data as well as a selection of previous theoretical calculations.

Quantum molecular dynamics of warm dense iron and a five-phase equation of state

NASA Astrophysics Data System (ADS)

Sjostrom, Travis; Crockett, Scott

2018-05-01

Through quantum molecular dynamics (QMD), utilizing both Kohn-Sham (orbital-based) and orbital-free density functional theory, we calculate the equation of state of warm dense iron in the density range 7 -30 g/cm 3 and temperatures from 1 to 100 eV. A critical examination of the iron pseudopotential is made, from which we find a significant improvement at high pressure to the previous QMD calculations of Wang et al. [Phys. Rev. E 89, 023101 (2014), 10.1103/PhysRevE.89.023101]. Our results also significantly extend the ranges of density and temperature that were attempted in that prior work. We calculate the shock Hugoniot and find very good agreement with experimental results to pressures over 20 TPa. These results are then incorporated with previous studies to generate a five-phase equation of state for iron.

12-h abstinence-induced functional connectivity density changes and craving in young smokers: a resting-state study.

PubMed

Zhao, Shuzhi; Li, Yangding; Li, Min; Wang, Ruonan; Bi, Yanzhi; Zhang, Yajuan; Lu, Xiaoqi; Yu, Dahua; Yang, Likun; Yuan, Kai

2018-06-20

Studying the neural correlates of craving to smoke is of great importance to improve treatment outcomes in smoking addiction. According to previous studies, the critical roles of striatum and frontal brain regions had been revealed in addiction. However, few studies focused on the hub of brain regions in the 12 h abstinence induced craving in young smokers. Thirty-one young male smokers were enrolled in the present study. A within-subject experiment design was carried out to compare functional connectivity density between 12-h smoking abstinence and smoking satiety conditions during resting state in young adult smokers by using functional connectivity density mapping (FCDM). Then, the functional connectivity density changes during smoking abstinence versus satiety were further used to examine correlations with abstinence-induced changes in subjective craving. We found young adult smokers in abstinence state (vs satiety) had higher local functional connectivity density (lFCD) and global functional connectivity density (gFCD) in brain regions including striatal subregions (i.e., bilateral caudate and putamen), frontal regions (i.e., anterior cingulate cortex (ACC) and orbital frontal cortex (OFC)) and bilateral insula. We also found higher lFCD during smoking abstinence (vs satiety) in bilateral thalamus. Additionally, the lFCD changes of the left ACC, bilateral caudate and right OFC were positively correlated with the changes in craving induced by abstinence (i.e., abstinence minus satiety) in young adult smokers. The present findings improve the understanding of the effects of acute smoking abstinence on the hubs of brain gray matter in the abstinence-induces craving and may contribute new insights into the neural mechanism of abstinence-induced craving in young smokers in smoking addiction.

Plasma Theory and Simulation Group Annual Progress Report for 1991

DTIC Science & Technology

1991-12-31

beam formation analitically : i) the resistance of the (low-density) to the final, high-density cylindrical wall can be approximated by the regime...model is developed that predicts the ion angular distribution function in a highly collisional sheath. In a previous study2, the normal ion velocity...gets a linear dispersion relation of the form W2 = k 2 (T + Ti/m. + m,), (40) which predicts ion acoustic waves. These waves have the highest frequency

Rates of Space Weathering in Lunar Regolith Grains

NASA Technical Reports Server (NTRS)

Zhang, S.; Keller, L. P.

2012-01-01

While the processes and products of lunar space weathering are reasonably well-studied, their accumulation rates in lunar soils are poorly constrained. Previously, we showed that the thickness of solar wind irradiated rims on soil grains is a smooth function of their solar flare particle track density, whereas the thickness of vapor-deposited rims was largely independent of track density [1]. Here, we have extended these preliminary results with data on additional grains from other mature soils.

Glass polymorphism in amorphous germanium probed by first-principles computer simulations

NASA Astrophysics Data System (ADS)

Mancini, G.; Celino, M.; Iesari, F.; Di Cicco, A.

2016-01-01

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions.

The Structure and Stability of Bn(+) Clusters

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The geometries of B+n clusters for n less than 14 have been optimized using density functional theory with the B3LYP functional. The most stable structure for each cluster is planar or quasi-planar. The B3LYP fragmentation energies are calibrated using coupled cluster theory. Overall, our corrected fragmentation energies are in reasonable agreement with experiment. Our results are compared with previous theoretical results.

Electric Field Induced Spectra of H sub 2 and D sub 2

NASA Technical Reports Server (NTRS)

Boyd, William Joseph

1974-01-01

The frequencies of four Q-branch lines of H2 and five Q-branch lines of D2 were measured as a function of density, and their shifts were observed to be in the linear region. The individual slopes and extrapolated zero density frequency of each line was determined. Hydrogen was measured for polarizability using the integrated intensity of the Q1(0) and S1(1), H2 absorption line. A highly automated technique for determining the response function of the spectrometer using digitally recorded data is presented. For the Q1(0) and Q1(1) lines of H2 the halfwidths were measured as a function of electric field intensity at constant pressure, and again at several densities and compared to previously measured widths. Technical and operational details of equipment built for this experiment, and for the five-meter Littrow spectrometer used, are described. Modifications of the spectrometer optics to accept the Stark cell are discussed.

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

PubMed

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Explore the reaction mechanism of the Maillard reaction: a density functional theory study.

PubMed

Ren, Ge-Rui; Zhao, Li-Jiang; Sun, Qiang; Xie, Hu-Jun; Lei, Qun-Fang; Fang, Wen-Jun

2015-05-01

The mechanism of Maillard reaction has been investigated by means of density functional theory calculations in the gaseous phase and aqueous solution. The Maillard reaction is a cascade of consecutive and parallel reaction. In the present model system study, glucose and glycine were taken as the initial reactants. On the basis of previous experimental results, the mechanisms of Maillard reaction have been proposed, and the possibility for the formation of different compounds have been evaluated through calculating the relative energy changes for different steps of reaction under different pH conditions. Our calculations reveal that the TS3 in Amadori rearrangement reaction is the rate-determining step of Maillard reaction with the activation barriers of about 66.7 and 68.8 kcal mol(-1) in the gaseous phase and aqueous solution, respectively. The calculation results are in good agreement with previous studies and could provide insights into the reaction mechanism of Maillard reaction, since experimental evaluation of the role of intermediates in the Maillard reaction is quite complicated.

Hybrid-exchange density-functional theory study of the electronic structure of MnV2O4 : Exotic orbital ordering in the cubic structure

NASA Astrophysics Data System (ADS)

Wu, Wei

2015-05-01

The electronic structures of cubic and tetragonal MnV2O4 have been studied using hybrid-exchange density-functional theory. The computed electronic structure of the tetragonal phase shows an antiferro-orbital ordering on V sites and a ferrimagnetic ground state (the spins on V and Mn are antialigned). These results are in good agreement with the previous theoretical result obtained from the local-density approximation + U methods [S. Sarkar et al., Phys. Rev. Lett. 102, 216405 (2009), 10.1103/PhysRevLett.102.216405]. Moreover, the electronic structure, especially the projected density of states of the cubic phase, has been predicted with good agreement with the recent soft x-ray spectroscopy experiment. Similar to the tetragonal phase, the spins on V and Mn in the cubic structure favor a ferrimagnetic configuration. Most interesting is that the computed charge densities of the spin-carrying orbitals on V in the cubic phase show an exotic orbital ordering, i.e., a ferro-orbital ordering along [110] but an antiferro-orbital ordering along [1 ¯10 ] .

Stellar Populations in the Central 0.5 pc of the Galaxy. I. A New Method for Constructing Luminosity Functions and Surface-density Profiles

NASA Astrophysics Data System (ADS)

Do, T.; Lu, J. R.; Ghez, A. M.; Morris, M. R.; Yelda, S.; Martinez, G. D.; Wright, S. A.; Matthews, K.

2013-02-01

We present new high angular resolution near-infrared spectroscopic observations of the nuclear star cluster surrounding the Milky Way's central supermassive black hole. Using the integral-field spectrograph OSIRIS on Keck II behind the laser-guide-star adaptive optics system, this spectroscopic survey enables us to separate early-type (young, 4-6 Myr) and late-type (old, >1 Gyr) stars with a completeness of 50% down to K' = 15.5 mag, which corresponds to ~10 M ⊙ for the early-type stars. This work increases the radial extent of reported OSIRIS/Keck measurements by more than a factor of three from 4'' to 14'' (0.16 to 0.56 pc), along the projected disk of young stars. For our analysis, we implement a new method of completeness correction using a combination of star-planting simulations and Bayesian inference. We assign probabilities for the spectral type of every source detected in deep imaging down to K' = 15.5 mag using information from spectra, simulations, number counts, and the distribution of stars. The inferred radial surface-density profiles, Σ(R)vpropR -Γ, for the young stars and late-type giants are consistent with earlier results (Γearly = 0.93 ± 0.09, Γlate = 0.16 ± 0.07). The late-type surface-density profile is approximately flat out to the edge of the survey. While the late-type stellar luminosity function is consistent with the Galactic bulge, the completeness-corrected luminosity function of the early-type stars has significantly more young stars at faint magnitudes compared with previous surveys with similar depth. This luminosity function indicates that the corresponding mass function of the young stars is likely less top-heavy than that inferred from previous surveys.

Functional Independent Scaling Relation for ORR/OER Catalysts

DOE PAGES

Christensen, Rune; Hansen, Heine A.; Dickens, Colin F.; ...

2016-10-11

A widely used adsorption energy scaling relation between OH* and OOH* intermediates in the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), has previously been determined using density functional theory and shown to dictate a minimum thermodynamic overpotential for both reactions. Here, we show that the oxygen–oxygen bond in the OOH* intermediate is, however, not well described with the previously used class of exchange-correlation functionals. By quantifying and correcting the systematic error, an improved description of gaseous peroxide species versus experimental data and a reduction in calculational uncertainty is obtained. For adsorbates, we find that the systematic error largelymore » cancels the vdW interaction missing in the original determination of the scaling relation. An improved scaling relation, which is fully independent of the applied exchange–correlation functional, is obtained and found to differ by 0.1 eV from the original. Lastly, this largely confirms that, although obtained with a method suffering from systematic errors, the previously obtained scaling relation is applicable for predictions of catalytic activity.« less

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

NASA Astrophysics Data System (ADS)

Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

2017-12-01

We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

Receiver function and gravity constraints on crustal structure and vertical movements of the Upper Mississippi Embayment and Ozark Uplift

NASA Astrophysics Data System (ADS)

Liu, Lin; Gao, Stephen S.; Liu, Kelly H.; Mickus, Kevin

2017-06-01

The Upper Mississippi Embayment (UME), where the seismically active New Madrid Seismic Zone resides, experienced two phases of subsidence commencing in the Late Precambrian and Cretaceous, respectively. To provide new constraints on models proposed for the mechanisms responsible for the subsidence, we computed and stacked P-to-S receiver functions recorded by 49 USArray and other seismic stations located in the UME and the adjacent Ozark Uplift and modeled Bouguer gravity anomaly data. The inferred thickness, density, and Vp/Vs of the upper and lower crustal layers suggest that the UME is characterized by a mafic and high-density upper crustal layer of ˜30 km thickness, which is underlain by a higher-density lower crustal layer of up to ˜15 km. Those measurements, in the background of previously published geological observations on the subsidence and uplift history of the UME, are in agreement with the model that the Cretaceous subsidence, which was suggested to be preceded by an approximately 2 km uplift, was the consequence of the passage of a previously proposed thermal plume. The thermoelastic effects of the plume would have induced wide-spread intrusion of mafic mantle material into the weak UME crust fractured by Precambrian rifting and increased its density, resulting in renewed subsidence after the thermal source was removed. In contrast, the Ozark Uplift has crustal density, thickness, and Vp/Vs measurements that are comparable to those observed on cratonic areas, suggesting an overall normal crust without significant modification by the proposed plume, probably owing to the relatively strong and thick lithosphere.

Human self-control and the density of reinforcement

PubMed Central

Flora, Stephen R.; Pavlik, William B.

1992-01-01

Choice responding in adult humans on a discrete-trial button-pressing task was examined as a function of amount, delay, and overall density (points per unit time) of reinforcement. Reinforcement consisted of points that were exchangeable for money. In T 0 conditions, an impulsive response produced 4 points immediately and a self-control response produced 10 points after a delay of 15 s. In T 15 conditions, a constant delay of 15 s was added to both prereinforcer delays. Postreinforcer delays, which consisted of 15 s added to the end of each impulsive trial, equated trial durations regardless of choice, and was manipulated in both T 0 and T 15 conditions. In all conditions, choice was predicted directly from the relative reinforcement densities of the alternatives. Self-control was observed in all conditions except T 0 without postreinforcer delays, where the impulsive choices produced the higher reinforcement density. These results support previous studies showing that choice is a direct function of the relative reinforcement densities when conditioned (point) reinforcers are used. In contrast, where responding produces intrinsic (immediately consumable) reinforcers, immediacy of reinforcement appears to account for preference when density does not. PMID:16812652

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Characteristics of cesium iodide for use as a particle discriminator for high energy cosmic rays

NASA Technical Reports Server (NTRS)

Crannell, C. J.; Kurz, R. J.; Viehmann, W.

1973-01-01

The possible use of CsI to discriminate between high energy cosmic ray electrons and interacting protons has been investigated. The pulse-shape properties as a function of ionization density, temperature, and spectral response are presented for thallium-activated CsI and as a function of ionization density for sodium-activated CsI. The results are based on previously published data and on corroborative measurements from the present work. Experimental results on the response of CsI to electron-induced electromagnetic cascades and to interacting hadrons are described. Bibliographies of publications dealing with the properties of CsI and with pulse-shape discrimination techniques are presented.

Calculation of the dielectric properties of semiconductors

NASA Astrophysics Data System (ADS)

Engel, G. E.; Farid, Behnam

1992-12-01

We report on numerical calculations of the dynamical dielectric function in silicon, using a continued-fraction expansion of the polarizability and a recently proposed representation of the inverse dielectric function in terms of plasmonlike excitations. A number of important technical refinements to further improve the computational efficiency of the method are introduced, making the ab initio calculation of the full energy dependence of the dielectric function comparable in cost to calculation of its static value. Physical results include the observation of previously unresolved features in the random-phase approximated dielectric function and its inverse within the framework of density-functional theory in the local-density approximation, which may be accessible to experiment. We discuss the dispersion of plasmon energies in silicon along the Λ and Δ directions and find improved agreement with experiment compared to earlier calculations. We also present quantitative evidence indicating the degree of violation of the Johnson f-sum rule for the dielectric function due to the nonlocality of the one-electron potential used in the underlying band-structure calculations.

Quadratic canonical transformation theory and higher order density matrices.

PubMed

Neuscamman, Eric; Yanai, Takeshi; Chan, Garnet Kin-Lic

2009-03-28

Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT's accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H(2)O and N(2) binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.

Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

NASA Astrophysics Data System (ADS)

Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

2018-04-01

Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

Self-consistent hybrid functionals for solids: a fully-automated implementation

NASA Astrophysics Data System (ADS)

Erba, A.

2017-08-01

A fully-automated algorithm for the determination of the system-specific optimal fraction of exact exchange in self-consistent hybrid functionals of the density-functional-theory is illustrated, as implemented into the public Crystal program. The exchange fraction of this new class of functionals is self-consistently updated proportionally to the inverse of the dielectric response of the system within an iterative procedure (Skone et al 2014 Phys. Rev. B 89, 195112). Each iteration of the present scheme, in turn, implies convergence of a self-consistent-field (SCF) and a coupled-perturbed-Hartree-Fock/Kohn-Sham (CPHF/KS) procedure. The present implementation, beside improving the user-friendliness of self-consistent hybrids, exploits the unperturbed and electric-field perturbed density matrices from previous iterations as guesses for subsequent SCF and CPHF/KS iterations, which is documented to reduce the overall computational cost of the whole process by a factor of 2.

Relative binding affinity of carboxylate-, phosphonate-, and bisphosphonate-functionalized gold nanoparticles targeted to damaged bone tissue

NASA Astrophysics Data System (ADS)

Ross, Ryan D.; Cole, Lisa E.; Roeder, Ryan K.

2012-10-01

Functionalized Au NPs have received considerable recent interest for targeting and labeling cells and tissues. Damaged bone tissue can be targeted by functionalizing Au NPs with molecules exhibiting affinity for calcium. Therefore, the relative binding affinity of Au NPs surface functionalized with either carboxylate ( l-glutamic acid), phosphonate (2-aminoethylphosphonic acid), or bisphosphonate (alendronate) was investigated for targeted labeling of damaged bone tissue in vitro. Targeted labeling of damaged bone tissue was qualitatively verified by visual observation and backscattered electron microscopy, and quantitatively measured by the surface density of Au NPs using field-emission scanning electron microscopy. The surface density of functionalized Au NPs was significantly greater within damaged tissue compared to undamaged tissue for each functional group. Bisphosphonate-functionalized Au NPs exhibited a greater surface density labeling damaged tissue compared to glutamic acid- and phosphonic acid-functionalized Au NPs, which was consistent with the results of previous work comparing the binding affinity of the same functionalized Au NPs to synthetic hydroxyapatite crystals. Targeted labeling was enabled not only by the functional groups but also by the colloidal stability in solution. Functionalized Au NPs were stabilized by the presence of the functional groups, and were shown to remain well dispersed in ionic (phosphate buffered saline) and serum (fetal bovine serum) solutions for up to 1 week. Therefore, the results of this study suggest that bisphosphonate-functionalized Au NPs have potential for targeted delivery to damaged bone tissue in vitro and provide motivation for in vivo investigation.

The inner magnetosphere ion composition and local time distribution over a solar cycle

NASA Astrophysics Data System (ADS)

Kistler, L. M.; Mouikis, C. G.

2016-03-01

Using the Cluster/Composition and Distribution Function (CODIF) analyzer data set from 2001 to 2013, a full solar cycle, we determine the ion distributions for H+, He+, and O+ in the inner magnetosphere (L < 12) over the energy range 40 eV to 40 keV as a function magnetic local time, solar EUV (F10.7), and geomagnetic activity (Kp). Concentrating on L = 6-7 for comparison with previous studies at geosynchronous orbit, we determine both the average flux at 90° pitch angle and the pitch angle anisotropy as a function of energy and magnetic local time. We clearly see the minimum in the H+ spectrum that results from the competition between eastward and westward drifts. The feature is weaker in O+ and He+, leading to higher O+/H+ and He+/H+ ratios in the affected region, and also to a higher pitch angle anisotropy, both features expected from the long-term effects of charge exchange. We also determine how the nightside L = 6-7 densities and temperatures vary with geomagnetic activity (Kp) and solar EUV (F10.7). Consistent with other studies, we find that the O+ density and relative abundance increase significantly with both Kp and F10.7. He+ density increases with F10.7, but not significantly with Kp. The temperatures of all species decrease with increasing F10.7. The O+ and He+ densities increase from L = 12 to L ~ 3-4, both absolutely and relative to H+, and then drop off sharply. The results give a comprehensive view of the inner magnetosphere using a contiguous long-term data set that supports much of the earlier work from GEOS, ISEE, Active Magnetospheric Particle Tracer Explorers, and Polar from previous solar cycles.

Calculation of nuclear spin-spin coupling constants using frozen density embedding

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

Götz, Andreas W., E-mail: agoetz@sdsc.edu; Autschbach, Jochen; Visscher, Lucas, E-mail: visscher@chem.vu.nl

2014-03-14

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects inmore » the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.« less

The energy dependence of the lateral dose response functions of detectors with various densities in photon-beam dosimetry.

PubMed

Looe, Hui Khee; Harder, Dietrich; Poppe, Björn

2017-02-07

The lateral dose response function is a general characteristic of the volume effect of a detector used for photon dosimetry in a water phantom. It serves as the convolution kernel transforming the true absorbed dose to water profile, which would be produced within the undisturbed water phantom, into the detector-measured signal profile. The shape of the lateral dose response function characterizes (i) the volume averaging attributable to the detector's size and (ii) the disturbance of the secondary electron field associated with the deviation of the electron density of the detector material from the surrounding water. In previous work, the characteristic dependence of the shape of the lateral dose response function upon the electron density of the detector material was studied for 6 MV photons by Monte Carlo simulation of a wall-less voxel-sized detector (Looe et al 2015 Phys. Med. Biol. 60 6585-07). This study is here continued for 60 Co gamma rays and 15 MV photons in comparison with 6 MV photons. It is found (1) that throughout these photon spectra the shapes of the lateral dose response functions are retaining their characteristic dependence on the detector's electron density, and (2) that their energy-dependent changes are only moderate. This appears as a practical advantage because the lateral dose response function can then be treated as practically invariant across a clinical photon beam in spite of the known changes of the photon spectrum with increasing distance from the beam axis.

Joint density-functional theory and its application to systems in solution

NASA Astrophysics Data System (ADS)

Petrosyan, Sahak A.

The physics of solvation, the interaction of water with solutes, plays a central role in chemistry and biochemistry, and it is essential for the very existence of life. Despite the central importance of water and the advent of the quantum theory early in the twentieth century, the link between the fundamental laws of physics and the observable properties of water remain poorly understood to this day. The central goal of this thesis is to develop a new formalism and framework to make the study of systems (solutes or surfaces) in contact with liquid water as practical and accurate as standard electronic structure calculations without the need for explicit averaging over large ensembles of configurations of water molecules. The thesis introduces a new form of density functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment. This theory rigorously joins an electron density-functional for the electrons of a solute with a classical density-functional theory for the liquid into a single variational principle for the free energy of the combined system. Using the new form of density-functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment, the thesis then presents the first detailed study of the impact of a solvent on the surface chemistry of Cr2O3, the passivating layer of stainless steel alloys. In comparison to a vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but has a dramatic effect on the binding of hydrogen to that surface. A key ingredient of a successful joint density functional theory is a good approximate functional for describing the solvent. We explore how the simplest examples of the best known class of approximate forms for the classical density functional fail when applied directly to water. The thesis then presents a computationally efficient density-functional theory for water which overcomes this difficulty and gives reasonable agreement with molecular dynamics simulation data for the solvation of hard spheres in water and sufficient agreement with experimental data for hydration of inert gas atoms to justify its use in a joint theory with standard approximate density functionals used in electronic structure calculations. The last study in the thesis combines the previous ideas and presenting an approximate model density functional which includes a description of cavitation effects through a classical density-functional theory; a description of dielectric effects through a non-local polarizability, and a description of the coupling of the solvent to the electrons of the solute through a pseudopotential. Without any empirical fitting of parameters to solvation data, this theory predicts solvation energies at least as well as state-of-the-art quantum-chemical cavity approaches, which do employ such fitting. Although this agreement without adjustable parameters is very encouraging and shows the promise of the joint density-functional approach, the functionals which we develop here are models and do not yet include all of the microscopic physics. The thesis concludes with a description of the directions future work should take to address this weakness.

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

Vidmer, Alexandre, E-mail: alexandre@vidmer.com; Sclauzero, Gabriele; Pasquarello, Alfredo

The infrared absorption spectra of jennite, tobermorite 14 Å, anomalous tobermorite 11 Å, and normal tobermorite 11 Å are simulated within a density-functional-theory scheme. The atomic coordinates and the cell parameters are optimized resulting in structures which agree with previous studies. The vibrational frequencies and modes are obtained for each mineral. The vibrational density of states is analyzed through extensive projections on silicon tetrahedra, oxygen atoms, OH groups, and water molecules. The coupling with the electric field is achieved through the use of density functional perturbation theory, which yields Born effective charges and dielectric constants. The simulated absorption spectra reproducemore » well the experimental spectra, thereby allowing for a detailed interpretation of the spectral features in terms of the underlying vibrational modes. In the far-infrared part of the absorption spectra, the interplay between Ca and Si related vibrations leads to differences which are sensitive to the calcium/silicon ratio of the mineral.« less

Equations of state and stability of MgSiO 3 perovskite and post-perovskite phases from quantum Monte Carlo simulations

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

Lin, Yangzheng; Cohen, Ronald E.; Stackhouse, Stephen

2014-11-10

In this study, we have performed quantum Monte Carlo (QMC) simulations and density functional theory calculations to study the equations of state of MgSiO 3 perovskite (Pv, bridgmanite) and post-perovskite (PPv) up to the pressure and temperature conditions of the base of Earth's lower mantle. The ground-state energies were derived using QMC simulations and the temperature-dependent Helmholtz free energies were calculated within the quasiharmonic approximation and density functional perturbation theory. The equations of state for both phases of MgSiO 3 agree well with experiments, and better than those from generalized gradient approximation calculations. The Pv-PPv phase boundary calculated from ourmore » QMC equations of state is also consistent with experiments, and better than previous local density approximation calculations. Lastly, we discuss the implications for double crossing of the Pv-PPv boundary in the Earth.« less

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Long-term supratentorial brain structure and cognitive function following cerebellar tumour resections in childhood.

PubMed

Moberget, T; Andersson, S; Lundar, T; Due-Tønnessen, B J; Heldal, A; Endestad, T; Westlye, L T

2015-03-01

The cerebellum is connected to extensive regions of the cerebrum, and cognitive deficits following cerebellar lesions may thus be related to disrupted cerebello-cerebral connectivity. Moreover, early cerebellar lesions could affect distal brain development, effectively inducing long-term changes in brain structure and cognitive function. Here, we characterize supratentorial brain structure and cognitive function in 20 adult patients treated for cerebellar tumours in childhood (mean age at surgery: 7.1 years) and 26 matched controls. Relative to controls, patients showed reduced cognitive function and increased grey matter density in bilateral cingulum, left orbitofrontal cortex and the left hippocampus. Within the patient group, increased grey matter density in these regions was associated with decreased performance on tests of processing speed and executive function. Further, diffusion tensor imaging revealed widespread alterations in white matter microstructure in patients. While current ventricle volume (an index of previous hydrocephalus severity it patients) was associated with grey matter density and white matter microstructure in patients, this could only partially account for the observed group differences in brain structure and cognitive function. In conclusion, our results show distal effects of cerebellar lesions on cerebral integrity and wiring, likely caused by a combination of neurodegenerative processes and perturbed neurodevelopment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dielectric function and plasmons in graphene: A self-consistent-field calculation within a Markovian master equation formalism

DOE PAGES

Karimi, F.; Davoody, A. H.; Knezevic, I.

2016-05-12

We introduce a method for calculating the dielectric function of nanostructures with an arbitrary band dispersion and Bloch wave functions. The linear response of a dissipative electronic system to an external electromagnetic field is calculated by a self-consistent-field approach within a Markovian master equation formalism (SCF-MMEF) coupled with full-wave electromagnetic equations. The SCF-MMEF accurately accounts for several concurrent scattering mechanisms. The method captures interband electron-hole-pair generation, as well as the interband and intraband electron scattering with phonons and impurities. We employ the SCF-MMEF to calculate the dielectric function, complex conductivity, and loss function for supported graphene. From the loss-function maximum,more » we obtain plasmon dispersion and propagation length for different substrate types [nonpolar diamondlike carbon (DLC) and polar SiO 2 and hBN], impurity densities, carrier densities, and temperatures. Plasmons on the two polar substrates are suppressed below the highest surface phonon energy, while the spectrum is broad on the nonpolar DLC. Plasmon propagation lengths are comparable on polar and nonpolar substrates and are on the order of tens of nanometers, considerably shorter than previously reported. As a result, they improve with fewer impurities, at lower temperatures, and at higher carrier densities.« less

Reply to ``Comment on `Spin- and charge-ordering in oxygen-vacancy-ordered mixed-valence Sr4Fe4O11 ' ''

NASA Astrophysics Data System (ADS)

Ravindran, P.; Vidya, R.; Fjellvåg, H.; Kjekshus, A.

2008-04-01

Recently, using density-functional theoretical calculations, we have reported [Phys. Rev. B 74, 054422 (2006)] that formal Fe3+ ions reside at the square-pyramidal site and Fe4+ ions in the octahedral site in Sr4Fe4O11 . Based on the interpretation of experimental structural and Mössbauer data from the literature, Adler concludes that our previous first-principles results disagree with experiments on the assignment of oxidation states to Fe in the square-pyramidal and octahedral environments in Sr4Fe4O11 . From a critical examination of the structure data for Sr4Fe4O11 and related oxides with Fe in different oxidation states and theoretically simulated Mössbauer parameters (hyperfine field, isomer shift, and quadrupole splitting), here we show that information on charges residing on the different constituents cannot be directly derived either from experimental structure or Mössbauer data. From additional analyses of the chemical bonding on the basis of charge density, charge transfer, electron localization function, crystal orbital Hamilton population, Born effective charge, and partial density of states, we substantiate our previous assignment of formal Fe3+ and Fe4+ to the square-pyramidal and octahedral sites, respectively, in Sr4Fe4O11 .

Monte Carlo simulation of hard spheres near random closest packing using spherical boundary conditions

NASA Astrophysics Data System (ADS)

Tobochnik, Jan; Chapin, Phillip M.

1988-05-01

Monte Carlo simulations were performed for hard disks on the surface of an ordinary sphere and hard spheres on the surface of a four-dimensional hypersphere. Starting from the low density fluid the density was increased to obtain metastable amorphous states at densities higher than previously achieved. Above the freezing density the inverse pressure decreases linearly with density, reaching zero at packing fractions equal to 68% for hard spheres and 84% for hard disks. Using these new estimates for random closest packing and coefficients from the virial series we obtain an equation of state which fits all the data up to random closest packing. Usually, the radial distribution function showed the typical split second peak characteristic of amorphous solids and glasses. High density systems which lacked this split second peak and showed other sharp peaks were interpreted as signaling the onset of crystal nucleation.

Lung function reductions associated with motor vehicle density in chronic obstructive pulmonary disease: a cross-sectional study.

PubMed

Nitschke, Monika; Appleton, Sarah L; Li, Qiaoyu; Tucker, Graeme R; Shah, Pushan; Bi, Peng; Pisaniello, Dino L; Adams, Robert J

2016-10-24

Motor vehicle-related air pollution can potentially impair lung function. The effect of pollution in people with compromised pulmonary function such as in COPD has not been previously investigated. To examine the association of lung function with motor vehicle density in people with spirometrically determined COPD in a cross-sectional study. In 2004-06, The North West Adelaide Health Study (NWAHS), a biomedical cohort of adults assessed pre and post-bronchodilator spirometry (n = 3,103). Traffic density, obtained from the motor vehicle inventory maintained by the South Australian Environment Protection Authority, was expressed as the daily numbers of vehicles travelling within a 200 m diameter zone around participants' geocoded residences. In subjects with COPD (FEV 1 /FVC <0.7, n = 221, 7.1 %), increasing daily vehicle density was associated with statistically significant decreases in lung function parameters after adjustment for smoking and socio-economic variables. Mean (95 % CI) post-bronchodilator % predicted FEV 1 was 81 % (76-87) in the low (≤7179/day) compared with 71 % (67-75) in the high (≥15,270/day) vehicle exposure group (p < 0.05). Linear regression analysis in all subjects with COPD showed significant decrements in post-bronchodilator FEV 1 /FVC ratio and % predicted FEV 1 of 0.03 and 0.05 % respectively per daily increase in 1000 vehicles. In men with COPD (n = 150), the corresponding reductions were 0.03 and 0.06 %. Smaller, non-significant decrements were seen in females. No difference was seen in those without COPD. Vehicle traffic density was associated with significant reductions in lung function in people with COPD. Urban planning should consider the health impacts for those with pre-existing respiratory conditions.

Effects of Varied Housing Density on a Hybrid Mouse Strain Followed for 20 Months

PubMed Central

Currer, Joanne M.

2016-01-01

To evaluate the effect of increased housing density in a hybrid mouse strain, we evaluated a panel of physiological and behavioral traits in animals that were housed in groups of 3, 5, 8, or 12, using cages that provide 78.1 in2 of floor space. Such groupings resulted in cage densities that ranged from half to almost twice the density recommended by the Guide for the Care and Use of Laboratory Animals. While previous studies have investigated physiological effects of increased housing density using inbred mouse strains, including C57BL/6J and 129S1/SvImJ, this study tested an F1 hybrid population of C57BL/6J x 129S1/SvImJ for changes resulting from either decreased or increased housing density. Mice were followed until they were 20 months old, a substantially longer duration than has been used in previous density studies. We evaluated mortality, growth, home cage behavior, blood pressure, body composition, clinical plasma chemistries, immune function, and organ weights (heart, kidney, adrenal glands, and testes) as endpoints of chronic stress that may arise from sub-optimal housing conditions. Few statistically different parameters were observed in this study, none of which describe chronic stress and all within normal physiological ranges for research mice, suggesting that this hybrid strain was not adversely affected by housing at twice the density currently recommended. PMID:26900840

A density-functional study of the phase diagram of cementite-type (Fe,Mn)3C at absolute zero temperature.

PubMed

Von Appen, Jörg; Eck, Bernhard; Dronskowski, Richard

2010-11-15

The phase diagram of (Fe(1-x) Mn(x))(3)C has been investigated by means of density-functional theory (DFT) calculations at absolute zero temperature. The atomic distributions of the metal atoms are not random-like as previously proposed but we find three different, ordered regions within the phase range. The key role is played by the 8d metal site which forms, as a function of the composition, differing magnetic layers, and these dominate the physical properties. We calculated the magnetic moments, the volumes, the enthalpies of mixing and formation of 13 different compositions and explain the changes of the macroscopic properties with changes in the electronic and magnetic structures by means of bonding analyses using the Crystal Orbital Hamilton Population (COHP) technique. 2010 Wiley Periodicals, Inc.

Quantification of ventricular β2 -adrenoceptor density and ligand binding affinity in wild sockeye salmon Oncorhynchus nerka smolts using a novel modification to the tritiated ligand technique.

PubMed

Goulding, A T; Farrell, A P

2016-05-01

A new, image-based, tritiated ligand technique for measuring cardiac β2 -adrenoceptor (β2 -AR) binding characteristics was developed and validated with adult rainbow trout Oncorhynchus mykiss hearts so that the tissue limitation of traditional receptor binding techniques could be overcome and measurements could be made in hearts nearly 14-times smaller than previously used. The myocardial cell-surface (functional) β2 -AR density of O. nerka smolts sampled at the headwaters of the Chilko River was 54·2 fmol mg protein(-1) and about half of that previously found in return migrating adults of the same population, but still more than twice that of adult hatchery O. mykiss (21·1 fmol mg protein(-1) ). This technique now opens the possibility of investigating cardiac receptor density in a much wider range of fish species and life stages. © 2016 The Fisheries Society of the British Isles.

Intraspecific Relationships among Wood Density, Leaf Structural Traits and Environment in Four Co-Occurring Species of Nothofagus in New Zealand

PubMed Central

Richardson, Sarah J.; Allen, Robert B.; Buxton, Rowan P.; Easdale, Tomás A.; Hurst, Jennifer M.; Morse, Christopher W.; Smissen, Rob D.; Peltzer, Duane A.

2013-01-01

Plant functional traits capture important variation in plant strategy and function. Recent literature has revealed that within-species variation in traits is greater than previously supposed. However, we still have a poor understanding of how intraspecific variation is coordinated among different traits, and how it is driven by environment. We quantified intraspecific variation in wood density and five leaf traits underpinning the leaf economics spectrum (leaf dry matter content, leaf mass per unit area, size, thickness and density) within and among four widespread Nothofagus tree species in southern New Zealand. We tested whether intraspecific relationships between wood density and leaf traits followed widely reported interspecific relationships, and whether variation in these traits was coordinated through shared responses to environmental factors. Sample sites varied widely in environmental variables, including soil fertility (25–900 mg kg–1 total P), precipitation (668–4875 mm yr–1), temperature (5.2–12.4 °C mean annual temperature) and latitude (41–46 °S). Leaf traits were strongly correlated with one another within species, but not with wood density. There was some evidence for a positive relationship between wood density and leaf tissue density and dry matter content, but no evidence that leaf mass or leaf size were correlated with wood density; this highlights that leaf mass per unit area cannot be used as a surrogate for component leaf traits such as tissue density. Trait variation was predicted by environmental factors, but not consistently among different traits; e.g., only leaf thickness and leaf density responded to the same environmental cues as wood density. We conclude that although intraspecific variation in wood density and leaf traits is strongly driven by environmental factors, these responses are not strongly coordinated among functional traits even across co-occurring, closely-related plant species. PMID:23527041

Identification of prominence ejecta by the proton distribution function and magnetic fine structure in interplanetary coronal mass ejections in the inner heliosphere

NASA Astrophysics Data System (ADS)

Yao, Shuo; Marsch, Eckart; Tu, Chuan-Yi; Schwenn, Rainer

2010-05-01

This work presents in situ solar wind observations of three magnetic clouds (MCs) that contain cold high-density material when Helios 2 was located at 0.3 AU on 9 May 1979, 0.5 AU on 30 March 1976, and 0.7 AU on 24 December 1978. In the cold high-density regions embedded in the interplanetary coronal mass ejections we find (1) that the number density of protons is higher than in other regions inside the magnetic cloud, (2) the possible existence of He+, (3) that the thermal velocity distribution functions are more isotropic and appear to be colder than in the other regions of the MC, and the proton temperature is lower than that of the ambient plasma, and (4) that the associated magnetic field configuration can for all three MC events be identified as a flux rope. This cold high-density region is located at the polarity inversion line in the center of the bipolar structure of the MC magnetic field (consistent with previous solar observation work that found that a prominence lies over the neutral line of the related bipolar solar magnetic field). Specifically, for the first magnetic cloud event on 8 May 1979, a coronal mass ejection (CME) was related to an eruptive prominence previously reported as a result of the observation of Solwind (P78-1). Therefore, we identify the cold and dense region in the MC as the prominence material. It is the first time that prominence ejecta were identified by both the plasma and magnetic field features inside 1 AU, and it is also the first time that the thermal ion velocity distribution functions were used to investigate the microstate of the prominence material. Moreover, from our three cases, we also found that this material tended to fall behind the magnetic cloud and become smaller as it propagated farther away from the Sun, which confirms speculations in previous work. Overall, our in situ observations are consistent with three-part CME models.

Einstein's equations and a cosmology with finite matter

NASA Astrophysics Data System (ADS)

Clavelli, L.; Goldstein, Gary R.

2015-05-01

We discuss various space-time metrics which are compatible with Einstein's equations and a previously suggested cosmology with a finite total mass.1 In this alternative cosmology, the matter density was postulated to be a spatial delta function at the time of the big bang thereafter diffusing outward with constant total mass. This proposal explores a departure from standard assumptions that the big bang occurred everywhere at once or was just one of an infinite number of previous and later transitions.

Quantification of the Relationship between Surrogate Fuel Structure and Performance

DTIC Science & Technology

2012-07-31

order to account for know deficiencies [18]. The frequencies are then used to calculate the zero point energy ( ZPE ). In the G3 theory HF/6-31G* was used...for the ZPE and the new procedure is likely to be more reliable. Also in contrast to previous G series composite methods, the Hartree–Fock energy...The total energy is obtained by adding the previously calculated ZPE . Durant and Rohlfing [38] reported that B3LYP density functional methods provide

Predicting the stability of ternary intermetallics with density functional theory and machine learning

NASA Astrophysics Data System (ADS)

Schmidt, Jonathan; Chen, Liming; Botti, Silvana; Marques, Miguel A. L.

2018-06-01

We use a combination of machine learning techniques and high-throughput density-functional theory calculations to explore ternary compounds with the AB2C2 composition. We chose the two most common intermetallic prototypes for this composition, namely, the tI10-CeAl2Ga2 and the tP10-FeMo2B2 structures. Our results suggest that there may be ˜10 times more stable compounds in these phases than previously known. These are mostly metallic and non-magnetic. While the use of machine learning reduces the overall calculation cost by around 75%, some limitations of its predictive power still exist, in particular, for compounds involving the second-row of the periodic table or magnetic elements.

Electronic, phonon and superconducting properties of LaPtBi half-Heusler compound

NASA Astrophysics Data System (ADS)

Shrivastava, Deepika; Sanyal, Sankar P.

2018-05-01

In the framework of density functional theory based on plane wave pseudopotential method and linear response technique, we have studied the electronic, phonon and superconducting properties of LaPtBi half-Heusler compound. The electronic band structure and density of states show that it is gapless semiconductor which is consistent with previous results. The positive phonon frequencies confirm the stability of this compound in cubic MgAgAs phase. Superconductivity is studied in terms of Eliashberg spectral function (α2F(ω)), electron-phonon coupling constants (λ). The value of electron-phonon coupling parameter is found to be 0.41 and the superconducting transition temperature is calculated to be 0.76 K, in excellent agreement with the experimentally reported values.

Statistical analysis of dislocations and dislocation boundaries from EBSD data.

PubMed

Moussa, C; Bernacki, M; Besnard, R; Bozzolo, N

2017-08-01

Electron BackScatter Diffraction (EBSD) is often used for semi-quantitative analysis of dislocations in metals. In general, disorientation is used to assess Geometrically Necessary Dislocations (GNDs) densities. In the present paper, we demonstrate that the use of disorientation can lead to inaccurate results. For example, using the disorientation leads to different GND density in recrystallized grains which cannot be physically justified. The use of disorientation gradients allows accounting for measurement noise and leads to more accurate results. Misorientation gradient is then used to analyze dislocations boundaries following the same principle applied on TEM data before. In previous papers, dislocations boundaries were defined as Geometrically Necessary Boundaries (GNBs) and Incidental Dislocation Boundaries (IDBs). It has been demonstrated in the past, through transmission electron microscopy data, that the probability density distribution of the disorientation of IDBs and GNBs can be described with a linear combination of two Rayleigh functions. Such function can also describe the probability density of disorientation gradient obtained through EBSD data as reported in this paper. This opens the route for determining IDBs and GNBs probability density distribution functions separately from EBSD data, with an increased statistical relevance as compared to TEM data. The method is applied on deformed Tantalum where grains exhibit dislocation boundaries, as observed using electron channeling contrast imaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Consistency criteria for generalized Cuddeford systems

NASA Astrophysics Data System (ADS)

Ciotti, Luca; Morganti, Lucia

2010-01-01

General criteria to check the positivity of the distribution function (phase-space consistency) of stellar systems of assigned density and anisotropy profile are useful starting points in Jeans-based modelling. Here, we substantially extend previous results, and present the inversion formula and the analytical necessary and sufficient conditions for phase-space consistency of the family of multicomponent Cuddeford spherical systems: the distribution function of each density component of these systems is defined as the sum of an arbitrary number of Cuddeford distribution functions with arbitrary values of the anisotropy radius, but identical angular momentum exponent. The radial trend of anisotropy that can be realized by these models is therefore very general. As a surprising byproduct of our study, we found that the `central cusp-anisotropy theorem' (a necessary condition for consistency relating the values of the central density slope and of the anisotropy parameter) holds not only at the centre but also at all radii in consistent multicomponent generalized Cuddeford systems. This last result suggests that the so-called mass-anisotropy degeneracy could be less severe than what is sometimes feared.

Density Functional Calculations of Native Defects in CH 3 NH 3 PbI 3 : Effects of Spin–Orbit Coupling and Self-Interaction Error

DOE PAGES

Du, Mao-Hua

2015-04-02

We know that native point defects play an important role in carrier transport properties of CH3NH3PbI3. However, the nature of many important defects remains controversial due partly to the conflicting results reported by recent density functional theory (DFT) calculations. In this Letter, we show that self-interaction error and the neglect of spin–orbit coupling (SOC) in many previous DFT calculations resulted in incorrect positions of valence and conduction band edges, although their difference, which is the band gap, is in good agreement with the experimental value. Moreover, this problem has led to incorrect predictions of defect-level positions. Hybrid density functional calculations,more » which partially correct the self-interaction error and include the SOC, show that, among native point defects (including vacancies, interstitials, and antisites), only the iodine vacancy and its complexes induce deep electron and hole trapping levels inside of the band gap, acting as nonradiative recombination centers.« less

Cetacean population density estimation from single fixed sensors using passive acoustics.

PubMed

Küsel, Elizabeth T; Mellinger, David K; Thomas, Len; Marques, Tiago A; Moretti, David; Ward, Jessica

2011-06-01

Passive acoustic methods are increasingly being used to estimate animal population density. Most density estimation methods are based on estimates of the probability of detecting calls as functions of distance. Typically these are obtained using receivers capable of localizing calls or from studies of tagged animals. However, both approaches are expensive to implement. The approach described here uses a MonteCarlo model to estimate the probability of detecting calls from single sensors. The passive sonar equation is used to predict signal-to-noise ratios (SNRs) of received clicks, which are then combined with a detector characterization that predicts probability of detection as a function of SNR. Input distributions for source level, beam pattern, and whale depth are obtained from the literature. Acoustic propagation modeling is used to estimate transmission loss. Other inputs for density estimation are call rate, obtained from the literature, and false positive rate, obtained from manual analysis of a data sample. The method is applied to estimate density of Blainville's beaked whales over a 6-day period around a single hydrophone located in the Tongue of the Ocean, Bahamas. Results are consistent with those from previous analyses, which use additional tag data. © 2011 Acoustical Society of America

IR spectra and properties of solid acetone, an interstellar and cometary molecule

NASA Astrophysics Data System (ADS)

Hudson, Reggie L.; Gerakines, Perry A.; Ferrante, Robert F.

2018-03-01

Mid-infrared spectra of amorphous and crystalline acetone are presented along with measurements of the refractive index and density for both forms of the compound. Infrared band strengths are reported for the first time for amorphous and crystalline acetone, along with IR optical constants. Vapor pressures and a sublimation enthalpy for crystalline acetone also are reported. Positions of 13C-labeled acetone are measured. Band strengths are compared to gas-phase values and to the results of a density-functional calculation. A 73% error in previous work is identified and corrected.

Quantum mechanical probability current as electromagnetic 4-current from topological EM fields

NASA Astrophysics Data System (ADS)

van der Mark, Martin B.

2015-09-01

Starting from a complex 4-potential A = αdβ we show that the 4-current density in electromagnetism and the probability current density in relativistic quantum mechanics are of identical form. With the Dirac-Clifford algebra Cl1,3 as mathematical basis, the given 4-potential allows topological solutions of the fields, quite similar to Bateman's construction, but with a double field solution that was overlooked previously. A more general nullvector condition is found and wave-functions of charged and neutral particles appear as topological configurations of the electromagnetic fields.

Gibbs measures based on 1d (an)harmonic oscillators as mean-field limits

NASA Astrophysics Data System (ADS)

Lewin, Mathieu; Nam, Phan Thành; Rougerie, Nicolas

2018-04-01

We prove that Gibbs measures based on 1D defocusing nonlinear Schrödinger functionals with sub-harmonic trapping can be obtained as the mean-field/large temperature limit of the corresponding grand-canonical ensemble for many bosons. The limit measure is supported on Sobolev spaces of negative regularity, and the corresponding density matrices are not trace-class. The general proof strategy is that of a previous paper of ours, but we have to complement it with Hilbert-Schmidt estimates on reduced density matrices.

Multiple-relaxation-time color-gradient lattice Boltzmann model for simulating two-phase flows with high density ratio

NASA Astrophysics Data System (ADS)

Ba, Yan; Liu, Haihu; Li, Qing; Kang, Qinjun; Sun, Jinju

2016-08-01

In this paper we propose a color-gradient lattice Boltzmann (LB) model for simulating two-phase flows with high density ratio and high Reynolds number. The model applies a multirelaxation-time (MRT) collision operator to enhance the stability of the simulation. A source term, which is derived by the Chapman-Enskog analysis, is added into the MRT LB equation so that the Navier-Stokes equations can be exactly recovered. Also, a form of the equilibrium density distribution function is used to simplify the source term. To validate the proposed model, steady flows of a static droplet and the layered channel flow are first simulated with density ratios up to 1000. Small values of spurious velocities and interfacial tension errors are found in the static droplet test, and improved profiles of velocity are obtained by the present model in simulating channel flows. Then, two cases of unsteady flows, Rayleigh-Taylor instability and droplet splashing on a thin film, are simulated. In the former case, the density ratio of 3 and Reynolds numbers of 256 and 2048 are considered. The interface shapes and spike and bubble positions are in good agreement with the results of previous studies. In the latter case, the droplet spreading radius is found to obey the power law proposed in previous studies for the density ratio of 100 and Reynolds number up to 500.

Partition-free approach to open quantum systems in harmonic environments: An exact stochastic Liouville equation

NASA Astrophysics Data System (ADS)

McCaul, G. M. G.; Lorenz, C. D.; Kantorovich, L.

2017-03-01

We present a partition-free approach to the evolution of density matrices for open quantum systems coupled to a harmonic environment. The influence functional formalism combined with a two-time Hubbard-Stratonovich transformation allows us to derive a set of exact differential equations for the reduced density matrix of an open system, termed the extended stochastic Liouville-von Neumann equation. Our approach generalizes previous work based on Caldeira-Leggett models and a partitioned initial density matrix. This provides a simple, yet exact, closed-form description for the evolution of open systems from equilibriated initial conditions. The applicability of this model and the potential for numerical implementations are also discussed.

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than being a function of the spin-up and spin-down densities. In work carried out so far, the multiconfigurational wave function is a multiconfiguration self-consistent-field wave function. The new formulation has the advantage that the reference wave function has the correct spatial and spin symmetry and can describe bond dissociation (of both single and multiple bonds) and electronic excitations in a formally and physically correct way. We then review the formulation of density functionals in terms of the on-top pair density. Finally we review successful applications of the theory to bond energies and bond dissociation potential energy curves of main-group and transition metal bonds, to barrier heights (including pericyclic reactions), to proton affinities, to the hydrogen bond energy of water dimer, to ground- and excited-state charge transfer, to valence and Rydberg excitations of molecules, and to singlet-triplet splittings of radicals. We find that that MC-PDFT can give accurate results not only with complete-active-space multiconfiguration wave functions but also with generalized-active-space multiconfiguration wave functions, which are practical for larger numbers of active electrons and active orbitals than are complete-active-space wave functions. The separated-pair approximation, which is a special case of generalized active space self-consistent-field theory, is especially promising. MC-PDFT, because it requires much less computer time and storage than pure WFT methods, has the potential to open larger and more complex strongly correlated systems to accurate simulation.

The density structure and star formation rate of non-isothermal polytropic turbulence

NASA Astrophysics Data System (ADS)

Federrath, Christoph; Banerjee, Supratik

2015-04-01

The interstellar medium of galaxies is governed by supersonic turbulence, which likely controls the star formation rate (SFR) and the initial mass function (IMF). Interstellar turbulence is non-universal, with a wide range of Mach numbers, magnetic fields strengths and driving mechanisms. Although some of these parameters were explored, most previous works assumed that the gas is isothermal. However, we know that cold molecular clouds form out of the warm atomic medium, with the gas passing through chemical and thermodynamic phases that are not isothermal. Here we determine the role of temperature variations by modelling non-isothermal turbulence with a polytropic equation of state (EOS), where pressure and temperature are functions of gas density, P˜ ρ ^Γ, T ˜ ρΓ - 1. We use grid resolutions of 20483 cells and compare polytropic exponents Γ = 0.7 (soft EOS), Γ = 1 (isothermal EOS) and Γ = 5/3 (stiff EOS). We find a complex network of non-isothermal filaments with more small-scale fragmentation occurring for Γ < 1, while Γ > 1 smoothes out density contrasts. The density probability distribution function (PDF) is significantly affected by temperature variations, with a power-law tail developing at low densities for Γ > 1. In contrast, the PDF becomes closer to a lognormal distribution for Γ ≲ 1. We derive and test a new density variance-Mach number relation that takes Γ into account. This new relation is relevant for theoretical models of the SFR and IMF, because it determines the dense gas mass fraction of a cloud, from which stars form. We derive the SFR as a function of Γ and find that it decreases by a factor of ˜5 from Γ = 0.7 to 5/3.

Controlled cell morphology and liver-specific function of engineered primary hepatocytes by fibroblast layer cell densities.

PubMed

Sakai, Yusuke; Koike, Makiko; Kawahara, Daisuke; Hasegawa, Hideko; Murai, Tomomi; Yamanouchi, Kosho; Soyama, Akihiko; Hidaka, Masaaki; Takatsuki, Mitsuhisa; Fujita, Fumihiko; Kuroki, Tamotsu; Eguchi, Susumu

2018-03-05

Engineered primary hepatocytes, including co-cultured hepatocyte sheets, are an attractive to basic scientific and clinical researchers because they maintain liver-specific functions, have reconstructed cell polarity, and have high transplantation efficiency. However, co-culture conditions regarding engineered primary hepatocytes were suboptimal in promoting these advantages. Here we report that the hepatocyte morphology and liver-specific function levels are controlled by the normal human diploid fibroblast (TIG-118 cell) layer cell density. Primary rat hepatocytes were plated onto TIG-118 cells, previously plated 3 days before at 1.04, 5.21, and 26.1×10 3  cells/cm 2 . Hepatocytes plated onto lower TIG-118 cell densities expanded better during the early culture period. The hepatocytes gathered as colonies and only exhibited small adhesion areas because of the pushing force from proliferating TIG-118 cells. The smaller areas of each hepatocyte result in the development of bile canaliculi. The highest density of TIG-118 cells downregulated albumin synthesis activity of hepatocytes. The hepatocytes may have undergone apoptosis associated with high TGF-β1 concentration and necrosis due to a lack of oxygen. These occurrences were supported by apoptotic chromatin condensation and high expression of both proteins HIF-1a and HIF-1b. Three types of engineered hepatocyte/fibroblast sheets comprising different TIG-118 cell densities were harvested after 4 days of hepatocyte culture and showed a complete cell sheet format without any holes. Hepatocyte morphology and liver-specific function levels are controlled by TIG-118 cell density, which helps to design better engineered hepatocytes for future applications such as in vitro cell-based assays and transplantable hepatocyte tissues. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Structural and configurational properties of nanoconfined monolayer ice from first principles

PubMed Central

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations. PMID:26728125

Structural and configurational properties of nanoconfined monolayer ice from first principles

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

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

PubMed

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

2015-01-07

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

Observation of a Charge Density Wave Incommensuration Near the Superconducting Dome in Cu x TiSe 2

DOE PAGES

Kogar, A.; de la Pena, G. A.; Lee, Sangjun; ...

2017-01-11

X-ray diffraction was employed to study the evolution of the charge density wave (CDW) in Cu xTiSe 2 as a function of copper intercalation in order to clarify the relationship between the CDW and superconductivity. In this paper, the results show a CDW incommensuration arising at an intercalation value coincident with the onset of superconductivity at around x = 0.055(5) . Additionally, it was found that the charge density wave persists to higher intercalant concentrations than previously assumed, demonstrating that the CDW does not terminate inside the superconducting dome. A charge density wave peak was observed in samples up tomore » x = 0.091(6) , the highest copper concentration examined in this study. Lastly, the phase diagram established in this work suggests that charge density wave incommensuration may play a role in the formation of the superconducting state.« less

The Rapidity Density Distributions and Longitudinal Expansion Dynamics of Identified Pions from the STAR Beam Energy Scan

NASA Astrophysics Data System (ADS)

Flores, Christopher E.

2016-12-01

The Beam Energy Scan (BES) at the Relativistic Heavy-Ion Collider was proposed to characterize the properties of the medium produced in heavy-ion interactions over a broad range of baryon chemical potential. The aptitude of the STAR detector for mid-rapidity measurements has previously been leveraged to measure identified particle yields and spectra to extract bulk properties for the BES energies for | y | ≤ 0.1. However, to extract information on expansion dynamics and full phase space particle production, it is necessary to study identified particle rapidity density distributions. We present the first rapidity density distributions of identified pions from Au+Au collisions at √{sNN} = 7.7 , 11.5, and 19.6 GeV from the BES program as measured by the STAR detector. We use these distributions to obtain the full phase space yields of the pions to provide additional information of the system's chemistry. Further, we report the width of the rapidity density distributions compared to the width expected from Landau hydrodynamics. Finally, we interpret the results as a function of collision energy and discuss them in the context of previous energy scans done at the AGS and SPS.

No difference in long-term trunk muscle strength, cross-sectional area, and density in patients with chronic low back pain 7 to 11 years after lumbar fusion versus cognitive intervention and exercises.

PubMed

Froholdt, Anne; Holm, Inger; Keller, Anne; Gunderson, Ragnhild B; Reikeraas, Olav; Brox, Jens I

2011-08-01

Reduced muscle strength and density observed at 1 year after lumbar fusion may deteriorate more in the long term. To compare the long-term effect of lumbar fusion and cognitive intervention and exercises on muscle strength, cross-sectional area, density, and self-rated function in patients with chronic low back pain (CLBP) and disc degeneration. Randomized controlled study with a follow-up examination at 8.5 years (range, 7-11 years). Patients with CLBP and disc degeneration randomized to either instrumented posterolateral fusion of one or both of the two lower lumbar levels or a 3-week cognitive intervention and exercise program were included. Isokinetic muscle strength was measured by a Cybex 6000 (Cybex-Lumex, Inc., Ronkonkoma, NY, USA). All patients had previous experience with the test procedure. The back extension (E) flexion (F) muscles were tested, and the E/F ratios were calculated. Cross-sectional area and density of the back muscles were measured at the L3-L4 segment by computed tomography. Patients rated their function by the General Function Score. Trunk muscle strength, cross-sectional area, density, and self-rated function. Fifty-five patients (90%) were included at long-term follow-up. There were no significant differences in cross-sectional area, density, muscle strength, or self-rated function between the two groups. The cognitive intervention and exercise group increased trunk muscle extension significantly (p<.05), and both groups performed significantly better on trunk muscle flexion tests (p<.01) at long-term follow-up. On average, self-rated function improved by 56%, cross-sectional area was reduced by 8.5%, and muscle density was reduced by 27%. Although this study did not assess the morphology of muscles likely damaged by surgery, trunk muscle strength and cross-sectional area above the surgical levels are not different between those who had lumbar fusion or cognitive intervention and exercises at 7- to 11-year follow-up. Copyright © 2011 Elsevier Inc. All rights reserved.

Ion transport controlled by nanoparticle-functionalized membranes.

PubMed

Barry, Edward; McBride, Sean P; Jaeger, Heinrich M; Lin, Xiao-Min

2014-12-17

From proton exchange membranes in fuel cells to ion channels in biological membranes, the well-specified control of ionic interactions in confined geometries profoundly influences the transport and selectivity of porous materials. Here we outline a versatile new approach to control a membrane's electrostatic interactions with ions by depositing ligand-coated nanoparticles around the pore entrances. Leveraging the flexibility and control by which ligated nanoparticles can be synthesized, we demonstrate how ligand terminal groups such as methyl, carboxyl and amine can be used to tune the membrane charge density and control ion transport. Further functionality, exploiting the ligands as binding sites, is demonstrated for sulfonate groups resulting in an enhancement of the membrane charge density. We then extend these results to smaller dimensions by systematically varying the underlying pore diameter. As a whole, these results outline a previously unexplored method for the nanoparticle functionalization of membranes using ligated nanoparticles to control ion transport.

Ion transport controlled by nanoparticle-functionalized membranes

NASA Astrophysics Data System (ADS)

Barry, Edward; McBride, Sean P.; Jaeger, Heinrich M.; Lin, Xiao-Min

2014-12-01

From proton exchange membranes in fuel cells to ion channels in biological membranes, the well-specified control of ionic interactions in confined geometries profoundly influences the transport and selectivity of porous materials. Here we outline a versatile new approach to control a membrane’s electrostatic interactions with ions by depositing ligand-coated nanoparticles around the pore entrances. Leveraging the flexibility and control by which ligated nanoparticles can be synthesized, we demonstrate how ligand terminal groups such as methyl, carboxyl and amine can be used to tune the membrane charge density and control ion transport. Further functionality, exploiting the ligands as binding sites, is demonstrated for sulfonate groups resulting in an enhancement of the membrane charge density. We then extend these results to smaller dimensions by systematically varying the underlying pore diameter. As a whole, these results outline a previously unexplored method for the nanoparticle functionalization of membranes using ligated nanoparticles to control ion transport.

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Obesity in Aging Exacerbates Neuroinflammation, Dysregulating Synaptic Function-related Genes and Altering Eicosanoid Synthesis in the Mouse Hippocampus: Potential Role in Impaired Synaptic Plasticity and Cognitive Decline.

PubMed

Valcarcel-Ares, Marta Noa; Tucsek, Zsuzsanna; Kiss, Tamas; Giles, Cory B; Tarantini, Stefano; Yabluchanskiy, Andriy; Balasubramanian, Priya; Gautam, Tripti; Galvan, Veronica; Ballabh, Praveen; Richardson, Arlan; Freeman, Willard M; Wren, Jonathan D; Deak, Ferenc; Ungvari, Zoltan; Csiszar, Anna

2018-06-08

There is strong evidence that obesity has deleterious effects on cognitive function of older adults. Previous preclinical studies demonstrate that obesity in aging is associated with a heightened state of systemic inflammation, which exacerbates blood brain barrier disruption, promoting neuroinflammation and oxidative stress. To test the hypothesis that synergistic effects of obesity and aging on inflammatory processes exert deleterious effects on hippocampal function, young and aged C57BL/6 mice were rendered obese by chronic feeding of a high fat diet followed by assessment of learning and memory function, measurement of hippocampal long-term potentiation (LTP), assessment of changes in hippocampal expression of genes relevant for synaptic function and determination of synaptic density. Because there is increasing evidence that altered production of lipid mediators modulate LTP, neuroinflammation and neurovascular coupling responses, the effects of obesity on hippocampal levels of relevant eicosanoid mediators were also assessed. We found that aging exacerbates obesity-induced microglia activation, which is associated with deficits in hippocampal-dependent learning and memory tests, impaired LTP, decreased synaptic density and dysregulation of genes involved in regulation of synaptic plasticity. Obesity in aging also resulted in an altered hippocampal eicosanoid profile, including decreases in vasodilator and pro-LTP epoxy-eicosatrienoic acids (EETs). Collectively, our results taken together with previous findings suggest that obesity in aging promotes hippocampal inflammation, which in turn may contribute to synaptic dysfunction and cognitive impairment.

Guaiacol hydrodeoxygenation mechanism on Pt(111): insights from density functional theory and linear free energy relations.

PubMed

Lee, Kyungtae; Gu, Geun Ho; Mullen, Charles A; Boateng, Akwasi A; Vlachos, Dionisios G

2015-01-01

Density functional theory is used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previous Brønsted-Evans-Polanyi (BEP) correlations for small open-chain molecules are inadequate in estimating the reaction barriers of phenolic compounds except for the side group (methoxy) carbon-dehydrogenation. New BEP relations are established using a select group of phenolic compounds. These relations are applied to construct a potential-energy surface of guaiacol-HDO to catechol. Analysis shows that catechol is mainly produced via dehydrogenation of the methoxy functional group followed by the CHx (x<3) removal of the functional group and hydrogenation of the ring carbon, in contrast to a hypothesis of a direct demethylation path. Dehydroxylation and demethoxylation are slow, implying that phenol is likely produced from catechol but not through its direct dehydroxylation followed by aromatic carbon-ring hydrogenation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of stretching on the ballistic conductance of Au nanocontacts in presence of CO: A density functional study

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dal Corso, Andrea; Smogunov, Alexander

2012-04-01

CO adsorption on an Au monatomic chain is studied within density functional theory in nanocontact geometries as a function of the contact stretching. We compare the bridge and atop adsorption sites of CO, finding that the bridge site is energetically favored at all strains studied here. Atop adsorption gives rise to an almost complete suppression of the ballistic conductance of the nanocontact, while adsorption at the bridge site results in a conductance value close to 0.6G0, in agreement with previous experimental data. We show that only the bridge site can qualitatively account for the evolution of the conductance as a function of the contact stretching observed in the experimental conductance traces. The numerical discrepancy between the theoretical and experimental conductance slopes is rationalized through a simple model for the elastic response of the metallic leads. We also verify that our conductance values are not affected by the specific choice of the nanocontact geometry by comparing two different atomistic models for the tips.

ELUCID. IV. Galaxy Quenching and its Relation to Halo Mass, Environment, and Assembly Bias

NASA Astrophysics Data System (ADS)

Wang, Huiyuan; Mo, H. J.; Chen, Sihan; Yang, Yang; Yang, Xiaohu; Wang, Enci; van den Bosch, Frank C.; Jing, Yipeng; Kang, Xi; Lin, Weipeng; Lim, S. H.; Huang, Shuiyao; Lu, Yi; Li, Shijie; Cui, Weiguang; Zhang, Youcai; Tweed, Dylan; Wei, Chengliang; Li, Guoliang; Shi, Feng

2018-01-01

We examine the quenched fraction of central and satellite galaxies as a function of galaxy stellar mass, halo mass, and the matter density of their large-scale environment. Matter densities are inferred from our ELUCID simulation, a constrained simulation of the local universe sampled by SDSS, while halo masses and central/satellite classification are taken from the galaxy group catalog of Yang et al. The quenched fraction for the total population increases systematically with the three quantities. We find that the “environmental quenching efficiency,” which quantifies the quenched fraction as a function of halo mass, is independent of stellar mass. And this independence is the origin of the stellar mass independence of density-based quenching efficiency found in previous studies. Considering centrals and satellites separately, we find that the two populations follow similar correlations of quenching efficiency with halo mass and stellar mass, suggesting that they have experienced similar quenching processes in their host halo. We demonstrate that satellite quenching alone cannot account for the environmental quenching efficiency of the total galaxy population, and that the difference between the two populations found previously arises mainly from the fact that centrals and satellites of the same stellar mass reside, on average, in halos of different mass. After removing these effects of halo mass and stellar mass, there remains a weak, but significant, residual dependence on environmental density, which is eliminated when halo assembly bias is taken into account. Our results therefore indicate that halo mass is the prime environmental parameter that regulates the quenching of both centrals and satellites.

Molecular simulation study of cavity-generated instabilities in the superheated Lennard-Jones liquid

NASA Astrophysics Data System (ADS)

Torabi, Korosh; Corti, David S.

2010-10-01

Previous equilibrium-based density-functional theory (DFT) analyses of cavity formation in the pure component superheated Lennard-Jones (LJ) liquid [S. Punnathanam and D. S. Corti, J. Chem. Phys. 119, 10224 (2003); M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007)] revealed that a thermodynamic limit of stability appears in which no liquidlike density profile can develop for cavity radii greater than some critical size (being a function of temperature and bulk density). The existence of these stability limits was also verified using isothermal-isobaric Monte Carlo (MC) simulations. To test the possible relevance of these limits of stability to a dynamically evolving system, one that may be important for homogeneous bubble nucleation, we perform isothermal-isobaric molecular dynamics (MD) simulations in which cavities of different sizes are placed within the superheated LJ liquid. When the impermeable boundary utilized to generate a cavity is removed, the MD simulations show that the cavity collapses and the overall density of the system remains liquidlike, i.e., the system is stable, when the initial cavity radius is below some certain value. On the other hand, when the initial radius is large enough, the cavity expands and the overall density of the system rapidly decreases toward vaporlike densities, i.e., the system is unstable. Unlike the DFT predictions, however, the transition between stability and instability is not infinitely sharp. The fraction of initial configurations that generate an instability (or a phase separation) increases from zero to unity as the initial cavity radius increases over a relatively narrow range of values, which spans the predicted stability limit obtained from equilibrium MC simulations. The simulation results presented here provide initial evidence that the equilibrium-based stability limits predicted in the previous DFT and MC simulation studies may play some role, yet to be fully determined, in the homogeneous nucleation and growth of embryos within metastable fluids.

Galaxy halo expansions: a new biorthogonal family of potential-density pairs

NASA Astrophysics Data System (ADS)

Lilley, Edward J.; Sanders, Jason L.; Evans, N. Wyn; Erkal, Denis

2018-05-01

Efficient expansions of the gravitational field of (dark) haloes have two main uses in the modelling of galaxies: first, they provide a compact representation of numerically constructed (or real) cosmological haloes, incorporating the effects of triaxiality, lopsidedness or other distortion. Secondly, they provide the basis functions for self-consistent field expansion algorithms used in the evolution of N-body systems. We present a new family of biorthogonal potential-density pairs constructed using the Hankel transform of the Laguerre polynomials. The lowest order density basis functions are double-power-law profiles cusped like ρ ˜ r-2+1/α at small radii with asymptotic density fall-off like ρ ˜ r-3-1/(2α). Here, α is a parameter satisfying α ≥ 1/2. The family therefore spans the range of inner density cusps found in numerical simulations, but has much shallower - and hence more realistic - outer slopes than the corresponding members of the only previously known family deduced by Zhao and exemplified by Hernquist & Ostriker. When α = 1, the lowest order density profile has an inner density cusp of ρ ˜ r-1 and an outer density slope of ρ ˜ r-3.5, similar to the famous Navarro, Frenk & White (NFW) model. For this reason, we demonstrate that our new expansion provides a more accurate representation of flattened NFW haloes than the competing Hernquist-Ostriker expansion. We utilize our new expansion by analysing a suite of numerically constructed haloes and providing the distributions of the expansion coefficients.

General framework for fluctuating dynamic density functional theory

NASA Astrophysics Data System (ADS)

Durán-Olivencia, Miguel A.; Yatsyshin, Peter; Goddard, Benjamin D.; Kalliadasis, Serafim

2017-12-01

We introduce a versatile bottom-up derivation of a formal theoretical framework to describe (passive) soft-matter systems out of equilibrium subject to fluctuations. We provide a unique connection between the constituent-particle dynamics of real systems and the time evolution equation of their measurable (coarse-grained) quantities, such as local density and velocity. The starting point is the full Hamiltonian description of a system of colloidal particles immersed in a fluid of identical bath particles. Then, we average out the bath via Zwanzig’s projection-operator techniques and obtain the stochastic Langevin equations governing the colloidal-particle dynamics. Introducing the appropriate definition of the local number and momentum density fields yields a generalisation of the Dean-Kawasaki (DK) model, which resembles the stochastic Navier-Stokes description of a fluid. Nevertheless, the DK equation still contains all the microscopic information and, for that reason, does not represent the dynamical law of observable quantities. We address this controversial feature of the DK description by carrying out a nonequilibrium ensemble average. Adopting a natural decomposition into local-equilibrium and nonequilibrium contribution, where the former is related to a generalised version of the canonical distribution, we finally obtain the fluctuating-hydrodynamic equation governing the time-evolution of the mesoscopic density and momentum fields. Along the way, we outline the connection between the ad hoc energy functional introduced in previous DK derivations and the free-energy functional from classical density-functional theory. The resultant equation has the structure of a dynamical density-functional theory (DDFT) with an additional fluctuating force coming from the random interactions with the bath. We show that our fluctuating DDFT formalism corresponds to a particular version of the fluctuating Navier-Stokes equations, originally derived by Landau and Lifshitz. Our framework thus provides the formal apparatus for ab initio derivations of fluctuating DDFT equations capable of describing the dynamics of soft-matter systems in and out of equilibrium.

An atomic orbital based real-time time-dependent density functional theory for computing electronic circular dichroism band spectra

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

Goings, Joshua J.; Li, Xiaosong, E-mail: xsli@uw.edu

2016-06-21

One of the challenges of interpreting electronic circular dichroism (ECD) band spectra is that different states may have different rotatory strength signs, determined by their absolute configuration. If the states are closely spaced and opposite in sign, observed transitions may be washed out by nearby states, unlike absorption spectra where transitions are always positive additive. To accurately compute ECD bands, it is necessary to compute a large number of excited states, which may be prohibitively costly if one uses the linear-response time-dependent density functional theory (TDDFT) framework. Here we implement a real-time, atomic-orbital based TDDFT method for computing the entiremore » ECD spectrum simultaneously. The method is advantageous for large systems with a high density of states. In contrast to previous implementations based on real-space grids, the method is variational, independent of nuclear orientation, and does not rely on pseudopotential approximations, making it suitable for computation of chiroptical properties well into the X-ray regime.« less

La 137 , 138 , 139 ( n , γ ) cross sections constrained with statistical decay properties of La 138 , 139 , 140 nuclei

DOE PAGES

Kheswa, B. V.; Wiedeking, M.; Brown, J. A.; ...

2017-04-21

The nuclear level densities and γ-ray strength functions of 138,139,140La were measured using the 139La( 3He,α), 139La( 3He,' 3He), and 139La(d,p) reactions. The particle-γ coincidences were recorded with the silicon particle telescope (SiRi) and NaI(Tl) (CACTUS) arrays. In the context of these experimental results, the low-energy enhancement in the A~140 region is discussed. The 137,138,139La(n,γ) cross sections were calculated at s- and p-process temperatures using the experimentally measured nuclear level densities and γ-ray strength functions. As a result, good agreement is found between 139La(n,γ) calculated cross sections and previous measurements.

La 137 , 138 , 139 ( n , γ ) cross sections constrained with statistical decay properties of La 138 , 139 , 140 nuclei

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

Kheswa, B. V.; Wiedeking, M.; Brown, J. A.

The nuclear level densities and γ-ray strength functions of 138,139,140La were measured using the 139La( 3He,α), 139La( 3He,' 3He), and 139La(d,p) reactions. The particle-γ coincidences were recorded with the silicon particle telescope (SiRi) and NaI(Tl) (CACTUS) arrays. In the context of these experimental results, the low-energy enhancement in the A~140 region is discussed. The 137,138,139La(n,γ) cross sections were calculated at s- and p-process temperatures using the experimentally measured nuclear level densities and γ-ray strength functions. As a result, good agreement is found between 139La(n,γ) calculated cross sections and previous measurements.

A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters

NASA Astrophysics Data System (ADS)

Heard, Christopher J.; Johnston, Roy L.

2013-02-01

The effect of doping on the energetics and dimensionality of eight atom coinage metal subnanometre particles is fully resolved using a genetic algorithm in tandem with on the fly density functional theory calculations to determine the global minima (GM) for Cu n Ag(8- n) and Cu n Au(8- n) clusters. Comparisons are made to previous ab initio work on mono- and bimetallic clusters, with excellent agreement found. Charge transfer and geometric arguments are considered to rationalise the stability of the particular permutational isomers found. An interesting transition between three dimensional and two dimensional GM structures is observed for copper-gold clusters, which is sharper and appears earlier in the doping series than is known for gold-silver particles.

137,138,139La(n ,γ ) cross sections constrained with statistical decay properties of 138,139,140La nuclei

NASA Astrophysics Data System (ADS)

Kheswa, B. V.; Wiedeking, M.; Brown, J. A.; Larsen, A. C.; Goriely, S.; Guttormsen, M.; Bello Garrote, F. L.; Bernstein, L. A.; Bleuel, D. L.; Eriksen, T. K.; Giacoppo, F.; Görgen, A.; Goldblum, B. L.; Hagen, T. W.; Koehler, P. E.; Klintefjord, M.; Malatji, K. L.; Midtbø, J. E.; Nyhus, H. T.; Papka, P.; Renstrøm, T.; Rose, S. J.; Sahin, E.; Siem, S.; Tornyi, T. G.

2017-04-01

The nuclear level densities and γ -ray strength functions of 138,139,140La were measured using the 139La(3He,α ), 139La(3He,3He' ), and 139La(d ,p ) reactions. The particle-γ coincidences were recorded with the silicon particle telescope (SiRi) and NaI(Tl) (CACTUS) arrays. In the context of these experimental results, the low-energy enhancement in the A ˜140 region is discussed. The 137,138,139La (n ,γ ) cross sections were calculated at s - and p -process temperatures using the experimentally measured nuclear level densities and γ -ray strength functions. Good agreement is found between 139La(n ,γ ) calculated cross sections and previous measurements.

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

Bemporad, G.A.; Rubin, H.

The development of internal waves and instabilities of the Kelvin Helmholtz-type may prevent the density gradient maintenance which allows the proper functioning of the Advanced Solar Pond (ASP). The properties and characteristics of internal waves, of constant and growing amplitude, are quantitatively described in this paper. The numerical simulations made in this study are in good agreement with previous theoretical and experimental results.

A spatially explicit capture-recapture estimator for single-catch traps.

PubMed

Distiller, Greg; Borchers, David L

2015-11-01

Single-catch traps are frequently used in live-trapping studies of small mammals. Thus far, a likelihood for single-catch traps has proven elusive and usually the likelihood for multicatch traps is used for spatially explicit capture-recapture (SECR) analyses of such data. Previous work found the multicatch likelihood to provide a robust estimator of average density. We build on a recently developed continuous-time model for SECR to derive a likelihood for single-catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multicatch estimator for various scenarios with nonconstant density surfaces. While the multicatch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height of the detection function. By contrast, the single-catch estimators of density, distribution, and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constant over the survey region, then the multicatch estimator performs well with single-catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single-catch estimator when trap saturation is above about 60%. The estimator's performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single-catch likelihood with unknown capture times remains intractable for now, researchers using single-catch traps should aim to incorporate timing devices with their traps.

Electronic and Optical Properties of Titanium Nitride Bulk and Surfaces from First Principles Calculations (Postprint)

DTIC Science & Technology

2015-11-18

thickness of the film, or substrate. In this work, we report calculations for titanium nitride ( TiN ), a promising material for plasmonic applications...stoichiometric bulk TiN , as well as of the TiN (100), TiN (110), and TiN (111) outermost surfaces. Density functional theory (DFT) and many-body GW methods...and the band structure for bulk TiN were shown to be consistent with previous work. Calculated dielectric functions, plasma frequencies, reflectivity

Evolution of statistical properties for a nonlinearly propagating sinusoid.

PubMed

Shepherd, Micah R; Gee, Kent L; Hanford, Amanda D

2011-07-01

The nonlinear propagation of a pure sinusoid is considered using time domain statistics. The probability density function, standard deviation, skewness, kurtosis, and crest factor are computed for both the amplitude and amplitude time derivatives as a function of distance. The amplitude statistics vary only in the postshock realm, while the amplitude derivative statistics vary rapidly in the preshock realm. The statistical analysis also suggests that the sawtooth onset distance can be considered to be earlier than previously realized. © 2011 Acoustical Society of America

Atom-scale covalent electrochemical modification of single-layer graphene on SiC substrates by diaryliodonium salts

DOE PAGES

Gearba, Raluca I.; Mueller, Kory M.; Veneman, Peter A.; ...

2015-05-09

Owing to its high conductivity, graphene holds promise as an electrode for energy devices such as batteries and photovoltaics. However, to this end, the work function and doping levels in graphene need to be precisely tuned. One promising route for modifying graphene’s electronic properties is via controlled covalent electrochemical grafting of molecules. We show that by employing diaryliodonium salts instead of the commonly used diazonium salts, spontaneous functionalization is avoided. This then allows for precise tuning of the grafting density. Moreover, by employing bis(4-nitrophenyl)iodonium(III) tetrafluoroborate (DNP) salt calibration curves, the surface functionalization density (coverage) of glassy carbon was controlled usingmore » cyclic voltammetry in varying salt concentrations. These electro-grafting conditions and calibration curves translated directly over to modifying single layer epitaxial graphene substrates (grown on insulating 6H-SiC (0 0 0 1)). In addition to quantifying the functionalization densities using electrochemical methods, samples with low grafting densities were characterized by low-temperature scanning tunneling microscopy (LT-STM). We show that the use of buffer-layer free graphene substrates is required for clear observation of the nitrophenyl modifications. Furthermore, atomically-resolved STM images of single site modifications were obtained, showing no preferential grafting at defect sites or SiC step edges as supposed previously in the literature. Most of the grafts exhibit threefold symmetry, but occasional extended modifications (larger than 4 nm) were observed as well.« less

Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes

PubMed Central

Mora, Camilo; Aburto-Oropeza, Octavio; Ayala Bocos, Arturo; Ayotte, Paula M.; Banks, Stuart; Bauman, Andrew G.; Beger, Maria; Bessudo, Sandra; Booth, David J.; Brokovich, Eran; Brooks, Andrew; Chabanet, Pascale; Cinner, Joshua E.; Cortés, Jorge; Cruz-Motta, Juan J.; Cupul Magaña, Amilcar; DeMartini, Edward E.; Edgar, Graham J.; Feary, David A.; Ferse, Sebastian C. A.; Friedlander, Alan M.; Gaston, Kevin J.; Gough, Charlotte; Graham, Nicholas A. J.; Green, Alison; Guzman, Hector; Hardt, Marah; Kulbicki, Michel; Letourneur, Yves; López Pérez, Andres; Loreau, Michel; Loya, Yossi; Martinez, Camilo; Mascareñas-Osorio, Ismael; Morove, Tau; Nadon, Marc-Olivier; Nakamura, Yohei; Paredes, Gustavo; Polunin, Nicholas V. C.; Pratchett, Morgan S.; Reyes Bonilla, Héctor; Rivera, Fernando; Sala, Enric; Sandin, Stuart A.; Soler, German; Stuart-Smith, Rick; Tessier, Emmanuel; Tittensor, Derek P.; Tupper, Mark; Usseglio, Paolo; Vigliola, Laurent; Wantiez, Laurent; Williams, Ivor; Wilson, Shaun K.; Zapata, Fernando A.

2011-01-01

Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a non-saturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world's coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas. PMID:21483714

Imaging of isotropic and anisotropic conductivities from power densities in three dimensions

NASA Astrophysics Data System (ADS)

Monard, François; Rim, Donsub

2018-07-01

We present numerical reconstructions of anisotropic conductivity tensors in three dimensions, from knowledge of a finite family of power density functionals. Such a problem arises in the coupled-physics imaging modality ultrasound modulated electrical impedance tomography for instance. We improve on the algorithms previously derived in Bal et al (2013 Inverse Problems Imaging 7 353–75) Monard and Bal (2013 Commun. PDE 38 1183–207) for both isotropic and anisotropic cases, and we address the well-known issue of vanishing determinants in particular. The algorithm is implemented and we provide numerical results that illustrate the improvements.

Multiple-relaxation-time color-gradient lattice Boltzmann model for simulating two-phase flows with high density ratio

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

Ba, Yan; Liu, Haihu; Li, Qing

2016-08-15

In this paper, we propose a color-gradient lattice Boltzmann (LB) model for simulating two-phase flows with high density ratio and high Reynolds number. The model applies a multi-relaxation-time (MRT) collision operator to enhance the stability of the simulation. A source term, which is derived by the Chapman-Enskog analysis, is added into the MRT LB equation so that the Navier-Stokes equations can be exactly recovered. Also, a new form of the equilibrium density distribution function is used to simplify the source term. To validate the proposed model, steady flows of a static droplet and the layered channel flow are first simulatedmore » with density ratios up to 1000. Small values of spurious velocities and interfacial tension errors are found in the static droplet test, and improved profiles of velocity are obtained by the present model in simulating channel flows. Then, two cases of unsteady flows, Rayleigh-Taylor instability and droplet splashing on a thin film, are simulated. In the former case, the density ratio of 3 and Reynolds numbers of 256 and 2048 are considered. The interface shapes and spike/bubble positions are in good agreement with the results of previous studies. In the latter case, the droplet spreading radius is found to obey the power law proposed in previous studies for the density ratio of 100 and Reynolds number up to 500.« less

Immunohistological features related to functional impairment in lymphangioleiomyomatosis.

PubMed

Nascimento, Ellen Caroline Toledo do; Baldi, Bruno Guedes; Mariani, Alessandro Wasum; Annoni, Raquel; Kairalla, Ronaldo Adib; Pimenta, Suzana Pinheiro; da Silva, Luiz Fernando Ferraz; Carvalho, Carlos Roberto Ribeiro; Dolhnikoff, Marisa

2018-05-08

Lymphangioleiomyomatosis (LAM) is a low-grade neoplasm characterized by the pulmonary infiltration of smooth muscle-like cells (LAM cells) and cystic destruction. Patients usually present with airway obstruction in pulmonary function tests (PFTs). Previous studies have shown correlations among histological parameters, lung function abnormalities and prognosis in LAM. We investigated the lung tissue expression of proteins related to the mTOR pathway, angiogenesis and enzymatic activity and its correlation with functional parameters in LAM patients. We analyzed morphological and functional parameters of thirty-three patients. Two groups of disease severity were identified according to FEV1 values. Lung tissue from open biopsies or lung transplants was immunostained for SMA, HMB-45, mTOR, VEGF-D, MMP-9 and D2-40. Density of cysts, density of nodules and protein expression were measured by image analysis and correlated with PFT parameters. There was no difference in the expression of D2-40 between the more severe and the less severe groups. All other immunohistological parameters showed significantly higher values in the more severe group (p ≤ 0.002). The expression of VEGF-D, MMP-9 and mTOR in LAM cells was associated with the density of both cysts and nodules. The density of cysts and nodules as well as the expression of MMP-9 and VEGF-D were associated with the impairment of PFT parameters. Severe LAM represents an active phase of the disease with high expression of VEGF-D, mTOR, and MMP-9, as well as LAM cell infiltration. Our findings suggest that the tissue expression levels of VEGF-D and MMP-9 are important parameters associated with the loss of pulmonary function and could be considered as potential severity markers in open lung biopsies of LAM patients.

Probing the Initial Mass Function in Extended Ultraviolet (XUV) Disks

NASA Astrophysics Data System (ADS)

Koda, Jin

2013-01-01

"The GALEX UV satellite discovered tantalizing evidence of star formation (SF) far beyond the optical edge of galactic disks (i.e. extended UV disk, or XUV disk). This discovery provides a new opportunity for studying SF in the exceedingly low-density environment (˜1/10 of typical SF density), spurring intense debate on the universality of the initial mass function (IMF) in such exceptional environments. Our pilot S-Cam study of M83’s XUV disk led to support for the universal IMF at least in M83 (Koda et al. 2012). We propose an expansion of the pilot study by about an order of magnitude, by observing 6 XUV disks in NA656(Hα), B, I, and R-band with S-Cam in S13B. In conjunction with GALEX UV bands, these images will reveal the presence of O stars (Hα) and O&B stars (UV) in stellar clusters -thus, constraining the high-mass end of the IMF. These multi-broadband images will enable us to determine the masses of the clusters with much improved accuracy (previously, relied only on R). The proposed observations will not only increase the statistical significance of our previous result, but also enable us to analyze the stochastic effect of IMF sampling in very low-mass - clusters (10^{2+3} M_sun) - the regime of ongoing debate. Previously allocated 1+2 nights were cancelled (telescope failures)."

Analytical mass formula and nuclear surface properties in the ETF approximation. Part I: symmetric nuclei

NASA Astrophysics Data System (ADS)

Aymard, François; Gulminelli, Francesca; Margueron, Jérôme

2016-08-01

The problem of determination of nuclear surface energy is addressed within the framework of the extended Thomas Fermi (ETF) approximation using Skyrme functionals. We propose an analytical model for the density profiles with variationally determined diffuseness parameters. In this first paper, we consider the case of symmetric nuclei. In this situation, the ETF functional can be exactly integrated, leading to an analytical formula expressing the surface energy as a function of the couplings of the energy functional. The importance of non-local terms is stressed and it is shown that they cannot be deduced simply from the local part of the functional, as it was suggested in previous works.

A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.

PubMed

Song, Yun S; Steinrücken, Matthias

2012-03-01

The transition density function of the Wright-Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright-Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation-selection balance.

The ionic versus metallic nature of 2D electrides: a density-functional description.

PubMed

Dale, Stephen G; Johnson, Erin R

2017-10-18

The two-dimensional (2D) electrides are a highly unusual class of materials, possessing interstitial electron layers sandwiched between cationic atomic layers of the solid. In this work, density-functional theory, with the exchange-hole dipole moment dispersion correction, is used to investigate exfoliation and interlayer sliding of the only two experimentally known 2D electrides: [Ca 2 N] + e - and [Y 2 C] 2+ (2e - ). Examination of the valence states during exfoliation identifies intercalated electrons in the bulk and weakly-bound surface-states in the fully-expanded case. The calculated exfoliation energies for the 2D electrides are found to be much higher than for typical 2D materials, which is attributed to the ionic nature of the electrides and the strong Coulomb forces governing the interlayer interactions. Conversely, the calculated sliding barriers are found to be quite low, comparable to those for typical 2D materials, and are effectively unchanged by exclusion of dispersion. We conjecture that the metallic nature of the interstitial electrons allows the atomic layers to move relative to each other without significantly altering the interlayer binding. Finally, comparison with previous works reveals the importance of a system-dependent dispersion correction in the density-functional treatment.

A Simple Method for Finding Explicit Analytic Transition Densities of Diffusion Processes with General Diploid Selection

PubMed Central

Song, Yun S.; Steinrücken, Matthias

2012-01-01

The transition density function of the Wright–Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright–Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation–selection balance. PMID:22209899

Efficient mixing scheme for self-consistent all-electron charge density

NASA Astrophysics Data System (ADS)

Shishidou, Tatsuya; Weinert, Michael

2015-03-01

In standard ab initio density-functional theory calculations, the charge density ρ is gradually updated using the ``input'' and ``output'' densities of the current and previous iteration steps. To accelerate the convergence, Pulay mixing has been widely used with great success. It expresses an ``optimal'' input density ρopt and its ``residual'' Ropt by a linear combination of the densities of the iteration sequences. In large-scale metallic systems, however, the long range nature of Coulomb interaction often causes the ``charge sloshing'' phenomenon and significantly impacts the convergence. Two treatments, represented in reciprocal space, are known to suppress the sloshing: (i) the inverse Kerker metric for Pulay optimization and (ii) Kerker-type preconditioning in mixing Ropt. In all-electron methods, where the charge density does not have a converging Fourier representation, treatments equivalent or similar to (i) and (ii) have not been described so far. In this work, we show that, by going through the calculation of Hartree potential, one can accomplish the procedures (i) and (ii) without entering the reciprocal space. Test calculations are done with a FLAPW method.

Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels

PubMed Central

2012-01-01

Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions. PMID:23316120

Generalized Maximum Entropy

NASA Technical Reports Server (NTRS)

Cheeseman, Peter; Stutz, John

2005-01-01

A long standing mystery in using Maximum Entropy (MaxEnt) is how to deal with constraints whose values are uncertain. This situation arises when constraint values are estimated from data, because of finite sample sizes. One approach to this problem, advocated by E.T. Jaynes [1], is to ignore this uncertainty, and treat the empirically observed values as exact. We refer to this as the classic MaxEnt approach. Classic MaxEnt gives point probabilities (subject to the given constraints), rather than probability densities. We develop an alternative approach that assumes that the uncertain constraint values are represented by a probability density {e.g: a Gaussian), and this uncertainty yields a MaxEnt posterior probability density. That is, the classic MaxEnt point probabilities are regarded as a multidimensional function of the given constraint values, and uncertainty on these values is transmitted through the MaxEnt function to give uncertainty over the MaXEnt probabilities. We illustrate this approach by explicitly calculating the generalized MaxEnt density for a simple but common case, then show how this can be extended numerically to the general case. This paper expands the generalized MaxEnt concept introduced in a previous paper [3].

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

The Riemann problem for the relativistic full Euler system with generalized Chaplygin proper energy density-pressure relation

NASA Astrophysics Data System (ADS)

Shao, Zhiqiang

2018-04-01

The relativistic full Euler system with generalized Chaplygin proper energy density-pressure relation is studied. The Riemann problem is solved constructively. The delta shock wave arises in the Riemann solutions, provided that the initial data satisfy some certain conditions, although the system is strictly hyperbolic and the first and third characteristic fields are genuinely nonlinear, while the second one is linearly degenerate. There are five kinds of Riemann solutions, in which four only consist of a shock wave and a centered rarefaction wave or two shock waves or two centered rarefaction waves, and a contact discontinuity between the constant states (precisely speaking, the solutions consist in general of three waves), and the other involves delta shocks on which both the rest mass density and the proper energy density simultaneously contain the Dirac delta function. It is quite different from the previous ones on which only one state variable contains the Dirac delta function. The formation mechanism, generalized Rankine-Hugoniot relation and entropy condition are clarified for this type of delta shock wave. Under the generalized Rankine-Hugoniot relation and entropy condition, we establish the existence and uniqueness of solutions involving delta shocks for the Riemann problem.

Aberrant patterns of local and long-range functional connectivity densities in schizophrenia

PubMed Central

Tian, Hongjun; Li, Jie; Qu, Hongru; Cheng, Langlang; Zhu, Jingjing; Zhuo, Chuanjun

2017-01-01

Schizophrenia is a disorder of brain dysconnectivity, and both the connection strength and connection number are disrupted in patients with schizophrenia. The functional connectivity density (FCD) can reflect alterations in the connection number. Alterations in the global FCD (gFCD) in schizophrenia were previously demonstrated; however, alterations in two other indices of the pathological characteristics of the brain, local FCD (lFCD) and long-range FCD (lrFCD), have not been revealed. To investigate lFCD and lrFCD alterations in patients with schizophrenia, 95 patients and 93 matched healthy controls were examined using structural and resting-state functional magnetic resonance imaging scanning. lFCD and lrFCD were measured using FCD mapping, and differences were identified using a two-sample t-test in a voxel-wise manner, with age and gender considered to increase variability. Multiple comparisons were performed using a false discovery rate method with a corrected threshold of P<0.05. Our analysis showed that lFCD was primarily decreased in the postcentral gyrus, right calcarine sulcus, and inferior occipital gyrus lobule, but increased in the bilateral subcortical regions. The differences in lFCD were more pronounced and complicated than those in lrFCD. In summary, in contrast with previous studies that focused on the connection strength, our findings, from the perspective of connection number, indicate that schizophrenia is a disorder of brain dysconnectivity, particularly affecting the local functional connectivity network, and support the hypothesis that schizophrenia is associated with a widespread cortical functional connectivity/activity deficit, with hyper- and/or hypo-connectivity/activity coexisting in some cortical or subcortical regions. PMID:28654893

Aberrant patterns of local and long-range functional connectivity densities in schizophrenia.

PubMed

Liu, Chuanxin; Zhang, Wei; Chen, Guangdong; Tian, Hongjun; Li, Jie; Qu, Hongru; Cheng, Langlang; Zhu, Jingjing; Zhuo, Chuanjun

2017-07-18

Schizophrenia is a disorder of brain dysconnectivity, and both the connection strength and connection number are disrupted in patients with schizophrenia. The functional connectivity density (FCD) can reflect alterations in the connection number. Alterations in the global FCD (gFCD) in schizophrenia were previously demonstrated; however, alterations in two other indices of the pathological characteristics of the brain, local FCD (lFCD) and long-range FCD (lrFCD), have not been revealed. To investigate lFCD and lrFCD alterations in patients with schizophrenia, 95 patients and 93 matched healthy controls were examined using structural and resting-state functional magnetic resonance imaging scanning. lFCD and lrFCD were measured using FCD mapping, and differences were identified using a two-sample t-test in a voxel-wise manner, with age and gender considered to increase variability. Multiple comparisons were performed using a false discovery rate method with a corrected threshold of P<0.05. Our analysis showed that lFCD was primarily decreased in the postcentral gyrus, right calcarine sulcus, and inferior occipital gyrus lobule, but increased in the bilateral subcortical regions. The differences in lFCD were more pronounced and complicated than those in lrFCD. In summary, in contrast with previous studies that focused on the connection strength, our findings, from the perspective of connection number, indicate that schizophrenia is a disorder of brain dysconnectivity, particularly affecting the local functional connectivity network, and support the hypothesis that schizophrenia is associated with a widespread cortical functional connectivity/activity deficit, with hyper- and/or hypo-connectivity/activity coexisting in some cortical or subcortical regions.

Trans-Ethnic Fine-Mapping of Lipid Loci Identifies Population-Specific Signals and Allelic Heterogeneity That Increases the Trait Variance Explained

PubMed Central

Wu, Ying; Waite, Lindsay L.; Jackson, Anne U.; Sheu, Wayne H-H.; Buyske, Steven; Absher, Devin; Arnett, Donna K.; Boerwinkle, Eric; Bonnycastle, Lori L.; Carty, Cara L.; Cheng, Iona; Cochran, Barbara; Croteau-Chonka, Damien C.; Dumitrescu, Logan; Eaton, Charles B.; Franceschini, Nora; Guo, Xiuqing; Henderson, Brian E.; Hindorff, Lucia A.; Kim, Eric; Kinnunen, Leena; Komulainen, Pirjo; Lee, Wen-Jane; Le Marchand, Loic; Lin, Yi; Lindström, Jaana; Lingaas-Holmen, Oddgeir; Mitchell, Sabrina L.; Narisu, Narisu; Robinson, Jennifer G.; Schumacher, Fred; Stančáková, Alena; Sundvall, Jouko; Sung, Yun-Ju; Swift, Amy J.; Wang, Wen-Chang; Wilkens, Lynne; Wilsgaard, Tom; Young, Alicia M.; Adair, Linda S.; Ballantyne, Christie M.; Bůžková, Petra; Chakravarti, Aravinda; Collins, Francis S.; Duggan, David; Feranil, Alan B.; Ho, Low-Tone; Hung, Yi-Jen; Hunt, Steven C.; Hveem, Kristian; Juang, Jyh-Ming J.; Kesäniemi, Antero Y.; Kuusisto, Johanna; Laakso, Markku; Lakka, Timo A.; Lee, I-Te; Leppert, Mark F.; Matise, Tara C.; Moilanen, Leena; Njølstad, Inger; Peters, Ulrike; Quertermous, Thomas; Rauramaa, Rainer; Rotter, Jerome I.; Saramies, Jouko; Tuomilehto, Jaakko; Uusitupa, Matti; Wang, Tzung-Dau; Mohlke, Karen L.

2013-01-01

Genome-wide association studies (GWAS) have identified ∼100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), respectively, in individuals of African American (n = 6,832), East Asian (n = 9,449), and European (n = 10,829) ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1×10−4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies. PMID:23555291

Spectroscopic investigations (FT-IR, UV, 1H and 13C NMR) and DFT/TD-DFT calculations of potential analgesic drug 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone

NASA Astrophysics Data System (ADS)

Sroczyński, Dariusz; Malinowski, Zbigniew

2017-12-01

The theoretical molecular geometry and the IR, UV, 1H and 13C NMR spectroscopic properties of 2-[2-(dimethylamino)ethyl]-6-methoxy-4-(pyridin-2-yl)-1(2H)-phthalazinone with the previously demonstrated in vivo analgesic activity were characterized. The conformational analysis, performed using the molecular mechanics method with the General AMBER Force Field (GAFF) and the Density Functional Theory (DFT) approach with the B3LYP hybrid functional and the 6-31 + g(d) basis sets, allowed to determine the most stable rotamer. The theoretical molecular geometry of this conformer was then calculated at the B3LYP/6-311++g(d,p) level of theory, and its phthalazinone core was compared with the experimental geometry of 1(2H)-phthalazinone. The calculated vibrational frequencies and the potential energy distribution enabled to assign the theoretical vibrational modes to the experimental FT-IR bands. The UV spectrum calculated with the Time-Dependent Density Functional Theory (TD-DFT) method in methanol identified the main electronic transitions and their character. 1H and 13C NMR chemical shifts simulated by the Gauge-Independent Atomic Orbital (GIAO) method in chloroform confirmed the previous assignment of the experimental resonance signals. The stability of the molecule was considered taking into account the hyperconjugation and electron density delocalization effects evaluated by the Natural Bond Orbital (NBO) method. The calculated spatial distribution of molecular electrostatic potential made possible to estimate the regions with nucleophilic and electrophilic properties. The results of the potentiodynamic polarization measurements were also indicated the corrosion inhibition activity of the title compound on 100Cr6 bearing steel in 1 mol dm-3 HCl solution.

Functional Reorganization in the Developing Lexicon: Separable and Changing Influences of Lexical and Phonological Variables on Children's Fast-Mapping

ERIC Educational Resources Information Center

McKean, Cristina; Letts, Carolyn; Howard, David

2013-01-01

Neighbourhood Density (ND) and Phonotactic Probability (PP) influence word learning in children. This influence appears to change over development but the separate developmental trajectories of influence of PP and ND on word learning have not previously been mapped. This study examined the cross-sectional developmental trajectories of influence of…

Structure-Property Relationships in Porous 3-D Nanostructures as a Function of Preparation Conditions: Isocyanate Cross-Linked Silica Aerogels

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Capadona, Lynn A.; McCorkle, Linda; Padadopoulos, Demetrios S.; Leventis, Nicholas

2007-01-01

Sol-gel derived silica aerogels are attractive candidates for many unique thermal, optical, catalytic, and chemical applications because of their low density and high mesoporosity. However, their inherent fragility has restricted use of aerogel monoliths to applications where they are not subject to any load. We have previously reported cross-linking the mesoporous silica structure of aerogels with di-isocyanates, styrenes or epoxies reacting with amine decorated silica surfaces. These approaches have been shown to significantly increase the strength of aerogels with only a small effect on density or porosity. Though density is a prime predictor of properties such as strength and thermal conductivity for aerogels, it is becoming clear from previous studies that varying the silica backbone and size of the polymer cross-link independently can give rise to combinations of properties which cannot be predicted from density alone. Herein, we examine the effects of four processing parameters for producing this type of polymer cross-linked aerogel on properties of the resulting monoliths. We focus on the results of C-13 CP-MAS NMR which gives insight to the size and structure of polymer cross-link present in the monoliths, and relates the size of the cross-links to microstructure, mechanical properties and other characteristics of the materials obtained.

Structure-Property Relationships in Porous 3-D Nanostructures as a Function of Preparation Conditions: Isocyanate Cross-Linked Silica Aerogels

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Capadona, Lynn A.; McCorkle, Linda; Papadopoulos, Demetrios S.; Leventis, Nicholas

2007-01-01

Sol-gel derived silica aerogels are attractive candidates for many unique thermal, optical, catalytic, and chemical applications because of their low density and high mesoporosity. However, their inherent fragility has restricted use of aerogel monoliths to applications where they are not subject to any load. We have previously reported cross-linking the mesoporous silica structure of aerogels with di-isocyanates, styrenes or epoxies reacting with amine decorated silica surfaces. These approaches have been shown to significantly increase the strength of aerogels with only a small effect on density or porosity. Though density is a prime predictor of properties such as strength and thermal conductivity for aerogels, it is becoming clear from previous studies that varying the silica backbone and size of the polymer cross-link independently can give rise to combinations of properties which cannot be predicted from density alone. Herein, we examine the effects of four processing parameters for producing this type of polymer cross-linked aerogel on properties of the resulting monoliths. We focus on the results of 13C CP-MAS NMR which gives insight to the size and structure of polymer cross-link present in the monoliths, and relates the size of the cross-links to microstructure, mechanical properties and other characteristics of the materials obtained.

Molecularly Engineered Azobenzene Derivatives for High Energy Density Solid-State Solar Thermal Fuels.

PubMed

Cho, Eugene N; Zhitomirsky, David; Han, Grace G D; Liu, Yun; Grossman, Jeffrey C

2017-03-15

Solar thermal fuels (STFs) harvest and store solar energy in a closed cycle system through conformational change of molecules and can release the energy in the form of heat on demand. With the aim of developing tunable and optimized STFs for solid-state applications, we designed three azobenzene derivatives functionalized with bulky aromatic groups (phenyl, biphenyl, and tert-butyl phenyl groups). In contrast to pristine azobenzene, which crystallizes and makes nonuniform films, the bulky azobenzene derivatives formed uniform amorphous films that can be charged and discharged with light and heat for many cycles. Thermal stability of the films, a critical metric for thermally triggerable STFs, was greatly increased by the bulky functionalization (up to 180 °C), and we were able to achieve record high energy density of 135 J/g for solid-state STFs, over a 30% improvement compared to previous solid-state reports. Furthermore, the chargeability in the solid state was improved, up to 80% charged from 40% charged in previous solid-state reports. Our results point toward molecular engineering as an effective method to increase energy storage in STFs, improve chargeability, and improve the thermal stability of the thin film.

Atomic structure of self-organizing iridium induced nanowires on Ge(001)

NASA Astrophysics Data System (ADS)

Kabanov, N. S.; Heimbuch, R.; Zandvliet, H. J. W.; Saletsky, A. M.; Klavsyuk, A. L.

2017-05-01

The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.

Density functional simulations of Sb-rich GeSbTe phase change alloys.

PubMed

Gabardi, S; Caravati, S; Bernasconi, M; Parrinello, M

2012-09-26

We generated models of the amorphous phase of Sb-rich GeSbTe phase change alloys by quenching from the melt within density functional molecular dynamics. We considered the two compositions Ge(1)Sb(1)Te(1) and Ge(2)Sb(4)Te(5). Comparison with previous results on the most studied Ge(2)Sb(2)Te(5) allowed us to draw some conclusions on the dependence of the structural properties of the amorphous phase on the alloy composition. Vibrational and electronic properties were also scrutinized. Phonons at high frequencies above 200 cm(-1) are localized in tetrahedra around Ge atoms in Sb-rich compounds as well as in Ge(2)Sb(2)Te(5). All compounds are semiconducting in the amorphous phase, with a band gap in the range 0.7-1.0 eV.

Density functional simulations of Sb-rich GeSbTe phase change alloys

NASA Astrophysics Data System (ADS)

Gabardi, S.; Caravati, S.; Bernasconi, M.; Parrinello, M.

2012-09-01

We generated models of the amorphous phase of Sb-rich GeSbTe phase change alloys by quenching from the melt within density functional molecular dynamics. We considered the two compositions Ge1Sb1Te1 and Ge2Sb4Te5. Comparison with previous results on the most studied Ge2Sb2Te5 allowed us to draw some conclusions on the dependence of the structural properties of the amorphous phase on the alloy composition. Vibrational and electronic properties were also scrutinized. Phonons at high frequencies above 200 cm-1 are localized in tetrahedra around Ge atoms in Sb-rich compounds as well as in Ge2Sb2Te5. All compounds are semiconducting in the amorphous phase, with a band gap in the range 0.7-1.0 eV.

Solving the Self-Interaction Problem in Kohn-Sham Density Functional Theory. Application to Atoms

DOE PAGES

Daene, M.; Gonis, A.; Nicholson, D. 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

New optimization scheme to obtain interaction potentials for oxide glasses

NASA Astrophysics Data System (ADS)

Sundararaman, Siddharth; Huang, Liping; Ispas, Simona; Kob, Walter

2018-05-01

We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational density of state of the glass, both obtained from ab initio simulations, as well as experimental data on the pressure dependence of the density of the glass. For the case of silica, we find that this new scheme facilitates finding pair potentials that are significantly more accurate than the previous ones even if the functional form is the same, thus demonstrating that even simple two-body potentials can be superior to more complex three-body potentials. We have tested the new potential by calculating the pressure dependence of the elastic moduli and found a good agreement with the corresponding experimental data.

Density functional theory study of 3R- and 2H-CuAlO2 under pressure

NASA Astrophysics Data System (ADS)

Liu, Qi-Jun; Liu, Zheng-Tang; Feng, Li-Ping; Tian, Hao; Liu, Wen-Ting; Yan, Feng

2010-10-01

We present a first-principles density-functional theory based study of the impact of pressure on the structural and elastic properties of bulk 3R- and 2H-CuAlO2. The ground state properties of 3R- and 2H-CuAlO2 are obtained, which are in good agreement with previous experimental and theoretical data. The analysis of enthalpy variation with pressure indicates the phase transition pressure between 3R and 2H is 15.4 GPa. The independent elastic constants of 3R- and 2H-CuAlO2 are calculated. As the applied pressure increases, the calculations show the presences of mechanical instability at 26.2 and 27.8 GPa for 3R- and 2H-CuAlO2, which are possibly related with the phase transitions.

Impaired lipoprotein processing in HIV patients on antiretroviral therapy: aberrant high-density lipoprotein lipids, stability, and function.

PubMed

Gillard, Baiba K; Raya, Joe L; Ruiz-Esponda, Raul; Iyer, Dinakar; Coraza, Ivonne; Balasubramanyam, Ashok; Pownall, Henry J

2013-07-01

HIV patients on antiretroviral therapy (HIV/ART) exhibit a unique atherogenic dyslipidemic profile with hypertriglyceridemia (HTG) and low plasma concentrations of high-density lipoprotein (HDL) cholesterol. In the Heart Positive Study of HIV/ART patients, a hypolipidemic therapy of fenofibrate, niacin, diet, and exercise reduced HTG and plasma non-HDL cholesterol concentrations and raised plasma HDL cholesterol and adiponectin concentrations. We tested the hypothesis that HIV/ART HDL have abnormal structures and properties and are dysfunctional. Hypolipidemic therapy reduced the TG contents of low-density lipoprotein and HDL. At baseline, HIV/ART low-density lipoproteins were more triglyceride (TG)-rich and HDL were more TG- and cholesteryl ester-rich than the corresponding lipoproteins from normolipidemic (NL) subjects. Very-low-density lipoproteins, low-density lipoprotein, and HDL were larger than the corresponding lipoproteins from NL subjects; HIV/ART HDL were less stable than NL HDL. HDL-[(3)H]cholesteryl ester uptake by Huh7 hepatocytes was used to assess HDL functionality. HIV/ART plasma were found to contain significantly less competitive inhibition activity for hepatocyte HDL-cholesteryl ester uptake than NL plasma were found to contain (P<0.001). Compared with NL subjects, lipoproteins from HIV/ART patients are larger and more neutral lipid-rich, and their HDL are less stable and less receptor-competent. On the basis of this work and previous studies of lipase activity in HIV, we present a model in which plasma lipolytic activities or hepatic cholesteryl ester uptake are impaired in HIV/ART patients. These findings provide a rationale to determine whether the distinctive lipoprotein structure, properties, and function of HIV/ART HDL predict atherosclerosis as assessed by carotid artery intimal medial thickness.

Exact density-potential pairs from complex-shifted axisymmetric systems

NASA Astrophysics Data System (ADS)

Ciotti, Luca; Marinacci, Federico

2008-07-01

In a previous paper, the complex-shift method has been applied to self-gravitating spherical systems, producing new analytical axisymmetric density-potential pairs. We now extend the treatment to the Miyamoto-Nagai disc and the Binney logarithmic halo, and we study the resulting axisymmetric and triaxial analytical density-potential pairs; we also show how to obtain the surface density of shifted systems from the complex shift of the surface density of the parent model. In particular, the systems obtained from Miyamoto-Nagai discs can be used to describe disc galaxies with a peanut-shaped bulge or with a central triaxial bar, depending on the direction of the shift vector. By using a constructive method that can be applied to generic axisymmetric systems, we finally show that the Miyamoto-Nagai and the Satoh discs, and the Binney logarithmic halo cannot be obtained from the complex shift of any spherical parent distribution. As a by-product of this study, we also found two new generating functions in closed form for even and odd Legendre polynomials, respectively.

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

DOE PAGES

Barja, Sara; Wickenburg, Sebastian; Liu, Zhen-Fei; ...

2016-04-18

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent densitymore » of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.« less

Density functional theory investigation of the geometric and electronic structures of [UO2(H2O)m(OH)n](2 - n) (n + m = 5).

PubMed

Ingram, Kieran I M; Häller, L Jonas L; Kaltsoyannis, Nikolas

2006-05-28

Gradient corrected density functional theory has been used to calculate the geometric and electronic structures of the family of molecules [UO2(H2O)m(OH)n](2 - n) (n + m = 5). Comparisons are made with previous experimental and theoretical structural and spectroscopic data. r(U-O(yl)) is found to lengthen as water molecules are replaced by hydroxides in the equatorial plane, and the nu(sym) and nu(asym) uranyl vibrational wavenumbers decrease correspondingly. GGA functionals (BP86, PW91 and PBE) are generally found to perform better for the cationic complexes than for the anions. The inclusion of solvent effects using continuum models leads to spurious low frequency imaginary vibrational modes and overall poorer agreement with experimental data for nu(sym) and nu(asym). Analysis of the molecular orbital structure is performed in order to trace the origin of the lengthening and weakening of the U-O(yl) bond as waters are replaced by hydroxides. No evidence is found to support previous suggestions of a competition for U 6d atomic orbitals in U-O(yl) and U-O(hydroxide)pi bonding. Rather, the lengthening and weakening of U-O(yl) is attributed to reduced ionic bonding generated in part by the sigma-donating ability of the hydroxide ligands.

Automatic breast tissue density estimation scheme in digital mammography images

NASA Astrophysics Data System (ADS)

Menechelli, Renan C.; Pacheco, Ana Luisa V.; Schiabel, Homero

2017-03-01

Cases of breast cancer have increased substantially each year. However, radiologists are subject to subjectivity and failures of interpretation which may affect the final diagnosis in this examination. The high density features in breast tissue are important factors related to these failures. Thus, among many functions some CADx (Computer-Aided Diagnosis) schemes are classifying breasts according to the predominant density. In order to aid in such a procedure, this work attempts to describe automated software for classification and statistical information on the percentage change in breast tissue density, through analysis of sub regions (ROIs) from the whole mammography image. Once the breast is segmented, the image is divided into regions from which texture features are extracted. Then an artificial neural network MLP was used to categorize ROIs. Experienced radiologists have previously determined the ROIs density classification, which was the reference to the software evaluation. From tests results its average accuracy was 88.7% in ROIs classification, and 83.25% in the classification of the whole breast density in the 4 BI-RADS density classes - taking into account a set of 400 images. Furthermore, when considering only a simplified two classes division (high and low densities) the classifier accuracy reached 93.5%, with AUC = 0.95.

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

DOE PAGES

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

2017-11-09

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Collective charge excitations and the metal-insulator transition in the square lattice Hubbard-Coulomb model

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

Ulybyshev, Maksim; Winterowd, Christopher; Zafeiropoulos, Savvas

Here in this article, we discuss the nontrivial collective charge excitations (plasmons) of the extended square lattice Hubbard model. Using a fully nonperturbative approach, we employ the hybrid Monte Carlo algorithm to simulate the system at half-filling. A modified Backus-Gilbert method is introduced to obtain the spectral functions via numerical analytic continuation. We directly compute the single-particle density of states which demonstrates the formation of Hubbard bands in the strongly correlated phase. The momentum-resolved charge susceptibility also is computed on the basis of the Euclidean charge-density-density correlator. In agreement with previous extended dynamical mean-field theory studies, we find that, atmore » high strength of the electron-electron interaction, the plasmon dispersion develops two branches.« less

Wave dynamics in an extended macroscopic traffic flow model with periodic boundaries

NASA Astrophysics Data System (ADS)

Wang, Yu-Qing; Chu, Xing-Jian; Zhou, Chao-Fan; Yan, Bo-Wen; Jia, Bin; Fang, Chen-Hao

2018-06-01

Motivated by the previous traffic flow model considering the real-time traffic state, a modified macroscopic traffic flow model is established. The periodic boundary condition is applied to the car-following model. Besides, the traffic state factor R is defined in order to correct the real traffic conditions in a more reasonable way. It is a key step that we introduce the relaxation time as a density-dependent function and provide corresponding evolvement of traffic flow. Three different typical initial densities, namely the high density, the medium one and the low one, are intensively investigated. It can be found that the hysteresis loop exists in the proposed periodic-boundary system. Furthermore, the linear and nonlinear stability analyses are performed in order to test the robustness of the system.

Cometary water-group ions in the region surrounding Comet Giacobini-Zinner - Distribution functions and bulk parameter estimates

NASA Astrophysics Data System (ADS)

Staines, K.; Balogh, A.; Cowley, S. W. H.; Hynds, R. J.; Yates, T. S.; Richardson, I. G.; Sanderson, T. R.; Wenzel, K. P.; McComas, D. J.; Tsurutani, B. T.

1991-03-01

The bulk parameters (number density and thermal energy density) of cometary water-group ions in the region surrounding Comet Giacobini-Zinner have been derived using data from the EPAS instrument on the ICE spacecraft. The derivation is based on the assumption that the pick-up ion distribution function is isotropic in the frame of the bulk flow, an approximation which has previously been shown to be reasonable within about 400,000 km of the comet nucleus along the spacecraft trajectory. The transition between the pick-up and mass-loaded regions occurs at the cometary shock, which was traversed at a cometocentric distance of about 100,000 km along the spacecraft track. Examination of the ion distribution functions in this region, transformed to the bulk flow frame, indicates the occurrence of a flattened distribution in the vicinity of the local pick-up speed, and a steeply falling tail at speeds above, which may be approximated as an exponential in ion speed.

Band structure calculations of CuAlO2, CuGaO2, CuInO2, and CuCrO2 by screened exchange

NASA Astrophysics Data System (ADS)

Gillen, Roland; Robertson, John

2011-07-01

We report density functional theory band structure calculations on the transparent conducting oxides CuAlO2, CuGaO2, CuInO2, and CuCrO2. The use of the hybrid functional screened-exchange local density approximation (sX-LDA) leads to considerably improved electronic properties compared to standard LDA and generalized gradient approximation (GGA) approaches. We show that the resulting electronic band gaps compare well with experimental values and previous quasiparticle calculations, and show the correct trends with respect to the atomic number of the cation (Al, Ga, In). The resulting energetic depths of Cu d and O p levels and the valence-band widths are considerable improvements compared to LDA and GGA and are in good agreement with available x-ray photoelectron spectroscopy data. Lastly, we show the calculated imaginary part of the dielectric function for all four systems.

A magnetic and electronic circular dichroism study of azurin, plastocyanin, cucumber basic protein, and nitrite reductase based on time-dependent density functional theory calculations.

PubMed

Zhekova, Hristina R; Seth, Michael; Ziegler, Tom

2010-06-03

The excitation, circular dichroism, magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of small models of four blue copper proteins are simulated on the TDDFT/BP86 level. X-Ray diffraction geometries are used for the modeling of the blue copper sites in azurin, plastocyanin, cucumber basic protein, and nitrite reductase. Comparison with experimental data reveals that the calculations reproduce most of the qualitative trends of the observed experimental spectra with some discrepancies in the orbital decompositions and the values of the excitation energies, the g( parallel) components of the g tensor, and the components of the A tensor. These discrepancies are discussed relative to deficiencies in the time-dependent density functional theory (TDDFT) methodology, as opposed to previous studies which address them as a result of insufficient model size or poor performance of the BP86 functional. In addition, attempts are made to elucidate the correlation between the MCD and EPR signals.

Surface reconstruction of InAs (001) depending on the pressure and temperature examined by density functional thermodynamics.

PubMed

Yeu, In Won; Park, Jaehong; Han, Gyuseung; Hwang, Cheol Seong; Choi, Jung-Hae

2017-09-06

A detailed understanding of the atomic configuration of the compound semiconductor surface, especially after reconstruction, is very important for the device fabrication and performance. While there have been numerous experimental studies using the scanning probe techniques, further theoretical studies on surface reconstruction are necessary to promote the clear understanding of the origins and development of such subtle surface structures. In this work, therefore, a pressure-temperature surface reconstruction diagram was constructed for the model case of the InAs (001) surface considering both the vibrational entropy and configurational entropy based on the density functional theory. Notably, the equilibrium fraction of various reconstructions was determined as a function of the pressure and temperature, not as a function of the chemical potential, which largely facilitated the direct comparison with the experiments. By taking into account the entropy effects, the coexistence of the multiple reconstructions and the fractional change of each reconstruction by the thermodynamic condition were predicted and were in agreement with the previous experimental observations. This work provides the community with a useful framework for such type of theoretical studies.

Restoring Cystic Fibrosis Transmembrane Conductance Regulator Function Reduces Airway Bacteria and Inflammation in People with Cystic Fibrosis and Chronic Lung Infections.

PubMed

Hisert, Katherine B; Heltshe, Sonya L; Pope, Christopher; Jorth, Peter; Wu, Xia; Edwards, Rachael M; Radey, Matthew; Accurso, Frank J; Wolter, Daniel J; Cooke, Gordon; Adam, Ryan J; Carter, Suzanne; Grogan, Brenda; Launspach, Janice L; Donnelly, Seamas C; Gallagher, Charles G; Bruce, James E; Stoltz, David A; Welsh, Michael J; Hoffman, Lucas R; McKone, Edward F; Singh, Pradeep K

2017-06-15

Previous work indicates that ivacaftor improves cystic fibrosis transmembrane conductance regulator (CFTR) activity and lung function in people with cystic fibrosis and G551D-CFTR mutations but does not reduce density of bacteria or markers of inflammation in the airway. These findings raise the possibility that infection and inflammation may progress independently of CFTR activity once cystic fibrosis lung disease is established. To better understand the relationship between CFTR activity, airway microbiology and inflammation, and lung function in subjects with cystic fibrosis and chronic airway infections. We studied 12 subjects with G551D-CFTR mutations and chronic airway infections before and after ivacaftor. We measured lung function, sputum bacterial content, and inflammation, and obtained chest computed tomography scans. Ivacaftor produced rapid decreases in sputum Pseudomonas aeruginosa density that began within 48 hours and continued in the first year of treatment. However, no subject eradicated their infecting P. aeruginosa strain, and after the first year P. aeruginosa densities rebounded. Sputum total bacterial concentrations also decreased, but less than P. aeruginosa. Sputum inflammatory measures decreased significantly in the first week of treatment and continued to decline over 2 years. Computed tomography scans obtained before and 1 year after ivacaftor treatment revealed that ivacaftor decreased airway mucous plugging. Ivacaftor caused marked reductions in sputum P. aeruginosa density and airway inflammation and produced modest improvements in radiographic lung disease in subjects with G551D-CFTR mutations. However, P. aeruginosa airway infection persisted. Thus, measures that control infection may be required to realize the full benefits of CFTR-targeting treatments.

Cost Modeling for Space Optical Telescope Assemblies

NASA Technical Reports Server (NTRS)

Stahl, H. Philip; Henrichs, Todd; Luedtke, Alexander; West, Miranda

2011-01-01

Parametric cost models are used to plan missions, compare concepts and justify technology investments. This paper reviews an on-going effort to develop cost modes for space telescopes. This paper summarizes the methodology used to develop cost models and documents how changes to the database have changed previously published preliminary cost models. While the cost models are evolving, the previously published findings remain valid: it costs less per square meter of collecting aperture to build a large telescope than a small telescope; technology development as a function of time reduces cost; and lower areal density telescopes cost more than more massive telescopes.

The Evolution of the Galaxy Rest-Frame Ultraviolet Luminosity Function Over the First Two Billion Years

NASA Technical Reports Server (NTRS)

Finkelstein, Steven L.; Ryan, Russell E., Jr.; Papovich, Casey; Dickinson, Mark; Song, Mimi; Somerville, Rachel; Ferguson, Henry C.; Salmon, Brett; Giavalisco, Mauro; Koekomoer, Anton M.;

Does the HI Mass Function Vary with Environment?

NASA Astrophysics Data System (ADS)

Minchin, Robert F.

2017-01-01

Based on analysis of a large dataset from the ALFALFA survey, Jones et al. (2016) recently claimed that the slope of the HI mass function is constant across different galactic environments, defined by their density. They point out that this finding is “perplexing” given that many previous studies have found that the HI mass functions of groups of galaxies have flat slopes, while the general field has a relatively steep slope. I argue that the analysis of Jones et al., and similar analyses in the past, is flawed as they examine the HI mass function of the galaxies found in environments with a given density, summed across the survey, not the HI mass function actually present in the individual structures at that density. If the position of the knee in the HI mass function were to vary between these structures, then the slope of the HI mass function found by summing across all of the structures with a given density would be steeper than the slope actually found in the individual structures. For example, if a survey were to contain three groups of galaxies, all with flat HI mass functions, but with the ‘knee’, at the mass of the largest galaxy in the group, at 108, 109 and 1010 solar masses, then the summed HI mass function would appear to have a knee at 1010 solar masses and a steep slope below this, rather than the flat slope that is actually present in the individual environments. It is not possible, therefore, to say from the analysis of Jones et al. that there is no dependence of the HI mass function on environment. This scenario explains the “seemingly contradictory findings” of Jones et al. and the earlier studies of individual groups as being due to differences in what is being studies, without having to invoke methodological errors in the derivation of the HI mass function.The Arecibo Observatory is operated by SRI International under a cooperative agreement with the National Science Foundation (AST-1100968), and in alliance with Ana G. Méndez-Universidad Metropolitana, and the Universities Space Research Association.

Use of the interior cavity of the P22 capsid for site-specific initiation of atom-transfer radical polymerization with high-density cargo loading

NASA Astrophysics Data System (ADS)

Lucon, Janice; Qazi, Shefah; Uchida, Masaki; Bedwell, Gregory J.; Lafrance, Ben; Prevelige, Peter E.; Douglas, Trevor

2012-10-01

Virus-like particles (VLPs) have emerged as important and versatile architectures for chemical manipulation in the development of functional hybrid nanostructures. Here we demonstrate a successful site-selective initiation of atom-transfer radical polymerization reactions to form an addressable polymer constrained within the interior cavity of a VLP. Potentially, this protein-polymer hybrid of P22 and cross-linked poly(2-aminoethyl methacrylate) could be useful as a new high-density delivery vehicle for the encapsulation and delivery of small-molecule cargos. In particular, the encapsulated polymer can act as a scaffold for the attachment of small functional molecules, such as fluorescein dye or the magnetic resonance imaging (MRI) contrast agent Gd-diethylenetriaminepentacetate, through reactions with its pendant primary amine groups. Using this approach, a significant increase in the labelling density of the VLP, compared to that of previous modifications of VLPs, can be achieved. These results highlight the use of multimeric protein-polymer conjugates for their potential utility in the development of VLP-based MRI contrast agents with the possibility of loading other cargos.

Self-consistent pseudopotential calculation of the bulk properties of Mo and W

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

Zunger, A.; Cohen, M.L.

The bulk properties of Mo and W are calculated using the recently developed momentum-space approach for calculating total energy via a nonlocal pseudopotential. This approach avoids any shape approximation to the variational charge density (e.g., muffin tins), is fully self-consistent, and replaces the multidimensional and multicenter integrals akin to real-space representations by simple and readily convergent reciprocal-space lattice sums. We use first-principles atomic pseudopotentials which have been previously demonstrated to yield band structures and charge densities for both semiconductors and transition metals in good agreement with experiment and all-electron calculations. Using a mixed-basis representation for the crystalline wave function, wemore » are able to accurately reproduce both the localized and itinerant features of the electronic states in these systems. These first-principles pseudopotentials, together with the self-consistent density-functional representation for both the exchange and the correlation screening, yields agreement with experiment of 0.2% in the lattice parameters, 2% and 11% for the binding energies of Mo and W, respectively, and 12% and 7% for the bulk moduli of Mo and W, respectively.« less

Properties of {sup 112}Cd from the (n,n'{gamma}) reaction: Levels and level densities

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

Garrett, P. E.; Lehmann, H.; Jolie, J.

2001-08-01

Levels in {sup 112}Cd have been studied through the (n,n'{gamma}) reaction with monoenergetic neutrons. An extended set of experiments that included excitation functions, {gamma}-ray angular distributions, and {gamma}{gamma} coincidence measurements was performed. A total of 375 {gamma} rays were placed in a level scheme comprising 200 levels (of which 238 {gamma}-ray assignments and 58 levels are newly established) up to 4 MeV in excitation. No evidence to support the existence of 47 levels as suggested in previous studies was found, and these have been removed from the level scheme. From the results, a comparison of the level density is mademore » with the constant temperature and back-shifted Fermi gas models. The back-shifted Fermi gas model with the Gilbert-Cameron spin cutoff parameter provided the best overall fit. Without using the neutron resonance information and only fitting the cumulative number of low-lying levels, the level density parameters extracted are a sensitive function of the maximum energy used in the fit.« less

Photoinduced charge-transfer electronic excitation of tetracyanoethylene/tetramethylethylene complex in dichloromethane

NASA Astrophysics Data System (ADS)

Xu, Long-Kun; Bi, Ting-Jun; Ming, Mei-Jun; Wang, Jing-Bo; Li, Xiang-Yuan

2017-07-01

Based on the previous work on nonequilibrium solvation model by the authors, Intermolecular charge-transfer electronic excitation of tetracyanoethylene (TCE)/tetramethylethylene (TME) π -stacked complex in dichloromethane (DCM) has been investigated. For weak interaction correction, dispersion corrected functional DFT-D3 is adopted for geometry optimization. In order to identify the excitation metric, dipole moment components of each Cartesian direction, atomic charge, charge separation and Δr index are analyzed for TCE/TME complex. Calculation shows that the calculated excitation energy is dependent on the functional choice, when conjuncted with suitable time-dependent density functional, the modified nonequilibrium expression gives satisfied results for intermolecular charge-transfer electronic excitation.

Minimizing antibody surface density on liposomes while sustaining cytokine-activated EC targeting.

PubMed

Almeda, Dariela; Wang, Biran; Auguste, Debra T

2015-02-01

Liposomes may be engineered to target inflamed endothelium by mimicking ligand-receptor interactions between leukocytes and cytokine-activated endothelial cells (ECs). The upregulation and assembly of vascular cell adhesion molecule-1 (VCAM1) and E-selectin on the cell membrane upon exposure to cytokines have shown potential for drug delivery vehicles to target sites of chronic endothelial inflammation, such as atherosclerosis and cancer. Herein, we characterized EC surfaces by measuring the E-selectin and VCAM1 surface densities and adhesion forces of aVCAM1 and aE-selectin to ECs. We quantified the antibody density, ratio, and diffusivity of liposomes to achieve significant binding and internalization. At 1 h, the 1:1 ratio of VCAM1:E-selectin antibodies was significantly higher than 1:0 and 0:1. Significant binding and uptake was achieved at aE-selectin densities as low as 400 molecules/μm(2). The highest levels of binding and uptake were achieved when using a 1:1 ratio of VCAM1:E-selectin antibodies at a density of 1000 molecules/μm(2); this density is 85% lower than previous reports. The binding and uptake of functionalized liposomes were reduced to levels comparable to IgG functionalized liposomes upon a 10-fold reduction in liposome membrane diffusivity. We conclude with a liposomal design that discriminates between healthy and inflamed endothelium while reducing antibody surface presentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Measuring the stellar luminosity function and spatial density profile of the inner 0.5 pc of the Milky Way nuclear star cluster

NASA Astrophysics Data System (ADS)

Do, Tuan; Ghez, Andrea; Lu, Jessica R.; Morris, Mark R.; Yelda, Sylvana; Martinez, Gregory D.; Peter, Annika H. G.; Wright, Shelley; Bullock, James; Kaplinghat, Manoj; Matthews, K.

2012-07-01

We report on measurements of the luminosity function of early (young) and late-type (old) stars in the central 0.5 pc of the Milky Way nuclear star cluster as well as the density profiles of both components. The young (~ 6 Myr) and old stars (> 1 Gyr) in this region provide different physical probes of the environment around a supermassive black hole; the luminosity function of the young stars offers us a way to measure the initial mass function from star formation in an extreme environment, while the density profile of the old stars offers us a probe of the dynamical interaction of a star cluster with a massive black hole. The two stellar populations are separated through a near-infrared spectroscopic survey using the integral-field spectrograph OSIRIS on Keck II behind the laser guide star adaptive optics system. This spectroscopic survey is able to separate early-type (young) and late-type (old) stars with a completeness of 50% at K' = 15.5. We describe our method of completeness correction using a combination of star planting simulations and Bayesian inference. The completeness corrected luminosity function of the early-type stars contains significantly more young stars at faint magnitudes compared to previous surveys with similar depth. In addition, by using proper motion and radial velocity measurements along with anisotropic spherical Jeans modeling of the cluster, it is possible to measure the spatial density profile of the old stars, which has been difficult to constrain with number counts alone. The most probable model shows that the spatial density profile, n(r) propto r-γ, to be shallow with γ = 0.4 ± 0.2, which is much flatter than the dynamically relaxed case of γ = 3/2 to 7/4, but does rule out a 'hole' in the distribution of old stars. We show, for the first time, that the spatial density profile, the black hole mass, and velocity anisotropy can be fit simultaneously to obtain a black hole mass that is consistent with that derived from individual orbits of stars at distances < 1000 AU from the Galactic center.

Inferring probabilistic stellar rotation periods using Gaussian processes

NASA Astrophysics Data System (ADS)

Angus, Ruth; Morton, Timothy; Aigrain, Suzanne; Foreman-Mackey, Daniel; Rajpaul, Vinesh

2018-02-01

Variability in the light curves of spotted, rotating stars is often non-sinusoidal and quasi-periodic - spots move on the stellar surface and have finite lifetimes, causing stellar flux variations to slowly shift in phase. A strictly periodic sinusoid therefore cannot accurately model a rotationally modulated stellar light curve. Physical models of stellar surfaces have many drawbacks preventing effective inference, such as highly degenerate or high-dimensional parameter spaces. In this work, we test an appropriate effective model: a Gaussian Process with a quasi-periodic covariance kernel function. This highly flexible model allows sampling of the posterior probability density function of the periodic parameter, marginalizing over the other kernel hyperparameters using a Markov Chain Monte Carlo approach. To test the effectiveness of this method, we infer rotation periods from 333 simulated stellar light curves, demonstrating that the Gaussian process method produces periods that are more accurate than both a sine-fitting periodogram and an autocorrelation function method. We also demonstrate that it works well on real data, by inferring rotation periods for 275 Kepler stars with previously measured periods. We provide a table of rotation periods for these and many more, altogether 1102 Kepler objects of interest, and their posterior probability density function samples. Because this method delivers posterior probability density functions, it will enable hierarchical studies involving stellar rotation, particularly those involving population modelling, such as inferring stellar ages, obliquities in exoplanet systems, or characterizing star-planet interactions. The code used to implement this method is available online.

Determination of Charge-Carrier Mobility in Disordered Thin-Film Solar Cells as a Function of Current Density

NASA Astrophysics Data System (ADS)

Mäckel, Helmut; MacKenzie, Roderick C. I.

2018-03-01

Charge-carrier mobility is a fundamental material parameter, which plays an important role in determining solar-cell efficiency. The higher the mobility, the less time a charge carrier will spend in a device and the less likely it is that it will be lost to recombination. Despite the importance of this physical property, it is notoriously difficult to measure accurately in disordered thin-film solar cells under operating conditions. We, therefore, investigate a method previously proposed in the literature for the determination of mobility as a function of current density. The method is based on a simple analytical model that relates the mobility to carrier density and transport resistance. By revising the theoretical background of the method, we clearly demonstrate what type of mobility can be extracted (constant mobility or effective mobility of electrons and holes). We generalize the method to any combination of measurements that is able to determine the mean electron and hole carrier density, and the transport resistance at a given current density. We explore the robustness of the method by simulating typical organic solar-cell structures with a variety of physical properties, including unbalanced mobilities, unbalanced carrier densities, and for high or low carrier trapping rates. The simulations reveal that near VOC and JSC , the method fails due to the limitation of determining the transport resistance. However, away from these regions (and, importantly, around the maximum power point), the method can accurately determine charge-carrier mobility. In the presence of strong carrier trapping, the method overestimates the effective mobility due to an underestimation of the carrier density.

Steady-state probability density function of the phase error for a DPLL with an integrate-and-dump device

NASA Technical Reports Server (NTRS)

Simon, M.; Mileant, A.

1986-01-01

The steady-state behavior of a particular type of digital phase-locked loop (DPLL) with an integrate-and-dump circuit following the phase detector is characterized in terms of the probability density function (pdf) of the phase error in the loop. Although the loop is entirely digital from an implementation standpoint, it operates at two extremely different sampling rates. In particular, the combination of a phase detector and an integrate-and-dump circuit operates at a very high rate whereas the loop update rate is very slow by comparison. Because of this dichotomy, the loop can be analyzed by hybrid analog/digital (s/z domain) techniques. The loop is modeled in such a general fashion that previous analyses of the Real-Time Combiner (RTC), Subcarrier Demodulator Assembly (SDA), and Symbol Synchronization Assembly (SSA) fall out as special cases.

Effects of plasmon pole models on the G0W0 electronic structure of various oxides

NASA Astrophysics Data System (ADS)

Miglio, A.; Waroquiers, D.; Antonius, G.; Giantomassi, M.; Stankovski, M.; Côté, M.; Gonze, X.; Rignanese, G.-M.

2012-09-01

The electronic properties of three different oxides (ZnO, SnO2 and SiO2) are investigated within many-body perturbation theory in the G 0 W 0 approximation. The frequency dependence of the dielectric function is either approximated using two different well-established plasmon-pole models (one of which enforces the fulfillment of the f-sum rule) or treated explicitly by means of the contour-deformation approach. Comparing these results, it is found that the plasmon-pole model enforcing the f-sum rule gives less accurate results for all three oxides. The calculated electronic properties are also compared with the available experimental data and previous ab initio results, focusing on the d state binding energies. The G 0 W 0 approach leads to significantly improved band gaps with respect to calculations based on the density functional theory in the local density approximation.

Diffusion in shear flow

NASA Astrophysics Data System (ADS)

Dufty, J. W.

1984-09-01

Diffusion of a tagged particle in a fluid with uniform shear flow is described. The continuity equation for the probability density describing the position of the tagged particle is considered. The diffusion tensor is identified by expanding the irreversible part of the probability current to first order in the gradient of the probability density, but with no restriction on the shear rate. The tensor is expressed as the time integral of a nonequilibrium autocorrelation function for the velocity of the tagged particle in its local fluid rest frame, generalizing the Green-Kubo expression to the nonequilibrium state. The tensor is evaluated from results obtained previously for the velocity autocorrelation function that are exact for Maxwell molecules in the Boltzmann limit. The effects of viscous heating are included and the dependence on frequency and shear rate is displayed explicitly. The mode-coupling contributions to the frequency and shear-rate dependent diffusion tensor are calculated.

Constrained variation in Jastrow method at high density

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

Owen, J.C.; Bishop, R.F.; Irvine, J.M.

1976-11-01

A method is derived for constraining the correlation function in a Jastrow variational calculation which permits the truncation of the cluster expansion after two-body terms, and which permits exact minimization of the two-body cluster by functional variation. This method is compared with one previously proposed by Pandharipande and is found to be superior both theoretically and practically. The method is tested both on liquid /sup 3/He, by using the Lennard--Jones potential, and on the model system of neutrons treated as Boltzmann particles (''homework'' problem). Good agreement is found both with experiment and with other calculations involving the explicit evaluation ofmore » higher-order terms in the cluster expansion. The method is then applied to a more realistic model of a neutron gas up to a density of 4 neutrons per F/sup 3/, and is found to give ground-state energies considerably lower than those of Pandharipande. (AIP)« less

Electronic structure and optical properties of CdSxSe1-x solid solution nanostructures from X-ray absorption near edge structure, X-ray excited optical luminescence, and density functional theory investigations

NASA Astrophysics Data System (ADS)

Murphy, M. W.; Yiu, Y. M.; Ward, M. J.; Liu, L.; Hu, Y.; Zapien, J. A.; Liu, Yingkai; Sham, T. K.

2014-11-01

The electronic structure and optical properties of a series of iso-electronic and iso-structural CdSxSe1-x solid solution nanostructures have been investigated using X-ray absorption near edge structure, extended X-ray absorption fine structure, and X-ray excited optical luminescence at various absorption edges of Cd, S, and Se. It is found that the system exhibits compositions, with variable local structure in-between that of CdS and CdSe accompanied by tunable optical band gap between that of CdS and CdSe. Theoretical calculation using density functional theory has been carried out to elucidate the observations. It is also found that luminescence induced by X-ray excitation shows new optical channels not observed previously with laser excitation. The implications of these observations are discussed.

Subcellular localization of celery mannitol dehydrogenase. A cytosolic metabolic enzyme in nuclei.

PubMed Central

Yamamoto, Y T; Zamski, E; Williamson, J D; Conkling, M A; Pharr, D M

1997-01-01

Mannitol dehydrogenase (MTD) is the first enzyme in mannitol catabolism in celery (Apium graveolens L. var dulce [Mill] Pers. cv Florida 638). Mannitol is an important photoassimilate, as well as providing plants with resistance to salt and osmotic stress. Previous work has shown that expression of the celery Mtd gene is regulated by many factors, such as hexose sugars, salt and osmotic stress, and salicylic acid. Furthermore, MTD is present in cells of sink organs, phloem cells, and mannitol-grown suspension cultures. Immunogold localization and biochemical analyses presented here demonstrate that celery MTD is localized in the cytosol and nuclei. Although the cellular density of MTD varies among different cell types, densities of nuclear and cytosolic MTD in a given cell are approximately equal. Biochemical analyses of nuclear extracts from mannitol-grown cultured cells confirmed that the nuclear-localized MTD is enzymatically active. The function(s) of nuclear-localized MTD is unknown. PMID:9414553

Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

NASA Astrophysics Data System (ADS)

Clay, Raymond; Morales, Miguel

2017-06-01

In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

A new efficient method for calculation of Frenkel exciton parameters in molecular aggregates

NASA Astrophysics Data System (ADS)

Plötz, Per-Arno; Niehaus, Thomas; Kühn, Oliver

2014-05-01

The Frenkel exciton Hamiltonian is at the heart of many simulations of excitation energy transfer in molecular aggregates. It separates the aggregate into Coulomb-coupled monomers. Here it is shown that the respective parameters, i.e., monomeric excitation energies and Coulomb couplings between transition densities can be efficiently calculated using time-dependent tight-binding-based density functional theory (TD-DFTB). Specifically, Coulomb couplings are expressed in terms of self-consistently determined Mulliken transition charges. The approach is applied to two dimer systems. First, formaldehyde oxime for which a detailed comparison with standard DFT using the B3LYP and the PBE functionals as well as with SCS-CC2 is provided. Second, the Coulomb coupling is explored in dependence on the intermolecular coordinates for a perylene bisimide dimer. This provides structural evidence for the previously observed biphasic aggregation behavior of this dye.

Energy level alignment of self-assembled linear chains of benzenediamine on Au(111) from first principles

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhen-Fei; Cooper, Valentino R.; Neaton, Jeffrey B.

2016-03-01

Using density functional theory (DFT) with a van der Waals density functional, we calculate the adsorption energetics and geometry of benzenediamine (BDA) molecules on Au(111) surfaces. Our results demonstrate that the reported self-assembled linear chain structure of BDA, stabilized via hydrogen bonds between amine groups, is energetically favored over previously studied monomeric phases. Moreover, using a model, which includes nonlocal polarization effects from the substrate and the neighboring molecules and incorporates many-body perturbation theory calculations within the GW approximation, we obtain approximate self-energy corrections to the DFT highest occupied molecular orbital (HOMO) energy associated with BDA adsorbate phases. We find that, independent of coverage, the HOMO energy of the linear chain phase is lower relative to the Fermi energy than that of the monomer phase, and in good agreement with values measured with ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy.

Comparative analysis of quantum cascade laser modeling based on density matrices and non-equilibrium Green's functions

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

Lindskog, M., E-mail: martin.lindskog@teorfys.lu.se; Wacker, A.; Wolf, J. M.

2014-09-08

We study the operation of an 8.5 μm quantum cascade laser based on GaInAs/AlInAs lattice matched to InP using three different simulation models based on density matrix (DM) and non-equilibrium Green's function (NEGF) formulations. The latter advanced scheme serves as a validation for the simpler DM schemes and, at the same time, provides additional insight, such as the temperatures of the sub-band carrier distributions. We find that for the particular quantum cascade laser studied here, the behavior is well described by simple quantum mechanical estimates based on Fermi's golden rule. As a consequence, the DM model, which includes second order currents,more » agrees well with the NEGF results. Both these simulations are in accordance with previously reported data and a second regrown device.« less

Probabilistic DHP adaptive critic for nonlinear stochastic control systems.

PubMed

Herzallah, Randa

2013-06-01

Following the recently developed algorithms for fully probabilistic control design for general dynamic stochastic systems (Herzallah & Káarnáy, 2011; Kárný, 1996), this paper presents the solution to the probabilistic dual heuristic programming (DHP) adaptive critic method (Herzallah & Káarnáy, 2011) and randomized control algorithm for stochastic nonlinear dynamical systems. The purpose of the randomized control input design is to make the joint probability density function of the closed loop system as close as possible to a predetermined ideal joint probability density function. This paper completes the previous work (Herzallah & Káarnáy, 2011; Kárný, 1996) by formulating and solving the fully probabilistic control design problem on the more general case of nonlinear stochastic discrete time systems. A simulated example is used to demonstrate the use of the algorithm and encouraging results have been obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Simplified curve fits for the thermodynamic properties of equilibrium air

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Tannehill, J. C.; Weilmuenster, K. J.

1987-01-01

New, improved curve fits for the thermodynamic properties of equilibrium air have been developed. The curve fits are for pressure, speed of sound, temperature, entropy, enthalpy, density, and internal energy. These curve fits can be readily incorporated into new or existing computational fluid dynamics codes if real gas effects are desired. The curve fits are constructed from Grabau-type transition functions to model the thermodynamic surfaces in a piecewise manner. The accuracies and continuity of these curve fits are substantially improved over those of previous curve fits. These improvements are due to the incorporation of a small number of additional terms in the approximating polynomials and careful choices of the transition functions. The ranges of validity of the new curve fits are temperatures up to 25 000 K and densities from 10 to the -7 to 10 to the 3d power amagats.

Refinement of the probability density function model for preferential concentration of aerosol particles in isotropic turbulence

NASA Astrophysics Data System (ADS)

Zaichik, Leonid I.; Alipchenkov, Vladimir M.

2007-11-01

The purposes of the paper are threefold: (i) to refine the statistical model of preferential particle concentration in isotropic turbulence that was previously proposed by Zaichik and Alipchenkov [Phys. Fluids 15, 1776 (2003)], (ii) to investigate the effect of clustering of low-inertia particles using the refined model, and (iii) to advance a simple model for predicting the collision rate of aerosol particles. The model developed is based on a kinetic equation for the two-point probability density function of the relative velocity distribution of particle pairs. Improvements in predicting the preferential concentration of low-inertia particles are attained due to refining the description of the turbulent velocity field of the carrier fluid by including a difference between the time scales of the of strain and rotation rate correlations. The refined model results in a better agreement with direct numerical simulations for aerosol particles.

Excess algal symbionts increase the susceptibility of reef corals to bleaching

NASA Astrophysics Data System (ADS)

Cunning, Ross; Baker, Andrew C.

2013-03-01

Rising ocean temperatures associated with global climate change are causing mass coral bleaching and mortality worldwide. Understanding the genetic and environmental factors that mitigate coral bleaching susceptibility may aid local management efforts to help coral reefs survive climate change. Although bleaching susceptibility depends partly on the genetic identity of a coral's algal symbionts, the effect of symbiont density, and the factors controlling it, remain poorly understood. By applying a new metric of symbiont density to study the coral Pocillopora damicornis during seasonal warming and acute bleaching, we show that symbiont cell ratio density is a function of both symbiont type and environmental conditions, and that corals with high densities are more susceptible to bleaching. Higher vulnerability of corals with more symbionts establishes a quantitative mechanistic link between symbiont density and the molecular basis for coral bleaching, and indicates that high densities do not buffer corals from thermal stress, as has been previously suggested. These results indicate that environmental conditions that increase symbiont densities, such as nutrient pollution, will exacerbate climate-change-induced coral bleaching, providing a mechanistic explanation for why local management to reduce these stressors will help coral reefs survive future warming.

Postsynaptic density levels of the NMDA receptor NR1 subunit and PSD-95 protein in prefrontal cortex from people with schizophrenia

PubMed Central

Catts, Vibeke Sørensen; Derminio, Dominique Suzanne; Hahn, Chang-Gyu; Weickert, Cynthia Shannon

2015-01-01

Background: There is converging evidence of involvement of N-methyl-d-aspartate (NMDA) receptor hypofunction in the pathophysiology of schizophrenia. Our group recently identified a decrease in total NR1 mRNA and protein expression in the dorsolateral prefrontal cortex in a case-control study of individuals with schizophrenia (n=37/group). The NR1 subunit is critical to NMDA receptor function at the postsynaptic density, a cellular structure rich in the scaffolding protein, PSD-95. The extent to which the NMDA receptor NR1 subunit is altered at the site of action, in the postsynaptic density, is not clear. Aims: To extend our previous results by measuring levels of NR1 and PSD-95 protein in postsynaptic density-enriched fractions of prefrontal cortex from the same individuals in the case-control study noted above. Methods: Postsynaptic density-enriched fractions were isolated from fresh-frozen prefrontal cortex (BA10) and subjected to western blot analysis for NR1 and PSD-95. Results: We found a 20% decrease in NR1 protein (t(66)=−2.874, P=0.006) and a 30% decrease in PSD-95 protein (t(63)=−2.668, P=0.010) in postsynaptic density-enriched fractions from individuals with schizophrenia relative to unaffected controls. Conclusions: Individuals with schizophrenia have less NR1 protein, and therefore potentially fewer functional NMDA receptors, at the postsynaptic density. The associated decrease in PSD-95 protein at the postsynaptic density suggests that not only are glutamate receptors compromised in individuals with schizophrenia, but the overall spine architecture and downstream signaling supported by PSD-95 may also be deficient. PMID:27336043

Postsynaptic density levels of the NMDA receptor NR1 subunit and PSD-95 protein in prefrontal cortex from people with schizophrenia.

PubMed

Catts, Vibeke Sørensen; Derminio, Dominique Suzanne; Hahn, Chang-Gyu; Weickert, Cynthia Shannon

2015-01-01

There is converging evidence of involvement of N-methyl-d-aspartate (NMDA) receptor hypofunction in the pathophysiology of schizophrenia. Our group recently identified a decrease in total NR1 mRNA and protein expression in the dorsolateral prefrontal cortex in a case-control study of individuals with schizophrenia (n=37/group). The NR1 subunit is critical to NMDA receptor function at the postsynaptic density, a cellular structure rich in the scaffolding protein, PSD-95. The extent to which the NMDA receptor NR1 subunit is altered at the site of action, in the postsynaptic density, is not clear. To extend our previous results by measuring levels of NR1 and PSD-95 protein in postsynaptic density-enriched fractions of prefrontal cortex from the same individuals in the case-control study noted above. Postsynaptic density-enriched fractions were isolated from fresh-frozen prefrontal cortex (BA10) and subjected to western blot analysis for NR1 and PSD-95. We found a 20% decrease in NR1 protein (t(66)=-2.874, P=0.006) and a 30% decrease in PSD-95 protein (t(63)=-2.668, P=0.010) in postsynaptic density-enriched fractions from individuals with schizophrenia relative to unaffected controls. Individuals with schizophrenia have less NR1 protein, and therefore potentially fewer functional NMDA receptors, at the postsynaptic density. The associated decrease in PSD-95 protein at the postsynaptic density suggests that not only are glutamate receptors compromised in individuals with schizophrenia, but the overall spine architecture and downstream signaling supported by PSD-95 may also be deficient.

CPB-K mice a mouse model of schizophrenia? Differences in dopaminergic, serotonergic and behavioral markers compared to BALB/cJ mice.

PubMed

Panther, P; Nullmeier, S; Dobrowolny, H; Schwegler, H; Wolf, R

2012-04-21

Schizophrenia is characterized by disturbances in social behavior, sensorimotor gating and cognitive function, that are discussed to be caused by a termination of different transmitter systems. Beside morphological alterations in cortical and subcortical areas reduced AMPA- NMDA-, 5-HT2-receptor densities and increased 5-HT1-receptor densities are found in the hippocampus.The two inbred mouse strains CPB-K and BALB/cJ are known to display considerable differences in cognitive function and prepulse inhibition, a stable marker of sensorimotor gating. Furthermore, CPB-K mice exhibit lower NMDA-, AMPA- and increased 5-HT-receptor densities in the hippocampus as compared to BALB/cJ mice. We investigated both mouse strains in social interaction test for differences in social behavior and with immuncytochemical approaches for alterations of dopaminergic and serotonergic parameters. Our results can be summarized as follows: compared to BALB/cJ, CPB-K mice showed:(1) significantly reduced traveling distance and number of contacts in social interaction test, (2) differences in the number of serotonin transporter-immunoreactive neurons and volume of raphe nuclei and a lower serotonergic fiber density in the ventral and dorsal hippocampal subfields CA1 and CA3, (3) no alterations of dopaminergic markers like neuron number, neuron density and volume in subregions of substantia nigra and ventral tegmental area, but a significantly higher dopaminergic fiber density in the dorsal hippocampus, the ventral hippocampus of CA1 and gyrus dentatus, (4) no significant differences in serotonergic and dopaminergic fiber densities in the amygdala.Based on our results and previous studies, CPB-K mice compared to BALB/cJ may serve as an important model to understand the interaction of the serotonergic and dopaminergic system and their impact on sensorimotor gating and cognitive function as related to neuropsychiatric disorders like schizophrenia. 2012 Elsevier B.V. All rights reserved.

A transient analysis of frost formation on a parallel plate evaporator

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

Martinez-Frias, J.; Aceves, S.M.; Hernandez-Guerrero, A.

1996-12-31

This paper presents the development of a transient model for evaluating frost formation on a parallel plate evaporator for heat pump applications. The model treats the frost layer as a porous substance, and applies the equations of conservation of mass, momentum and energy to calculate the growth and densification of the frost layer. Empirical correlations for thermal conductivity and tortuosity as a function of density are incorporated from previous studies. Frost growth is calculated as a function of time, Reynolds number, longitudinal location, plate temperature, and ambient air temperature and humidity. The main assumptions are: ideal gas behavior for airmore » and water vapor, uniform frost density and thermal conductivity across the thickness of the frost layer; and quasi-steady conditions during the whole process. The mathematical model is validated by comparing the predicted values of frost thickness and frost density with results obtained in recent experimental studies. A good agreement was obtained in the comparison. The frost formation model calculates pressure drop and heat transfer resistance that result from the existence of the frost layer, and it can therefore be incorporated into a heat pump model to evaluate performance losses due to frosting as a function of weather conditions and time of operation since the last evaporator defrost.« less

Influence of spatial heterogeneity on the type of zooplankton functional response: A study based on field observations

NASA Astrophysics Data System (ADS)

Morozov, Andrew; Arashkevich, Elena; Reigstad, Marit; Falk-Petersen, Stig

2008-10-01

Mathematical models of plankton dynamics are sensitive to the choice of type of zooplankton functional response, i.e., to how the rate of intake of food varies with the food density. Conventionally, the conclusion on the actual type of functional response for a given zooplankton species is made based upon laboratory analysis on experimental feeding. In this paper, we show that such an approach can be too simplistic and misleading. Based on real ocean data obtained from three expeditions of R/V Jan Mayen in the Barents Sea in 2003-2005, we demonstrate that vertical heterogeneity in algal distribution as well as active vertical movement of herbivorous zooplankton can modify the type of trophic response completely. In particular, we found that the rate of average intake of algae by Calanus glacialis exhibits a Holling type III response, instead of Holling type I or II found previously in laboratory experiments. We argue that this conceptual discrepancy is due to the ability of the zooplankton to feed in layers with high algal density and to avoid depths with lower algal density. Since theoretical studies would predict enhancing in system stability in the case of Holling type III, our results may be of importance for understanding the main factors controlling plankton dynamics.

Uniform electron gases. III. Low-density gases on three-dimensional spheres.

PubMed

Agboola, Davids; Knol, Anneke L; Gill, Peter M W; Loos, Pierre-François

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGF centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids - the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) - and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.

Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors

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

Shin, Ilgyou; Carter, Emily A., E-mail: eac@princeton.edu

2014-05-14

We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect andmore » (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.« less

Discontinuous Galerkin finite element method for solving population density functions of cortical pyramidal and thalamic neuronal populations.

PubMed

Huang, Chih-Hsu; Lin, Chou-Ching K; Ju, Ming-Shaung

2015-02-01

Compared with the Monte Carlo method, the population density method is efficient for modeling collective dynamics of neuronal populations in human brain. In this method, a population density function describes the probabilistic distribution of states of all neurons in the population and it is governed by a hyperbolic partial differential equation. In the past, the problem was mainly solved by using the finite difference method. In a previous study, a continuous Galerkin finite element method was found better than the finite difference method for solving the hyperbolic partial differential equation; however, the population density function often has discontinuity and both methods suffer from a numerical stability problem. The goal of this study is to improve the numerical stability of the solution using discontinuous Galerkin finite element method. To test the performance of the new approach, interaction of a population of cortical pyramidal neurons and a population of thalamic neurons was simulated. The numerical results showed good agreement between results of discontinuous Galerkin finite element and Monte Carlo methods. The convergence and accuracy of the solutions are excellent. The numerical stability problem could be resolved using the discontinuous Galerkin finite element method which has total-variation-diminishing property. The efficient approach will be employed to simulate the electroencephalogram or dynamics of thalamocortical network which involves three populations, namely, thalamic reticular neurons, thalamocortical neurons and cortical pyramidal neurons. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification of prominence ejecta by the proton distribution function and magnetic fine structure in ICMEs in the inner heliosphere

NASA Astrophysics Data System (ADS)

Marsch, Eckart; Yao, Shuo; Tu, Chuanyi; Schwenn, Rainer

This work presents in-situ solar wind observations of three magnetic clouds that contain certain cold high-density material, when Helios 2 was located at 0.3 AU, on 9 May 1979, 0.5 AU on 30 March 1976, and 0.7 AU on 24 December 1978, respectively. In the cold high-density regions embedded in the ICMEs we find that (1) the number density of protons is higher than in other regions inside the magnetic cloud (MC), (2)the possible existence of He+, (3) the thermal velocity distribution functions (VDFs) are more isotropic and appear to be colder than in the other regions of the MC, and the proton temperature is lower than that of the ambient plasma, (4) the associated magnetic field configuration can for all three MC events be identified as a flux rope. This cold high-density region is located at the polarity inversion line in the center of the bipolar structure of the MC magnetic field (consistent with previous work of solar observation that a prominence lies over the neutral line of the related bipolar solar magnetic field ). It is the first time that prominence ejecta are identified by both the plasma and magnetic field features inside 1 AU, and that thermal ion velocity distribution functions are used to investigate the microstate of the prominence material. Overall, our in situ observations are consistent with the three-part CME models.

Assessing the spatial relationship between fixation and foveal specializations.

PubMed

Wilk, Melissa A; Dubis, Adam M; Cooper, Robert F; Summerfelt, Phyllis; Dubra, Alfredo; Carroll, Joseph

2017-03-01

Increased cone photoreceptor density, an avascular zone (FAZ), and the displacement of inner retinal neurons to form a pit are distinct features of the human fovea. As the fovea provides the majority of our vision, appreciating how these anatomical specializations are related is important for understanding foveal development, normal visual function, and retinal disease. Here we evaluated the relationship between these specializations and their location relative to the preferred retinal locus of fixation (PRL). We measured foveal pit volume, FAZ area, peak cone density, and location of the PRL in 22 subjects with normal vision using optical coherence tomography and adaptive optics scanning light ophthalmoscopy. Foveal pit volume was positively correlated with FAZ area; however, peak cone density was not correlated with pit volume. In addition, there was no systematic offset of the location of any of these specializations relative to PRL, and there was no correlation between the magnitude of the offset from PRL and the corresponding foveal specialization measurements (pit volume, FAZ area, peak cone density). The standard deviation of our PRL measurements was consistent with previous measurements of fixational stability. These data provide insight into the sequence of events during foveal development and may have implications for visual function and retinal disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Competition of density waves and quantum multicritical behavior in Dirac materials from functional renormalization

NASA Astrophysics Data System (ADS)

Classen, Laura; Herbut, Igor F.; Janssen, Lukas; Scherer, Michael M.

2016-03-01

We study the competition of spin- and charge-density waves and their quantum multicritical behavior for the semimetal-insulator transitions of low-dimensional Dirac fermions. Employing the effective Gross-Neveu-Yukawa theory with two order parameters as a model for graphene and a growing number of other two-dimensional Dirac materials allows us to describe the physics near the multicritical point at which the semimetallic and the spin- and charge-density-wave phases meet. With the help of a functional renormalization group approach, we are able to reveal a complex structure of fixed points, the stability properties of which decisively depend on the number of Dirac fermions Nf. We give estimates for the critical exponents and observe crucial quantitative corrections as compared to the previous first-order ɛ expansion. For small Nf, the universal behavior near the multicritical point is determined by the chiral Heisenberg universality class supplemented by a decoupled, purely bosonic, Ising sector. At large Nf, a novel fixed point with nontrivial couplings between all sectors becomes stable. At intermediate Nf, including the graphene case (Nf=2 ), no stable and physically admissible fixed point exists. Graphene's phase diagram in the vicinity of the intersection between the semimetal, antiferromagnetic, and staggered density phases should consequently be governed by a triple point exhibiting first-order transitions.

Correction to the Beer-Lambert-Bouguer law for optical absorption.

PubMed

Abitan, Haim; Bohr, Henrik; Buchhave, Preben

2008-10-10

The Beer-Lambert-Bouguer absorption law, known as Beer's law for absorption in an optical medium, is precise only at power densities lower than a few kW. At higher power densities this law fails because it neglects the processes of stimulated emission and spontaneous emission. In previous models that considered those processes, an analytical expression for the absorption law could not be obtained. We show here that by utilizing the Lambert W-function, the two-level energy rate equation model is solved analytically, and this leads into a general absorption law that is exact because it accounts for absorption as well as stimulated and spontaneous emission. The general absorption law reduces to Beer's law at low power densities. A criterion for its application is given along with experimental examples. (c) 2008 Optical Society of America

The Luminosity Function and Star Formation Rate Between Redshifts of 0.07 and 1.47 for Narrow-band Emitters in the Subaru Deep Field

NASA Astrophysics Data System (ADS)

Ly, Chun; Malkan, M.; Kashikawa, N.; Shimasaku, K.; Doi, M.; Nagao, T.; Iye, M.; Kodama, T.; Morokuma, T.; Motohara, K.

2006-06-01

Subaru Deep Field line-emitting galaxies in four narrow-band filters at low and intermediate redshifts are presented. Broad-band colors, follow-up optical spectroscopy, and multiple narrow-band filters are used to distinguish Hα, [OII], and [OIII] emitters between redshifts of 0.07 and 1.47 to construct their averaged rest-frame optical-to-UV SED and luminosity functions. These luminosity functions are derived down to faint magnitudes, which allows for a more accurate determination of the faint end slope. With a large (N 200-900) sample for each redshift interval, a Schechter profile is fitted to each luminosity function. Prior to dust extinction corrections, the [OIII] and [OII] luminosity functions reported in this paper agree reasonably well with those of Hippelein et al (2003). The z=0.066-0.092 Hα LF agrees with those of Jones & Bland-Hawthorn (2001), but for z=0.24 and 0.40, their number density is higher by a factor of two or more. The z=0.08 Hα LF, which reaches two orders of magnitude fainter than Gallego et al. (1995), is steeper by 25%. This indicates that there are more low luminosity star-forming galaxies for z<0.1 than predicted. The faint end slope α and φ* show a strong evolution with redshift while L* show little evolution. The evolution in α indicates that low-luminosity galaxies have a stronger evolution compared to brighter ones. Integrated star formation rate densities are derived via Hα for 0.07

Synchronous changes in coral chromatophore tissue density and skeletal banding as an adaptive response to environmental change

NASA Astrophysics Data System (ADS)

Ardisana, R. N.; Miller, C. A.; Sivaguru, M.; Fouke, B. W.

2013-12-01

Corals are a key reservoir of biodiversity in coastal, shallow water tropical marine environments, and density banding in their aragonite skeletons is used as a sensitive record of paleoclimate. Therefore, the cellular response of corals to environmental change and its expression in skeletal structure is of significant importance. Chromatophores, pigment-bearing cells within the ectoderm of hermatypic corals, serve to both enhance the photosynthetic activity of zooxanthellae symbionts, as well as protect the coral animal from harmful UV radiation. Yet connections have not previously been drawn between chromatophore tissue density and the development of skeletal density bands. A histological analysis of the coral Montastrea faveolata has therefore been conducted across a bathymetric gradient of 1-20 m on the southern Caribbean island of Curaçao. A combination of field and laboratory photography, serial block face imaging (SBFI), two-photon laser scanning microscopy (TPLSM), and 3D image analysis has been applied to test whether M. faveolata adapts to increasing water depth and decreasing photosynthetically active radiation by shifting toward a more heterotrophic lifestyle (decreasing zooxanthellae tissue density, increasing mucocyte tissue density, and decreasing chromatophores density). This study is among the first to collect and evaluate histological data in the spatial context of an entire unprocessed coral polyp. TPLSM was used to optically thin section unprocessed tissue biopsies with quantitative image analysis to yield a nanometer-scale three-dimensional map of the quantity and distribution of the symbionts (zooxanthellae) and a host fluorescent pigments (chromatophores), which is thought to have photoprotective properties, within the context of an entire coral polyp. Preliminary results have offered new insight regarding the three-dimensional distribution and abundance of chromatophores and have identified: (1) M. faveolata tissue collected from 8M SWD do not contain the abundant chromatophores present in M. faveolata collected from 20M SWD; and (2) a distinct difference in size and distribution of chromatophores between M. faveolata collected from 8-20M SWD. These results suggest that chromatophore cells may have an important photoenhancing function (reflection of light to help facilitate the collection of usable light that reaches the symbiotic algae for effective photosynthesis) rather than a photoinhibitive function (absorbing or refract light that may be harmful to zooxanthellae) which has been previously hypothesized.

Introducing PROFESS 2.0: A parallelized, fully linear scaling program for orbital-free density functional theory calculations

NASA Astrophysics Data System (ADS)

Hung, Linda; Huang, Chen; Shin, Ilgyou; Ho, Gregory S.; Lignères, Vincent L.; Carter, Emily A.

2010-12-01

Orbital-free density functional theory (OFDFT) is a first principles quantum mechanics method to find the ground-state energy of a system by variationally minimizing with respect to the electron density. No orbitals are used in the evaluation of the kinetic energy (unlike Kohn-Sham DFT), and the method scales nearly linearly with the size of the system. The PRinceton Orbital-Free Electronic Structure Software (PROFESS) uses OFDFT to model materials from the atomic scale to the mesoscale. This new version of PROFESS allows the study of larger systems with two significant changes: PROFESS is now parallelized, and the ion-electron and ion-ion terms scale quasilinearly, instead of quadratically as in PROFESS v1 (L. Hung and E.A. Carter, Chem. Phys. Lett. 475 (2009) 163). At the start of a run, PROFESS reads the various input files that describe the geometry of the system (ion positions and cell dimensions), the type of elements (defined by electron-ion pseudopotentials), the actions you want it to perform (minimize with respect to electron density and/or ion positions and/or cell lattice vectors), and the various options for the computation (such as which functionals you want it to use). Based on these inputs, PROFESS sets up a computation and performs the appropriate optimizations. Energies, forces, stresses, material geometries, and electron density configurations are some of the values that can be output throughout the optimization. New version program summaryProgram Title: PROFESS Catalogue identifier: AEBN_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBN_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 68 721 No. of bytes in distributed program, including test data, etc.: 1 708 547 Distribution format: tar.gz Programming language: Fortran 90 Computer: Intel with ifort; AMD Opteron with pathf90 Operating system: Linux Has the code been vectorized or parallelized?: Yes. Parallelization is implemented through domain composition using MPI. RAM: Problem dependent, but 2 GB is sufficient for up to 10,000 ions. Classification: 7.3 External routines: FFTW 2.1.5 ( http://www.fftw.org) Catalogue identifier of previous version: AEBN_v1_0 Journal reference of previous version: Comput. Phys. Comm. 179 (2008) 839 Does the new version supersede the previous version?: Yes Nature of problem: Given a set of coordinates describing the initial ion positions under periodic boundary conditions, recovers the ground state energy, electron density, ion positions, and cell lattice vectors predicted by orbital-free density functional theory. The computation of all terms is effectively linear scaling. Parallelization is implemented through domain decomposition, and up to ˜10,000 ions may be included in the calculation on just a single processor, limited by RAM. For example, when optimizing the geometry of ˜50,000 aluminum ions (plus vacuum) on 48 cores, a single iteration of conjugate gradient ion geometry optimization takes ˜40 minutes wall time. However, each CG geometry step requires two or more electron density optimizations, so step times will vary. Solution method: Computes energies as described in text; minimizes this energy with respect to the electron density, ion positions, and cell lattice vectors. Reasons for new version: To allow much larger systems to be simulated using PROFESS. Restrictions: PROFESS cannot use nonlocal (such as ultrasoft) pseudopotentials. A variety of local pseudopotential files are available at the Carter group website ( http://www.princeton.edu/mae/people/faculty/carter/homepage/research/localpseudopotentials/). Also, due to the current state of the kinetic energy functionals, PROFESS is only reliable for main group metals and some properties of semiconductors. Running time: Problem dependent: the test example provided with the code takes less than a second to run. Timing results for large scale problems are given in the PROFESS paper and Ref. [1].

A new all-sky map of Galactic high-velocity clouds from the 21-cm HI4PI survey

NASA Astrophysics Data System (ADS)

Westmeier, Tobias

2018-02-01

High-velocity clouds (HVCs) are neutral or ionized gas clouds in the vicinity of the Milky Way that are characterized by high radial velocities inconsistent with participation in the regular rotation of the Galactic disc. Previous attempts to create a homogeneous all-sky H I map of HVCs have been hampered by a combination of poor angular resolution, limited surface brightness sensitivity and suboptimal sampling. Here, a new and improved H I map of Galactic HVCs based on the all-sky HI4PI survey is presented. The new map is fully sampled and provides significantly better angular resolution (16.2 versus 36 arcmin) and column density sensitivity (2.3 versus 3.7 × 1018 cm-2 at the native resolution) than the previously available LAB survey. The new HVC map resolves many of the major HVC complexes in the sky into an intricate network of narrow H I filaments and clumps that were not previously resolved by the LAB survey. The resulting sky coverage fraction of high-velocity H I emission above a column density level of 2 × 1018 cm-2 is approximately 15 per cent, which reduces to about 13 per cent when the Magellanic Clouds and other non-HVC emission are removed. The differential sky coverage fraction as a function of column density obeys a truncated power law with an exponent of -0.93 and a turnover point at about 5 × 1019 cm-2. H I column density and velocity maps of the HVC sky are made publicly available as FITS images for scientific use by the community.

Inhibition of NMDA Receptors Prevents the Loss of BDNF Function Induced by Amyloid β.

PubMed

Tanqueiro, Sara R; Ramalho, Rita M; Rodrigues, Tiago M; Lopes, Luísa V; Sebastião, Ana M; Diógenes, Maria J

2018-01-01

Brain-derived neurotrophic factor (BDNF) plays important functions in cell survival and differentiation, neuronal outgrowth and plasticity. In Alzheimer's disease (AD), BDNF signaling is known to be impaired, partially because amyloid β (Aβ) induces truncation of BDNF main receptor, TrkB-full length (TrkB-FL). We have previously shown that such truncation is mediated by calpains, results in the formation of an intracellular domain (ICD) fragment and causes BDNF loss of function. Since calpains are Ca 2+ -dependent proteases, we hypothesized that excessive intracellular Ca 2+ build-up could be due to dysfunctional N-methyl-d-aspartate receptors (NMDARs) activation. To experimentally address this hypothesis, we investigated whether TrkB-FL truncation by calpains and consequent BDNF loss of function could be prevented by NMDAR blockade. We herein demonstrate that a NMDAR antagonist, memantine, prevented excessive calpain activation and TrkB-FL truncation induced by Aβ 25-35 . When calpains were inhibited by calpastatin, BDNF was able to increase the dendritic spine density of neurons exposed to Aβ 25135 . Moreover, NMDAR inhibition by memantine also prevented Aβ-driven deleterious impact of BDNF loss of function on structural (spine density) and functional outcomes (synaptic potentiation). Collectively, these findings support NMDAR/Ca 2+ /calpains mechanistic involvement in Aβ-triggered BDNF signaling disruption.

Redshift-space distortions with the halo occupation distribution - II. Analytic model

NASA Astrophysics Data System (ADS)

Tinker, Jeremy L.

2007-01-01

We present an analytic model for the galaxy two-point correlation function in redshift space. The cosmological parameters of the model are the matter density Ωm, power spectrum normalization σ8, and velocity bias of galaxies αv, circumventing the linear theory distortion parameter β and eliminating nuisance parameters for non-linearities. The model is constructed within the framework of the halo occupation distribution (HOD), which quantifies galaxy bias on linear and non-linear scales. We model one-halo pairwise velocities by assuming that satellite galaxy velocities follow a Gaussian distribution with dispersion proportional to the virial dispersion of the host halo. Two-halo velocity statistics are a combination of virial motions and host halo motions. The velocity distribution function (DF) of halo pairs is a complex function with skewness and kurtosis that vary substantially with scale. Using a series of collisionless N-body simulations, we demonstrate that the shape of the velocity DF is determined primarily by the distribution of local densities around a halo pair, and at fixed density the velocity DF is close to Gaussian and nearly independent of halo mass. We calibrate a model for the conditional probability function of densities around halo pairs on these simulations. With this model, the full shape of the halo velocity DF can be accurately calculated as a function of halo mass, radial separation, angle and cosmology. The HOD approach to redshift-space distortions utilizes clustering data from linear to non-linear scales to break the standard degeneracies inherent in previous models of redshift-space clustering. The parameters of the occupation function are well constrained by real-space clustering alone, separating constraints on bias and cosmology. We demonstrate the ability of the model to separately constrain Ωm,σ8 and αv in models that are constructed to have the same value of β at large scales as well as the same finger-of-god distortions at small scales.

Random sequential adsorption of cubes

NASA Astrophysics Data System (ADS)

Cieśla, Michał; Kubala, Piotr

2018-01-01

Random packings built of cubes are studied numerically using a random sequential adsorption algorithm. To compare the obtained results with previous reports, three different models of cube orientation sampling were used. Also, three different cube-cube intersection algorithms were tested to find the most efficient one. The study focuses on the mean saturated packing fraction as well as kinetics of packing growth. Microstructural properties of packings were analyzed using density autocorrelation function.

Beyond Zipf's Law: The Lavalette Rank Function and Its Properties.

PubMed

Fontanelli, Oscar; Miramontes, Pedro; Yang, Yaning; Cocho, Germinal; Li, Wentian

Although Zipf's law is widespread in natural and social data, one often encounters situations where one or both ends of the ranked data deviate from the power-law function. Previously we proposed the Beta rank function to improve the fitting of data which does not follow a perfect Zipf's law. Here we show that when the two parameters in the Beta rank function have the same value, the Lavalette rank function, the probability density function can be derived analytically. We also show both computationally and analytically that Lavalette distribution is approximately equal, though not identical, to the lognormal distribution. We illustrate the utility of Lavalette rank function in several datasets. We also address three analysis issues on the statistical testing of Lavalette fitting function, comparison between Zipf's law and lognormal distribution through Lavalette function, and comparison between lognormal distribution and Lavalette distribution.

Probing the Initial Mass Function in Extended Ultraviolet (XUV) Disks

NASA Astrophysics Data System (ADS)

Koda, Jin

2012-01-01

"The GALEX UV satellite discovered tantalizing evidence of star formation (SF) far beyond the optical edge of galactic disks (i.e. extended UV disk, or XUV disk). This discovery provides a new opportunity for studying SF in the exceedingly low-density environment (˜1/10 of typical SF density), spurring intense debate on the universality of the initial mass function (IMF) in such exceptional environments. Our pilot S-Cam study of M83’s XUV disk led to support for the universal IMF at least in M83 (Koda et al. 2012). We propose an expansion of the pilot study, observing 6 XUV disks in NA656(Hα), B, I, and R-band with S-Cam. In conjunction with GALEX UV bands, these images will reveal the presence of O stars (Hα; NA656-R) and O&B stars (UV) in stellar clusters -thus, constraining the high-mass end of the IMF. The multi-broadband images will enable us to determine the masses of the clusters with much improved accuracy (previously, relied only on R). The proposed observations will not only increase the statistical significance of our previous result, but also enable us to analyze the stochastic effect of IMF sampling in very low-mass clusters (10^{2+3} M_sun) - the regime about which there is much ongoing debate."

Characterization of crack-tip microstructures via synchrotron fractography in Mo and Mo-Nb alloy crystals

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

Hmelo, A.B.

1987-01-01

The nature of the plastic relaxation associated with the semi-brittle cleavage fracture of a series of pre-cracked molybdenum-niobium alloy single crystals was investigated as a function of composition and temperature from 77/sup 0/ to 298/sup 0/K. Conventional optical microscopy and white-beam Synchrotron X-Ray Fractography (SXRF) were used to examined the structure of a thin layer a few microns thick at the remnant of the precursor crack plastic zone. The plastic work of fracture was evaluated by measuring the lattice curvature associated with networks of dislocations beneath the cleavage surface. Using SXRF, lattice curvature is detected as asterism on photographic plates,more » and is associated with an excess density of edge dislocations of one sign. The results are in qualitative agreement with a previous determination of the fracture toughness of these specimens. Excess edge-dislocation density of one sign has been shown to vary as a function of temperature and composition, in a way consistent with previous studies of total dislocation content in these materials. Unlike the etch-pit analysis that can reveal the total dislocation content only, the tensor bases analysis described here allows the activity on individual slip systems to be distinguished.« less

Hybrid density functional study of organic magnetic crystals: bi-metallic CrIII cyanides and rhombohedral C60

NASA Astrophysics Data System (ADS)

Chan, J. A.; Montanari, B.; Chan, W. L.; Harrison, N. M.

Periodic hybrid-exchange density functional theory calculations have been used to investigate the magnetic properties of two classes of organic magnets, namely the bi-metallic CrIII cyanides and the polymerized rhombohedral C60 fullerenes (Rh-C60). For the systems KMII[CrIII(CN)6] with M II=V, Mn, Ni and CrIII[CrIII(CN)6], the magnetic ordering energies, Mulliken populations, and spin density plots are reported for the optimized geometries. The qualitative nature of the magnetic coupling mechanism is consistent with that observed in previous unrestricted Hartree-Fock calculations, but the coupling energies computed here are significantly higher. The increased coupling is found to be a result of both changes in the geometry and the electronic structure resulting from the more reliable treatment of electronic exchange and correlation effects. The existence of long-range coupling between local spin moments is investigated in three different defective Rh-C60 structures: (i) a previously proposed prototype structure, where an atom is removed from the C60 cage; (ii) a related structure in which vacancies in nearby cages are brought closer together in pairs; and (iii) a structure where the intra-fullerene bond between the two inter-fullerene bonds is broken spontaneously after applying isotropic pressure to one layer of the Rh-C60 structure. All of these structures are characterized by low flat spin polarized bands at the Fermi edge and localized spin moments around the defects, but no evidence of long-range magnetic coupling is found.

Centella asiatica increases hippocampal synaptic density and improves memory and executive function in aged mice.

PubMed

Gray, Nora E; Zweig, Jonathan A; Caruso, Maya; Martin, Marjoen D; Zhu, Jennifer Y; Quinn, Joseph F; Soumyanath, Amala

2018-06-19

Centella asiatica is a plant used for centuries to enhance memory. We have previously shown that a water extract of Centella asiatica (CAW) attenuates age-related spatial memory deficits in mice and improves neuronal health. Yet the effect of CAW on other cognitive domains remains unexplored as does its mechanism of improving age-related cognitive impairment. This study investigates the effects of CAW on a variety of cognitive tasks as well as on synaptic density and mitochondrial and antioxidant pathways. Twenty-month-old CB6F1 mice were treated with CAW (2 mg/ml) in their drinking water for 2 weeks prior to behavioral testing. Learning, memory, and executive function were assessed using the novel object recognition task (NORT), object location memory task (OLM), and odor discrimination reversal learning (ODRL) test. Tissue was collected for Golgi analysis of spine density as well as assessment of mitochondrial, antioxidant, and synaptic proteins. CAW improved performance in all behavioral tests suggesting effects on hippocampal and cortical dependent memory as well as on prefrontal cortex mediated executive function. There was also an increase in synaptic density in the treated animals, which was accompanied by increased expression of the antioxidant response gene NRF2 as well as the mitochondrial marker porin. These data show that CAW can increase synaptic density as well as antioxidant and mitochondrial proteins and improve multiple facets of age-related cognitive impairment. Because mitochondrial dysfunction and oxidative stress also accompany cognitive impairment in many pathological conditions this suggests a broad therapeutic utility of CAW. © 2018 The Authors. Brain and Behavior published by Wiley Periodicals, Inc.

Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20

DOE PAGES

Michael, J. Robert; Volkov, Anatoliy

2015-03-01

The widely used pseudoatom formalism in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens. It was shown that the analytical form for normalization coefficients is available primarily forl ≤ 4. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7.more » In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle–Coppens method in the Wolfram Mathematicasoftware to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.« less

Chemical-to-Electricity Carbon: Water Device.

PubMed

He, Sisi; Zhang, Yueyu; Qiu, Longbin; Zhang, Longsheng; Xie, Yun; Pan, Jian; Chen, Peining; Wang, Bingjie; Xu, Xiaojie; Hu, Yajie; Dinh, Cao Thang; De Luna, Phil; Banis, Mohammad Norouzi; Wang, Zhiqiang; Sham, Tsun-Kong; Gong, Xingao; Zhang, Bo; Peng, Huisheng; Sargent, Edward H

2018-05-01

The ability to release, as electrical energy, potential energy stored at the water:carbon interface is attractive, since water is abundant and available. However, many previous reports of such energy converters rely on either flowing water or specially designed ionic aqueous solutions. These requirements restrict practical application, particularly in environments with quiescent water. Here, a carbon-based chemical-to-electricity device that transfers the chemical energy to electrical form when coming into contact with quiescent deionized water is reported. The device is built using carbon nanotube yarns, oxygen content of which is modulated using oxygen plasma-treatment. When immersed in water, the device discharges electricity with a power density that exceeds 700 mW m -2 , one order of magnitude higher than the best previously published result. X-ray absorption and density functional theory studies support a mechanism of operation that relies on the polarization of sp 2 hybridized carbon atoms. The devices are incorporated into a flexible fabric for powering personal electronic devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermal characteristics of the lunar surface layer.

NASA Technical Reports Server (NTRS)

Cremers, C. J.; Birkebak, R. C.; White, J. E.

1972-01-01

The thermophysical properties of the fines from the Apollo 12 landing site have been determined as a function of their relevant parameters. These properties include the thermal conductivity, thermal diffusivity, directional reflectance and emittance. The density used was the same as that observed from the returned core-tube samples and so should be close to the true density of the surface layer at the Apollo 12 site. The measured properties are used to calculate the diurnal temperature variation of the moon's surface as well as for several depths below the surface. The maximum surface of 389 K is obtained at lunar noon while the minimum temperature of 86.1 K is obtained at sunrise. It is shown that the most significant effects on temperature, as compared with previous calculations, are caused by using the directional reflectance which controls the amount of solar energy absorption during the day in place of a constant hemispherical reflectance. The results are compared with previous analyses and remote measurements.

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

PubMed

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Precipitation, density, and population dynamics of desert bighorn sheep on San Andres National Wildlife Refuge, New Mexico

USGS Publications Warehouse

Bender, L.C.; Weisenberger, M.E.

2005-01-01

Understanding the determinants of population size and performance for desert bighorn sheep (Ovis canadensis mexicana) is critical to develop effective recovery and management strategies. In arid environments, plant communities and consequently herbivore populations are strongly dependent upon precipitation, which is highly variable seasonally and annually. We conducted a retrospective exploratory analysis of desert bighorn sheep population dynamics on San Andres National Wildlife Refuge (SANWR), New Mexico, 1941-1976, by modeling sheep population size as a function of previous population sizes and precipitation. Population size and trend of desert bighorn were best and well described (R 2=0.89) by a model that included only total annual precipitation as a covariate. Models incorporating density-dependence, delayed density-dependence, and combinations of density and precipitation were less informative than the model containing precipitation alone (??AlCc=8.5-22.5). Lamb:female ratios were positively related to precipitation (current year: F1,34=7.09, P=0.012; previous year: F1,33=3.37, P=0.075) but were unrelated to population size (current year. F1,34=0.04, P=0.843; previous year: F1,33 =0.14, P=0.715). Instantaneous population rate of increase (r) was related to population size (F1,33=5.55; P=0.025). Precipitation limited populations of desert bighorn sheep on SANWR primarily in a density-independent manner by affecting production or survival of lambs, likely through influences on forage quantity and quality. Habitat evaluations and recovery plans for desert bighorn sheep need to consider fundamental influences on desert bighorn populations such as precipitation and food, rather than focus solely on proximate issues such as security cover, predation, and disease. Moreover, the concept of carrying capacity for desert bighorn sheep may need re-evaluation in respect to highly variable (CV =35.6%) localized precipitation patterns. On SANWR carrying capacity for desert bighorn sheep was zero when total annual precipitation was <28.2 cm.

High-carrier-density phase in LaTiO3/SrTiO3 superlattices

NASA Astrophysics Data System (ADS)

Park, Se Young; Rabe, Karin; Millis, Andrew

2015-03-01

We investigate superlattices composed of alternating layers of Mott insulating LaTiO3 and band insulating SrTiO3 from first principles, using the density functional theory plus U (DFT+U) method. For values of U above a critical threshold, we find that melting of the Mott-insulating phase can extend from the interface into the LaTiO3 layer, resulting in a sheet carrier density exceeding the density of 0.5 electrons per in-plane unit cell found in previous studies. The critical U for the melting transition is larger than the critical Coulomb correlation required for the insulating LaTiO3, suggesting the existence of a high sheet carrier density phase in LaTiO3/SrTiO3 superlattices. The effects of in-plane strain and varying layer thickness on the melting transition are discussed. For insulating superlattices, we study the strain and thickness dependence of the polarization and its relation to near-interface local atomic distortions. Support: DOE ER 046169, ONR N00014-11-0666.

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Galaxy evolution and large-scale structure in the far-infrared. I - IRAS pointed observations

NASA Astrophysics Data System (ADS)

Lonsdale, Carol J.; Hacking, Perry B.

1989-04-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained in terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution.

Galaxy evolution and large-scale structure in the far-infrared. I. IRAS pointed observations

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

Lonsdale, C.J.; Hacking, P.B.

1989-04-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained inmore » terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution. 81 refs.« less

Galaxy evolution and large-scale structure in the far-infrared. I - IRAS pointed observations

NASA Technical Reports Server (NTRS)

Lonsdale, Carol J.; Hacking, Perry B.

1989-01-01

Redshifts for 66 galaxies were obtained from a sample of 93 60-micron sources detected serendipitously in 22 IRAS deep pointed observations, covering a total area of 18.4 sq deg. The flux density limit of this survey is 150 mJy, 4 times fainter than the IRAS Point Source Catalog (PSC). The luminosity function is similar in shape with those previously published for samples selected from the PSC, with a median redshift of 0.048 for the fainter sample, but shifted to higher space densities. There is evidence that some of the excess number counts in the deeper sample can be explained in terms of a large-scale density enhancement beyond the Pavo-Indus supercluster. In addition, the faintest counts in the new sample confirm the result of Hacking et al. (1989) that faint IRAS 60-micron source counts lie significantly in excess of an extrapolation of the PSC counts assuming no luminosity or density evolution.

The transition to the metallic state in low density hydrogen

DOE PAGES

McMinis, Jeremy; Morales, Miguel A.; Ceperley, David M.; ...

2015-11-18

Solid atomic hydrogen is one of the simplest systems to undergo a metal-insulator transition. Near the transition, the electronic degrees of freedom become strongly correlated and their description provides a difficult challenge for theoretical methods. As a result, the order and density of the phase transition are still subject to debate. In this work we use diffusion quantum Monte Carlo to benchmark the transition between the paramagnetic and anti-ferromagnetic phases of ground state body centered cubic atomic hydrogen. We locate the density of the transition by computing the equation of state for these two phases and identify the phase transitionmore » order by computing the band gap near the phase transition. These benchmark results show that the phase transition is continuous and occurs at a Wigner-Seitz radius of r s = 2.27(3)a 0. As a result, we compare our results to previously reported density functional theory, Hedin s GW approximation, and dynamical mean field theory results.« less

Nonlinear calculations of the time evolution of black hole accretion disks

NASA Technical Reports Server (NTRS)

Luo, C.

1994-01-01

Based on previous works on black hole accretion disks, I continue to explore the disk dynamics using the finite difference method to solve the highly nonlinear problem of time-dependent alpha disk equations. Here a radially zoned model is used to develop a computational scheme in order to accommodate functional dependence of the viscosity parameter alpha on the disk scale height and/or surface density. This work is based on the author's previous work on the steady disk structure and the linear analysis of disk dynamics to try to apply to x-ray emissions from black candidates (i.e., multiple-state spectra, instabilities, QPO's, etc.).

Aeolian transport in the field: A comparison of the effects of different surface treatments

NASA Astrophysics Data System (ADS)

Dong, Zhibao; Lv, Ping; Zhang, Zhengcai; Qian, Guangqiang; Luo, Wanyin

2012-05-01

Aeolian transport represents the result of wind-surface interactions, and therefore depends strongly on variations in the characteristics of the sediment surface. We conducted field observations of aeolian transport of typical dune sand in three 80 m × 80 m plots with different surface treatments: gravel-covered sand, enclosed shifting sand, and open (unprotected) shifting sand. The study was performed at the Shapotou Aeolian Experiment Site in the southeastern part of China's Tengger Desert to compare the effects of these different surface treatments on aeolian transport. To do so, we analyzed the flux density profiles and transport rates above each surface. The flux density profiles for all three treatments followed the exponential decay law that was proposed by most previous researchers to describe the saltation flux density profiles. Coefficients of the exponential decay function were defined as a function of the surface and the wind velocity. The enclosed and open plots with shifting sand had similar flux density profiles, but the flux density above gravel-covered plots showed that transport decayed more slowly with increasing height, producing flux density profiles with a higher average saltation height. The transport rate above the three treatment plots tended to increase proportionally with the cube of the mean wind velocity and with the maximum wind velocity during the observation period, but was more strongly correlated with the square of drift potential. Transport rates above the plot with open shifting sand were greater than those above the plots with enclosed shifting sand and the gravel-covered plot.

The evolving far-IR galaxy luminosity function and dust-obscured star formation rate density out to z≃5.

NASA Astrophysics Data System (ADS)

Koprowski, M. P.; Dunlop, J. S.; Michałowski, M. J.; Coppin, K. E. K.; Geach, J. E.; McLure, R. J.; Scott, D.; van der Werf, P. P.

2017-11-01

We present a new measurement of the evolving galaxy far-IR luminosity function (LF) extending out to redshifts z ≃ 5, with resulting implications for the level of dust-obscured star formation density in the young Universe. To achieve this, we have exploited recent advances in sub-mm/mm imaging with SCUBA-2 on the James Clerk Maxwell Telescope and the Atacama Large Millimeter/Submillimeter Array, which together provide unconfused imaging with sufficient dynamic range to provide meaningful coverage of the luminosity-redshift plane out to z > 4. Our results support previous indications that the faint-end slope of the far-IR LF is sufficiently flat that comoving luminosity density is dominated by bright objects (≃L*). However, we find that the number density/luminosity of such sources at high redshifts has been severely overestimated by studies that have attempted to push the highly confused Herschel SPIRE surveys beyond z ≃ 2. Consequently, we confirm recent reports that cosmic star formation density is dominated by UV-visible star formation at z > 4. Using both direct (1/Vmax) and maximum likelihood determinations of the LF, we find that its high-redshift evolution is well characterized by continued positive luminosity evolution coupled with negative density evolution (with increasing redshift). This explains why bright sub-mm sources continue to be found at z > 5, even though their integrated contribution to cosmic star formation density at such early times is very small. The evolution of the far-IR galaxy LF thus appears similar in form to that already established for active galactic nuclei, possibly reflecting a similar dependence on the growth of galaxy mass.

The glass transition temperature of thin films: A molecular dynamics study for a bead-spring model.

PubMed

Stevenson, Craig S; Curro, John G; McCoy, John D

2017-05-28

Molecular dynamics simulations were carried out on free-standing liquid films of different thicknesses h using a bead-spring model of 10 beads per chain. The glass transition temperatures, T g , of the various films were determined from plots of the internal energy versus temperature. We used these simulations to test the validity of our earlier conjecture that the glass transition of a confined liquid could be approximated by pre-averaging over the non-uniform density profile of the film. Using the density profiles from our simulations, we computed the average density of the free-standing films as a function of temperature. In all our film simulations we found, within the error of the simulation, that T g of the film occurred at the same density (or packing fraction) as the bulk system at the bulk glass transition temperature T g B . By equating these densities at their respective glass transition temperatures, as suggested by the simulations, we deduced that T g /T g B is proportional to h 0 /h. This is consistent with previous simulations and experimental data. Moreover, the parameter h 0 is determinable in our model from the density profile of the films.

Local-spin-density calculations for iron: Effect of spin interpolation on ground-state properties

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

MacLaren, J.M.; Clougherty, D.P.; Albers, R.C.

1990-08-15

Scalar-relativistic self-consistent linear muffin-tin orbital (LMTO) calculations for bcc and fcc Fe have been performed with several different local approximations to the exchange and correlation energy density and potential. Overall, in contrast to the conclusions of previous studies, we find that the local-spin-density approximation to exchange and correlation can provide an adequate description of bulk Fe {ital provided} that a proper parametrization of the correlation energy density and potential of the homogeneous electron gas over both spin and density is used. Lattice constants, found from the position of the minimum of the total energy as a function of Wigner-Seitz radius,more » agree to within 1% (for {ital s},{ital p},{ital d} LMTO's only) and within 1--2% (for {ital s},{ital p},{ital d},{ital f} LMTO's) of the experimental lattice constants for all forms used for the local correlation. The best agreement, however, was obtained using a local correlation potential derived from the Vosko-Wilk-Nusair form for the spin dependence of the correlation energy density. The calculation performed with this correlation potential was also the only calculation to correctly predict a bcc ferromagnetic ground state.« less

First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement

PubMed Central

Vicente-Dólera, Nelly; Troadec, Christelle; Moya, Manuel; del Río-Celestino, Mercedes; Pomares-Viciana, Teresa; Bendahmane, Abdelhafid; Picó, Belén; Román, Belén; Gómez, Pedro

2014-01-01

Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding. PMID:25386735

Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment

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

Meng, Da; Zheng, Bin; Lin, Guang

2014-08-29

We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is themore » number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.« less

The multifacet graphically contracted function method. I. Formulation and implementation

NASA Astrophysics Data System (ADS)

Shepard, Ron; Gidofalvi, Gergely; Brozell, Scott R.

2014-08-01

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that both the energy and the gradient computation scale as O(N2n4) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N2 dissociation, cubic H8 dissociation, the symmetric dissociation of H2O, and the insertion of Be into H2. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.

The multifacet graphically contracted function method. I. Formulation and implementation.

PubMed

Shepard, Ron; Gidofalvi, Gergely; Brozell, Scott R

2014-08-14

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that both the energy and the gradient computation scale as O(N(2)n(4)) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N2 dissociation, cubic H8 dissociation, the symmetric dissociation of H2O, and the insertion of Be into H2. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.

The surface structure of silver-coated gold nanocrystals and its influence on shape control

DOE PAGES

Padmos, J. Daniel; Personick, Michelle L.; Tang, Qing; ...

2015-07-08

Understanding the surface structure of metal nanocrystals with specific facet indices is important due to its impact on controlling nanocrystal shape and functionality. However, this is particularly challenging for halide-adsorbed nanocrystals due to the difficulty in analysing interactions between metals and light halides (for example, chloride). Here we uncover the surface structures of chloride-adsorbed, silver-coated gold nanocrystals with {111}, {110}, {310} and {720} indexed facets by X-ray absorption spectroscopy and density functional theory modelling. The silver–chloride, silver–silver and silver–gold bonding structures are markedly different between the nanocrystal surfaces, and are sensitive to their formation mechanism and facet type. A uniquemore » approach of combining the density functional theory and experimental/simulated X-ray spectroscopy further verifies the surface structure models and identifies the previously indistinguishable valence state of silver atoms on the nanocrystal surfaces. Overall, this work elucidates the thus-far unknown chloride–metal nanocrystal surface structures and sheds light onto the halide-induced growth mechanism of anisotropic nanocrystals.« less

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

Yu, Kuang; Libisch, Florian; Carter, Emily A., E-mail: eac@princeton.edu

We report a new implementation of the density functional embedding theory (DFET) in the VASP code, using the projector-augmented-wave (PAW) formalism. Newly developed algorithms allow us to efficiently perform optimized effective potential optimizations within PAW. The new algorithm generates robust and physically correct embedding potentials, as we verified using several test systems including a covalently bound molecule, a metal surface, and bulk semiconductors. We show that with the resulting embedding potential, embedded cluster models can reproduce the electronic structure of point defects in bulk semiconductors, thereby demonstrating the validity of DFET in semiconductors for the first time. Compared to ourmore » previous version, the new implementation of DFET within VASP affords use of all features of VASP (e.g., a systematic PAW library, a wide selection of functionals, a more flexible choice of U correction formalisms, and faster computational speed) with DFET. Furthermore, our results are fairly robust with respect to both plane-wave and Gaussian type orbital basis sets in the embedded cluster calculations. This suggests that the density functional embedding method is potentially an accurate and efficient way to study properties of isolated defects in semiconductors.« less

Evaluating a linearized Euler equations model for strong turbulence effects on sound propagation.

PubMed

Ehrhardt, Loïc; Cheinet, Sylvain; Juvé, Daniel; Blanc-Benon, Philippe

2013-04-01

Sound propagation outdoors is strongly affected by atmospheric turbulence. Under strongly perturbed conditions or long propagation paths, the sound fluctuations reach their asymptotic behavior, e.g., the intensity variance progressively saturates. The present study evaluates the ability of a numerical propagation model based on the finite-difference time-domain solving of the linearized Euler equations in quantitatively reproducing the wave statistics under strong and saturated intensity fluctuations. It is the continuation of a previous study where weak intensity fluctuations were considered. The numerical propagation model is presented and tested with two-dimensional harmonic sound propagation over long paths and strong atmospheric perturbations. The results are compared to quantitative theoretical or numerical predictions available on the wave statistics, including the log-amplitude variance and the probability density functions of the complex acoustic pressure. The match is excellent for the evaluated source frequencies and all sound fluctuations strengths. Hence, this model captures these many aspects of strong atmospheric turbulence effects on sound propagation. Finally, the model results for the intensity probability density function are compared with a standard fit by a generalized gamma function.

Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory.

PubMed

Grofe, Adam; Chen, Xin; Liu, Wenjian; Gao, Jiali

2017-10-05

Kohn-Sham density functional theory has been tremendously successful in chemistry and physics. Yet, it is unable to describe the energy degeneracy of spin-multiplet components with any approximate functional. This work features two contributions. (1) We present a multistate density functional theory (MSDFT) to represent spin-multiplet components and to determine multiplet energies. MSDFT is a hybrid approach, taking advantage of both wave function theory and density functional theory. Thus, the wave functions, electron densities and energy density-functionals for ground and excited states and for different components are treated on the same footing. The method is illustrated on valence excitations of atoms and molecules. (2) Importantly, a key result is that for cases in which the high-spin components can be determined separately by Kohn-Sham density functional theory, the transition density functional in MSDFT (which describes electronic coupling) can be defined rigorously. The numerical results may be explored to design and optimize transition density functionals for configuration coupling in multiconfigurational DFT.

Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

2014-09-09

The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation.

B97-3c: A revised low-cost variant of the B97-D density functional method

NASA Astrophysics Data System (ADS)

Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas; Grimme, Stefan

2018-02-01

A revised version of the well-established B97-D density functional approximation with general applicability for chemical properties of large systems is proposed. Like B97-D, it is based on Becke's power-series ansatz from 1997 and is explicitly parametrized by including the standard D3 semi-classical dispersion correction. The orbitals are expanded in a modified valence triple-zeta Gaussian basis set, which is available for all elements up to Rn. Remaining basis set errors are mostly absorbed in the modified B97 parametrization, while an established atom-pairwise short-range potential is applied to correct for the systematically too long bonds of main group elements which are typical for most semi-local density functionals. The new composite scheme (termed B97-3c) completes the hierarchy of "low-cost" electronic structure methods, which are all mainly free of basis set superposition error and account for most interactions in a physically sound and asymptotically correct manner. B97-3c yields excellent molecular and condensed phase geometries, similar to most hybrid functionals evaluated in a larger basis set expansion. Results on the comprehensive GMTKN55 energy database demonstrate its good performance for main group thermochemistry, kinetics, and non-covalent interactions, when compared to functionals of the same class. This also transfers to metal-organic reactions, which is a major area of applicability for semi-local functionals. B97-3c can be routinely applied to hundreds of atoms on a single processor and we suggest it as a robust computational tool, in particular, for more strongly correlated systems where our previously published "3c" schemes might be problematic.

Adjusting the surface areal density of click-reactive azide groups by kinetic control of the azide substitution reaction on bromine-functional SAMs.

PubMed

Zhang, Shuo; Maidenberg, Yanir; Luo, Kai; Koberstein, Jeffrey T

2014-06-03

Azide-alkyne click chemistry has emerged as an important and versatile means for tethering a wide variety of guest molecules to virtually any substrate. In many of these applications, it is important to exercise control over the areal density of surface functional groups to achieve a desired areal density of the tethered guest molecule of interest. We demonstrate herein that the areal density of surface azide groups on flat germanium surfaces and nanoparticle substrates (silica and iron oxide) can be controlled kinetically by appropriately timed quenching of the S(N)2 substitution reaction of bromo-alkane-silane monolayers induced by the addition of sodium azide. The kinetics of the azide substitution reaction on monolayers formed on flat Ge substrates, determined by attenuated total reflection infrared spectroscopy (ATR-IR), are found to be identical to those for monolayers formed on both silica and iron oxide nanoparticles, the latter determined by transmission infrared spectroscopy. To validate the method, the percentages of surface bromine groups converted to azide groups after various reaction times were measured by quenching the S(N)2 reaction followed by analysis with ATR-IR (for Ge) and thermogravimetric analysis (after a subsequent click reaction with an alkyne-terminal polymer) for the nanoparticle substrates. The conversions found after quenching agree well with those expected from the standard kinetic curves. The latter result suggests that the kinetic method for the control of azide group areal density is a versatile means for functionalizing substrates with a prescribed areal density of azide groups for subsequent click reactions, and that the method is universal for any substrate, flat or nanoparticle, that can be modified with bromo-alkane-silane monolayers. Regardless of the surface geometry, we find that the azide substitution reaction is complete within 2-3 h, in sharp contrast to previous reports that indicate times of 48-60 h required for completion of the reaction.

Structural and Functional Plasticity within the Nucleus Accumbens and Prefrontal Cortex Associated with Time-Dependent Increases in Food Cue-Seeking Behavior.

PubMed

Dingess, Paige M; Darling, Rebecca A; Derman, Rifka C; Wulff, Shaun S; Hunter, Melissa L; Ferrario, Carrie R; Brown, Travis E

2017-11-01

Urges to consume food can be driven by stimuli in the environment that are associated with previous food experience. Identifying adaptations within brain reward circuits that facilitate cue-induced food seeking is critical for understanding and preventing the overconsumption of food and subsequent weight gain. Utilizing electrophysiological, biochemical, and DiI labeling, we examined functional and structural changes in the nucleus accumbens (NAc) and prefrontal cortex (PFC) associated with time-dependent increases in food craving ('incubation of craving'). Rats self-administered 60% high fat or chow 45 mg pellets and were then tested for incubation of craving either 1 or 30 days after training. High fat was chosen for comparison to determine whether palatability differentially affected incubation and/or plasticity. Rats showed robust incubation of craving for both food rewards, although responding for cues previously associated with high fat was greater than chow at both 1 and 30 days. In addition, previous experience with high-fat consumption reduced dendritic spine density in the PFC at both time points. In contrast, incubation was associated with an increase in NAc spine density and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated transmission at 30 days in both groups. Finally, incubation of craving for chow and high fat was accompanied by an increase in calcium-permeable and calcium-impermeable AMPARs, respectively. Our results suggest that incubation of food craving alters brain reward circuitry and macronutrient composition specifically induces cortical changes in a way that may facilitate maladaptive food-seeking behaviors.

Symbiosis regulation in a facultatively symbiotic temperate coral: zooxanthellae division and expulsion

NASA Astrophysics Data System (ADS)

Dimond, J.; Carrington, E.

2008-09-01

Zooxanthellae mitotic index (MI) and expulsion rates were measured in the facultatively symbiotic scleractinian Astrangia poculata during winter and summer off the southern New England coast, USA. While MI was significantly higher in summer than in winter, mean expulsion rates were comparable between seasons. Corals therefore appear to allow increases in symbiont density when symbiosis is advantageous during the warm season, followed by a net reduction during the cold season when zooxanthellae may draw resources from the coral. Given previous reports that photosynthesis in A. poculata symbionts does not occur below approximately 6°C, considerable zooxanthellae division at 3°C and in darkness suggests that zooxanthellae are heterotrophic at low seasonal temperatures. Finally, examination of expulsion as a function of zooxanthellae density revealed that corals with very low zooxanthellae densities export a significantly greater proportion of their symbionts, apparently allowing them to persist in a stable azooxanthellate state.

First-principles investigations on structural, elastic, electronic properties and Debye temperature of orthorhombic Ni3Ta under pressure

NASA Astrophysics Data System (ADS)

Li, Pan; Zhang, Jianxin; Ma, Shiyu; Jin, Huixin; Zhang, Youjian; Zhang, Wenyang

2018-06-01

The structural, elastic, electronic properties and Debye temperature of Ni3Ta under different pressures are investigated using the first-principles method based on density functional theory. Our calculated equilibrium lattice parameters at 0 GPa well agree with the experimental and previous theoretical results. The calculated negative formation enthalpies and elastic constants both indicate that Ni3Ta is stable under different pressures. The bulk modulus B, shear modulus G, Young's modulus E and Poisson's ratio ν are calculated by the Voigt-Reuss-Hill method. The bigger ratio of B/G indicates Ni3Ta is ductile and the pressure can improve the ductility of Ni3Ta. In addition, the results of density of states and the charge density difference show that the stability of Ni3Ta is improved by the increasing pressure. The Debye temperature ΘD calculated from elastic modulus increases along with the pressure.

Ground state structure of high-energy-density polymeric carbon monoxide

NASA Astrophysics Data System (ADS)

Xia, Kang; Sun, Jian; Pickard, Chris J.; Klug, Dennis D.; Needs, Richard J.

2017-04-01

Crystal structure prediction methods and first-principles calculations have been used to explore low-energy structures of carbon monoxide (CO). Contrary to the standard wisdom, the most stable structure of CO at ambient pressure was found to be a polymeric structure of P n a 21 symmetry rather than a molecular solid. This phase is formed from six-membered (four carbon + two oxygen) rings connected by C=C double bonds with two double-bonded oxygen atoms attached to each ring. Interestingly, the polymeric P n a 21 phase of CO has a much higher energy density than trinitrotoluene (TNT). On compression to about 7 GPa, P n a 21 is found to transform into another chainlike phase of C c symmetry which has similar ring units to P n a 21 . On compression to 12 GPa, it is energetically favorable for CO to polymerize into a purely single bonded C m c a phase, which is stable over a wide pressure range and transforms into the previously known C m c m phase at around 100 GPa. Thermodynamic stability of these structures was verified using calculations with different density functionals, including hybrid and van der Waals corrected functionals.

Continuous Sound Velocity Measurements along the Shock Hugoniot Curve of Quartz

NASA Astrophysics Data System (ADS)

Li, Mu; Zhang, Shuai; Zhang, Hongping; Zhang, Gongmu; Wang, Feng; Zhao, Jianheng; Sun, Chengwei; Jeanloz, Raymond

2018-05-01

We report continuous measurements of the sound velocity along the principal Hugoniot curve of α quartz between 0.25 and 1.45 TPa, as determined from lateral release waves intersecting the shock front as a function of time in decaying-shock experiments. The measured sound velocities are lower than predicted by prior models, based on the properties of stishovite at densities below ˜7 g /cm3 , but agree with density functional theory molecular dynamics calculations and an empirical wide-regime equation of state presented here. The Grüneisen parameter calculated from the sound velocity decreases from γ ˜1 .3 at 0.25 TPa to 0.66 at 1.45 TPa. In combination with evidence for increased (configurational) specific heat and decreased bulk modulus, the values of γ suggest a high thermal expansion coefficient at ˜0. 25 - 0 .65 TPa , where SiO2 is thought to be a bonded liquid. From our measurements, dissociation of the molecular bonds persists to ˜0. 65 - 1 .0 TPa , consistent with estimates by other methods. At higher densities, the sound velocity is close to predictions from previous models, and the Grüneisen parameter approaches the ideal gas value.

Nanostructured magnesium has fewer detrimental effects on osteoblast function.

PubMed

Weng, Lucy; Webster, Thomas J

2013-01-01

Efforts have been made recently to implement nanoscale surface features on magnesium, a biodegradable metal, to increase bone formation. Compared with normal magnesium, nanostructured magnesium has unique characteristics, including increased grain boundary properties, surface to volume ratio, surface roughness, and surface energy, which may influence the initial adsorption of proteins known to promote the function of osteoblasts (bone-forming cells). Previous studies have shown that one way to increase nanosurface roughness on magnesium is to soak the metal in NaOH. However, it has not been determined if degradation of magnesium is altered by creating nanoscale features on its surface to influence osteoblast density. The aim of the present in vitro study was to determine the influence of degradation of nanostructured magnesium, created by soaking in NaOH, on osteoblast density. Our results showed a less detrimental effect of magnesium degradation on osteoblast density when magnesium was treated with NaOH to create nanoscale surface features. The detrimental degradation products of magnesium are of significant concern when considering use of magnesium as an orthopedic implant material, and this study identified a surface treatment, ie, soaking in NaOH to create nanoscale features for magnesium that can improve its use in numerous orthopedic applications.

Nanostructured magnesium has fewer detrimental effects on osteoblast function

PubMed Central

Weng, Lucy; Webster, Thomas J

2013-01-01

Efforts have been made recently to implement nanoscale surface features on magnesium, a biodegradable metal, to increase bone formation. Compared with normal magnesium, nanostructured magnesium has unique characteristics, including increased grain boundary properties, surface to volume ratio, surface roughness, and surface energy, which may influence the initial adsorption of proteins known to promote the function of osteoblasts (bone-forming cells). Previous studies have shown that one way to increase nanosurface roughness on magnesium is to soak the metal in NaOH. However, it has not been determined if degradation of magnesium is altered by creating nanoscale features on its surface to influence osteoblast density. The aim of the present in vitro study was to determine the influence of degradation of nanostructured magnesium, created by soaking in NaOH, on osteoblast density. Our results showed a less detrimental effect of magnesium degradation on osteoblast density when magnesium was treated with NaOH to create nanoscale surface features. The detrimental degradation products of magnesium are of significant concern when considering use of magnesium as an orthopedic implant material, and this study identified a surface treatment, ie, soaking in NaOH to create nanoscale features for magnesium that can improve its use in numerous orthopedic applications. PMID:23674891

Improvement of physiochemical properties of the tetrahydroazepinoindole series of farnesoid X receptor (FXR) agonists: beneficial modulation of lipids in primates.

PubMed

Lundquist, Joseph T; Harnish, Douglas C; Kim, Callain Y; Mehlmann, John F; Unwalla, Rayomand J; Phipps, Kristin M; Crawley, Matthew L; Commons, Thomas; Green, Daniel M; Xu, Weixin; Hum, Wah-Tung; Eta, Julius E; Feingold, Irene; Patel, Vikram; Evans, Mark J; Lai, Kehdih; Borges-Marcucci, Lisa; Mahaney, Paige E; Wrobel, Jay E

2010-02-25

In an effort to develop orally active farnesoid X receptor (FXR) agonists, a series of tetrahydroazepinoindoles with appended solubilizing amine functionalities were synthesized. The crystal structure of the previously disclosed FXR agonist, 1 (FXR-450), aided in the design of compounds with tethered solubilizing functionalities designed to reach the solvent cavity around the hFXR receptor. These compounds were soluble in 0.5% methylcellulose/2% Tween-80 in water (MC/T) for oral administration. In vitro and in vivo optimization led to the identification of 14dd and 14cc, which in a dose-dependent fashion regulated low density lipoprotein cholesterol (LDLc) in low density lipoprotein receptor knockout (LDLR(-/-)) mice. Compound 14cc was dosed in female rhesus monkeys for 4 weeks at 60 mg/kg daily in MC/T vehicle. After 7 days, triglyceride (TG) levels and very low density lipoprotein cholesterol (VLDLc) levels were significantly decreased and LDLc was decreased 63%. These data are the first to demonstrate the dramatic lowering of serum LDLc levels by a FXR agonist in primates and supports the potential utility of 14cc in treating dyslipidemia in humans beyond just TG lowering.

Microscopic origin of the charge transfer in single crystals based on thiophene derivatives: A combined NEXAFS and density functional theory approach

NASA Astrophysics Data System (ADS)

Chernenkaya, A.; Morherr, A.; Backes, S.; Popp, W.; Witt, S.; Kozina, X.; Nepijko, S. A.; Bolte, M.; Medjanik, K.; Öhrwall, G.; Krellner, C.; Baumgarten, M.; Elmers, H. J.; Schönhense, G.; Jeschke, H. O.; Valentí, R.

2016-07-01

We have investigated the charge transfer mechanism in single crystals of DTBDT-TCNQ and DTBDT-F4TCNQ (where DTBDT is dithieno[2,3-d;2',3'-d'] benzo[1,2-b;4,5-b']dithiophene) using a combination of near-edge X-ray absorption spectroscopy (NEXAFS) and density functional theory calculations (DFT) including final state effects beyond the sudden state approximation. In particular, we find that a description that considers the partial screening of the electron-hole Coulomb correlation on a static level as well as the rearrangement of electronic density shows excellent agreement with experiment and allows to uncover the details of the charge transfer mechanism in DTBDT-TCNQ and DTBDT-F4 TCNQ, as well as a reinterpretation of previous NEXAFS data on pure TCNQ. Finally, we further show that almost the same quality of agreement between theoretical results and experiment is obtained by the much faster Z+1/2 approximation, where the core hole effects are simulated by replacing N or F with atomic number Z with the neighboring atom with atomic number Z+1/2.

The galaxy UV luminosity function at z ≃ 2-4; new results on faint-end slope and the evolution of luminosity density

NASA Astrophysics Data System (ADS)

Parsa, Shaghayegh; Dunlop, James S.; McLure, Ross J.; Mortlock, Alice

2016-03-01

We present a new, robust measurement of the evolving rest-frame ultraviolet (UV) galaxy luminosity function (LF) over the key redshift range from z ≃ 2 to z ≃ 4. Our results are based on the high dynamic range provided by combining the Hubble Ultra Deep Field (HUDF), CANDELS/GOODS-South, and UltraVISTA/COSMOS surveys. We utilize the unparalleled multifrequency photometry available in this survey `wedding cake' to compile complete galaxy samples at z ≃ 2, 3, 4 via photometric redshifts (calibrated against the latest spectroscopy) rather than colour-colour selection, and to determine accurate rest-frame UV absolute magnitudes (M1500) from spectral energy distribution (SED) fitting. Our new determinations of the UV LF extend from M1500 ≃ -22 (AB mag) down to M1500 = -14.5, -15.5 and -16 at z ≃ 2, 3 and 4, respectively (thus, reaching ≃ 3-4 mag fainter than previous blank-field studies at z ≃ 2,3). At z ≃ 2, 3, we find a much shallower faint-end slope (α = -1.32 ± 0.03) than reported in some previous studies (α ≃ -1.7), and demonstrate that this new measurement is robust. By z ≃ 4, the faint-end slope has steepened slightly, to α = -1.43 ± 0.04, and we show that these measurements are consistent with the overall evolutionary trend from z = 0 to 8. Finally, we find that while characteristic number density (φ*) drops from z ≃ 2 to z ≃ 4, characteristic luminosity (M*) brightens by ≃ 1 mag. This, combined with the new flatter faint-end slopes, has the consequence that UV luminosity density (and hence unobscured star formation density) peaks at z ≃ 2.5-3, when the Universe was ≃ 2.5 Gyr old.

Shock Initiation and Equation of State of Ammonium Nitrate

NASA Astrophysics Data System (ADS)

Robbins, David; Sheffield, Steve; Dattelbaum, Dana; Chellappa, Raja; Velisavljevic, Nenad

2013-06-01

Ammonium nitrate (AN) is a widely used fertilizer and mining explosive commonly found in ammonium nitrate-fuel oil. Neat AN is a non-ideal explosive with measured detonation velocities approaching 4 km/s. Previously, we reported a thermodynamically-complete equation of state for AN based on its maximum density, and showed that near-full density AN did not initiate when subjected to shock input conditions up to 22 GPa. In this work, we extend these initial results, by presenting new Hugoniot data for intermediate density neat AN obtained from gas gun-driven plate impact experiments. AN at densities from 1.8 to 1.5 g/cm3 were impacted into LiF windows using a two-stage light gas gun. Dual VISARs were used to measure the interfacial particle velocity wave profile as a function of time following impact. The new Hugoniot data, in addition to updates to thermodynamic parameters derived from structural analysis and vibrational spectroscopy measurements in high pressure diamond anvil cell experiments, are used to refine the unreacted EOS for AN. Furthermore, shock initiation of neat AN was observed as the initial porosity increased (density decreased). Insights into the relationship(s) between initial density and shock initiation sensitivity are also presented, from evidence of shock initiation in the particle velocity profiles obtained for the lower density AN samples.

Damped and sub-damped Lyman-α absorbers in z > 4 QSOs

NASA Astrophysics Data System (ADS)

Guimarães, R.; Petitjean, P.; de Carvalho, R. R.; Djorgovski, S. G.; Noterdaeme, P.; Castro, S.; Poppe, P. C. Da R.; Aghaee, A.

2009-12-01

We present the results of a survey of damped (DLA, log~N(H i)>20.3) and sub-damped Lyman-α systems (19.5 2.55 along the lines-of-sight to 77 quasars with emission redshifts in the range 419.5 were detected of which 40 systems are damped Lyman-α systems for an absorption length of Δ X = 378. About half of the lines of sight of this homogeneous survey have never been investigated for DLAs. We study the evolution with redshift of the cosmological density of the neutral gas and find, consistent with previous studies at similar resolution, that ΩDLA, H_I decreases at z>3.5. The overall cosmological evolution of Ω_HI shows a peak around this redshift. The H i column density distribution for log N(H i)≥20.3 is fitted, consistent with previous surveys, with a single power-law of index α ˜ -1.8 ±0.25. This power-law overpredicts data at the high-end and a second, much steeper, power-law (or a gamma function) is needed. There is a flattening of the function at lower H i column densities with an index of α ˜ -1.4 for the column density range log N(H i)=19.5-21. The fraction of H i mass in sub-DLAs is of the order of 30%. The H i column density distribution does not evolve strongly from z˜ 2.5 to z˜ 4.5. The observations reported here were obtained with the W. M. Keck Observatory, which is operated by the California Association for Research in Astronomy, a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. Tables 1, 2 and Appendices are only available in electronic form at http://www.aanda.org

Association between power law coefficients of the anatomical noise power spectrum and lesion detectability in breast imaging modalities

NASA Astrophysics Data System (ADS)

Chen, Lin; Abbey, Craig K.; Boone, John M.

2013-03-01

Previous research has demonstrated that a parameter extracted from a power function fit to the anatomical noise power spectrum, β, may be predictive of breast mass lesion detectability in x-ray based medical images of the breast. In this investigation, the value of β was compared with a number of other more widely used parameters, in order to determine the relationship between β and these other parameters. This study made use of breast CT data sets, acquired on two breast CT systems developed in our laboratory. A total of 185 breast data sets in 183 women were used, and only the unaffected breast was used (where no lesion was suspected). The anatomical noise power spectrum computed from two-dimensional region of interests (ROIs), was fit to a power function (NPS(f) = α f-β), and the exponent parameter (β) was determined using log/log linear regression. Breast density for each of the volume data sets was characterized in previous work. The breast CT data sets analyzed in this study were part of a previous study which evaluated the receiver operating characteristic (ROC) curve performance using simulated spherical lesions and a pre-whitened matched filter computer observer. This ROC information was used to compute the detectability index as well as the sensitivity at 95% specificity. The fractal dimension was computed from the same ROIs which were used for the assessment of β. The value of β was compared to breast density, detectability index, sensitivity, and fractal dimension, and the slope of these relationships was investigated to assess statistical significance from zero slope. A statistically significant non-zero slope was considered to be a positive association in this investigation. All comparisons between β and breast density, detectability index, sensitivity at 95% specificity, and fractal dimension demonstrated statistically significant association with p < 0.001 in all cases. The value of β was also found to be associated with patient age and breast diameter, parameters both related to breast density. In all associations between other parameters, lower values of β were associated with increased breast cancer detection performance. Specifically, lower values of β were associated with lower breast density, higher detectability index, higher sensitivity, and lower fractal dimension values. While causality was not and probably cannot be demonstrated, the strong, statistically significant association between the β metric and the other more widely used parameters suggest that β may be considered as a surrogate measure for breast cancer detection performance. These findings are specific to breast parenchymal patterns and mass lesions only.

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

PubMed

Gruden, Maja; Andjeklović, Ljubica; Jissy, Akkarapattiakal Kuriappan; Stepanović, Stepan; Zlatar, Matija; Cui, Qiang; Elstner, Marcus

2017-09-30

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

STAR FORMATION AT Z = 2.481 IN THE LENSED GALAXY SDSS J1110+6459: STAR FORMATION DOWN TO 30 PARSEC SCALES.

PubMed

Johnson, Traci L; Rigby, Jane R; Sharon, Keren; Gladders, Michael D; Florian, Michael; Bayliss, Matthew B; Wuyts, Eva; Whitaker, Katherine E; Livermore, Rachael; Murray, Katherine T

2017-07-10

We present measurements of the surface density of star formation, the star-forming clump luminosity function, and the clump size distribution function, for the lensed galaxy SGAS J111020.0+645950.8 at a redshift of z =2.481. The physical size scales that we probe, radii r = 30-50 pc, are considerably smaller scales than have yet been studied at these redshifts. The star formation surface density we find within these small clumps is consistent with surface densities measured previously for other lensed galaxies at similar redshift. Twenty-two percent of the rest-frame ultraviolet light in this lensed galaxy arises from small clumps, with r <100 pc. Within the range of overlap, the clump luminosity function measured for this lensed galaxy is remarkably similar to those of z ∼ 0 galaxies. In this galaxy, star-forming regions smaller than 100 pc-physical scales not usually resolved at these redshifts by current telescopes-are important locations of star formation in the distant universe. If this galaxy is representative, this may contradict the theoretical picture in which the critical size scale for star formation in the distant universe is of order 1 kiloparsec. Instead, our results suggest that current telescopes have not yet resolved the critical size scales of star-forming activity in galaxies over most of cosmic time.

Uniform electron gases. III. Low-density gases on three-dimensional spheres

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

Agboola, Davids; Knol, Anneke L.; Gill, Peter M. W., E-mail: peter.gill@anu.edu.au

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGFmore » centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids — the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) — and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.« less

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

Grid-texture mechanisms in human vision: Contrast detection of regular sparse micro-patterns requires specialist templates.

PubMed

Baker, Daniel H; Meese, Tim S

2016-07-27

Previous work has shown that human vision performs spatial integration of luminance contrast energy, where signals are squared and summed (with internal noise) over area at detection threshold. We tested that model here in an experiment using arrays of micro-pattern textures that varied in overall stimulus area and sparseness of their target elements, where the contrast of each element was normalised for sensitivity across the visual field. We found a power-law improvement in performance with stimulus area, and a decrease in sensitivity with sparseness. While the contrast integrator model performed well when target elements constituted 50-100% of the target area (replicating previous results), observers outperformed the model when texture elements were sparser than this. This result required the inclusion of further templates in our model, selective for grids of various regular texture densities. By assuming a MAX operation across these noisy mechanisms the model also accounted for the increase in the slope of the psychometric function that occurred as texture density decreased. Thus, for the first time, mechanisms that are selective for texture density have been revealed at contrast detection threshold. We suggest that these mechanisms have a role to play in the perception of visual textures.

Long-Term Effects of Concussion on Electrophysiological Indices of Attention in Varsity College Athletes: An Event-Related Potential and Standardized Low-Resolution Brain Electromagnetic Tomography Approach.

PubMed

Ledwidge, Patrick S; Molfese, Dennis L

2016-12-01

This study investigated the effects of a past concussion on electrophysiological indices of attention in college athletes. Forty-four varsity football athletes (22 with at least one past concussion) participated in three neuropsychological tests and a two-tone auditory oddball task while undergoing high-density event-related potential (ERP) recording. Athletes previously diagnosed with a concussion experienced their most recent injury approximately 4 years before testing. Previously concussed and control athletes performed equivalently on three neuropsychological tests. Behavioral accuracy and reaction times on the oddball task were also equivalent across groups. However, athletes with a concussion history exhibited significantly larger N2 and P3b amplitudes and longer P3b latencies. Source localization using standardized low-resolution brain electromagnetic tomography indicated that athletes with a history of concussion generated larger electrical current density in the left inferior parietal gyrus compared to control athletes. These findings support the hypothesis that individuals with a past concussion recruit compensatory neural resources in order to meet executive functioning demands. High-density ERP measures combined with source localization provide an important method to detect long-term neural consequences of concussion in the absence of impaired neuropsychological performance.

Long-Term Effects of Concussion on Electrophysiological Indices of Attention in Varsity College Athletes: An Event-Related Potential and Standardized Low-Resolution Brain Electromagnetic Tomography Approach

PubMed Central

Molfese, Dennis L.

2016-01-01

Abstract This study investigated the effects of a past concussion on electrophysiological indices of attention in college athletes. Forty-four varsity football athletes (22 with at least one past concussion) participated in three neuropsychological tests and a two-tone auditory oddball task while undergoing high-density event-related potential (ERP) recording. Athletes previously diagnosed with a concussion experienced their most recent injury approximately 4 years before testing. Previously concussed and control athletes performed equivalently on three neuropsychological tests. Behavioral accuracy and reaction times on the oddball task were also equivalent across groups. However, athletes with a concussion history exhibited significantly larger N2 and P3b amplitudes and longer P3b latencies. Source localization using standardized low-resolution brain electromagnetic tomography indicated that athletes with a history of concussion generated larger electrical current density in the left inferior parietal gyrus compared to control athletes. These findings support the hypothesis that individuals with a past concussion recruit compensatory neural resources in order to meet executive functioning demands. High-density ERP measures combined with source localization provide an important method to detect long-term neural consequences of concussion in the absence of impaired neuropsychological performance. PMID:27025905

Magnetic and Electrical Characteristics of Permalloy Thin Tape Bobbin Cores

NASA Technical Reports Server (NTRS)

Schwarze, Gene E.; Wieserman, William R.; Niedra, Janis M.

2005-01-01

The core loss, that is, the power loss, of a soft ferromagnetic material is a function of the flux density, frequency, temperature, excitation type (voltage or current), excitation waveform (sine, square, etc.) and lamination or tape thickness. In previously published papers we have reported on the specific core loss and dynamic B-H loop results for several polycrystalline, nanocrystalline, and amorphous soft magnetic materials. In this previous research we investigated the effect of flux density, frequency, temperature, and excitation waveform for voltage excitation on the specific core loss and dynamic B-H loop. In this paper, we will report on an experimental study to investigate the effect of tape thicknesses of 1, 1/2, 1/4, and 1/8-mil Permalloy type magnetic materials on the specific core loss. The test cores were fabricated by winding the thin tapes on ceramic bobbin cores. The specific core loss tests were conducted at room temperature and over the frequency range of 10 kHz to 750 kHz using sine wave voltage excitation. The results of this experimental investigation will be presented primarily in graphical form to show the effect of tape thickness, frequency, and magnetic flux density on the specific core loss. Also, the experimental results when applied to power transformer design will be briefly discussed.

Grid-texture mechanisms in human vision: Contrast detection of regular sparse micro-patterns requires specialist templates

PubMed Central

Baker, Daniel H.; Meese, Tim S.

2016-01-01

Previous work has shown that human vision performs spatial integration of luminance contrast energy, where signals are squared and summed (with internal noise) over area at detection threshold. We tested that model here in an experiment using arrays of micro-pattern textures that varied in overall stimulus area and sparseness of their target elements, where the contrast of each element was normalised for sensitivity across the visual field. We found a power-law improvement in performance with stimulus area, and a decrease in sensitivity with sparseness. While the contrast integrator model performed well when target elements constituted 50–100% of the target area (replicating previous results), observers outperformed the model when texture elements were sparser than this. This result required the inclusion of further templates in our model, selective for grids of various regular texture densities. By assuming a MAX operation across these noisy mechanisms the model also accounted for the increase in the slope of the psychometric function that occurred as texture density decreased. Thus, for the first time, mechanisms that are selective for texture density have been revealed at contrast detection threshold. We suggest that these mechanisms have a role to play in the perception of visual textures. PMID:27460430

Diffusion of finite-sized hard-core interacting particles in a one-dimensional box: Tagged particle dynamics.

PubMed

Lizana, L; Ambjörnsson, T

2009-11-01

We solve a nonequilibrium statistical-mechanics problem exactly, namely, the single-file dynamics of N hard-core interacting particles (the particles cannot pass each other) of size Delta diffusing in a one-dimensional system of finite length L with reflecting boundaries at the ends. We obtain an exact expression for the conditional probability density function rhoT(yT,t|yT,0) that a tagged particle T (T=1,...,N) is at position yT at time t given that it at time t=0 was at position yT,0. Using a Bethe ansatz we obtain the N -particle probability density function and, by integrating out the coordinates (and averaging over initial positions) of all particles but particle T , we arrive at an exact expression for rhoT(yT,t|yT,0) in terms of Jacobi polynomials or hypergeometric functions. Going beyond previous studies, we consider the asymptotic limit of large N , maintaining L finite, using a nonstandard asymptotic technique. We derive an exact expression for rhoT(yT,t|yT,0) for a tagged particle located roughly in the middle of the system, from which we find that there are three time regimes of interest for finite-sized systems: (A) for times much smaller than the collision time ttaucoll but times smaller than the equilibrium time ttaue , rhoT(yT,t|yT,0) approaches a polynomial-type equilibrium probability density function. Notably, only regimes (A) and (B) are found in the previously considered infinite systems.

Demographic response of black bears at Cold Lake, Alberta, to the removal of adult males

USGS Publications Warehouse

Sargeant, Glen A.; Ruff, Robert L.

2001-01-01

Previous reports described an increase in population density following the removal of 23 adult male black bears (Ursus americanus) from a 218-km2 study area near Cold Lake, Alberta (the CLSA). This finding plays a central role in continuing debates over population regulation in bears, but has recently been criticized because density estimates were based on assumptions that were not met. Moreover, subsequent discussion has been predicated on conjecture that human exploitation had minimal influence on population dynamics. Our reanalysis supports previous descriptions of trends in bear density at Cold Lake. However, survival records revealed heavier exploitation than previously suspected. An underlying assumption of previous interpretationsCthat the Cold Lake bear population was naturally regulated near carrying capacityCno longer seems reasonable. Adult males deterred bears in other sex-age groups from using the CLSA; however, we found no evidence that birth or death rates were affected. The observed increase in local density should not be construed as a density-dependent response. Abrupt changes in local density might not have occurred if males had been removed from a larger area encompassing the CLSA.

Atomic kinetic energy, momentum distribution, and structure of solid neon at zero temperature

NASA Astrophysics Data System (ADS)

Cazorla, C.; Boronat, J.

2008-01-01

We report on the calculation of the ground-state atomic kinetic energy Ek and momentum distribution of solid Ne by means of the diffusion Monte Carlo method and Aziz HFD-B pair potential. This approach is shown to perform notably for this crystal since we obtain very good agreement with respect to experimental thermodynamic data. Additionally, we study the structural properties of solid Ne at densities near the equilibrium by estimating the radial pair-distribution function, Lindemann’s ratio, and atomic density profile around the positions of the perfect crystalline lattice. Our value for Ek at the equilibrium density is 41.51(6)K , which agrees perfectly with the recent prediction made by Timms , 41(2)K , based on their deep-inelastic neutron scattering experiments carried out over the temperature range 4-20K , and also with previous path integral Monte Carlo results obtained with the Lennard-Jones and Aziz HFD-C2 atomic pairwise interactions. The one-body density function of solid Ne is calculated accurately and found to fit perfectly, within statistical uncertainty, to a Gaussian curve. Furthermore, we analyze the degree of anharmonicity of solid Ne by calculating some of its microscopic ground-state properties within traditional harmonic approaches. We provide insightful comparison to solid He4 in terms of the Debye model in order to assess the relevance of anharmonic effects in Ne.

Trap densities and transport properties of pentacene metal-oxide-semiconductor transistors: II—Numerical modeling of dc characteristics

NASA Astrophysics Data System (ADS)

Basile, A. F.; Kyndiah, A.; Biscarini, F.; Fraboni, B.

2014-06-01

A numerical procedure to calculate the drain-current (ID) vs. gate-voltage (VG) characteristics from numerical solutions of the Poisson equation for organic Thin-Film Transistors (TFTs) is presented. Polaron transport is modeled as two-dimensional charge transport in a semiconductor having free-carrier density of states proportional to the density of molecules and traps with energy equal to the polaron-hopping barrier. The simulated ID-VG curves are proportional to the product of the density of free carriers, calculated as a function of VG, and the intrinsic mobility, assumed to be a constant independent of temperature. The presence of traps in the oxide was also taken into account in the model, which was applied to a TFT made with six monolayers of pentacene grown on an oxide substrate. The polaron-hopping barrier determines the temperature dependence of the simulated ID-VG curves, trapping in the oxide is responsible for current reduction at high bias and the slope of the characteristics near threshold is related to the metal-semiconductor work-function difference. The values of the model parameters yielding the best match between calculations and experiments are consistent with previous experimental results and theoretical predictions. Therefore, this model enables to extract both physical and technological properties of thin-film devices from the temperature-dependent dc characteristics.

Reformulation of Density Functional Theory for N-Representable Densities and the Resolution of the v-Representability Problem

DOE PAGES

Gonis, A.; Zhang, X. G.; Stocks, G. 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

Studies of the electron density in the highest occupied molecular orbitals of PH 3, PF 3 and P(CH 3) 3 by electron momentum spectroscopy and Hartree-Fock, MRSD-CI and DFT calculations

NASA Astrophysics Data System (ADS)

Rolke, J.; Brion, C. E.

1996-06-01

The spherically averaged momentum profiles for the highest occupied molecular orbitals of PF 3 and P(CH 3) 3 have been obtained by electron momentum spectroscopy. The measurements provide a stringent test of basis set effects and the quality of ab-initio methods in the description of these larger molecular systems. As in previous work on the methyl-substituted amines, intuitive arguments fail to predict the correct amount of s- and p-type contributions to the momentum profile while delocalized molecular orbital concepts provide a more adequate description of the HOMOs. The experimental momentum profiles have been compared with theoretical momentum profiles calculated at the level of the target Hartree-Fock approximation with a range of basis sets. New Hartree-Fock calculations are also presented for the HOMO of PH 3 and compared to previously published experimental and theoretical momentum profiles. The experimental momentum profiles have further been compared to calculations at the level of the target Kohn-Sham approximation using density functional theory with the local density approximation and also with gradient corrected (non-local) exchange correlation potentials. In addition, total energies and dipole moments have been calculated for all three molecules by the various theoretical methods and compared to experimental values. Calculated 'density difference maps' show the regions where the HOMO momentum and position electron densities of PF 3 and P(CH 3) 3 change relative to the corresponding HOMO density of PH 3. The results suggest that methyl groups have an electron-attracting effect (relative to H) on the HOMO charge density in trimethyl phosphines. These conclusions are supported by a consideration of dipole moments and the 31P NMR chemical shifts for PH 3, PF 3 and P(CH 3) 3.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

DOE PAGES

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

2017-11-20

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Ye, Lin-Hui; Duan, Yuhua

2017-12-01

The primary goal of Kohn-Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao-Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree-Fock density yields the exchange and correlation energies in good agreement with the Optimized Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Finally, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

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

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Kernel Density Surface Modelling as a Means to Identify Significant Concentrations of Vulnerable Marine Ecosystem Indicators

PubMed Central

Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

2014-01-01

The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify “significant concentrations” of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere. PMID:25289667

Kernel density surface modelling as a means to identify significant concentrations of vulnerable marine ecosystem indicators.

PubMed

Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

2014-01-01

The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify "significant concentrations" of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere.

Subchondral bone density distribution of the talus in clinically normal Labrador Retrievers.

PubMed

Dingemanse, W; Müller-Gerbl, M; Jonkers, I; Vander Sloten, J; van Bree, H; Gielen, I

2016-03-15

Bones continually adapt their morphology to their load bearing function. At the level of the subchondral bone, the density distribution is highly correlated with the loading distribution of the joint. Therefore, subchondral bone density distribution can be used to study joint biomechanics non-invasively. In addition physiological and pathological joint loading is an important aspect of orthopaedic disease, and research focusing on joint biomechanics will benefit veterinary orthopaedics. This study was conducted to evaluate density distribution in the subchondral bone of the canine talus, as a parameter reflecting the long-term joint loading in the tarsocrural joint. Two main density maxima were found, one proximally on the medial trochlear ridge and one distally on the lateral trochlear ridge. All joints showed very similar density distribution patterns and no significant differences were found in the localisation of the density maxima between left and right limbs and between dogs. Based on the density distribution the lateral trochlear ridge is most likely subjected to highest loads within the tarsocrural joint. The joint loading distribution is very similar between dogs of the same breed. In addition, the joint loading distribution supports previous suggestions of the important role of biomechanics in the development of OC lesions in the tarsus. Important benefits of computed tomographic osteoabsorptiometry (CTOAM), i.e. the possibility of in vivo imaging and temporal evaluation, make this technique a valuable addition to the field of veterinary orthopaedic research.

SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.; Thorne, Daniel T.; Dausman, Alyssa M.; Sukop, Michael C.; Guo, Weixing

2008-01-01

The SEAWAT program is a coupled version of MODFLOW and MT3DMS designed to simulate three-dimensional, variable-density, saturated ground-water flow. Flexible equations were added to the program to allow fluid density to be calculated as a function of one or more MT3DMS species. Fluid density may also be calculated as a function of fluid pressure. The effect of fluid viscosity variations on ground-water flow was included as an option. Fluid viscosity can be calculated as a function of one or more MT3DMS species, and the program includes additional functions for representing the dependence on temperature. Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport, temperature can be simulated as one of the species by entering appropriate transport coefficients. For example, the process of heat conduction is mathematically analogous to Fickian diffusion. Heat conduction can be represented in SEAWAT by assigning a thermal diffusivity for the temperature species (instead of a molecular diffusion coefficient for a solute species). Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption. By combining flexible equations for fluid density and viscosity with multi-species transport, SEAWAT Version 4 represents variable-density ground-water flow coupled with multi-species solute and heat transport. SEAWAT Version 4 is based on MODFLOW-2000 and MT3DMS and retains all of the functionality of SEAWAT-2000. SEAWAT Version 4 also supports new simulation options for coupling flow and transport, and for representing constant-head boundaries. In previous versions of SEAWAT, the flow equation was solved for every transport timestep, regardless of whether or not there was a large change in fluid density. A new option was implemented in SEAWAT Version 4 that allows users to control how often the flow field is updated. New options were also implemented for representing constant-head boundaries with the Time-Variant Constant-Head (CHD) Package. These options allow for increased flexibility when using CHD flow boundaries with the zero-dispersive flux solute boundaries implemented by MT3DMS at constant-head cells. This report contains revised input instructions for the MT3DMS Dispersion (DSP) Package, Variable-Density Flow (VDF) Package, Viscosity (VSC) Package, and CHD Package. The report concludes with seven cases of an example problem designed to highlight many of the new features.

Accurate Ionization Energies for Mononuclear Copper Complexes Remain a Challenge for Density Functional Theory.

PubMed

Dereli, Büsra; Ortuño, Manuel A; Cramer, Christopher J

2018-04-17

Copper is ubiquitous and its one-electron redox chemistry is central to many catalytic processes. Modeling such chemistry requires electronic structure methods capable of the accurate prediction of ionization energies (IEs) for compounds including copper in different oxidation states and supported by various ligands. Herein, we estimate IEs for 12 mononuclear Cu species previously reported in the literature by using 21 modern density functionals and the DLPNO-CCSD(T) wave function theory model; we consider extrapolated values of the latter to provide reference values of acceptable accuracy. Our results reveal a considerable diversity in functional performance. Although there is nearly always at least one functional that performs well for any given species, there are none that do so for every member of the test set, and certain cases are particularly pathological. Over the entire test set, the SOGGA11-X functional performs best with a mean unsigned error (MUE) of 0.22 eV. PBE0, ωB97X-D, CAM-B3LYP, M11-L, B3LYP, and M11 exhibit MUEs ranging between 0.23 and 0.34 eV. When including relativistic effects with the zero-order regular approximation, ωB97X-D, CAM-B3LYP, and PBE0 are found to provide the best accuracy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrophysiological heterogeneity of pacemaker cells in the rabbit intercaval region, including the SA node: insights from recording multiple ion currents in each cell.

PubMed

Monfredi, Oliver; Tsutsui, Kenta; Ziman, Bruce; Stern, Michael D; Lakatta, Edward G; Maltsev, Victor A

2018-03-01

Cardiac pacemaker cells, including cells of the sinoatrial node, are heterogeneous in size, morphology, and electrophysiological characteristics. The exact extent to which these cells differ electrophysiologically is unclear yet is critical to understanding their functioning. We examined major ionic currents in individual intercaval pacemaker cells (IPCs) sampled from the paracristal, intercaval region (including the sinoatrial node) that were spontaneously beating after enzymatic isolation from rabbit hearts. The beating rate was measured at baseline and after inhibition of the Ca 2+ pump with cyclopiazonic acid. Thereafter, in each cell, we consecutively measured the density of funny current ( I f ), delayed rectifier K + current ( I K ) (a surrogate of repolarization capacity), and L-type Ca 2+ current ( I Ca,L ) using whole cell patch clamp . The ionic current densities varied to a greater extent than previously appreciated, with some IPCs demonstrating very small or zero I f . The density of none of the currents was correlated with cell size, while I Ca,L and I f densities were related to baseline beating rates. I f density was correlated with I K density but not with that of I Ca,L . Inhibition of Ca 2+ cycling had a greater beating rate slowing effect in IPCs with lower I f densities. Our numerical model simulation indicated that 1) IPCs with small (or zero) I f or small I Ca,L can operate via a major contribution of Ca 2+ clock, 2) I f -Ca 2+ -clock interplay could be important for robust pacemaking function, and 3) coupled I f - I K function could regulate maximum diastolic potential. Thus, we have demonstrated marked electrophysiological heterogeneity of IPCs. This heterogeneity is manifested in basal beating rate and response to interference of Ca 2+ cycling, which is linked to I f . NEW & NOTEWORTHY In the present study, a hitherto unrecognized range of heterogeneity of ion currents in pacemaker cells from the intercaval region is demonstrated. Relationships between basal beating rate and L-type Ca 2+ current and funny current ( I f ) density are uncovered, along with a positive relationship between I f and delayed rectifier K + current. Links are shown between the response to Ca 2+ cycling blockade and I f density.

Method of deep drilling

DOEpatents

Colgate, Stirling A.

1984-01-01

Deep drilling is facilitated by the following steps practiced separately or in any combination: (1) Periodically and sequentially fracturing zones adjacent the bottom of the bore hole with a thixotropic fastsetting fluid that is accepted into the fracture to overstress the zone, such fracturing and injection being periodic as a function of the progression of the drill. (2) Casing the bore hole with ductile, pre-annealed casing sections, each of which is run down through the previously set casing and swaged in situ to a diameter large enough to allow the next section to run down through it. (3) Drilling the bore hole using a drill string of a low density alloy and a high density drilling mud so that the drill string is partially floated.

Maximum time-dependent space-charge limited diode currents

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

Griswold, M. E.; Fisch, N. J.

Recent papers claim that a one dimensional (1D) diode with a time-varying voltage drop can transmit current densities that exceed the Child-Langmuir (CL) limit on average, apparently contradicting a previous conjecture that there is a hard limit on the average current density across any 1D diode, as t → ∞, that is equal to the CL limit. However, these claims rest on a different definition of the CL limit, namely, a comparison between the time-averaged diode current and the adiabatic average of the expression for the stationary CL limit. If the current were considered as a function of the maximummore » applied voltage, rather than the average applied voltage, then the original conjecture would not have been refuted.« less

Self-Interaction Error in Density Functional Theory: An Appraisal.

PubMed

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

A Combined Density Functional Theory and Spectrophotometry Study of the Bonding Interactions of [NpO 2·M] 4+ Cation–Cation Complexes

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

Freiderich, John W.; Burn, Adam G.; Martin, Leigh R.

The equilibrium constants for [NpO 2M∙] 4+ (M = Al 3+, In 3+, Sc 3+, Fe 3+) in μ = 10 M nitric acid and [NpO 2∙Ga] 4+ in μ = 10 M hydrochloric acid media have been determined. The trend in the interaction strength follows: Fe 3+ > Sc 3+ In 3+ > Ga 3+ Al 3+. These equilibrium constants are compared to those of previously reported values for NpO 2 + complexes with Cr 3+ and Rh 3+ within the literature. Thermodynamic parameters and bonding modes are discussed, with density functional theory and natural bond orbital analysis indicatingmore » that the NpO 2 + dioxocation acts as a -donor with transition-metal cations and a sigma donor with group 13 cations. The small changes in electron-donating ability is modulated by the overlap with the coordinating metal ion's valence atomic orbitals.« less

Reconsideration of the Detection and Fluorescence Mechanism of a Pyrene-Based Chemosensor for TNT.

PubMed

Lu, Meiheng; Zhou, Panwang; Ma, Yinhua; Tang, Zhe; Yang, Yanqiang; Han, Keli

2018-02-08

The rapid detection of chemical explosives is crucial for national security and public safety, and the investigation of sensing mechanisms is important for designing highly efficient chemosensors. This study theoretically investigates the detection and fluorescence mechanism of a newly synthesized pyrene-based chemosensor for the detection of trinitrotoluene (TNT) through density-functional-theory (DFT) and time-dependent density-functional-theory (TDDFT) methods and suggests a different interaction product of the probe and TNT from previously reported ones [ Mosca et al. J. Am. Chem. Soc. 2015 , 137 , 7967 ]. Instead of forming Meisenheimer complexes, the energies of which are beyond those of the reactants, a low-energy product generated by a π-π-stacking interaction is more rational and favorable. The fluorescence-quenching property further confirms that the π-π-stacking product is the predicted one rather than luminescent Meisenheimer complexes. Frontier-molecular-orbital (FMO)-analysis results show that photoinduced electron transfer (PET) is the mechanism underlying the luminescence quenching of the probe upon exposure to TNT.

A density functional study on adsorption and dissociation of O 2 on Ir(1 0 0) surface

NASA Astrophysics Data System (ADS)

Erikat, I. A.; Hamad, B. A.; Khalifeh, J. M.

2011-06-01

The adsorption and the reaction barrier for the dissociation of O 2 on Ir(1 0 0) surface are studied using periodic self-consistent density functional theory (DFT) calculations. Dissociative adsorption is found to be energetically more favorable compared to molecular adsorption. Parallel approaches Prl1 and Prl2 on a hollow site with the same adsorption energy of -3.93 eV for both of them are found to have the most energetically preferred sites of adsorptions among all the studied cases. Hybridization between p-O 2 and d-metal orbitals is responsible for the dissociative adsorption. The minimum energy path is determined by using the nudge elastic band method (NEB). We found that the dissociation occurs immediately and very early in the dissociation path with a small activation barrier (0.26 eV), which means that molecular adsorption of O 2 on Ir(1 0 0) surface occurs at very low temperatures; this is consistent with previous experimental and theoretical studies on Ir surfaces.

Density Functional Theory Study of Spirodienone Stereoisomers in Lignin

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

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.

The spirodienone structure in lignin is a relatively recent discovery, and it has been found to occur in lignin of various plant species at concentrations of ~3%, which is sufficiently high to be important for better understanding of its properties and reactivity. The cyclic structure, with a ..beta..-1 bond, has been proposed to be a precursor for acyclic ..beta..-1 linkages in lignin. Previous analytical work has revealed the presence, but not the absolute configuration, of two stereoisomeric forms of spirodienone. The objective of the current work was to determine if there are thermodynamic differences that could help identify the experimentallymore » observed stereoisomers. Results from density functional theory calculations reveal the presence of clusters of stereoisomers with varying stability that may be of use in narrowing the list of possible structures. Furthermore, the bond dissociation enthalpy of the cyclic ring exhibited a particularly high value for the C-O cleavage reaction relative to more conventional ether bonds in lignin, perhaps due to limited electron delocalization possibilities.« less

Density Functional Theory Study of Spirodienone Stereoisomers in Lignin

DOE PAGES

Elder, Thomas; Berstis, Laura; Beckham, Gregg T.; ...

2017-06-28

The spirodienone structure in lignin is a relatively recent discovery, and it has been found to occur in lignin of various plant species at concentrations of ~3%, which is sufficiently high to be important for better understanding of its properties and reactivity. The cyclic structure, with a ..beta..-1 bond, has been proposed to be a precursor for acyclic ..beta..-1 linkages in lignin. Previous analytical work has revealed the presence, but not the absolute configuration, of two stereoisomeric forms of spirodienone. The objective of the current work was to determine if there are thermodynamic differences that could help identify the experimentallymore » observed stereoisomers. Results from density functional theory calculations reveal the presence of clusters of stereoisomers with varying stability that may be of use in narrowing the list of possible structures. Furthermore, the bond dissociation enthalpy of the cyclic ring exhibited a particularly high value for the C-O cleavage reaction relative to more conventional ether bonds in lignin, perhaps due to limited electron delocalization possibilities.« less

Computing approximate random Delta v magnitude probability densities. [for spacecraft trajectory correction

NASA Technical Reports Server (NTRS)

Chadwick, C.

1984-01-01

This paper describes the development and use of an algorithm to compute approximate statistics of the magnitude of a single random trajectory correction maneuver (TCM) Delta v vector. The TCM Delta v vector is modeled as a three component Cartesian vector each of whose components is a random variable having a normal (Gaussian) distribution with zero mean and possibly unequal standard deviations. The algorithm uses these standard deviations as input to produce approximations to (1) the mean and standard deviation of the magnitude of Delta v, (2) points of the probability density function of the magnitude of Delta v, and (3) points of the cumulative and inverse cumulative distribution functions of Delta v. The approximates are based on Monte Carlo techniques developed in a previous paper by the author and extended here. The algorithm described is expected to be useful in both pre-flight planning and in-flight analysis of maneuver propellant requirements for space missions.

Ecosystem-scale plant hydraulic strategies inferred from remotely-sensed soil moisture

NASA Astrophysics Data System (ADS)

Bassiouni, M.; Good, S. P.; Higgins, C. W.

2017-12-01

Characterizing plant hydraulic strategies at the ecosystem scale is important to improve estimates of evapotranspiration and to understand ecosystem productivity and resilience. However, quantifying plant hydraulic traits beyond the species level is a challenge. The probability density function of soil moisture observations provides key information about the soil moisture states at which evapotranspiration is reduced by water stress. Here, an inverse Bayesian approach is applied to a standard bucket model of soil column hydrology forced with stochastic precipitation inputs. Through this approach, we are able to determine the soil moisture thresholds at which stomata are open or closed that are most consistent with observed soil moisture probability density functions. This research utilizes remotely-sensed soil moisture data to explore global patterns of ecosystem-scale plant hydraulic strategies. Results are complementary to literature values of measured hydraulic traits of various species in different climates and previous estimates of ecosystem-scale plant isohydricity. The presented approach provides a novel relation between plant physiological behavior and soil-water dynamics.

Diffusion of hydrogen into and through γ-iron by density functional theory

NASA Astrophysics Data System (ADS)

Chohan, Urslaan K.; Koehler, Sven P. K.; Jimenez-Melero, Enrique

2018-06-01

This study is concerned with the early stages of hydrogen embrittlement on an atomistic scale. We employed density functional theory to investigate hydrogen diffusion through the (100), (110) and (111) surfaces of γ-Fe. The preferred adsorption sites and respective energies for hydrogen adsorption were established for each plane, as well as a minimum energy pathway for diffusion. The H atoms adsorb on the (100), (110) and (111) surfaces with energies of ∼4.06 eV, ∼3.92 eV and ∼4.05 eV, respectively. The barriers for bulk-like diffusion for the (100), (110) and (111) surfaces are ∼0.6 eV, ∼0.5 eV and ∼0.7 eV, respectively. We compared these calculated barriers with previously obtained experimental data in an Arrhenius plot, which indicates good agreement between experimentally measured and theoretically predicted activation energies. Texturing austenitic steels such that the (111) surfaces of grains are preferentially exposed at the cleavage planes may be a possibility to reduce hydrogen embrittlement.

A Combined Density Functional Theory and Spectrophotometry Study of the Bonding Interactions of [NpO 2·M] 4+ Cation–Cation Complexes

DOE PAGES

Freiderich, John W.; Burn, Adam G.; Martin, Leigh R.; ...

2017-04-14

The equilibrium constants for [NpO 2M∙] 4+ (M = Al 3+, In 3+, Sc 3+, Fe 3+) in μ = 10 M nitric acid and [NpO 2∙Ga] 4+ in μ = 10 M hydrochloric acid media have been determined. The trend in the interaction strength follows: Fe 3+ > Sc 3+ In 3+ > Ga 3+ Al 3+. These equilibrium constants are compared to those of previously reported values for NpO 2 + complexes with Cr 3+ and Rh 3+ within the literature. Thermodynamic parameters and bonding modes are discussed, with density functional theory and natural bond orbital analysis indicatingmore » that the NpO 2 + dioxocation acts as a -donor with transition-metal cations and a sigma donor with group 13 cations. The small changes in electron-donating ability is modulated by the overlap with the coordinating metal ion's valence atomic orbitals.« less

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Understanding Middle School Students' Difficulties in Explaining Density Differences from a Language Perspective

ERIC Educational Resources Information Center

Seah, Lay Hoon; Clarke, David; Hart, Christina

2015-01-01

This study examines how a class of Grade 7 students employed linguistic resources to explain density differences. Drawing from the same data-set as a previous study by, we take a language perspective to investigate the challenges students face in learning the concept of density. Our study thus complements previous research on learning about…

Structure, strain, and the ground state of the LaTiO3/LaAlO3 superlattice

NASA Astrophysics Data System (ADS)

Lee, Alex Taekyung; Han, Myung Joon

2014-03-01

The first-principles density functional theory calculations have been performed to understand LaTiO3/LaAlO3 superlattice. By taking into account of the structural distortions, U dependence, and the exchange correlation functional dependence, we show that the ferromagnetic spin and antiferro-orbital ordering is stabilized in the wide range of strains, which is notably different from the previous reports on the titanate systems. The ground-state spin and orbital configurations critically depend on the structural properties. Our results suggest a possible strain control of the magnetic property in transition-metal oxide heterostructures.

Ionizing gas breakdown waves in strong electric fields.

NASA Technical Reports Server (NTRS)

Klingbeil, R.; Tidman, D. A.; Fernsler, R. F.

1972-01-01

A previous analysis by Albright and Tidman (1972) of the structure of an ionizing potential wave driven through a dense gas by a strong electric field is extended to include atomic structure details of the background atoms and radiative effects, especially, photoionization. It is found that photoionization plays an important role in avalanche propagation. Velocities, electron densities, and temperatures are presented as a function of electric field for both negative and positive breakdown waves in nitrogen.

Probing the Initial Mass Function in Extended Ultraviolet (XUV) Disks

NASA Astrophysics Data System (ADS)

Koda, Jin

2013-01-01

"The GALEX UV satellite discovered tantalizing evidence of star formation (SF) far beyond the optical edge of galactic disks (i.e. extended UV disk, or XUV disk). This discovery provides a new opportunity for studying SF in the exceedingly low-density environment (˜1/10 of typical SF density), spurring intense debate on the universality of the initial mass function (IMF) in such exceptional environments. Our pilot S-Cam study of M83’s XUV disk led to support for the universal IMF at least in M83 (Koda et al. 2012). We propose an expansion of the pilot study by an order of magnitude, by observing additional 6 XUV disks in NA656(Hα), B, I, and R-band with S-Cam in S13A. In conjunction with GALEX UV bands, these images will reveal the presence of O stars (Hα; NA656-R) and O&B stars (UV) in stellar clusters -thus, constraining the high-mass end of the IMF. These multi-broadband images will enable us to determine the masses of the clusters with much improved accuracy (previously, relied only on R). The proposed observations will not only increase the statistical significance of our previous result, but also enable us to analyze the stochastic effect of IMF sampling in very low-mass - clusters (10^(2+3) M_sun) - the regime about which there is much ongoing debate."

Probing the Initial Mass Function in Extended Ultraviolet (XUV) Disks

NASA Astrophysics Data System (ADS)

Koda, Jin

2014-01-01

The GALEX UV satellite discovered tantalizing evidence of star formation (SF) far beyond the optical edge of galactic disks (i.e. XUV disk). This discovery provides a new opportunity for studying SF in the exceedingly low-density environment (~1/10 of typical SF density), spurring intense debate on the universality of the initial mass function (IMF) in such exceptional environments. Our pilot study led to support for the universal IMF at least in M83’s XUV disk (Koda et al. 2012). We propose an expansion of the pilot study by about an order of magnitude, by observing total ~ 10 XUV disks (6 disks in S14A) in NA656(Halpha), B, I, and R-band with S-Cam. In conjunction with GALEX UV bands, these images will reveal the presence of O stars (Halpha) and O&B stars (UV) in stellar clusters -thus, constraining the high-mass end of the IMF. These multi-broadband images will enable us to determine the masses of the clusters with much improved accuracy (previously, relied only on R). This project will not only increase the statistical significance of our previous result, but also enable us to analyze the stochastic effect of IMF sampling in very low-mass clusters (102-3 Msun) - the regime of ongoing debate. This proposal will complete this on-going project with S-Cam.

Perinatal MAO Inhibition Produces Long-Lasting Impairment of Serotonin Function in Offspring.

PubMed

Burke, Mark W; Fillion, Myriam; Mejia, Jose; Ervin, Frank R; Palmour, Roberta M

2018-06-11

In addition to transmitter functions, many neuroamines have trophic or ontogenetic regulatory effects important to both normal and disordered brain development. In previous work (Mejia et al., 2002), we showed that pharmacologically inhibiting monoamine oxidase (MAO) activity during murine gestation increases the prevalence of behaviors thought to reflect impulsivity and aggression. The goal of the present study was to determine the extent to which this treatment influences dopamine and serotonin innervation of murine cortical and subcortical areas, as measured by regional density of dopamine (DAT) and serotonin transporters (SERT). We measured DAT and SERT densities at 3 developmental times (PND 14, 35 and 90) following inhibition of MAO A, or MAO B or both throughout murine gestation and early post-natal development. DAT binding was unaltered within the nigrostriatal pathway, but concurrent inhibition of MAO-A and MAO-B significantly and specifically reduced SERT binding by 10⁻25% in both the frontal cortex and raphe nuclei. Low levels of SERT binding persisted (PND 35, 90) after the termination (PND 21) of exposure to MAO inhibitors and was most marked in brain structures germane to the previously described behavioral changes. The relatively modest level of enzyme inhibition (25⁻40%) required to produce these effects mandates care in the use of any compound which might inhibit MAO activity during gestation.

Modified free volume theory of self-diffusion and molecular theory of shear viscosity of liquid carbon dioxide.

PubMed

Nasrabad, Afshin Eskandari; Laghaei, Rozita; Eu, Byung Chan

2005-04-28

In previous work on the density fluctuation theory of transport coefficients of liquids, it was necessary to use empirical self-diffusion coefficients to calculate the transport coefficients (e.g., shear viscosity of carbon dioxide). In this work, the necessity of empirical input of the self-diffusion coefficients in the calculation of shear viscosity is removed, and the theory is thus made a self-contained molecular theory of transport coefficients of liquids, albeit it contains an empirical parameter in the subcritical regime. The required self-diffusion coefficients of liquid carbon dioxide are calculated by using the modified free volume theory for which the generic van der Waals equation of state and Monte Carlo simulations are combined to accurately compute the mean free volume by means of statistical mechanics. They have been computed as a function of density along four different isotherms and isobars. A Lennard-Jones site-site interaction potential was used to model the molecular carbon dioxide interaction. The density and temperature dependence of the theoretical self-diffusion coefficients are shown to be in excellent agreement with experimental data when the minimum critical free volume is identified with the molecular volume. The self-diffusion coefficients thus computed are then used to compute the density and temperature dependence of the shear viscosity of liquid carbon dioxide by employing the density fluctuation theory formula for shear viscosity as reported in an earlier paper (J. Chem. Phys. 2000, 112, 7118). The theoretical shear viscosity is shown to be robust and yields excellent density and temperature dependence for carbon dioxide. The pair correlation function appearing in the theory has been computed by Monte Carlo simulations.

Formation and properties of surface-anchored polymer assemblies with tunable physico-chemical characteristics

NASA Astrophysics Data System (ADS)

Wu, Tao

We describe two new methodologies leading to the formation of novel surface-anchored polymer assemblies on solid substrates. While the main goal is to understand the fundamentals pertaining to the preparation and properties of the surface-bound polymer assemblies (including neutral and chargeable polymers), several examples also are mentioned throughout the Thesis that point out to practical applications of such structures. The first method is based on generating assemblies comprising anchored polymers with a gradual variation of grafting densities on solid substrates. These structures are prepared by first covering the substrate with a molecular gradient of the polymerization initiator, followed by polymerization from these substrate-bound initiator centers ("grafting from"). We apply this technique to prepare grafting density gradients of poly(acryl amide) (PAAm) and poly(acrylic acid) (PAA) on silica-covered substrates. We show that using the grafting density gradient geometry, the characteristics of surface-anchored polymers in both the low grafting density ("mushroom") regime as well as the high grafting density ("brush") regime can be accessed conveniently on a single sample. We use a battery of experimental methods, including Fourier transform infrared spectroscopy (FTIR), Near-edge absorption fine structure spectroscopy (NEXAFS), contact angle, ellipsometry, to study the characteristics of the surface-bound polymer layers. We also probe the scaling laws of neutral polymer as a function of grafting density, and for weak polyelectrolyte, in addition to the grafting density, we study the affect of solution ionic strength and pH values. In the second novel method, which we coined as "mechanically assisted polymer assembly" (MAPA), we form surface anchored polymers by "grafting from" polymerization initiators deposited on elastic surfaces that have been previously extended uniaxially by a certain length increment, Deltax. Upon releasing the strain in the substrate after completion of polymerization, we show the grafting density of the polymers grafted to flexible substrates can be tuned as a function of Deltax.

GAMA/G10-COSMOS/3D-HST: the 0 < z < 5 cosmic star formation history, stellar-mass, and dust-mass densities

NASA Astrophysics Data System (ADS)

Driver, Simon P.; Andrews, Stephen K.; da Cunha, Elisabete; Davies, Luke J.; Lagos, Claudia; Robotham, Aaron S. G.; Vinsen, Kevin; Wright, Angus H.; Alpaslan, Mehmet; Bland-Hawthorn, Joss; Bourne, Nathan; Brough, Sarah; Bremer, Malcolm N.; Cluver, Michelle; Colless, Matthew; Conselice, Christopher J.; Dunne, Loretta; Eales, Steve A.; Gomez, Haley; Holwerda, Benne; Hopkins, Andrew M.; Kafle, Prajwal R.; Kelvin, Lee S.; Loveday, Jon; Liske, Jochen; Maddox, Steve J.; Phillipps, Steven; Pimbblet, Kevin; Rowlands, Kate; Sansom, Anne E.; Taylor, Edward; Wang, Lingyu; Wilkins, Stephen M.

2018-04-01

We use the energy-balance code MAGPHYS to determine stellar and dust masses, and dust corrected star formation rates for over 200 000 GAMA galaxies, 170 000 G10-COSMOS galaxies, and 200 000 3D-HST galaxies. Our values agree well with previously reported measurements and constitute a representative and homogeneous data set spanning a broad range in stellar-mass (108-1012 M⊙), dust-mass (106-109 M⊙), and star formation rates (0.01-100 M⊙yr-1), and over a broad redshift range (0.0 < z < 5.0). We combine these data to measure the cosmic star formation history (CSFH), the stellar-mass density (SMD), and the dust-mass density (DMD) over a 12 Gyr timeline. The data mostly agree with previous estimates, where they exist, and provide a quasi-homogeneous data set using consistent mass and star formation estimators with consistent underlying assumptions over the full time range. As a consequence our formal errors are significantly reduced when compared to the historic literature. Integrating our CSFH we precisely reproduce the SMD with an interstellar medium replenishment factor of 0.50 ± 0.07, consistent with our choice of Chabrier initial mass function plus some modest amount of stripped stellar mass. Exploring the cosmic dust density evolution, we find a gradual increase in dust density with lookback time. We build a simple phenomenological model from the CSFH to account for the dust-mass evolution, and infer two key conclusions: (1) For every unit of stellar mass which is formed 0.0065-0.004 units of dust mass is also formed. (2) Over the history of the Universe approximately 90-95 per cent of all dust formed has been destroyed and/or ejected.

Development and validation of a subject-specific finite element model of the functional spinal unit to predict vertebral strength.

PubMed

Lee, Chu-Hee; Landham, Priyan R; Eastell, Richard; Adams, Michael A; Dolan, Patricia; Yang, Lang

2017-09-01

Finite element models of an isolated vertebral body cannot accurately predict compressive strength of the spinal column because, in life, compressive load is variably distributed across the vertebral body and neural arch. The purpose of this study was to develop and validate a patient-specific finite element model of a functional spinal unit, and then use the model to predict vertebral strength from medical images. A total of 16 cadaveric functional spinal units were scanned and then tested mechanically in bending and compression to generate a vertebral wedge fracture. Before testing, an image processing and finite element analysis framework (SpineVox-Pro), developed previously in MATLAB using ANSYS APDL, was used to generate a subject-specific finite element model with eight-node hexahedral elements. Transversely isotropic linear-elastic material properties were assigned to vertebrae, and simple homogeneous linear-elastic properties were assigned to the intervertebral disc. Forward bending loading conditions were applied to simulate manual handling. Results showed that vertebral strengths measured by experiment were positively correlated with strengths predicted by the functional spinal unit finite element model with von Mises or Drucker-Prager failure criteria ( R 2  = 0.80-0.87), with areal bone mineral density measured by dual-energy X-ray absorptiometry ( R 2  = 0.54) and with volumetric bone mineral density from quantitative computed tomography ( R 2  = 0.79). Large-displacement non-linear analyses on all specimens did not improve predictions. We conclude that subject-specific finite element models of a functional spinal unit have potential to estimate the vertebral strength better than bone mineral density alone.

Reexamining cluster radioactivity in trans-lead nuclei with consideration of specific density distributions in daughter nuclei and clusters

NASA Astrophysics Data System (ADS)

Qian, Yibin; Ren, Zhongzhou; Ni, Dongdong

2016-08-01

We further investigate the cluster emission from heavy nuclei beyond the lead region in the framework of the preformed cluster model. The refined cluster-core potential is constructed by the double-folding integral of the density distributions of the daughter nucleus and the emitted cluster, where the radius or the diffuseness parameter in the Fermi density distribution formula is determined according to the available experimental data on the charge radii and the neutron skin thickness. The Schrödinger equation of the cluster-daughter relative motion is then solved within the outgoing Coulomb wave-function boundary conditions to obtain the decay width. It is found that the present decay width of cluster emitters is clearly enhanced as compared to that in the previous case, which involved the fixed parametrization for the density distributions of daughter nuclei and clusters. Among the whole procedure, the nuclear deformation of clusters is also introduced into the calculations, and the degree of its influence on the final decay half-life is checked to some extent. Moreover, the effect from the bubble density distribution of clusters on the final decay width is carefully discussed by using the central depressed distribution.

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.

PubMed

Sabatti, Chiara; Service, Susan K; Hartikainen, Anna-Liisa; Pouta, Anneli; Ripatti, Samuli; Brodsky, Jae; Jones, Chris G; Zaitlen, Noah A; Varilo, Teppo; Kaakinen, Marika; Sovio, Ulla; Ruokonen, Aimo; Laitinen, Jaana; Jakkula, Eveliina; Coin, Lachlan; Hoggart, Clive; Collins, Andrew; Turunen, Hannu; Gabriel, Stacey; Elliot, Paul; McCarthy, Mark I; Daly, Mark J; Järvelin, Marjo-Riitta; Freimer, Nelson B; Peltonen, Leena

2009-01-01

Genome-wide association studies (GWAS) of longitudinal birth cohorts enable joint investigation of environmental and genetic influences on complex traits. We report GWAS results for nine quantitative metabolic traits (triglycerides, high-density lipoprotein, low-density lipoprotein, glucose, insulin, C-reactive protein, body mass index, and systolic and diastolic blood pressure) in the Northern Finland Birth Cohort 1966 (NFBC1966), drawn from the most genetically isolated Finnish regions. We replicate most previously reported associations for these traits and identify nine new associations, several of which highlight genes with metabolic functions: high-density lipoprotein with NR1H3 (LXRA), low-density lipoprotein with AR and FADS1-FADS2, glucose with MTNR1B, and insulin with PANK1. Two of these new associations emerged after adjustment of results for body mass index. Gene-environment interaction analyses suggested additional associations, which will require validation in larger samples. The currently identified loci, together with quantified environmental exposures, explain little of the trait variation in NFBC1966. The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci.

Plasma lipoprotein and apolipoprotein distribution as a function of density in the rainbow trout (Salmo gairdneri).

PubMed Central

Babin, P J

1987-01-01

I have previously described [Babin (1987) J. Biol. Chem. 262, 4290-4296] the apolipoprotein composition of the major classes of trout plasma lipoproteins. The present work describes the use of an isopycnic density gradient centrifugation procedure and sequential flotation ultracentrifugation to show: (1) the presence of intermediate density lipoproteins (IDL) in the plasma, between 1.015 and 1.040 g/ml; (2) the existence of a single type of Mr 240,000 apoB-like in the low density lipoproteins (LDL, 1.040 less than p less than 1.085 g/ml); (3) the presence of apoA-I-like (Mr 25,000) in the densest LDL; (4) the adequacy of 1.085 g/ml as a cutoff between the LDL and high density lipoproteins (HDL); (5) the accumulation of Mr 55,000 and 76,000 apolipoproteins and apoA-like apolipoproteins in the 1.21 g/ml infranatant. The fractionation of trout lipoprotein spectrum thus furnishes the distribution of the different lipoprotein classes and leads to the description of the constituent apolipoproteins, which account for about 36% of circulating plasma proteins in this species. Images Fig. 2. Fig. 3. PMID:3689318

Detachment experiments in new DIII-D upper divertor

NASA Astrophysics Data System (ADS)

Moser, A. L.; Leonard, A. W.; Groebner, R. J.; Guo, H.; Wang, H.; Watkins, J. G.; McLean, A. G.; Fenstermacher, M. E.; Shafer, M. W.; Briesemeister, A. R.; Hinson, E. T.

2017-10-01

Installation of the Small Angle Slot (SAS) in the upper divertor of DIII-D enables new studies of the effect of target and baffle geometry on divertor detachment. This structure provides a more-closed upper divertor as well as the SAS divertor itself. Initial SAS experiment results indicate that divertor detachment occurs at a lower line-averaged density than in the more-open, lower single null divertor configurations on DIII-D. In contrast, the increased divertor closure of the new installation did not reduce the upstream density required for detachment beyond that achieved with the previous upper divertor structure. Particle pumping in the upper divertor structure is found to produce a 10 % reduction in the pedestal density required for detachment compared to the case with no pumping. Comparisons focus on both the onset of detachment (measured by in-target Langmuir probes) as a function of upstream density, as well as the effect of the new divertor configurations on pedestal density profiles. Work supported by US DOE under DE-FC02-04ER54698, DE-AC05-00OR22725, DE-AC04-94AL85000, DE-AC52-07NA27344, and DE-SC00013911.

The structural, electronic and dynamic properties of the L1{sub 2}- type Co{sub 3}Ti alloy

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

Arikan, Nihat; Özduran, Mustafa

2014-10-06

The structural, electronic and dynamic properties of the cubic Co{sub 3}Ti alloy in L1{sub 2} structure have been investigated using a pseudopotential plane wave (PP-PW) method within the generalized gradient approximation proposed by Perdew–Burke–Ernzerhof (GGA-PBE). The structural properties, including the lattice constant, the bulk modulus and its pressure derivative agree reasonably with the previous results. The density of state (DOS), projected density of state (PDOS) and electronic band structure are also reported. The DOS shows that Co{sub 3}Ti alloy has a metallic character since the energy bands cross the Fermi level. The density of states at Fermi level mainly comesmore » from the Co-3d states. Phonon dispersion curves and their corresponding total densities of states were obtained using a linear response in the framework of the density functional perturbation theory. All computed phonon frequencies are no imaginer and thus, Co{sub 3}Ti alloy is dynamically stable. The zone center phonon modes have been founded to be 9.307, 9.626 and 13.891 THz for Co{sub 3}Ti.« less

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

PubMed

Serwer, Philip; Wright, Elena T; Demeler, Borries; Jiang, Wen

2018-04-01

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

Serum high-density lipoprotein is associated with better cognitive function in a cross-sectional study of aging women.

PubMed

Bates, Kristyn A; Sohrabi, Hamid R; Rainey-Smith, Stephanie R; Weinborn, Michael; Bucks, Romola S; Rodrigues, Mark; Beilby, John; Howard, Matthew; Taddei, Kevin; Martins, Georgia; Paton, Athena; Shah, Tejal; Dhaliwal, Satvinder S; Foster, Jonathan K; Martins, Ian J; Lautenschlager, Nicola T; Mastaglia, Frank L; Gandy, Samuel E; Martins, Ralph N

2017-03-01

Purpose/Aim of the study: Poor cardiovascular health, including obesity and altered lipid profiles at mid-life, are linked to increased risk of Alzheimer's disease (AD). The biological mechanisms linking cardiovascular health and cognitive function are unclear though are likely to be multifactorial. This study examined the association between various lipoproteins and cognitive functioning in ageing women. We investigated the relationship between readily available biomarkers (i.e. serum lipoprotein) and cognitive decline in domains associated with increased risk of AD (e.g. episodic verbal memory performance and subjective memory complaint). We report cross-sectional data investigating the relationship between serum total cholesterol, triglycerides, high-density lipoprotein (HDL-C) and low-density lipoprotein with verbal memory and learning ability in 130 women with and without memory complaints (n = 71 and 59, respectively) drawn from a study investigating cognitively healthy Western Australians (average age 62.5 years old). After statistical modelling that controlled for the effects of age, depression and apolipoprotein E genotype, HDL-C was significantly associated with better verbal learning and memory performance, specifically short and long delay-free recalls (F = 3.062; p < .05 and F = 3.2670; p < .05, respectively). Our cross-sectional findings suggest that the positive effect of HDL-C on verbal memory may be present much earlier than previously reported and provide further support for the role of HDL-C in healthy brain ageing. Further exploration of the protective effect of HDL-C on cognitive function in ageing is warranted through follow-up, longitudinal studies.

A draft annotation and overview of the human genome

PubMed Central

Wright, Fred A; Lemon, William J; Zhao, Wei D; Sears, Russell; Zhuo, Degen; Wang, Jian-Ping; Yang, Hee-Yung; Baer, Troy; Stredney, Don; Spitzner, Joe; Stutz, Al; Krahe, Ralf; Yuan, Bo

2001-01-01

Background The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. Results We report here a functionally annotated human gene index placed directly on the genome. The index is based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. Such a global approach had previously been described only for chromosomes 21 and 22, which together account for 2.2% of the genome. Conclusions We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a comprehensive gene index requires the synthesis of all available computational and experimental evidence. PMID:11516338

Environmental conditions and biotic interactions influence ecosystem structure and function in a drying stream

USGS Publications Warehouse

Ludlam, J.P.; Magoulick, D.D.

2010-01-01

Benthic consumers influence stream ecosystem structure and function, but these interactions depend on environmental context. We experimentally quantified the effects of central stoneroller minnows (Campostoma anomalum (Rafinesque) and Meek's crayfish (Orconectes meeki meeki (Faxon)) on benthic communities using electric exclusion quadrats in Little Mulberry Creek before (June) and during (August) seasonal stream drying. Unglazed ceramic tiles were deployed in June and August to measure periphyton and invertebrate abundance, and leafpack decomposition and primary production were also measured in August. Relationships between stoneroller and crayfish density and the size of consumer effects were evaluated with multiple linear regression models. Average chlorophyll a abundance was greater on exposed than exclusion tiles in August, but not in June. Sediment dry mass, periphyton ash-free dry mass (AFDM), and chironomid densities on tiles did not differ among treatments in either period. Leaf packs decayed faster in exposed than exclusion treatments (kexposed = 0.038 ?? 0.013, kexclusion = 0.007 ?? 0.002), but consumer effects were stronger in some pools than others. Leafpack invertebrate biomass and abundance and tile primary productivity did not differ among treatments. Consumer effects on chlorophyll a were related to crayfish and stoneroller density, and effects on chironomid density were related to stoneroller density. These results contrast with a previous exclusion experiment in Little Mulberry Creek that demonstrated strong consumer effects. The influence of stream drying on consumer effects appears to have been reduced by strong spates, underscoring the importance of conducting multi-year studies to determine the magnitude of variability in ecological interactions. ?? US Government: USGS 2010.

The competition of particle-vibration coupling and tensor interaction in spherical nuclei

NASA Astrophysics Data System (ADS)

Afanasjev, Anatoli; Litvinova, Elena

2014-09-01

The search for missing terms in the energy density functionals (EDF) is one of the leading directions in the development of nuclear density functional theory (DFT). Tensor force is one of possible candidates. However, despite extensive studies the questions about its effective strength and unambiguous signals still remain open. One of the main experimental benchmarks for the studies of tensor interaction is provided by the data on the single-particle states in the N = 82 and Z = 50 isotopes. The energy splittings of the proton h11 / 2 and g7 / 2 states in the Z = 50 isotopes and neutron 1i13 / 2 and 1h9 / 2 states in the N = 82 isotones are used in the definition of tensor force in the Skyrme DFT. However, in experiment these states are not ``mean-field'' states because of coupling with vibrations. Employing relativistic particle-vibration coupling (PVC) model we show that many features of these splittings can be reproduced when PVC is taken into account. This suggests the competition of PVC and tensor interaction and that tensor interaction should be weaker as compared with previous estimates. The search for missing terms in the energy density functionals (EDF) is one of the leading directions in the development of nuclear density functional theory (DFT). Tensor force is one of possible candidates. However, despite extensive studies the questions about its effective strength and unambiguous signals still remain open. One of the main experimental benchmarks for the studies of tensor interaction is provided by the data on the single-particle states in the N = 82 and Z = 50 isotopes. The energy splittings of the proton h11 / 2 and g7 / 2 states in the Z = 50 isotopes and neutron 1i13 / 2 and 1h9 / 2 states in the N = 82 isotones are used in the definition of tensor force in the Skyrme DFT. However, in experiment these states are not ``mean-field'' states because of coupling with vibrations. Employing relativistic particle-vibration coupling (PVC) model we show that many features of these splittings can be reproduced when PVC is taken into account. This suggests the competition of PVC and tensor interaction and that tensor interaction should be weaker as compared with previous estimates. This work has been supported by the U.S. Department of Energy under the Grant DE-FG02-07ER41459 and National Science Foundation Award PHY-1204486.

Differential localization of SAP102 and PSD-95 is revealed in hippocampal spines using super-resolution light microscopy.

PubMed

Zheng, Chan-Ying; Wang, Ya-Xia; Kachar, Bechara; Petralia, Ronald S

2011-01-01

Synapse-associated protein 102 (SAP102) and postsynaptic density 95 (PSD-95) are two major cytoskeleton proteins in the postsynaptic density (PSD). Both of them belong to the membrane-associated guanylate kinase (MAGUK) family, which clusters and anchors glutamate receptors and other proteins at synapses. In our previous study, we found that SAP102 and PSD-95 have different distributions, using combined light/electron microscopy (LM/EM) methods.1 Here, we double labeled endogenous SAP102 and PSD-95 in mature hippocampal neurons, and then took images by two different kinds of super resolution microscopy-Stimulated Emission Depletion microscopy (STED) and DeltaVision OMX 3D super resolution microscopy. We found that our 2D and 3D super resolution data were consistent with our previous LM/EM data, showing significant differences in the localization of SAP102 and PSD-95 in spines: SAP102 is distributed in both the PSD and cytoplasm of spines, while PSD-95 is concentrated only in the PSD area. These results indicate functional differences between SAP102 and PSD-95 in synaptic organization and plasticity.

Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents

DOE PAGES

McNally, Joshua S.; Noll, Bruce; Orme, Christopher J.; ...

2015-05-04

Here, a density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An x-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction withmore » the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo-six membered ring which included both protons.« less

Density-functional theory for internal magnetic fields

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

The multifacet graphically contracted function method. I. Formulation and implementation

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

Shepard, Ron; Brozell, Scott R.; Gidofalvi, Gergely

2014-08-14

The basic formulation for the multifacet generalization of the graphically contracted function (MFGCF) electronic structure method is presented. The analysis includes the discussion of linear dependency and redundancy of the arc factor parameters, the computation of reduced density matrices, Hamiltonian matrix construction, spin-density matrix construction, the computation of optimization gradients for single-state and state-averaged calculations, graphical wave function analysis, and the efficient computation of configuration state function and Slater determinant expansion coefficients. Timings are given for Hamiltonian matrix element and analytic optimization gradient computations for a range of model problems for full-CI Shavitt graphs, and it is observed that bothmore » the energy and the gradient computation scale as O(N{sup 2}n{sup 4}) for N electrons and n orbitals. The important arithmetic operations are within dense matrix-matrix product computational kernels, resulting in a computationally efficient procedure. An initial implementation of the method is used to present applications to several challenging chemical systems, including N{sub 2} dissociation, cubic H{sub 8} dissociation, the symmetric dissociation of H{sub 2}O, and the insertion of Be into H{sub 2}. The results are compared to the exact full-CI values and also to those of the previous single-facet GCF expansion form.« less

17β Estradiol increases resilience and improves hippocampal synaptic function in helpless ovariectomized rats

PubMed Central

Bredemann, Teruko M.; McMahon, Lori L.

2014-01-01

Summary Memory impairment is the most commonly reported cognitive symptom associated with major depressive disorder. Decreased hippocampal volume and neurogenesis in depression link hippocampal dysfunction with deficits in memory. Stress decreases hippocampal dendritic spine density and long-term potentiation (LTP) at glutamate synapses, a cellular correlate of learning and memory. However, elevated plasma levels of 17β estradiol (E2) during proestrus increase hippocampal structure and function, directly opposing the negative consequences of stress. In women, significant fluctuations in ovarian hormones likely increase vulnerability of hippocampal circuits to stress, potentially contributing to the greater incidence of depression compared to men. Using the learned helplessness model of depression and ovariectomized female rats, we investigated whether acquisition of helplessness and hippocampal synaptic dysfunction is differentially impacted by the presence or absence of plasma E2. We find that inescapable shock induces a greater incidence of helplessness in vehicle- versus E2-treated OVX rats. In the vehicle-treated group, LTP was absent at CA3-CA1 synapses in slices only from helpless rats, and CA1 spine density was decreased compared to resilient rats. In contrast, significant LTP was observed in slices from E2-treated helpless rats; importantly, spine density was not different between E2-treated helpless and resilient rats, dissociating spine density from the LTP magnitude. We also find that E2 replacement can reverse previously established helpless behavior. Thus, our results show that E2 replacement in OVX rats increases resilience and improves hippocampal plasticity, suggesting that E2 therapy may increase resilience to stress and preserve hippocampal function in women experiencing large fluctuations in plasma estrogen levels. PMID:24636504

Topics in QCD at Nonzero Temperature and Density

NASA Astrophysics Data System (ADS)

Pangeni, Kamal

Understanding the behavior of matter at ultra-high density such as neutron stars require the knowledge of ground state properties of Quantum chromodynamics (QCD) at finite chemical potential. However, this task has turned out to be very difficult because of two main reasons: 1) QCD may still be strongly coupled at those regimes making perturbative calculations unreliable and 2) QCD at finite density suffers from the sign problem that makes the use of lattice simulation problematic and it even affects phenomenological models. In the first part of this thesis, we show that the sign problem in analytical calculations of finite density models can be solved by considering the CK-symmetric, where C is charge conjugation and K is complex conjugation, complex saddle points of the effective action. We then explore the properties and consequences of such complex saddle points at non-zero temperature and density. Due to CK symmetry, the mass matrix eigenvalues in these models are not always real but can be complex, which results in damped oscillation of the density-density correlation function, a new feature of finite density models. To address the generality of such behavior, we next consider a lattice model of QCD with static quarks at strong-coupling. Computation of the mass spectrum confirms the existence of complex eigenvalues in much of temperature-chemical potential plane. This provides an independent confirmation of our results obtained using phenomenological models of QCD. The existence of regions in parameter space where density-density correlation function exhibit damped oscillation is one of the hallmarks of typical liquid-gas system. The formalism developed to tackle the sign problem in QCD models actually gives a simple understanding for the existence of such behavior in liquid-gas system. To this end, we develop a generic field theoretic model for the treatment of liquid-gas phase transition. An effective field theory at finite density derived from a fundamental four dimensional field theory turns out to be complex but CK symmetric. The existence of CK symmetry results in complex mass eigenvalues, which in turn leads to damped oscillatory behavior of the density-density correlation function. In the last part of this thesis, we study the effect of large amplitude density oscillations on the transport properties of superfluid nuclear matter. In nuclear matter at neutron-star densities and temperature, Cooper pairing leads to the formations of a gap in the nucleon excitation spectra resulting in exponentially strong Boltzmann suppression of many transport coefficients. Previous calculations have shown evidence that density oscillations of sufficiently large amplitude can overcome this suppression for flavor-changing beta processes via the mechanism of "gap-bridging". We address the simplifications made in that initial work, and show that gap bridging can counteract Boltzmann suppression of neutrino emissivity for the realistic case of modified Urca processes in matter with 3 P2 neutron pairing.

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

PubMed

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.

In Search of Sleep Biomarkers of Alzheimer’s Disease: K-Complexes Do Not Discriminate between Patients with Mild Cognitive Impairment and Healthy Controls

PubMed Central

Reda, Flaminia; Gorgoni, Maurizio; Lauri, Giulia; Truglia, Ilaria; Cordone, Susanna; Scarpelli, Serena; Mangiaruga, Anastasia; D’Atri, Aurora; Ferrara, Michele; Lacidogna, Giordano; Marra, Camillo; Rossini, Paolo Maria; De Gennaro, Luigi

2017-01-01

The K-complex (KC) is one of the hallmarks of Non-Rapid Eye Movement (NREM) sleep. Recent observations point to a drastic decrease of spontaneous KCs in Alzheimer’s disease (AD). However, no study has investigated when, in the development of AD, this phenomenon starts. The assessment of KC density in mild cognitive impairment (MCI), a clinical condition considered a possible transitional stage between normal cognitive function and probable AD, is still lacking. The aim of the present study was to compare KC density in AD/MCI patients and healthy controls (HCs), also assessing the relationship between KC density and cognitive decline. Twenty amnesic MCI patients underwent a polysomnographic recording of a nocturnal sleep. Their data were compared to those of previously recorded 20 HCs and 20 AD patients. KCs during stage 2 NREM sleep were visually identified and KC densities of the three groups were compared. AD patients showed a significant KC density decrease compared with MCI patients and HCs, while no differences were observed between MCI patients and HCs. KC density was positively correlated with Mini-Mental State Examination (MMSE) scores. Our results point to the existence of an alteration of KC density only in a full-blown phase of AD, which was not observable in the early stage of the pathology (MCI), but linked with cognitive deterioration. PMID:28468235

Quantifying Individual Brain Connectivity with Functional Principal Component Analysis for Networks.

PubMed

Petersen, Alexander; Zhao, Jianyang; Carmichael, Owen; Müller, Hans-Georg

2016-09-01

In typical functional connectivity studies, connections between voxels or regions in the brain are represented as edges in a network. Networks for different subjects are constructed at a given graph density and are summarized by some network measure such as path length. Examining these summary measures for many density values yields samples of connectivity curves, one for each individual. This has led to the adoption of basic tools of functional data analysis, most commonly to compare control and disease groups through the average curves in each group. Such group differences, however, neglect the variability in the sample of connectivity curves. In this article, the use of functional principal component analysis (FPCA) is demonstrated to enrich functional connectivity studies by providing increased power and flexibility for statistical inference. Specifically, individual connectivity curves are related to individual characteristics such as age and measures of cognitive function, thus providing a tool to relate brain connectivity with these variables at the individual level. This individual level analysis opens a new perspective that goes beyond previous group level comparisons. Using a large data set of resting-state functional magnetic resonance imaging scans, relationships between connectivity and two measures of cognitive function-episodic memory and executive function-were investigated. The group-based approach was implemented by dichotomizing the continuous cognitive variable and testing for group differences, resulting in no statistically significant findings. To demonstrate the new approach, FPCA was implemented, followed by linear regression models with cognitive scores as responses, identifying significant associations of connectivity in the right middle temporal region with both cognitive scores.

Are Strong Zonal Winds in Giant Planets Caused by Density-Stratification?

NASA Astrophysics Data System (ADS)

Verhoeven, J.; Stellmach, S.

2012-12-01

One of the most striking features of giant planets like Jupiter and Saturn are the zonal wind patterns observed on their surfaces. The mechanism that drives this differential rotation is still not clearly identified and is currently strongly debated in the astro- and geophysics community. Different mechanisms have been proposed over the last decades. Here, a recently discovered mechanism based on background density stratification (Glatzmaier et al., 2009) is investigated. This mechanism has the potential to overcome known difficulties of previous explanations and its efficiency has been demonstrated in 2-d simulations covering equatorial planes. By performing highly resolved numerical simulations in a local Cartesian geometry, we are able to test the efficiency and functionality of this mechanism in turbulent, rotating convection in three spatial dimensions. The choice of a Cartesian model geometry naturally excludes other known mechanisms capable of producing differential rotation, thus allowing us to investigate the role of density stratification in isolation. Typically, the dynamics can be classified into two main regimes: A regime exhibiting strong zonal winds for weak to moderate thermal driving and a regime where zonal winds are largely absent in the case of a strong thermal forcing. Our results indicate that previous 2-d results must be handled with care and can only explain parts of the full 3-d behavior. We show that the density-stratification mechanism tends to operate in a more narrow parameter range in 3-d as compared to 2-d simulations. The dynamics of the regime transition is shown to differ in both cases, which renders scaling laws derived from two-dimensional studies questionable. Based on our results, we provide estimates for the importance of the density-stratification mechanism for giant planets like Jupiter (strong density stratification), for systems like the Earth's core (weak density stratification) and compare its efficiency with other suggested mechanisms for driving differential rotation. Gary A. Glatzmaier, Martha Evonuk and Tamara M. Rogers (2009), Differential rotation in giant planets maintained by density-stratified turbulent convection. Geophysical and Astrophysical Fluid Dynamics, Vol. 103, No. 1, 31-51.

Effect of water temperature and population density on the population dynamics of Schistosoma mansoni intermediate host snails.

PubMed

McCreesh, Nicky; Arinaitwe, Moses; Arineitwe, Wilber; Tukahebwa, Edridah M; Booth, Mark

2014-11-12

Mathematical models can be used to identify areas at risk of increased or new schistosomiasis transmission as a result of climate change. The results of these models can be very different when parameterised to different species of host snail, which have varying temperature preferences. Currently, the experimental data needed by these models are available for only a few species of snail. The choice of density-dependent functions can also affect model results, but the effects of increasing densities on Biomphalaria populations have only previously been investigated in artificial aquariums. Laboratory experiments were conducted to estimate Biomphalaria sudanica mortality, fecundity and growth rates at ten different constant water temperatures, ranging from 13-32°C. Snail cages were used to determine the effects of snail densities on B. sudanica and B. stanleyi mortality and fecundity rates in semi-natural conditions in Lake Albert. B. sudanica survival and fecundity were highest at 20°C and 22°C respectively. Growth in shell diameter was estimated to be highest at 23°C in small and medium sized snails, but the relationship between temperature and growth was not clear. The fecundity of both B. sudanica and B. stanleyi decreased by 72-75% with a four-fold increase in population density. Increasing densities four-fold also doubled B. stanleyi mortality rates, but had no effect on the survival of B. sudanica. The optimum temperature for fecundity was lower for B. sudanica than for previously studied species of Biomphalaria. In contrast to other Biomphalaria species, B. sudanica have a distinct peak temperature for survival, as opposed to a plateau of highly suitable temperatures. For both B. stanleyi and B. sudanica, fecundity decreased with increasing population densities. This means that snail populations may experience large fluctuations in numbers, even in the absence of any external factors such as seasonal temperature changes. Survival also decreased with increasing density for B. stanleyi, in contrast to B. sudanica and other studied Biomphalaria species where only fecundity has been shown to decrease.

The relative efficiency of modular and non-modular networks of different size

PubMed Central

Tosh, Colin R.; McNally, Luke

2015-01-01

Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a range of sizes. We conduct a detailed analysis of efficiency in networks of two size classes: ‘small’ and ‘large’, and a less detailed analysis across a range of network sizes. The former analysis reveals that while the modular network is less efficient than one of the two non-modular networks considered when networks are small, it is usually equally or more efficient than both non-modular networks when networks are large. The latter analysis shows that in networks of small to intermediate size, modular networks are much more efficient that non-modular networks of the same (low) connective density. If connective density must be kept low to reduce energy needs for example, this could promote modularity. We have shown how relative functionality/performance scales with network size, but the precise nature of evolutionary relationship between network size and prevalence of modularity will depend on the costs of connectivity. PMID:25631996

Ginzburg-Landau theory for the solid-liquid interface of bcc elements. II - Application to the classical one-component plasma, the Wigner crystal, and He-4

NASA Technical Reports Server (NTRS)

Zeng, X. C.; Stroud, D.

1989-01-01

The previously developed Ginzburg-Landau theory for calculating the crystal-melt interfacial tension of bcc elements to treat the classical one-component plasma (OCP), the charged fermion system, and the Bose crystal. For the OCP, a direct application of the theory of Shih et al. (1987) yields for the surface tension 0.0012(Z-squared e-squared/a-cubed), where Ze is the ionic charge and a is the radius of the ionic sphere. Bose crystal-melt interface is treated by a quantum extension of the classical density-functional theory, using the Feynman formalism to estimate the relevant correlation functions. The theory is applied to the metastable He-4 solid-superfluid interface at T = 0, with a resulting surface tension of 0.085 erg/sq cm, in reasonable agreement with the value extrapolated from the measured surface tension of the bcc solid in the range 1.46-1.76 K. These results suggest that the density-functional approach is a satisfactory mean-field theory for estimating the equilibrium properties of liquid-solid interfaces, given knowledge of the uniform phases.

Replication of associations between LRP5 and ESRRA variants and bone density in premenopausal women.

PubMed

Giroux, S; Elfassihi, L; Cole, D E C; Rousseau, F

2008-12-01

Replication is a critical step to validate positive genetic associations. In this study, we tested two previously reported positive associations. The low density lipoprotein receptor-related protein 5 (LRP5) Val667Met and lumbar spine bone density are replicated. This result is in line with results from large consortiums such as Genomos. However, the estrogen-related receptor alpha (ESRRA) repeat in the promoter is not replicated although the polymorphism studied was functional and could have been a causative variant. We sought to validate associations previously reported between LRP5 V667M polymorphism and lumbar spine (LS, p = 0.013) and femoral neck (FN, p = 0.0002) bone mineral density (BMD), and between ESRRA 23 base pair repeat polymorphism and LS BMD (p = 0.0036) in a sample of premenopausal Caucasian women using an independent sample. For the replication sample, we recruited 673 premenopausal women from the Toronto metropolitan area. All women were Caucasian and had BMD measured. LRP5 V667M was genotyped by allele-specific PCR and ESRRA repeats by sizing of PCR products on agarose gels. We reproduced the same association as we reported previously between LRP5 V667M and LS BMD (p = 0.015) but not with FN BMD (p = 0.254). The combined data from the two populations indicate an effect size of 0.28SD for LS BMD (p = 0.00048) and an effect size of 0.26 SD for FN BMD (p = 0.00037). In contrast, the association we reported earlier between ESRRA repeats and LS BMD was not replicated in the sample from Toronto (p = 0.645). The association between LRP5 V667M and LS BMD is confirmed but not that between ESRRA repeats and LS BMD. This result indicates that it is imperative to validate any positive association in an independent sample.

Reconstitution of Homomeric GluA2flop Receptors in Supported Lipid Membranes

PubMed Central

Baranovic, Jelena; Ramanujan, Chandra S.; Kasai, Nahoko; Midgett, Charles R.; Madden, Dean R.; Torimitsu, Keiichi; Ryan, John F.

2013-01-01

AMPA receptors (AMPARs) are glutamate-gated ion channels ubiquitous in the vertebrate central nervous system, where they mediate fast excitatory neurotransmission and act as molecular determinants of memory formation and learning. Together with detailed analyses of individual AMPAR domains, structural studies of full-length AMPARs by electron microscopy and x-ray crystallography have provided important insights into channel assembly and function. However, the correlation between the structure and functional states of the channel remains ambiguous particularly because these functional states can be assessed only with the receptor bound within an intact lipid bilayer. To provide a basis for investigating AMPAR structure in a membrane environment, we developed an optimized reconstitution protocol using a receptor whose structure has previously been characterized by electron microscopy. Single-channel recordings of reconstituted homomeric GluA2flop receptors recapitulate key electrophysiological parameters of the channels expressed in native cellular membranes. Atomic force microscopy studies of the reconstituted samples provide high-resolution images of membrane-embedded full-length AMPARs at densities comparable to those in postsynaptic membranes. The data demonstrate the effect of protein density on conformational flexibility and dimensions of the receptors and provide the first structural characterization of functional membrane-embedded AMPARs, thus laying the foundation for correlated structure-function analyses of the predominant mediators of excitatory synaptic signals in the brain. PMID:23382380

Measurement of electron density using reactance cutoff probe

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

You, K. H.; Seo, B. H.; Kim, J. H.

2016-05-15

This paper proposes a new measurement method of electron density using the reactance spectrum of the plasma in the cutoff probe system instead of the transmission spectrum. The highly accurate reactance spectrum of the plasma-cutoff probe system, as expected from previous circuit simulations [Kim et al., Appl. Phys. Lett. 99, 131502 (2011)], was measured using the full two-port error correction and automatic port extension methods of the network analyzer. The electron density can be obtained from the analysis of the measured reactance spectrum, based on circuit modeling. According to the circuit simulation results, the reactance cutoff probe can measure themore » electron density more precisely than the previous cutoff probe at low densities or at higher pressure. The obtained results for the electron density are presented and discussed for a wide range of experimental conditions, and this method is compared with previous methods (a cutoff probe using the transmission spectrum and a single Langmuir probe).« less

Properties of density and magnetic fluctuations occurring in density striations in the new LAPD

NASA Astrophysics Data System (ADS)

Maggs, J. E.; Morales, G. J.

2001-10-01

Previous studies of density striations (long, narrow magnetic-field-aligned density depletions) in the LAPD plasma device at UCLA revealed an eigenmode structure to fluctuations driven by the pressure gradient in the striation wall (Maggs and Morales, Phys. Plasmas, 4, 1997). The nature of these fluctuations depended on the plasma beta external to the striation, with shear Alfvén wave turbulence developing at betas less than the mass ratio and drift-Alfvén waves at betas above the mass ratio. These fluctuations were found to have a direct connection to turbulence observed at the plasma edge. The new LAPD is 18 meters in length with a background field up to twice previously attainable values. We report on the properties of fluctuations associated with density striations in the new device over a wider range of beta, and compare them to previous results. The behavior of fluctuations in density striations created in flared-field and magnetic-mirror geometries will also be presented. Research sponsored by ONR and NSF

Structural and electronic stability of a volleyball-shaped B80 fullerene

NASA Astrophysics Data System (ADS)

Wang, Xiao-Qian

2010-10-01

We have studied the structural and electronic characteristics of a volleyball-shaped B80 cage using first-principles density-functional calculations. In contrast to the popularly ratified “magic” B80 buckyball with 20 hexagonal pyramids and 12 hollow pentagons, the volleyball-shaped B80 constitutes 12 pentagonal pyramids, 8 hexagonal pyramids, and 12 hollow hexagons. The B80 volleyball is markedly more stable than the previously assumed magic B80 buckyball, which is attributed to the improved aromaticity associated with the distinct configuration.

Adsorption of O_{2} on Ag(111): Evidence of Local Oxide Formation.

PubMed

Andryushechkin, B V; Shevlyuga, V M; Pavlova, T V; Zhidomirov, G M; Eltsov, K N

2016-07-29

The atomic structure of the disordered phase formed by oxygen on Ag(111) at low coverage is determined by a combination of low-temperature scanning tunneling microscopy and density functional theory. We demonstrate that the previous assignment of the dark objects in STM to chemisorbed oxygen atoms is incorrect and incompatible with trefoil-like structures observed in atomic-resolution images in current work. In our model, each object is an oxidelike ring formed by six oxygen atoms around the vacancy in Ag(111).

Investigation of structural stability and elastic properties of CrH and MnH: A first principles study

NASA Astrophysics Data System (ADS)

Kanagaprabha, S.; Rajeswarapalanichamy, R.; Sudhapriyanga, G.; Murugan, A.; Santhosh, M.; Iyakutti, K.

2015-06-01

The structural and mechanical properties of CrH and MnH are investigated using first principles calculation based on density functional theory as implemented in VASP code with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and other theoretical results. A structural phase transition from NaCl to NiAs phase at a pressure of 76 GPa is predicted for both CrH and MnH.

Collisionless dissociation and isotopic enrichment of SF6 using high-powered CO2 laser radiation

NASA Technical Reports Server (NTRS)

Gower, M. C.; Billman, K. W.

1977-01-01

Dissociation of S-32F6 and the resultant isotopic enrichment of S-34F6 using high-powered CO2 laser radiation has been studied with higher experimental sensitivity than previously reported. Enrichment factors have been measured as a function of laser pulse number, wavelength, energy and time duration. A geometry independent dissociation cross section is introduced and measured values are presented. Threshold energy densities, below which no dissociation was observed, were also determined.

Rough Interface Effects on N-S Proximity-Contact Systems

NASA Astrophysics Data System (ADS)

Nagato, Yasushi; Nagai, Katsuhiko

2003-03-01

We discuss the influence of atomic scale roughness of the interface on the properties of the N-S contact systems. To treat the interface roughness effects we extend our previous quasi-classical theory of the rough surface effect and construct a formal solution for the quasi-classical Green's function. We apply the formulation to N-S systems with two-dimensional anisotropic dx2-y2 superconductor and calculate the self-consistent pair potential and the density of states at the interface.

Geometric structure of anatase Ti O2(101 )

NASA Astrophysics Data System (ADS)

Treacy, Jon P. W.; Hussain, Hadeel; Torrelles, Xavier; Grinter, David C.; Cabailh, Gregory; Bikondoa, Oier; Nicklin, Christopher; Selcuk, Sencer; Selloni, Annabella; Lindsay, Robert; Thornton, Geoff

2017-02-01

Surface x-ray diffraction has been used to determine the quantitative structure of the (101) termination of anatase Ti O2 . The atomic displacements from the bulk-terminated structure are significantly different from those previously calculated with density functional theory (DFT) methods with discrepancies for the Ti displacements in the [10 1 ¯] direction of up to 0.3 Å . DFT calculations carried out as part of the current paper provide a much better agreement through improved accuracy and thicker slab models.

[Changes in mammographic features of breast cancer--comparison with previous films].

PubMed

Matsunaga, T; Hagiwara, K; Kimura, K; Kusama, M

1992-11-25

Mammographic features of 87 breast cancer patients were studied in comparison with their previous survey films. Changes in the mammographic features included microcalicification (28 cases), tumor shadow (35 cases) and intratumorous microcalicifications (6 cases). Seven cases had several extremely faint calcifications on the previous films, and three of six cases with clustered and scattered microcalcifications that extended over an entire breast quadrant had increased in number, density and extent. Eight cases in which clustered microcalcifications had increased in number, density and extent suggested a relationship between the increase in the extent of microcalcifications and length of time between visits. In most cases with tumor shadow, a slight localized increase in mammary gland density, irregular margins and straightened trabeculae were overlooked because of breast density.

A note on the accuracy of KS-DFT densities

NASA Astrophysics Data System (ADS)

Ranasinghe, Duminda S.; Perera, Ajith; Bartlett, Rodney J.

2017-11-01

The accuracy of the density of wave function methods and Kohn-Sham (KS) density functionals is studied using moments of the density, ⟨rn ⟩ =∫ ρ (r )rnd τ =∫0∞4 π r2ρ (r ) rnd r ,where n =-1 ,-2,0,1,2 ,and 3 provides information about the short- and long-range behavior of the density. Coupled cluster (CC) singles, doubles, and perturbative triples (CCSD(T)) is considered as the reference density. Three test sets are considered: boron through neon neutral atoms, two and four electron cations, and 3d transition metals. The total density and valence only density are distinguished by dropping appropriate core orbitals. Among density functionals tested, CAMQTP00 and ωB97x show the least deviation for boron through neon neutral atoms. They also show accurate eigenvalues for the HOMO indicating that they should have a more correct long-range behavior for the density. For transition metals, some density functional approximations outperform some wave function methods, suggesting that the KS determinant could be a better starting point for some kinds of correlated calculations. By using generalized many-body perturbation theory (MBPT), the convergence of second-, third-, and fourth-order KS-MBPT for the density is addressed as it converges to the infinite-order coupled cluster result. For the transition metal test set, the deviations in the KS density functional theory methods depend on the amount of exact exchange the functional uses. Functionals with exact exchange close to 25% show smaller deviations from the CCSD(T) density.

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

PubMed Central

Milton, James A.; Patole, Samson; Yin, Huabing; Xiao, Qiang; Brown, Tom; Melvin, Tracy

2013-01-01

Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies. PMID:23361467

The intrapair electron correlation in natural orbital functional theory

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

Piris, M.; Donostia International Physics Center; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao

2013-12-21

A previously proposed [M. Piris, X. Lopez, F. Ruipérez, J. M. Matxain, and J. M. Ugalde, J. Chem. Phys. 134, 164102 (2011)] formulation of the two-particle cumulant, based on an orbital-pairing scheme, is extended here for including more than two natural orbitals. This new approximation is used to reconstruct the two-particle reduced density matrix (2-RDM) constrained to the D, Q, and G positivity necessary conditions of the N-representable 2-RDM. In this way, we have derived an extended version of the Piris natural orbital functional 5 (PNOF5e). An antisymmetrized product of strongly orthogonal geminals with the expansion coefficients explicitly expressed bymore » the occupation numbers is also used to generate the PNOF5e. The theory is applied to the homolytic dissociation of selected diatomic molecules: H{sub 2}, LiH, and Li{sub 2}. The Bader's theory of atoms in molecules is used to analyze the electron density and the presence of non-nuclear maxima in the case of a set of light atomic clusters: Li{sub 2}, Li {sub 3}{sup +}, Li {sub 4}{sup 2+}, and H{sub 3}{sup +}. The improvement of PNOF5e over PNOF5 was observed by visualizing the electron densities.« less

Segmentation Algorithms for Detection of Targets in IR Imagery (Algorithmes de Segmentation pour la Detection de Cibles sur Images IR),

DTIC Science & Technology

1981-01-01

This fact being established, leptokurtic and platykurtic density functions are defined in terms of deviations from the normal density function. Thus...the usual definitions (Ref. 6) are: Leptokurtic - A density function that is peaked, K > 0, [18] and Platykurtic - A density function that is flat, K...has long Deen accepted that a symmetrical platykurtic density function, with K<O, is characterized by a flatter top and more abrupt terminals than the

Testing the molecular-hydrogen Kennicutt-Schmidt law in the low-density environments of extended ultraviolet disc galaxies

NASA Astrophysics Data System (ADS)

Watson, Linda C.; Martini, Paul; Lisenfeld, Ute; Böker, Torsten; Schinnerer, Eva

2016-01-01

Studying star formation beyond the optical radius of galaxies allows us to test empirical relations in extreme conditions with low average gas density and low molecular fraction. Previous studies discovered galaxies with extended ultraviolet (XUV) discs, which often contain star-forming regions with lower Hα-to-far-UV (FUV) flux ratios compared to inner disc star-forming regions. However, most previous studies lack measurements of molecular gas, which is presumably the component of the interstellar medium out of which stars form. We analysed published CO measurements and upper limits for 15 star-forming regions in the XUV or outer disc of three nearby spiral galaxies and a new CO upper limit from the IRAM (Institut de Radioastronomie Millimétrique) 30 m telescope in one star-forming region at r = 3.4r25 in the XUV disc of NGC 4625. We found that the star-forming regions are in general consistent with the same molecular-hydrogen Kennicutt-Schmidt law that applies within the optical radius, independent of whether we used Hα or FUV as the star formation rate (SFR) tracer. However, a number of the CO detections are significantly offset towards higher SFR surface density for their molecular-hydrogen surface density. Deeper CO data may enable us to use the presence or absence of molecular gas as an evolutionary probe to break the degeneracy between age and stochastic sampling of the initial mass function as the explanation for the low Hα-to-FUV flux ratios in XUV discs.

Linear Stability Analysis of Gravitational Effects on a Low-Density Gas Jet Injected into a High-Density Medium

NASA Technical Reports Server (NTRS)

Lawson, Anthony L.; Parthasarathy, Ramkumar N.

2005-01-01

The objective of this study was to determine the effects of buoyancy on the absolute instability of low-density gas jets injected into high-density gas mediums. Most of the existing analyses of low-density gas jets injected into a high-density ambient have been carried out neglecting effects of gravity. In order to investigate the influence of gravity on the near-injector development of the flow, a spatio-temporal stability analysis of a low-density round jet injected into a high-density ambient gas was performed. The flow was assumed to be isothermal and locally parallel; viscous and diffusive effects were ignored. The variables were represented as the sum of the mean value and a normal-mode small disturbance. An ordinary differential equation governing the amplitude of the pressure disturbance was derived. The velocity and density profiles in the shear layer, and the Froude number (signifying the effects of gravity) were the three important parameters in this equation. Together with the boundary conditions, an eigenvalue problem was formulated. Assuming that the velocity and density profiles in the shear layer to be represented by hyperbolic tangent functions, the eigenvalue problem was solved for various values of Froude number. The Briggs-Bers criterion was combined with the spatio-temporal stability analysis to determine the nature of the absolute instability of the jet whether absolutely or convectively unstable. The roles of the density ratio, Froude number, Schmidt number, and the lateral shift between the density and velocity profiles on the absolute instability of the jet were determined. Comparisons of the results with previous experimental studies show good agreement when the effects of these variables are combined together. Thus, the combination of these variables determines how absolutely unstable the jet will be.

Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands

NASA Astrophysics Data System (ADS)

Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.

2018-01-01

The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.

Computation of Nonretarded London Dispersion Coefficients and Hamaker Constants of Copper Phthalocyanine.

PubMed

Zhao, Yan; Ng, Hou T; Hanson, Eric; Dong, Jiannan; Corti, David S; Franses, Elias I

2010-02-09

A time-dependent density functional theory (TDDFT) scheme has been validated for predictions of the dispersion coefficients of five molecules (H2O, NH3, CO2, C6H6, and pentane) and for predictions of the static dipole polarizabilities of three organometallic compounds (TiCl4, OsO4, and Ge(CH3)4). The convergence of grid spacing has been examined, and two types of pseudopotentials and 13 density functionals have been tested. The nonretarded Hamaker constants A11 are calculated by employing a semiempirical parameter a along with the standard Hamaker constant equation. The parameter a is optimized against six accurate Hamaker constants obtained from the full Lifshitz theory. The dispersion coefficients of copper phthalocyanine CuPc and CuPc-SO3H are then computed. Using the theoretical densities of ρ1 = 1.63 and 1.62 g/cm(3), the Hamaker constants A11 of crystalline α-CuPc and β-CuPc are found to be 14.73 × 10(-20) and 14.66 × 10(-20) J, respectively. Using the experimentally derived density of ρ1 = 1.56 g/cm(3) for a commercially available β-CuPc (nanoparticles of ∼90 nm hydrodynamic diameter), A11 = 13.52 × 10(-20) J is found. Its corresponding effective Hamaker constant in water (A121) is calculated to be 3.07 × 10(-20) J. All computed A11 values for CuPc are noted to be higher than those reported previously.

Symmetries, invariants and generating functions: higher-order statistics of biased tracers

NASA Astrophysics Data System (ADS)

Munshi, Dipak

2018-01-01

Gravitationally collapsed objects are known to be biased tracers of an underlying density contrast. Using symmetry arguments, generalised biasing schemes have recently been developed to relate the halo density contrast δh with the underlying density contrast δ, divergence of velocity θ and their higher-order derivatives. This is done by constructing invariants such as s, t, ψ,η. We show how the generating function formalism in Eulerian standard perturbation theory (SPT) can be used to show that many of the additional terms based on extended Galilean and Lifshitz symmetry actually do not make any contribution to the higher-order statistics of biased tracers. Other terms can also be drastically simplified allowing us to write the vertices associated with δh in terms of the vertices of δ and θ, the higher-order derivatives and the bias coefficients. We also compute the cumulant correlators (CCs) for two different tracer populations. These perturbative results are valid for tree-level contributions but at an arbitrary order. We also take into account the stochastic nature bias in our analysis. Extending previous results of a local polynomial model of bias, we express the one-point cumulants Script SN and their two-point counterparts, the CCs i.e. Script Cpq, of biased tracers in terms of that of their underlying density contrast counterparts. As a by-product of our calculation we also discuss the results using approximations based on Lagrangian perturbation theory (LPT).

Study of the Auger line shape of polyethylene and diamond

NASA Technical Reports Server (NTRS)

Dayan, M.; Pepper, S. V.

1984-01-01

The KVV Auger electron line shapes of carbon in polyethylene and diamond have been studied. The spectra were obtained in derivative form by electron beam excitation. They were treated by background subtraction, integration and deconvolution to produce the intrinsic Auger line shape. Electron energy loss spectra provided the response function in the deconvolution procedure. The line shape from polyethylene is compared with spectra from linear alkanes and with a previous spectrum of Kelber et al. Both spectra are compared with the self-convolution of their full valence band densities of states and of their p-projected densities. The experimental spectra could not be understood in terms of existing theories. This is so even when correlation effects are qualitatively taken into account account to the theories of Cini and Sawatzky and Lenselink.

Phase transitions in four-dimensional binary hard hypersphere mixtures

NASA Astrophysics Data System (ADS)

Bishop, Marvin; Whitlock, Paula A.

2013-02-01

Previous Monte Carlo investigations of binary hard hyperspheres in four-dimensional mixtures are extended to higher densities where the systems may solidify. The ratios of the diameters of the hyperspheres examined were 0.4, 0.5, and 0.6. Only the 0.4 system shows a clear two phase, solid-liquid transition and the larger component solidifies into a D4 crystal state. Its pair correlation function agrees with that of a one component fluid at an appropriately scaled density. The 0.5 systems exhibit states that are a mix of D4 and A4 regions. The 0.6 systems behave similarly to a jammed state rather than solidifying into a crystal. No demixing into two distinct fluid phases was observed for any of the simulations.

Ionospheric and Birkeland current distributions inferred from the MAGSAT magnetometer data

NASA Technical Reports Server (NTRS)

Zanetti, L. J.; Potemra, T. A.; Baumjohann, W.

1983-01-01

Ionospheric and field-aligned sheet current density distributions are presently inferred by means of MAGSAT vector magnetometer data, together with an accurate magnetic field model. By comparing Hall current densities inferred from the MAGSAT data and those inferred from simultaneously recorded ground based data acquired by the Scandinavian magnetometer array, it is determined that the former have previously been underestimated due to high damping of magnetic variations with high spatial wave numbers between the ionosphere and the MAGSAT orbit. Among important results of this study is noted the fact that the Birkeland and electrojet current systems are colocated. The analyses have shown a tendency for triangular rather than constant electrojet current distributions as a function of latitude, consistent with the statistical, uniform regions 1 and 2 Birkeland current patterns.

Ionisation density effects following optical excitation in LiF:Mg, Ti (TLD-100).

PubMed

Weiss, D; Horowitz, Y; Oster, L

2007-01-01

The TL signal following 5 eV photon excitation of previously irradiated and readout material has been studied as a function of ionisation density and various experimental parameters: (i) maximum temperature of the first readout; (ii) photon fluence; (iii) photon energy and (iv) beta ray dose. Following alpha particle irradiation, the ratio of the second-readout to first-readout TL signal, epsilon(alpha,) has been found to be 10-20 times higher than that following beta irradiation, indicative of the possibility of using the double ratio epsilon(alpha)/epsilon(beta) as a mixed-field discriminator. The beginning of an attempt to explain this unusual effect is offered in the framework of the track structure theory and kinetic modelling of the beta ray dose-response of the first and second readouts.

Ab-initio calculations of the Ruddlesden Popper phases CaMnO3, CaO(CaMnO3) and CaO(CaMnO3)2

NASA Astrophysics Data System (ADS)

Cardoso, C.; Borges, R. P.; Gasche, T.; Godinho, M.

2008-01-01

The present work reports ab-initio density functional theory calculations for the Ruddlesden-Popper phase CaO(CaMnO3)n compounds. In order to study the evolution of the properties with the number of perovskite layers, a detailed analysis of the densities of states calculated for each compound and for several magnetic configurations was performed. The effect of distortions of the crystal structure on the magnetic ground state is also analysed and the exchange constants and transition temperatures are calculated for the three compounds using a mean field model. The calculated magnetic ground state structures and magnetic moments are in good agreement with experimental results and previous calculations.

Five- and six-electron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1-matrix functionals

NASA Astrophysics Data System (ADS)

Cioslowski, Jerzy; Strasburger, Krzysztof

2018-04-01

Electronic properties of several states of the five- and six-electron harmonium atoms are obtained from large-scale calculations employing explicitly correlated basis functions. The high accuracy of the computed energies (including their components), natural spinorbitals, and their occupation numbers makes them suitable for testing, calibration, and benchmarking of approximate formalisms of quantum chemistry and solid state physics. In the case of the five-electron species, the availability of the new data for a wide range of the confinement strengths ω allows for confirmation and generalization of the previously reached conclusions concerning the performance of the presently known approximations for the electron-electron repulsion energy in terms of the 1-matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three low-lying states of the six-electron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1-matrix functionals not revealed by previous studies. In general, the previously published assessment of the present implementations of DMFT being of poor accuracy is found to hold. Extending the present work to harmonically confined systems with even more electrons is most likely counterproductive as the steep increase in computational cost required to maintain sufficient accuracy of the calculated properties is not expected to be matched by the benefits of additional information gathered from the resulting benchmarks.

Brief communication: Hair density and body mass in mammals and the evolution of human hairlessness.

PubMed

Sandel, Aaron A

2013-09-01

Humans are unusual among mammals in appearing hairless. Several hypotheses propose explanations for this phenotype, but few data are available to test these hypotheses. To elucidate the evolutionary history of human "hairlessness," a comparative approach is needed. One previous study on primate hair density concluded that great apes have systematically less dense hair than smaller primates. While there is a negative correlation between body size and hair density, it remains unclear whether great apes have less dense hair than is expected for their body size. To revisit the scaling relationship between hair density and body size in mammals, I compiled data from the literature on 23 primates and 29 nonprimate mammals and conducted Phylogenetic Generalized Least Squares regressions. Among anthropoids, there is a significant negative correlation between hair density and body mass. Chimpanzees display the largest residuals, exhibiting less dense hair than is expected for their body size. There is a negative correlation between hair density and body mass among the broader mammalian sample, although the functional significance of this scaling relationship remains to be tested. Results indicate that all primates, and chimpanzees in particular, are relatively hairless compared to other mammals. This suggests that there may have been selective pressures acting on the ancestor of humans and chimpanzees that led to an initial reduction in hair density. To further understand the evolution of human hairlessness, a systematic study of hair density and physiology in a wide range of species is necessary. Copyright © 2013 Wiley Periodicals, Inc.

Exact models for isotropic matter

NASA Astrophysics Data System (ADS)

Thirukkanesh, S.; Maharaj, S. D.

2006-04-01

We study the Einstein-Maxwell system of equations in spherically symmetric gravitational fields for static interior spacetimes. The condition for pressure isotropy is reduced to a recurrence equation with variable, rational coefficients. We demonstrate that this difference equation can be solved in general using mathematical induction. Consequently, we can find an explicit exact solution to the Einstein-Maxwell field equations. The metric functions, energy density, pressure and the electric field intensity can be found explicitly. Our result contains models found previously, including the neutron star model of Durgapal and Bannerji. By placing restrictions on parameters arising in the general series, we show that the series terminate and there exist two linearly independent solutions. Consequently, it is possible to find exact solutions in terms of elementary functions, namely polynomials and algebraic functions.

Selectivity for CO2 over CH4 on a functionalized periodic mesoporous phenylene-silica explained by transition state theory

NASA Astrophysics Data System (ADS)

Kunkel, Christian; Viñes, Francesc; Lourenço, Mirtha A. O.; Ferreira, Paula; Gomes, José R. B.; Illas, Francesc

2017-03-01

Efficient separation of CO2/CH4 is critical in biogas upgrading, requiring highly selective adsorbents. Based on the adsorption energies of -0.30 and -0.14 eV, previously calculated by dispersion corrected density functional theory for adsorption/desorption of CO2 and CH4 on the functionalized periodic mesoporous phenylene-silica material APTMS@Ph-PMO, respectively, transition state theory rates were derived and used to simulate the adsorption/desorption rates of these two gases on APTMS@Ph-PMO. The latter yielded an estimation of initial CO2/CH4 selectivity at various temperatures. At T = 298 K, selectivity of 32.2 agrees to an experimental value of 26.1, which validates the method used for evaluating CO2/CH4 adsorption selectivities.

Dynamic Structure Factor: An Introduction

NASA Astrophysics Data System (ADS)

Sturm, K.

1993-02-01

The doubly differential cross-section for weak inelastic scattering of waves or particles by manybody systems is derived in Born approximation and expressed in terms of the dynamic structure factor according to van Hove. The application of this very general scheme to scattering of neutrons, x-rays and high-energy electrons is discussed briefly. The dynamic structure factor, which is the space and time Fourier transform of the density-density correlation function, is a property of the many-body system independent of the external probe and carries information on the excitation spectrum of the system. The relation of the electronic structure factor to the density-density response function defined in linear-response theory is shown using the fluctuation-dissipation theorem. This is important for calculations, since the response function can be calculated approximately from the independent-particle response function in self-consistent field approximations, such as the random-phase approximation or the local-density approximation of the density functional theory. Since the density-density response function also determines the dielectric function, the dynamic structure can be expressed by the dielectric function.

MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

PubMed

Yu, Haoyu S; He, Xiao; Truhlar, Donald G

2016-03-08

Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Local and linear chemical reactivity response functions at finite temperature in density functional theory

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

Franco-Pérez, Marco, E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, E-mail: avela@cinvestav.mx; Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340; Ayers, Paul W., E-mail: francopj@mcmaster.ca, E-mail: ayers@mcmaster.ca, E-mail: jlgm@xanum.uam.mx, 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 dualmore » 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.« less

Local and linear chemical reactivity response functions at finite temperature in density functional theory.

PubMed

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.

The Molecular Structure of cis-FONO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

First-principles simulations of shock front propagation in liquid deuterium

NASA Astrophysics Data System (ADS)

Gygi, Francois; Galli, Giulia

2001-03-01

We present large-scale first-principles molecular dynamics simulations of the formation and propagation of a shock front in liquid deuterium. Molecular deuterium was subjected to supersonic impacts at velocities ranging from 10 to 30 km/s. We used Density Functional Theory in the local density approximation, and simulation cells containing 1320 deuterium atoms. The formation of a shock front was observed and its velocity was measured and compared with the results of laser-driven shock experiments [1]. The pressure and density in the compressed fluid were also computed directly from statistical averages in appropriate regions of the simulation cell, and compared with previous first-principles calculations performed at equilibrium [2]. Details of the electronic structure at the shock front, and their influence on the properties of the compressed fluid will be discussed. [1] J.W.Collins et al. Science 281, 1178 (1998). [2] G.Galli, R.Q.Hood, A.U.Hazi and F.Gygi, Phys.Rev. B61, 909 (2000).

Heat transfer to and from vegetated surfaces - An analytical method for the bulk exchange coefficients

NASA Technical Reports Server (NTRS)

Massman, William J.

1987-01-01

The semianalytical model outlined in a previous study (Massman, 1987) to describe momentum exchange between the atmosphere and vegetated surfaces is extended to include the exchange of heat. The methods employed are based on one-dimensional turbulent diffusivities, and use analytical solutions to the steady-state diffusion equation. The model is used to assess the influence that the canopy foliage structure and density, the wind profile structure within the canopy, and the shelter factor can have upon the inverse surface Stanton number (kB exp -1), as well as to explore the consequences of introducing a scalar displacement height which can be different from the momentum displacement height. In general, the triangular foliage area density function gives results which agree more closely with observations than that for constant foliage area density. The intended application of this work is for parameterizing the bulk aerodynamic resistances for heat and momentum exchange for use within large-scale models of plant-atmosphere exchanges.

Higher-order ionospheric error at Arecibo, Millstone, and Jicamarca

NASA Astrophysics Data System (ADS)

Matteo, N. A.; Morton, Y. T.

2010-12-01

The ionosphere is a dominant source of Global Positioning System receiver range measurement error. Although dual-frequency receivers can eliminate the first-order ionospheric error, most second- and third-order errors remain in the range measurements. Higher-order ionospheric error is a function of both electron density distribution and the magnetic field vector along the GPS signal propagation path. This paper expands previous efforts by combining incoherent scatter radar (ISR) electron density measurements, the International Reference Ionosphere model, exponential decay extensions of electron densities, the International Geomagnetic Reference Field, and total electron content maps to compute higher-order error at ISRs in Arecibo, Puerto Rico; Jicamarca, Peru; and Millstone Hill, Massachusetts. Diurnal patterns, dependency on signal direction, seasonal variation, and geomagnetic activity dependency are analyzed. Higher-order error is largest at Arecibo with code phase maxima circa 7 cm for low-elevation southern signals. The maximum variation of the error over all angles of arrival is circa 8 cm.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

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.

Revealing Asymmetries in the HD181327 Debris Disk: A Recent Massive Collision or Interstellar Medium Warping

NASA Technical Reports Server (NTRS)

Stark, Christopher C.; Schneider, Glenn; Weinberger, Alycia J.; Debes, John H.; Grady, Carol A.; Jang-Condell, Hannah; Kuchner, Marc J.

2014-01-01

New multi-roll coronagraphic images of the HD181327 debris disk obtained using the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope reveal the debris ring in its entirety at high signal-to-noise ratio and unprecedented spatial resolution. We present and apply a new multi-roll image processing routine to identify and further remove quasi-static point-spread function-subtraction residuals and quantify systematic uncertainties. We also use a new iterative image deprojection technique to constrain the true disk geometry and aggressively remove any surface brightness asymmetries that can be explained without invoking dust density enhancements/ deficits. The measured empirical scattering phase function for the disk is more forward scattering than previously thought and is not well-fit by a Henyey-Greenstein function. The empirical scattering phase function varies with stellocentric distance, consistent with the expected radiation pressured-induced size segregation exterior to the belt. Within the belt, the empirical scattering phase function contradicts unperturbed debris ring models, suggesting the presence of an unseen planet. The radial profile of the flux density is degenerate with a radially varying scattering phase function; therefore estimates of the ring's true width and edge slope may be highly uncertain.We detect large scale asymmetries in the disk, consistent with either the recent catastrophic disruption of a body with mass greater than 1% the mass of Pluto, or disk warping due to strong interactions with the interstellar medium.

Revealing asymmetries in the HD 181327 debris disk: A recent massive collision or interstellar medium warping

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

Stark, Christopher C.; Kuchner, Marc J.; Schneider, Glenn

New multi-roll coronagraphic images of the HD 181327 debris disk obtained using the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope reveal the debris ring in its entirety at high signal-to-noise ratio and unprecedented spatial resolution. We present and apply a new multi-roll image processing routine to identify and further remove quasi-static point-spread function-subtraction residuals and quantify systematic uncertainties. We also use a new iterative image deprojection technique to constrain the true disk geometry and aggressively remove any surface brightness asymmetries that can be explained without invoking dust density enhancements/deficits. The measured empirical scattering phase function for themore » disk is more forward scattering than previously thought and is not well-fit by a Henyey-Greenstein function. The empirical scattering phase function varies with stellocentric distance, consistent with the expected radiation pressured-induced size segregation exterior to the belt. Within the belt, the empirical scattering phase function contradicts unperturbed debris ring models, suggesting the presence of an unseen planet. The radial profile of the flux density is degenerate with a radially varying scattering phase function; therefore estimates of the ring's true width and edge slope may be highly uncertain. We detect large scale asymmetries in the disk, consistent with either the recent catastrophic disruption of a body with mass >1% the mass of Pluto, or disk warping due to strong interactions with the interstellar medium.« less

Revealing Asymmetries in the HD 181327 Debris Disk: A Recent Massive Collision or Interstellar Medium Warping

NASA Astrophysics Data System (ADS)

Stark, Christopher C.; Schneider, Glenn; Weinberger, Alycia J.; Debes, John H.; Grady, Carol A.; Jang-Condell, Hannah; Kuchner, Marc J.

2014-07-01

New multi-roll coronagraphic images of the HD 181327 debris disk obtained using the Space Telescope Imaging Spectrograph on board the Hubble Space Telescope reveal the debris ring in its entirety at high signal-to-noise ratio and unprecedented spatial resolution. We present and apply a new multi-roll image processing routine to identify and further remove quasi-static point-spread function-subtraction residuals and quantify systematic uncertainties. We also use a new iterative image deprojection technique to constrain the true disk geometry and aggressively remove any surface brightness asymmetries that can be explained without invoking dust density enhancements/deficits. The measured empirical scattering phase function for the disk is more forward scattering than previously thought and is not well-fit by a Henyey-Greenstein function. The empirical scattering phase function varies with stellocentric distance, consistent with the expected radiation pressured-induced size segregation exterior to the belt. Within the belt, the empirical scattering phase function contradicts unperturbed debris ring models, suggesting the presence of an unseen planet. The radial profile of the flux density is degenerate with a radially varying scattering phase function; therefore estimates of the ring's true width and edge slope may be highly uncertain. We detect large scale asymmetries in the disk, consistent with either the recent catastrophic disruption of a body with mass >1% the mass of Pluto, or disk warping due to strong interactions with the interstellar medium.

On the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures.

PubMed

Santra, Biswajit; Klimes, Jirí; Tkatchenko, Alexandre; Alfè, Dario; Slater, Ben; Michaelides, Angelos; Car, Roberto; Scheffler, Matthias

2013-10-21

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimeš, D. Alfè, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water.

Monte Carlo simulations of liquid tetrahydrofuran including pseudorotationa)

NASA Astrophysics Data System (ADS)

Chandrasekhar, Jayaraman; Jorgensen, William L.

1982-11-01

Monte Carlo statistical mechanics simulations have been carried out for liquid tetrahydrofuran (THF) with and without pseudorotation at 1 atm and 25 °C. The intermolecular potential functions consisted of Lennard-Jones and Coulomb terms in the TIPS format reported previously for ethers. Pseudorotation of the ring was described using the generalized coordinates defined by Cremer and Pople, viz., the puckering amplitude and the phase angle of the ring. The corresponding intramolecular potential function was derived from molecular mechanics (MM2) calculations. Compared to the gas phase, the rings tend to be more flat and the population of the C2 twist geometry is slightly higher in liquid THF. However, pseudorotation has negligible effect on the calculated intermolecular structure and thermodynamic properties. The computed density, heat of vaporization, and heat capacity are in good agreement with experiment. The results are also compared with those from previous simulations of acyclic ethers. The present study provides the foundation for investigations of the solvating ability of THF.

Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB)

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

Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Bannwarth, Christoph

2016-08-07

The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the wellmore » established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H–Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first benchmarked for vertical excitation energies of open- and closed-shell systems in comparison to other semi-empirical methods and applied to exemplary problems in electronic spectroscopy. As side products of the development, a robust and efficient valence electron TB method for the accurate determination of atomic charges as well as a more accurate calculation scheme of dipole rotatory strengths within the Tamm-Dancoff approximation is proposed.« less

Three-dimensional culture of rat calvarial osteoblasts in porous biodegradable polymers

NASA Technical Reports Server (NTRS)

Ishaug-Riley, S. L.; Crane-Kruger, G. M.; Yaszemski, M. J.; Mikos, A. G.

1998-01-01

Neonatal rat calvarial osteoblasts were cultured in 90% porous, 75:25 poly(DL-lactic-co-glycolic acid) (PLGA) foam scaffolds for up to 56 days to examine the effects of the cell seeding density, scaffold pore size, and foam thickness on the proliferation and function of the cells in this three-dimensional environment. Osteoblasts were seeded at either 11.1 x 10(5) or 22.1 x 10(5) cells per cm2 onto PLGA scaffolds having pore sizes in the range of 150-300 or 500-710 microm with a thickness of either 1.9 or 3.2 mm. After 1 day in culture, 75.6 and 68.6% of the seeded cells attached and proliferated on the 1.9 mm thick scaffolds of 150-300 microm pore size for the low and high seeding densities, respectively. The number of osteoblasts continued to increase throughout the study and eventually leveled off near 56 days, as indicated by a quantitative DNA assay. Osteoblast/foam constructs with a low cell seeding density achieved comparable DNA content and alkaline phosphatase (ALPase) activity after 14 days, and mineralization results after 56 days to those with a high cell seeding density. A maximum penetration depth of osseous tissue of 220+/-40 microm was reached after 56 days in the osteoblast/foam constructs of 150-300 microm pore size initially seeded with a high cell density. For constructs of 500-710 microm pore size, the penetration depth was 190+/-40 microm under the same conditions. Scaffold pore size and thickness did not significantly affect the proliferation or function of osteoblasts as demonstrated by DNA content, ALPase activity, and mineralized tissue formation. These data show that comparable bone-like tissues can be engineered in vitro over a 56 day period using different rat calvarial osteoblast seeding densities onto biodegradable polymer scaffolds with pore sizes in the range of 150-710 microm. When compared with the results of a previous study where similar polymer scaffolds were seeded and cultured with marrow stromal cells, this study demonstrates that PLGA foams are suitable substrates for osteoblast growth and differentiated function independent of cell source.

Structure, strain, and control of ground state property in LaTiO3/LaAlO3 superlattice

NASA Astrophysics Data System (ADS)

Lee, Alex Taekyung; Han, Myung Joon

2014-03-01

We examined the ground state property of LaTiO3/LaAlO3 superlattice through density functional band calculations. Total energy calculations, including the structural distortions, U dependence, and the exchange correlation functional dependence, clearly showed that the spin and orbital ground state can be controlled systematically by the epitaxial strain. In the wide range of strain, the ferromagnetic-spin and antiferro-orbital order are stabilized, which is notably different from the previously reported ground state in the titanate systems. By applying +2.8% of tensile strains, we showed that the antiferromagnetic-spin and ferro-orbital ordered phase become stabilized.

LUMINOUS AND HIGH STELLAR MASS CANDIDATE GALAXIES AT z Almost-Equal-To 8 DISCOVERED IN THE COSMIC ASSEMBLY NEAR-INFRARED DEEP EXTRAGALACTIC LEGACY SURVEY

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

Yan Haojing; Finkelstein, Steven L.; Huang, Kuang-Han

One key goal of the Hubble Space Telescope Cosmic Assembly Near-Infrared Deep Extragalactic Legacy Survey is to track galaxy evolution back to z Almost-Equal-To 8. Its two-tiered ''wide and deep'' strategy bridges significant gaps in existing near-infrared surveys. Here we report on z Almost-Equal-To 8 galaxy candidates selected as F105W-band dropouts in one of its deep fields, which covers 50.1 arcmin{sup 2} to 4 ks depth in each of three near-infrared bands in the Great Observatories Origins Deep Survey southern field. Two of our candidates have J < 26.2 mag, and are >1 mag brighter than any previously known F105W-dropouts.more » We derive constraints on the bright end of the rest-frame ultraviolet luminosity function of galaxies at z Almost-Equal-To 8, and show that the number density of such very bright objects is higher than expected from the previous Schechter luminosity function estimates at this redshift. Another two candidates are securely detected in Spitzer Infrared Array Camera images, which are the first such individual detections at z Almost-Equal-To 8. Their derived stellar masses are on the order of a few Multiplication-Sign 10{sup 9} M{sub Sun }, from which we obtain the first measurement of the high-mass end of the galaxy stellar mass function at z Almost-Equal-To 8. The high number density of very luminous and very massive galaxies at z Almost-Equal-To 8, if real, could imply a large stellar-to-halo mass ratio and an efficient conversion of baryons to stars at such an early time.« less

Physical exercise in overweight to obese individuals induces metabolic- and neurotrophic-related structural brain plasticity

PubMed Central

Mueller, Karsten; Möller, Harald E.; Horstmann, Annette; Busse, Franziska; Lepsien, Jöran; Blüher, Matthias; Stumvoll, Michael; Villringer, Arno; Pleger, Burkhard

2015-01-01

Previous cross-sectional studies on body-weight-related alterations in brain structure revealed profound changes in the gray matter (GM) and white matter (WM) that resemble findings obtained from individuals with advancing age. This suggests that obesity may lead to structural brain changes that are comparable with brain aging. Here, we asked whether weight-loss-dependent improved metabolic and neurotrophic functioning parallels the reversal of obesity-related alterations in brain structure. To this end we applied magnetic resonance imaging (MRI) together with voxel-based morphometry and diffusion-tensor imaging in overweight to obese individuals who participated in a fitness course with intensive physical training twice a week over a period of 3 months. After the fitness course, participants presented, with inter-individual heterogeneity, a reduced body mass index (BMI), reduced serum leptin concentrations, elevated high-density lipoprotein-cholesterol (HDL-C), and alterations of serum brain-derived neurotrophic factor (BDNF) concentrations suggesting changes of metabolic and neurotrophic function. Exercise-dependent changes in BMI and serum concentration of BDNF, leptin, and HDL-C were related to an increase in GM density in the left hippocampus, the insular cortex, and the left cerebellar lobule. We also observed exercise-dependent changes of diffusivity parameters in surrounding WM structures as well as in the corpus callosum. These findings suggest that weight-loss due to physical exercise in overweight to obese participants induces profound structural brain plasticity, not primarily of sensorimotor brain regions involved in physical exercise, but of regions previously reported to be structurally affected by an increased body weight and functionally implemented in gustation and cognitive processing. PMID:26190989

BH-DFTB/DFT calculations for iron clusters

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

Aktürk, Abdurrahman; Sebetci, Ali, E-mail: asebetci@mevlana.edu.tr

2016-05-15

We present a study on the structural, electronic, and magnetic properties of Fe{sub n}(n  =  2  −  20) clusters by performing density functional tight binding (DFTB) calculations within a basin hopping (BH) global optimization search followed by density functional theory (DFT) investigations. The structures, total energies and total spin magnetic moments are calculated and compared with previously reported theoretical and experimental results. Two basis sets SDD with ECP and 6-31G** are employed in the DFT calculations together with BLYP GGA exchange-correlation functional. The results indicate that the offered BH-DFTB/DFT strategy collects all the global minima of which different minima havemore » been reported in the previous studies by different groups. Small Fe clusters have three kinds of packing; icosahedral (Fe{sub 9−13}), centered hexagonal antiprism (Fe{sub 14−17}, Fe{sub 20}), and truncated decahedral (Fe{sub 17(2)}, Fe{sub 18−19}). It is obtained in a qualitative agreement with the time of flight mass spectra that the magic numbers for the small Fe clusters are 7, 13, 15, and 19 and with the collision induced dissociation experiments that the sizes 6, 7, 13, 15, and 19 are thermodynamically more stable than their neighboring sizes. The spin magnetic moment per atom of Fe{sub n}(n = 2 − 20) clusters is between 2.4 and 3.6 μ{sub B} for the most of the sizes. The antiferromagnetic coupling between the central and the surface atoms of the Fe{sub 13} icosahedron, which have already been reported by experimental and theoretical studies, is verified by our calculations as well. The quantitative disagreements between the calculations and measurements of the magnetic moments of the individual sizes are still to be resolved.« less

Hydra effects in discrete-time models of stable communities.

PubMed

Cortez, Michael H

2016-12-21

A species exhibits a hydra effect when, counter-intuitively, increased mortality of the species causes an increase in its abundance. Hydra effects have been studied in many continuous time (differential equation) multispecies models, but only rarely have hydra effects been observed in or studied with discrete time (difference equation) multispecies models. In addition most discrete time theory focuses on single-species models. Thus, it is unclear what unifying characteristics determine when hydra effects arise in discrete time models. Here, using discrete time multispecies models (where total abundance is the single variable describing each population), I show that a species exhibits a hydra effect in a stable system only when fixing that species' density at its equilibrium density destabilizes the system. This general characteristic is referred to as subsystem instability. I apply this result to two-species models and identify specific mechanisms that cause hydra effects in stable communities, e.g., in host--parasitoid models, host Allee effects and saturating parasitoid functional responses can cause parasitoid hydra effects. I discuss how the general characteristic can be used to identify mechanisms causing hydra effects in communities with three or more species. I also show that the condition for hydra effects at stable equilibria implies the system is reactive (i.e., density perturbations can grow before ultimately declining). This study extends previous work on conditions for hydra effects in single-species models by identifying necessary conditions for stable systems and sufficient conditions for cyclic systems. In total, these results show that hydra effects can arise in many more communities than previously appreciated and that hydra effects were present, but unrecognized, in previously studied discrete time models. Copyright © 2016 Elsevier Ltd. All rights reserved.

Large scale IRAM 30 m CO-observations in the giant molecular cloud complex W43

NASA Astrophysics Data System (ADS)

Carlhoff, P.; Nguyen Luong, Q.; Schilke, P.; Motte, F.; Schneider, N.; Beuther, H.; Bontemps, S.; Heitsch, F.; Hill, T.; Kramer, C.; Ossenkopf, V.; Schuller, F.; Simon, R.; Wyrowski, F.

2013-12-01

We aim to fully describe the distribution and location of dense molecular clouds in the giant molecular cloud complex W43. It was previously identified as one of the most massive star-forming regions in our Galaxy. To trace the moderately dense molecular clouds in the W43 region, we initiated W43-HERO, a large program using the IRAM 30 m telescope, which covers a wide dynamic range of scales from 0.3 to 140 pc. We obtained on-the-fly-maps in 13CO (2-1) and C18O (2-1) with a high spectral resolution of 0.1 km s-1 and a spatial resolution of 12''. These maps cover an area of ~1.5 square degrees and include the two main clouds of W43 and the lower density gas surrounding them. A comparison to Galactic models and previous distance calculations confirms the location of W43 near the tangential point of the Scutum arm at approximately 6 kpc from the Sun. The resulting intensity cubes of the observed region are separated into subcubes, which are centered on single clouds and then analyzed in detail. The optical depth, excitation temperature, and H2 column density maps are derived out of the 13CO and C18O data. These results are then compared to those derived from Herschel dust maps. The mass of a typical cloud is several 104 M⊙ while the total mass in the dense molecular gas (>102 cm-3) in W43 is found to be ~1.9 × 106 M⊙. Probability distribution functions obtained from column density maps derived from molecular line data and Herschel imaging show a log-normal distribution for low column densities and a power-law tail for high densities. A flatter slope for the molecular line data probability distribution function may imply that those selectively show the gravitationally collapsing gas. Appendices are available in electronic form at http://www.aanda.orgThe final datacubes (13CO and C18O) for the entire survey are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/560/A24

Exact free oscillation spectra, splitting functions and the resolvability of Earth's density structure

NASA Astrophysics Data System (ADS)

Akbarashrafi, F.; Al-Attar, D.; Deuss, A.; Trampert, J.; Valentine, A. P.

2018-04-01

Seismic free oscillations, or normal modes, provide a convenient tool to calculate low-frequency seismograms in heterogeneous Earth models. A procedure called `full mode coupling' allows the seismic response of the Earth to be computed. However, in order to be theoretically exact, such calculations must involve an infinite set of modes. In practice, only a finite subset of modes can be used, introducing an error into the seismograms. By systematically increasing the number of modes beyond the highest frequency of interest in the seismograms, we investigate the convergence of full-coupling calculations. As a rule-of-thumb, it is necessary to couple modes 1-2 mHz above the highest frequency of interest, although results depend upon the details of the Earth model. This is significantly higher than has previously been assumed. Observations of free oscillations also provide important constraints on the heterogeneous structure of the Earth. Historically, this inference problem has been addressed by the measurement and interpretation of splitting functions. These can be seen as secondary data extracted from low frequency seismograms. The measurement step necessitates the calculation of synthetic seismograms, but current implementations rely on approximations referred to as self- or group-coupling and do not use fully accurate seismograms. We therefore also investigate whether a systematic error might be present in currently published splitting functions. We find no evidence for any systematic bias, but published uncertainties must be doubled to properly account for the errors due to theoretical omissions and regularization in the measurement process. Correspondingly, uncertainties in results derived from splitting functions must also be increased. As is well known, density has only a weak signal in low-frequency seismograms. Our results suggest this signal is of similar scale to the true uncertainties associated with currently published splitting functions. Thus, it seems that great care must be taken in any attempt to robustly infer details of Earth's density structure using current splitting functions.

Normal order and extended Wick theorem for a multiconfiguration reference wave function

NASA Astrophysics Data System (ADS)

Kutzelnigg, Werner; Mukherjee, Debashis

1997-07-01

A generalization of normal ordering and of Wick's theorem with respect to an arbitrary reference function Φ as some generalized "physical vacuum" is formulated in a different (but essentially equivalent) way than that suggested previously by one of the present authors. Guiding principles are that normal order operators with respect to any reference state must be expressible as linear combinations of those with respect to the genuine vacuum, that the vacuum expectation value of a normal order operator must vanish (with respect to the vacuum to which it is in normal order), and that the well-known formalism for a single Slater determinant as physical vacuum must be contained as a special case. The derivation is largely based on the concepts of "Quantum Chemistry in Fock space," which means that particle-number-conserving operators (excitation operators) play a central role. Nevertheless, the contraction rules in the frame of a generalized Wick theorem are derived, that hold for non-particle-number-conserving operators as well. The contraction rules are formulated and illustrated in terms of diagrams. The contractions involve the "residual n-particle density matrices" λ, which are the irreducible (non-factorizable) parts of the conventional n-particle density matrices γ, in the sense of a cumulant expansion for the density. A spinfree formulation is presented as well. The expression of the Hamiltonian in normal order with respect to a multiconfiguration reference function leads to a natural definition of a generalized Fock operator. MC-SCF-theory is easily worked out in this context. The paper concludes with a discussion of the excited configurations and the first-order interacting space, that underlies a perturbative coupled cluster type correction to the MCSCF function for an arbitrary reference function, and with general implications of the new formalism, that is related to "internally contracted multireference configuration interaction." The present generalization of normal ordering is not only valid for arbitrary reference functions, but also if the reference state is an ensemble state.

Magnetic-Field Density-Functional Theory (BDFT): Lessons from the Adiabatic Connection.

PubMed

Reimann, Sarah; Borgoo, Alex; Tellgren, Erik I; Teale, Andrew M; Helgaker, Trygve

2017-09-12

We study the effects of magnetic fields in the context of magnetic field density-functional theory (BDFT), where the energy is a functional of the electron density ρ and the magnetic field B. We show that this approach is a worthwhile alternative to current-density functional theory (CDFT) and may provide a viable route to the study of many magnetic phenomena using density-functional theory (DFT). The relationship between BDFT and CDFT is developed and clarified within the framework of the four-way correspondence of saddle functions and their convex and concave parents in convex analysis. By decomposing the energy into its Kohn-Sham components, we demonstrate that the magnetizability is mainly determined by those energy components that are related to the density. For existing density functional approximations, this implies that, for the magnetizability, improvements of the density will be more beneficial than introducing a magnetic-field dependence in the correlation functional. However, once a good charge density is achieved, we show that high accuracy is likely only obtainable by including magnetic-field dependence. We demonstrate that adiabatic-connection (AC) curves at different field strengths resemble one another closely provided each curve is calculated at the equilibrium geometry of that field strength. In contrast, if all AC curves are calculated at the equilibrium geometry of the field-free system, then the curves change strongly with increasing field strength due to the increasing importance of static correlation. This holds also for density functional approximations, for which we demonstrate that the main error encountered in the presence of a field is already present at zero field strength, indicating that density-functional approximations may be applied to systems in strong fields, without the need to treat additional static correlation.

Determination of the absolute configurations of natural products via density functional theory calculations of optical rotation, electronic circular dichroism, and vibrational circular dichroism: the cytotoxic sesquiterpene natural products quadrone, suberosenone, suberosanone, and suberosenol A acetate.

PubMed

Stephens, P J; McCann, D M; Devlin, F J; Smith, A B

2006-07-01

The determination of the absolute configurations (ACs) of chiral molecules using the chiroptical techniques of optical rotation (OR), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) has been revolutionized by the development of density functional theory (DFT) methods for the prediction of these properties. Here, we demonstrate the significance of these advances for the stereochemical characterization of natural products. Time-dependent DFT (TDDFT) calculations of the specific rotations, [alpha](D), of four cytotoxic natural products, quadrone (1), suberosenone (2), suberosanone (3), and suberosenol A acetate (4), are used to assign their ACs. TDDFT calculations of the ECD of 1 are used to assign its AC. The VCD spectrum of 1 is reported and also used, together with DFT calculations, to assign its AC. The ACs of 1 derived from its [alpha](D), ECD, and VCD are identical and in agreement with the AC previously determined via total synthesis. The previously undetermined ACs of 2-4, derived from their [alpha](D) values, have absolute configurations of their tricyclic cores identical to that of 1. Further studies of the ACs of these molecules using ECD and, especially, VCD are recommended to establish more definitively this finding. Our studies of the OR, ECD, and VCD of quadrone are the first to utilize DFT calculations of all three properties for the determination of the AC of a chiral natural product molecule.

An improved interatomic potential for xenon in UO2: a combined density functional theory/genetic algorithm approach.

PubMed

Thompson, Alexander E; Meredig, Bryce; Wolverton, C

2014-03-12

We have created an improved xenon interatomic potential for use with existing UO2 potentials. This potential was fit to density functional theory calculations with the Hubbard U correction (DFT + U) using a genetic algorithm approach called iterative potential refinement (IPR). We examine the defect energetics of the IPR-fitted xenon interatomic potential as well as other, previously published xenon potentials. We compare these potentials to DFT + U derived energetics for a series of xenon defects in a variety of incorporation sites (large, intermediate, and small vacant sites). We find the existing xenon potentials overestimate the energy needed to add a xenon atom to a wide set of defect sites representing a range of incorporation sites, including failing to correctly rank the energetics of the small incorporation site defects (xenon in an interstitial and xenon in a uranium site neighboring uranium in an interstitial). These failures are due to problematic descriptions of Xe-O and/or Xe-U interactions of the previous xenon potentials. These failures are corrected by our newly created xenon potential: our IPR-generated potential gives good agreement with DFT + U calculations to which it was not fitted, such as xenon in an interstitial (small incorporation site) and xenon in a double Schottky defect cluster (large incorporation site). Finally, we note that IPR is very flexible and can be applied to a wide variety of potential forms and materials systems, including metals and EAM potentials.

Coarse graining the distribution function of cold dark matter - II

NASA Astrophysics Data System (ADS)

Henriksen, R. N.

2004-12-01

We study analytically the coarse- and fine-grained distribution function (DF) established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase-space sheet substructure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best-fitting analytic density function is likely to be provided by a high-order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. As we find that the central flattening is progressive in time, dynamically young systems such as galaxy clusters may well possess a Navarro, Frenk and White type density profile, while primordial dwarf galaxies, for example, are expected to have cores. This progressive flattening is expected to end either in the non-singular isothermal sphere, or in the non-singular metastable polytropic cores; as the DFs associated with each of these arise naturally in the bulk halo during the infall. We suggest, based on previous studies of the evolution of de-stabilized polytropes, that a collisionless system may pass through a family of polytropes of increasing order, finally approaching the limit of the non-singular isothermal sphere, if the `violent' collective relaxation is frequently re-excited by `merger' events. Thus central dominant (cD) galaxies, and indeed all bright galaxies that have grown in this fashion, should be in polytropic states. Our results suggest that no physics beyond that of wave-particle scattering is necessary to explain the nature of dark matter density profiles. However, this may be assisted by the scattering of particles from the centre of the system by the infall of dwarf galaxies, galactic nuclei or black holes (e.g. Nakano & Makino), all of which would restart pure dynamical relaxation.

Studying the varied shapes of gold clusters by an elegant optimization algorithm that hybridizes the density functional tight-binding theory and the density functional theory

NASA Astrophysics Data System (ADS)

Yen, Tsung-Wen; Lim, Thong-Leng; Yoon, Tiem-Leong; Lai, S. K.

2017-11-01

We combined a new parametrized density functional tight-binding (DFTB) theory (Fihey et al. 2015) with an unbiased modified basin hopping (MBH) optimization algorithm (Yen and Lai 2015) and applied it to calculate the lowest energy structures of Au clusters. From the calculated topologies and their conformational changes, we find that this DFTB/MBH method is a necessary procedure for a systematic study of the structural development of Au clusters but is somewhat insufficient for a quantitative study. As a result, we propose an extended hybridized algorithm. This improved algorithm proceeds in two steps. In the first step, the DFTB theory is employed to calculate the total energy of the cluster and this step (through running DFTB/MBH optimization for given Monte-Carlo steps) is meant to efficiently bring the Au cluster near to the region of the lowest energy minimum since the cluster as a whole has explicitly considered the interactions of valence electrons with ions, albeit semi-quantitatively. Then, in the second succeeding step, the energy-minimum searching process will continue with a skilledly replacement of the energy function calculated by the DFTB theory in the first step by one calculated in the full density functional theory (DFT). In these subsequent calculations, we couple the DFT energy also with the MBH strategy and proceed with the DFT/MBH optimization until the lowest energy value is found. We checked that this extended hybridized algorithm successfully predicts the twisted pyramidal structure for the Au40 cluster and correctly confirms also the linear shape of C8 which our previous DFTB/MBH method failed to do so. Perhaps more remarkable is the topological growth of Aun: it changes from a planar (n =3-11) → an oblate-like cage (n =12-15) → a hollow-shape cage (n =16-18) and finally a pyramidal-like cage (n =19, 20). These varied forms of the cluster's shapes are consistent with those reported in the literature.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Cross sections of proton-induced nuclear reactions on bismuth and lead up to 100 MeV

NASA Astrophysics Data System (ADS)

Mokhtari Oranj, L.; Jung, N. S.; Bakhtiari, M.; Lee, A.; Lee, H. S.

2017-04-01

Production cross sections of 209Bi(p , x n )207,206,205,204,203Po, 209Bi(p , pxn) 207,206,205,204,203,202Bi, and natPb(p , x n ) 206,205,204,203,202,201Bi reactions were measured to fill the gap in the excitation functions up to 100 MeV as well as to figure out the effects of different nuclear properties on proton-induced reactions including heavy nuclei. The targets were arranged in two different stacks consisting of Bi, Pb, Al, Au foils and Pb plates. The proton beam intensity was determined by the activation analysis method using 27Al(p ,3 p n )24Na, 197Au(p ,p n )196Au, and 197Au(p , p 3 n )194Au monitor reactions in parallel as well as the Gafchromic film dosimetry method. The activities of produced radionuclei in the foils were measured by the HPGe spectroscopy system. Over 40 new cross sections were measured in the investigated energy range. A satisfactory agreement was observed between the present experimental data and the previously published data. Excitation functions of mentioned reactions were calculated by using the theoretical model based on the latest version of the TALYS code and compared to the new data as well as with other data in the literature. Additionally, the effects of various combinations of the nuclear input parameters of different level density models, optical model potentials, and γ-ray strength functions were considered. It was concluded that if certain level density models are used, the calculated cross sections could be comparable to the measured data. Furthermore, the effects of optical model potential and γ-ray strength functions were considerably lower than that of nuclear level densities.

Characterizing water-metal interfaces and machine learning potential energy surfaces

NASA Astrophysics Data System (ADS)

Ryczko, Kevin

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

Low-Dimensional Materials for Optoelectronic and Bioelectronic Applications

NASA Astrophysics Data System (ADS)

Hong, Tu

In this thesis, we first discuss the fundamentals of ab initio electronic structure theory and density functional theory (DFT). We also discuss statistics related to computing thermodynamic averages of molecular dynamics (MD). We then use this theory to analyze and compare the structural, dynamical, and electronic properties of liquid water next to prototypical metals including platinum, graphite, and graphene. Our results are built on Born-Oppenheimer molecular dynamics (BOMD) generated using density functional theory (DFT) which explicitly include van der Waals (vdW) interactions within a first principles approach. All calculations reported use large simulation cells, allowing for an accurate treatment of the water-electrode interfaces. We have included vdW interactions through the use of the optB86b-vdW exchange correlation functional. Comparisons with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional are also shown. We find an initial peak, due to chemisorption, in the density profile of the liquid water-Pt interface not seen in the liquid water-graphite interface, liquid watergraphene interface, nor interfaces studied previously. To further investigate this chemisorption peak, we also report differences in the electronic structure of single water molecules on both Pt and graphite surfaces. We find that a covalent bond forms between the single water molecule and the platinum surface, but not between the single water molecule and the graphite surface. We also discuss the effects that defects and dopants in the graphite and graphene surfaces have on the structure and dynamics of liquid water. Lastly, we introduce artificial neural networks (ANNs), and demonstrate how they can be used to machine learn electronic structure calculations. As a proof of principle, we show the success of an ANN potential energy surfaces for a dimer molecule with a Lennard-Jones potential.

Effects of a mixture of chloromethylisothiazolinone and methylisothiazolinone on peripheral airway dysfunction in children

PubMed Central

Cho, Hyun-Ju; Park, Dong-Uk; Yoon, Jisun; Lee, Eun; Yang, Song-I; Kim, Young-Ho; Lee, So-Yeon

2017-01-01

Background Children who were only exposed to a mixture of chloromethylisothiazolinone (CMIT) and methylisothiazolinone (MIT) as humidifier disinfectant (HD) components were evaluated for humidifier disinfectant-associated lung injury (HDLI) from 2012. This study was to evaluate the pulmonary function using, impulse oscillometry (IOS) for children exposed to a mixture of CMIT/MIT from HD. Methods Twenty-four children who were only exposed to a mixture of CMIT/MIT, with no previous underlying disease, were assessed by IOS. Diagnostic criteria for HDLI were categorized as definite, probable, possible, or unlikely. Home visits and administration of a standardized questionnaire were arranged to assess exposure characteristics. Results Definite and probable cases showed higher airborne disinfectant exposure intensity during sleep (32.4 ± 8.7 μg/m3) and younger age at initial exposure (3.5 ± 3.3 months) compared with unlikely cases (17.3 ± 11.0 μg/m3, p = 0.026; 22.5 ± 26.2 months, p = 0.039, respectively). Reactance at 5 Hz was significantly more negative in those with high-density exposure during sleep (mean, -0.463 kPa/L/s vs. low density, -0.296, p = 0.001). The reactance area was also higher with high-density exposure during sleep (mean, 3.240 kPa/L vs. low density, 1.922, p = 0.039). The mean bronchodilator response with high-density exposure was within the normal range for reactance. Conclusions Significant peripheral airway dysfunction were found in children with high levels of inhalation exposure to a mixture of CMIT/MIT during sleep. Strict regulation of a mixture of CMIT/MIT exposure were associated with positive effects on lung function of children. PMID:28453578

The Next Generation of Mars-GRAM and Its Role in the Autonomous Aerobraking Development Plan

NASA Technical Reports Server (NTRS)

Justh, Hilary L.; Justus, Carl G.; Ramey, Holly S.

2011-01-01

The Mars Global Reference Atmospheric Model (Mars-GRAM) is an engineering-level atmospheric model widely used for diverse mission applications. Mars-GRAM 2010 is currently being used to develop the onboard atmospheric density estimator that is part of the Autonomous Aerobraking Development Plan. In previous versions, Mars-GRAM was less than realistic when used for sensitivity studies for Thermal Emission Spectrometer (TES) MapYear=0 and large optical depth values, such as tau=3. A comparison analysis has been completed between Mars-GRAM, TES and data from the Planetary Data System (PDS) resulting in updated coefficients for the functions relating density, latitude, and longitude of the sun. The adjustment factors are expressed as a function of height (z), Latitude (Lat) and areocentric solar longitude (Ls). The latest release of Mars-GRAM 2010 includes these adjustment factors that alter the in-put data from MGCM and MTGCM for the Mapping Year 0 (user-controlled dust) case. The greatest adjustment occurs at large optical depths such as tau greater than 1. The addition of the adjustment factors has led to better correspondence to TES Limb data from 0-60 km as well as better agreement with MGS, ODY and MRO data at approximately 90-135 km. Improved simulations utilizing Mars-GRAM 2010 are vital to developing the onboard atmospheric density estimator for the Autonomous Aerobraking Development Plan. Mars-GRAM 2010 was not the only planetary GRAM utilized during phase 1 of this plan; Titan-GRAM and Venus-GRAM were used to generate density data sets for Aerobraking Design Reference Missions. These data sets included altitude profiles (both vertical and along a trajectory), GRAM perturbations (tides, gravity waves, etc.) and provided density and scale height values for analysis by other Autonomous Aero-braking team members.

Production of a high-efficiency TILLING population through polyploidization.

PubMed

Tsai, Helen; Missirian, Victor; Ngo, Kathie J; Tran, Robert K; Chan, Simon R; Sundaresan, Venkatesan; Comai, Luca

2013-04-01

Targeting Induced Local Lesions in Genomes (TILLING) provides a nontransgenic method for reverse genetics that is widely applicable, even in species where other functional resources are missing or expensive to build. The efficiency of TILLING, however, is greatly facilitated by high mutation density. Species vary in the number of mutations induced by comparable mutagenic treatments, suggesting that genetic background may affect the response. Allopolyploid species have often yielded higher mutation density than diploids. To examine the effect of ploidy, we autotetraploidized the Arabidopsis (Arabidopsis thaliana) ecotype Columbia, whose diploid has been used for TILLING extensively, and mutagenized it with 50 mm ethylmethane sulfonate. While the same treatment sterilized diploid Columbia, the tetraploid M1 plants produced good seed. To determine the mutation density, we searched 528 individuals for induced mutations in 15 genes for which few or no knockout alleles were previously available. We constructed tridimensional pools from the genomic DNA of M2 plants, amplified target DNA, and subjected them to Illumina sequencing. The results were analyzed with an improved version of the mutation detection software CAMBa that accepts any pooling scheme. This small population provided a rich resource with approximately 25 mutations per queried 1.5-kb fragment, including on average four severe missense and 1.3 truncation mutations. The overall mutation density of 19.4 mutations Mb(-1) is 4 times that achieved in the corresponding diploid accession, indicating that genomic redundancy engenders tolerance to high mutation density. Polyploidization of diploids will allow the production of small populations, such as less than 2,000, that provide allelic series from knockout to mild loss of function for virtually all genes.

Periodic Density Functional Theory Study of the Structure, Raman Spectrum, and Mechanical Properties of Schoepite Mineral.

PubMed

Colmenero, Francisco; Cobos, Joaquín; Timón, Vicente

2018-04-16

The structure and Raman spectrum of schoepite mineral, [(UO 2 ) 8 O 2 (OH) 12 ]·12H 2 O, was studied by means of theoretical calculations. The computations were carried out by using density functional theory with plane waves and pseudopotentials. A norm-conserving pseudopotential specific for the U atom developed in a previous work was employed. Because it was not possible to locate H atoms directly from X-ray diffraction (XRD) data by structure refinement in previous experimental studies, all of the positions of the H atoms in the full unit cell were determined theoretically. The structural results, including the lattice parameters, bond lengths, bond angles, and powder XRD pattern, were found to be in good agreement with their experimental counterparts. However, the calculations performed using the unit cell designed by Ostanin and Zeller in 2007, involving half of the atoms of the full unit cell, led to significant errors in the computed powder XRD pattern. Furthermore, Ostanin and Zeller's unit cell contains hydronium ions, H 3 O + , which are incompatible with the experimental information. Therefore, while the use of this schoepite model may be a very useful approximation requiring a much smaller amount of computational effort, the full unit cell should be used to study this mineral accurately. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum. The results were also in agreement with the experimental data. A normal-mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment significantly improved the current empirical assignment of the bands of the Raman spectrum of schoepite mineral. In addition, the equation of state and elastic properties of this mineral were determined. The crystal structure of schoepite was found to be stable mechanically and dynamically. Schoepite can be described as a brittle material exhibiting small anisotropy and large compressibility in the direction perpendicular to the layers, which characterize its structure. The calculated bulk modulus, B, was ∼35 GPa.

Vibrational Properties of Bulk Boric Acid 2A and 3T Polymorphs and Their Two-Dimensional Layers: Measurements and Density Functional Theory Calculations.

PubMed

Bezerra da Silva, M; Santos, R C R; Freire, P T C; Caetano, E W S; Freire, V N

2018-02-08

Boric acid (H 3 BO 3 ) is being used effectively nowadays in traps/baits for the management of Aedes aegypti L. and Aedes albopictus Skuse species of mosquitoes, which are the main spreading vectors worldwide for diseases such as malaria, dengue, and zika. Previously, we published results on the structural, electronic, and optical properties of its molecular triclinic H 3 BO 3 -2A and trigonal H 3 BO 3 -3T polymorphs within the framework of density functional theory (DFT). Because of the renewed importance of these materials, the focus of this work is on the vibrational properties of the bulk boric acid 2A and 3T polymorphs. We measured the infrared and Raman spectra of the former, which was accompanied and interpreted through state-of-the-art DFT calculations, supplemented by computations regarding the H 3 BO 3 molecule and two-dimensional layers based on the bulk structures. We identify/assign their normal modes and find vibrational signatures for each polymorph as well as in- and out-of-plane motions and molecular vibrations, unveiling a nice agreement between the DFT level of theory employed and our improved spectroscopic measurements in the wavenumber ranges of 400-2000 cm -1 (infrared) and 0-1500 cm -1 (Raman). We show that a dispersion-corrected DFT functional within the generalized gradient approximation (GGA) can be very accurate in describing the vibrational properties of the boric acid polymorphs. Besides, several issues left open/not clearly resolved in previously published works on the vibrational mode assignments of the bulk and 2D sheets of boric acid are explained satisfactorily. Finally, phonon dispersions and associated densities of states were also evaluated for each polymorph along with their temperature-dependent DFT-calculated entropy, enthalpy, free energy, heat capacity, and Debye temperature. In particular, our DFT calculations suggest a possible way to differentiate the 2A and 3T boric acid polymorphs through Raman spectroscopy and heat capacity measurements.

Ontogenetic development of the inner ear saccule and utricle in the Lusitanian toadfish: Potential implications for auditory sensitivity.

PubMed

Chaves, Patrícia P; Valdoria, Ciara M C; Amorim, M Clara P; Vasconcelos, Raquel O

2017-09-01

Studies addressing structure-function relationships of the fish auditory system during development are sparse compared to other taxa. The Batrachoididae has become an important group to investigate mechanisms of auditory plasticity and evolution of auditory-vocal systems. A recent study reported ontogenetic improvements in the inner ear saccule sensitivity of the Lusitanian toadfish, Halobatrachus didactylus, but whether this results from changes in the sensory morphology remains unknown. We investigated how the macula and organization of auditory receptors in the saccule and utricle change during growth in this species. Inner ear sensory epithelia were removed from the end organs of previously PFA-fixed specimens, from non-vocal posthatch fry (<1.4 cm, standard length) to adults (>23 cm). Epithelia were phalloidin-stained and analysed for area, shape, number and orientation patterns of hair cells (HC), and number and size of saccular supporting cells (SC). Saccular macula area expanded 41x in total, and significantly more (relative to body length) among vocal juveniles (2.3-2.9 cm). Saccular HC number increased 25x but HC density decreased, suggesting that HC addition is slower relative to epithelial growth. While SC density decreased, SC apical area increased, contributing to the epithelial expansion. The utricule revealed increased HC density (striolar region) and less epithelial expansion (5x) with growth, contrasting with the saccule that may have a different developmental pattern due to its larger size and main auditory functions. Both macula shape and HC orientation patterns were already established in the posthatch fry and retained throughout growth in both end organs. We suggest that previously reported ontogenetic improvements in saccular sensitivity might be associated with changes in HC number (not density), size and/or molecular mechanisms controlling HC sensitivity. This is one of the first studies investigating the ontogenetic development of the saccule and utricle in a vocal fish and how it potentially relates to auditory enhancement for acoustic communication. Copyright © 2017 Elsevier B.V. All rights reserved.

On the probability distribution function of the mass surface density of molecular clouds. II.

NASA Astrophysics Data System (ADS)

Fischera, Jörg

2014-11-01

The probability distribution function (PDF) of the mass surface density of molecular clouds provides essential information about the structure of molecular cloud gas and condensed structures out of which stars may form. In general, the PDF shows two basic components: a broad distribution around the maximum with resemblance to a log-normal function, and a tail at high mass surface densities attributed to turbulence and self-gravity. In a previous paper, the PDF of condensed structures has been analyzed and an analytical formula presented based on a truncated radial density profile, ρ(r) = ρc/ (1 + (r/r0)2)n/ 2 with central density ρc and inner radius r0, widely used in astrophysics as a generalization of physical density profiles. In this paper, the results are applied to analyze the PDF of self-gravitating, isothermal, pressurized, spherical (Bonnor-Ebert spheres) and cylindrical condensed structures with emphasis on the dependence of the PDF on the external pressure pext and on the overpressure q-1 = pc/pext, where pc is the central pressure. Apart from individual clouds, we also consider ensembles of spheres or cylinders, where effects caused by a variation of pressure ratio, a distribution of condensed cores within a turbulent gas, and (in case of cylinders) a distribution of inclination angles on the mean PDF are analyzed. The probability distribution of pressure ratios q-1 is assumed to be given by P(q-1) ∝ q-k1/ (1 + (q0/q)γ)(k1 + k2) /γ, where k1, γ, k2, and q0 are fixed parameters. The PDF of individual spheres with overpressures below ~100 is well represented by the PDF of a sphere with an analytical density profile with n = 3. At higher pressure ratios, the PDF at mass surface densities Σ ≪ Σ(0), where Σ(0) is the central mass surface density, asymptotically approaches the PDF of a sphere with n = 2. Consequently, the power-law asymptote at mass surface densities above the peak steepens from Psph(Σ) ∝ Σ-2 to Psph(Σ) ∝ Σ-3. The corresponding asymptote of the PDF of cylinders for the large q-1 is approximately given by Pcyl(Σ) ∝ Σ-4/3(1 - (Σ/Σ(0))2/3)-1/2. The distribution of overpressures q-1 produces a power-law asymptote at high mass surface densities given by ∝ Σ-2k2 - 1 (spheres) or ∝ Σ-2k2 (cylinders). Appendices are available in electronic form at http://www.aanda.org

Contribution of HI-bearing ultra-diffuse galaxies to the cosmic number density of galaxies

NASA Astrophysics Data System (ADS)

Jones, M. G.; Papastergis, E.; Pandya, V.; Leisman, L.; Romanowsky, A. J.; Yung, L. Y. A.; Somerville, R. S.; Adams, E. A. K.

2018-06-01

We estimate the cosmic number density of the recently identified class of HI-bearing ultra-diffuse sources (HUDs) based on the completeness limits of the ALFALFA survey. These objects have HI masses approximately in the range 8.5 < logMHI/M⊙ < 9.5, average r-band surface brightnesses fainter than 24 mag arcsec-2, half-light radii greater than 1.5 kpc, and are separated from neighbours by at least 350 kpc. In this work we demonstrate that they contribute at most 6% of the population of HI-bearing dwarfs detected by ALFALFA (with similar HI masses), have a total cosmic number density of (1.5 ± 0.6) × 10-3 Mpc-3, and an HI mass density of (6.0 ± 0.8) × 105 M⊙ Mpc-3. We estimate that this is similar to the total cosmic number density of ultra-diffuse galaxies (UDGs) in groups and clusters, and conclude that the relation between the number of UDGs hosted in a halo and the halo mass must have a break below M200 1012 M⊙ in order to account for the abundance of HUDs in the field. The distribution of the velocity widths of HUDs rises steeply towards low values, indicating a preference for slow rotation rates compared to the global HI-rich dwarf population. These objects were already included in previous measurements of the HI mass function, but have been absent from measurements of the galaxy stellar mass function owing to their low surface brightness. However, we estimate that due to their low number density the inclusion of HUDs would constitute a correction of less than 1%. Comparison with the Santa Cruz semi-analytic model shows that it produces HI-rich central UDGs that have similar colours to HUDs, but that these UDGs are currently produced in a much greater number. While previous results from this sample have favoured formation scenarios where HUDs form in high spin-parameter halos, comparisons with recent results which invoke that formation mechanism reveal that this model produces an order of magnitude more field UDGs than we observe in the HUD population, and these have an occurrence rate (relative to other dwarfs) that is approximately double what we observe. In addition, the colours of HUDs are bluer than predicted, although we suspect this is due to a systematic problem in reproducing the star formation histories of low-mass galaxies rather than being specific to the ultra-diffuse nature of these sources.

Multiconfiguration Pair-Density Functional Theory Is as Accurate as CASPT2 for Electronic Excitation.

PubMed

Hoyer, Chad E; Ghosh, Soumen; Truhlar, Donald G; Gagliardi, Laura

2016-02-04

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.

Synthesis of two-dimensional titanium nitride Ti4N3 (MXene)

NASA Astrophysics Data System (ADS)

Urbankowski, Patrick; Anasori, Babak; Makaryan, Taron; Er, Dequan; Kota, Sankalp; Walsh, Patrick L.; Zhao, Mengqiang; Shenoy, Vivek B.; Barsoum, Michel W.; Gogotsi, Yury

2016-06-01

We report on the synthesis of the first two-dimensional transition metal nitride, Ti4N3-based MXene. In contrast to the previously reported MXene synthesis methods - in which selective etching of a MAX phase precursor occurred in aqueous acidic solutions - here a molten fluoride salt is used to etch Al from a Ti4AlN3 powder precursor at 550 °C under an argon atmosphere. We further delaminated the resulting MXene to produce few-layered nanosheets and monolayers of Ti4N3Tx, where T is a surface termination (F, O, or OH). Density functional theory calculations of bare, non-terminated Ti4N3 and terminated Ti4N3Tx were performed to determine the most energetically stable form of this MXene. Bare and functionalized Ti4N3 are predicted to be metallic. Bare Ti4N3 is expected to show magnetism, which is significantly reduced in the presence of functional groups.We report on the synthesis of the first two-dimensional transition metal nitride, Ti4N3-based MXene. In contrast to the previously reported MXene synthesis methods - in which selective etching of a MAX phase precursor occurred in aqueous acidic solutions - here a molten fluoride salt is used to etch Al from a Ti4AlN3 powder precursor at 550 °C under an argon atmosphere. We further delaminated the resulting MXene to produce few-layered nanosheets and monolayers of Ti4N3Tx, where T is a surface termination (F, O, or OH). Density functional theory calculations of bare, non-terminated Ti4N3 and terminated Ti4N3Tx were performed to determine the most energetically stable form of this MXene. Bare and functionalized Ti4N3 are predicted to be metallic. Bare Ti4N3 is expected to show magnetism, which is significantly reduced in the presence of functional groups. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02253g

Influence of the exchange and correlation functional on the structure of amorphous InSb and In3SbTe2 compounds

NASA Astrophysics Data System (ADS)

Gabardi, Silvia; Caravati, Sebastiano; Los, Jan H.; Kühne, Thomas D.; Bernasconi, Marco

2016-05-01

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In3SbTe2 compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtained with the most commonly used Perdew-Becke-Ernzerhof functional. This outcome is at odd with the properties of Ge2Sb2Te5 phase change compound for which the two exchange-correlation functionals yield very similar results on the structure of the amorphous phase.

Influence of the exchange and correlation functional on the structure of amorphous InSb and In3SbTe2 compounds.

PubMed

Gabardi, Silvia; Caravati, Sebastiano; Los, Jan H; Kühne, Thomas D; Bernasconi, Marco

2016-05-28

We have investigated the structural, vibrational, and electronic properties of the amorphous phase of InSb and In3SbTe2 compounds of interest for applications in phase change non-volatile memories. Models of the amorphous phase have been generated by quenching from the melt by molecular dynamics simulations based on density functional theory. In particular, we have studied the dependence of the structural properties on the choice of the exchange-correlation functional. It turns out that the use of the Becke-Lee-Yang-Parr functional provides models with a much larger fraction of In atoms in a tetrahedral bonding geometry with respect to previous results obtained with the most commonly used Perdew-Becke-Ernzerhof functional. This outcome is at odd with the properties of Ge2Sb2Te5 phase change compound for which the two exchange-correlation functionals yield very similar results on the structure of the amorphous phase.

On the use of the noncentral chi-square density function for the distribution of helicopter spectral estimates

NASA Technical Reports Server (NTRS)

Garber, Donald P.

1993-01-01

A probability density function for the variability of ensemble averaged spectral estimates from helicopter acoustic signals in Gaussian background noise was evaluated. Numerical methods for calculating the density function and for determining confidence limits were explored. Density functions were predicted for both synthesized and experimental data and compared with observed spectral estimate variability.

Focal high cell density generates a gradient of patterns in self-organizing vascular mesenchymal cells.

PubMed

Cheng, Henry; Reddy, Aneela; Sage, Andrew; Lu, Jinxiu; Garfinkel, Alan; Tintut, Yin; Demer, Linda L

2012-01-01

In embryogenesis, structural patterns, such as vascular branching, may form via a reaction-diffusion mechanism in which activator and inhibitor morphogens guide cells into periodic aggregates. We previously found that vascular mesenchymal cells (VMCs) spontaneously aggregate into nodular structures and that morphogen pairs regulate the aggregation into patterns of spots and stripes. To test the effect of a focal change in activator morphogen on VMC pattern formation, we created a focal zone of high cell density by plating a second VMC layer within a cloning ring over a confluent monolayer. After 24 h, the ring was removed and pattern formation monitored by phase-contrast microscopy. At days 2-8, the patterns progressed from uniform distributions to swirl, labyrinthine and spot patterns. Within the focal high-density zone (HDZ) and a narrow halo zone, cells aggregated into spot patterns, whilst in the outermost zone of the plate, cells formed a labyrinthine pattern. The area occupied by aggregates was significantly greater in the outermost zone than in the HDZ or halo. The rate of pattern progression within the HDZ increased as a function of its plating density. Thus, focal differences in cell density may drive pattern formation gradients in tissue architecture, such as vascular branching. Copyright © 2012 S. Karger AG, Basel.

Supernova Driving. II. Compressive Ratio in Molecular-cloud Turbulence

NASA Astrophysics Data System (ADS)

Pan, Liubin; Padoan, Paolo; Haugbølle, Troels; Nordlund, Åke

2016-07-01

The compressibility of molecular cloud (MC) turbulence plays a crucial role in star formation models, because it controls the amplitude and distribution of density fluctuations. The relation between the compressive ratio (the ratio of powers in compressive and solenoidal motions) and the statistics of turbulence has been previously studied systematically only in idealized simulations with random external forces. In this work, we analyze a simulation of large-scale turbulence (250 pc) driven by supernova (SN) explosions that has been shown to yield realistic MC properties. We demonstrate that SN driving results in MC turbulence with a broad lognormal distribution of the compressive ratio, with a mean value ≈0.3, lower than the equilibrium value of ≈0.5 found in the inertial range of isothermal simulations with random solenoidal driving. We also find that the compressibility of the turbulence is not noticeably affected by gravity, nor are the mean cloud radial (expansion or contraction) and solid-body rotation velocities. Furthermore, the clouds follow a general relation between the rms density and the rms Mach number similar to that of supersonic isothermal turbulence, though with a large scatter, and their average gas density probability density function is described well by a lognormal distribution, with the addition of a high-density power-law tail when self-gravity is included.

Measurement of electron density transients in pulsed RF discharges using a frequency boxcar hairpin probe

NASA Astrophysics Data System (ADS)

Peterson, David; Coumou, David; Shannon, Steven

2015-11-01

Time resolved electron density measurements in pulsed RF discharges are shown using a hairpin resonance probe using low cost electronics, on par with normal Langmuir probe boxcar mode operation. Time resolution of 10 microseconds has been demonstrated. A signal generator produces the applied microwave frequency; the reflected waveform is passed through a directional coupler and filtered to remove the RF component. The signal is heterodyned with a frequency mixer and rectified to produce a DC signal read by an oscilloscope. At certain points during the pulse, the plasma density is such that the applied frequency is the same as the resonance frequency of the probe/plasma system, creating reflected signal dips. The applied microwave frequency is shifted in small increments in a frequency boxcar routine to determine the density as a function of time. A dc sheath correction is applied for the grounded probe, producing low cost, high fidelity, and highly reproducible electron density measurements. The measurements are made in both inductively and capacitively coupled systems, the latter driven by multiple frequencies where a subset of these frequencies are pulsed. Measurements are compared to previous published results, time resolved OES, and in-line measurement of plasma impedance. This work is supported by the NSF DOE partnership on plasma science, the NSF GOALI program, and MKS Instruments.

A Faint Flux-limited Ly α Emitter Sample at z ∼ 0.3

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

Wold, Isak G. B.; Finkelstein, Steven L.; Barger, Amy J.

2017-10-20

We present a flux-limited sample of z ∼ 0.3 Ly α emitters (LAEs) from Galaxy Evolution Explorer ( GALEX ) grism spectroscopic data. The published GALEX z ∼ 0.3 LAE sample is pre-selected from continuum-bright objects and thus is biased against high equivalent width (EW) LAEs. We remove this continuum pre-selection and compute the EW distribution and the luminosity function of the Ly α emission line directly from our sample. We examine the evolution of these quantities from z ∼ 0.3 to 2.2 and find that the EW distribution shows little evidence for evolution over this redshift range. As shownmore » by previous studies, the Ly α luminosity density from star-forming (SF) galaxies declines rapidly with declining redshift. However, we find that the decline in Ly α luminosity density from z = 2.2 to z = 0.3 may simply mirror the decline seen in the H α luminosity density from z = 2.2 to z = 0.4, implying little change in the volumetric Ly α escape fraction. Finally, we show that the observed Ly α luminosity density from AGNs is comparable to the observed Ly α luminosity density from SF galaxies at z = 0.3. We suggest that this significant contribution from AGNs to the total observed Ly α luminosity density persists out to z ∼ 2.2.« less

Stretched hydrogen molecule from a constrained-search density-functional perspective

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

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 themore » 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.« less

Neuroprotective Effect of Tauroursodeoxycholic Acid on N-Methyl-D-Aspartate-Induced Retinal Ganglion Cell Degeneration

PubMed Central

Fernández-Sánchez, Laura; Rondón, Netxibeth; Esquiva, Gema; Germain, Francisco; de la Villa, Pedro; Cuenca, Nicolás

2015-01-01

Retinal ganglion cell degeneration underlies the pathophysiology of diseases affecting the retina and optic nerve. Several studies have previously evidenced the anti-apoptotic properties of the bile constituent, tauroursodeoxycholic acid, in diverse models of photoreceptor degeneration. The aim of this study was to investigate the effects of systemic administration of tauroursodeoxycholic acid on N-methyl-D-aspartate (NMDA)-induced damage in the rat retina using a functional and morphological approach. Tauroursodeoxycholic acid was administered intraperitoneally before and after intravitreal injection of NMDA. Three days after insult, full-field electroretinograms showed reductions in the amplitudes of the positive and negative-scotopic threshold responses, scotopic a- and b-waves and oscillatory potentials. Quantitative morphological evaluation of whole-mount retinas demonstrated a reduction in the density of retinal ganglion cells. Systemic administration of tauroursodeoxycholic acid attenuated the functional impairment induced by NMDA, which correlated with a higher retinal ganglion cell density. Our findings sustain the efficacy of tauroursodeoxycholic acid administration in vivo, suggesting it would be a good candidate for the pharmacological treatment of degenerative diseases coursing with retinal ganglion cell loss. PMID:26379056

Analytical second derivatives of excited-state energy within the time-dependent density functional theory coupled with a conductor-like polarizable continuum model.

PubMed

Liu, Jie; Liang, WanZhen

2013-01-14

This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with a conductor-like polarizable continuum model (CPCM). The formalism, implementation, and application of analytical first and second energy derivatives of TDDFT/CPCM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of excitation energies, excited-state geometries, and harmonic vibrational frequencies for a number of benchmark systems. The calculated results are in good agreement with the corresponding experimental data or other theoretical calculations, indicating the reliability of the current computer implementation of the developed algorithms. Then we made some preliminary applications to calculate the resonant Raman spectrum of 4-hydroxybenzylidene-2,3-dimethyl-imidazolinone in ethanol solution and the infrared spectra of ground and excited states of 9-fluorenone in methanol solution.

Photovoltaic Properties of Two-Dimensional (CH3NH3)2Pb(SCN)2I2 Perovskite: A Combined Experimental and Density Functional Theory Study.

PubMed

Xiao, Zewen; Meng, Weiwei; Saparov, Bayrammurad; Duan, Hsin-Sheng; Wang, Changlei; Feng, Chunbao; Liao, Weiqiang; Ke, Weijun; Zhao, Dewei; Wang, Jianbo; Mitzi, David B; Yan, Yanfa

2016-04-07

We explore the photovoltaic-relevant properties of the 2D MA2Pb(SCN)2I2 (where MA = CH3NH3(+)) perovskite using a combination of materials synthesis, characterization and density functional theory calculation, and determine electronic properties of MA2Pb(SCN)2I2 that are significantly different from those previously reported in literature. The layered perovskite with mixed-anions exhibits an indirect bandgap of ∼2.04 eV, with a slightly larger direct bandgap of ∼2.11 eV. The carriers (both electrons and holes) are also found to be confined within the 2D layers. Our results suggest that the 2D MA2Pb(SCN)2I2 perovskite may not be among the most promising absorbers for efficient single-junction solar cell applications; however, use as an absorber for the top cell of a tandem solar cell may still be a possibility if films are grown with the 2D layers aligned perpendicular to the substrates.

Direct vs. indirect pathway for nitrobenzene reduction reaction on a Ni catalyst surface: a density functional study.

PubMed

Mahata, Arup; Rai, Rohit K; Choudhuri, Indrani; Singh, Sanjay K; Pathak, Biswarup

2014-12-21

Density functional theory (DFT) calculations are performed to understand and address the previous experimental results that showed the reduction of nitrobenzene to aniline prefers direct over indirect reaction pathways irrespective of the catalyst surface. Nitrobenzene to aniline conversion occurs via the hydroxyl amine intermediate (direct pathway) or via the azoxybenzene intermediate (indirect pathway). Through our computational study we calculated the spin polarized and dispersion corrected reaction energies and activation barriers corresponding to various reaction pathways for the reduction of nitrobenzene to aniline over a Ni catalyst surface. The adsorption behaviour of the substrate, nitrobenzene, on the catalyst surface was also considered and the energetically most preferable structural orientation was elucidated. Our study indicates that the parallel adsorption behaviour of the molecules over a catalyst surface is preferable over vertical adsorption behaviour. Based on the reaction energies and activation barrier of the various elementary steps involved in direct or indirect reaction pathways, we find that the direct reduction pathway of nitrobenzene over the Ni(111) catalyst surface is more favourable than the indirect reaction pathway.

Optimizing the Ar-Xe infrared laser on the Naval Research Laboratory's Electra generator

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

Apruzese, J. P.; Giuliani, J. L.; Wolford, M. F.

2008-07-01

The Ar-Xe infrared laser has been investigated in several series of experiments carried out on the Naval Research Laboratory's Electra generator. Our primary goals were to optimize the efficiency of the laser (within Electra's capabilities) and to gain understanding of the main physical processes underlying the laser's output as a function of controllable parameters such as Xe fraction, power deposition, and gas pressure. We find that the intrinsic efficiency maximizes at {approx}3% at a total pressure of 2.5 atm, Xe fraction of 1%, and electron beam power deposition density of 50-100 kW cm{sup -3}. We deployed an interferometer to measuremore » the electron density during lasing; the ionization fractions of 10{sup -5}-10{sup -4} that it detected well exceed previous theoretical estimates. Some trends in the data as a function of beam power and xenon fraction are not fully understood. The as-yet incomplete picture of Ar-Xe laser physics is likely traceable in large part to significant uncertainties still present in many important rates influencing the atomic and molecular kinetics.« less

Adsorptive desulfurization with metal-organic frameworks: A density functional theory investigation

NASA Astrophysics Data System (ADS)

Chen, Zhiping; Ling, Lixia; Wang, Baojun; Fan, Huiling; Shangguan, Ju; Mi, Jie

2016-11-01

The contribution of each fragment of metal-organic frameworks (MOFs) to the adsorption of sulfur compounds were investigated using density functional theory (DFT). The involved sulfur compounds are dimethyl sulfide (CH3SCH3), ethyl mercaptan (CH3CH2SH) and hydrogen sulfide (H2S). MOFs with different organic ligands (NH2-BDC, BDC and NDC), metal centers structures (M, M-M and M3O) and metal ions (Zn, Cu and Fe) were used to study their effects on sulfur species adsorption. The results revealed that, MOFs with coordinatively unsaturated sites (CUS) have the strongest binding strength with sulfur compounds, MOFs with NH2-BDC substituent group ligand comes second, followed by that with saturated metal center, and the organic ligands without substituent group has the weakest adsorption strength. Moreover, it was also found that, among different metal ions (Fe, Zn and Cu), MOFs with unsaturated Fe has the strongest adsorption strength for sulfur compounds. These results are consistent with our previous experimental observations, and therefore provide insights on the better design of MOFs for desulfurization application.

Accessing protein conformational ensembles using room-temperature X-ray crystallography

PubMed Central

Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

2011-01-01

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold.

PubMed

Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

2006-03-07

We present results for a simulated inelastic electron-tunneling spectra (IETS) from calculations using the "gDFTB" code. The geometric and electronic structure is obtained from calculations using a local-basis density-functional scheme, and a nonequilibrium Green's function formalism is employed to deal with the transport aspects of the problem. The calculated spectrum of octanedithiol on gold(111) shows good agreement with experimental results and suggests further details in the assignment of such spectra. We show that some low-energy peaks, unassigned in the experimental spectrum, occur in a region where a number of molecular modes are predicted to be active, suggesting that these modes are the cause of the peaks rather than a matrix signal, as previously postulated. The simulations also reveal the qualitative nature of the processes dominating IETS. It is highly sensitive only to the vibrational motions that occur in the regions of the molecule where there is electron density in the low-voltage conduction channel. This result is illustrated with an examination of the predicted variation of IETS with binding site and alkane chain length.

Grain boundaries in bcc-Fe: a density-functional theory and tight-binding study

NASA Astrophysics Data System (ADS)

Wang, Jingliang; Madsen, Georg K. H.; Drautz, Ralf

2018-02-01

Grain boundaries (GBs) have a significant influence on material properties. In the present paper, we calculate the energies of eleven low-Σ ({{Σ }}≤slant 13) symmetrical tilt GBs and two twist GBs in ferromagnetic bcc iron using first-principles density functional theory (DFT) calculations. The results demonstrate the importance of a sufficient sampling of initial rigid body translations in all three directions. We show that the relative GB energies can be explained by the miscoordination of atoms at the GB region. While the main features of the studied GB structures were captured by previous empirical interatomic potential calculations, it is shown that the absolute values of GB energies calculated were substantially underestimated. Based on DFT-calculated GB structures and energies, we construct a new d-band orthogonal tight-binding (TB) model for bcc iron. The TB model is validated by its predictive power on all the studied GBs. We apply the TB model to block boundaries in lath martensite and demonstrate that the experimentally observed GB character distribution can be explained from the viewpoint of interface energy.

Charged-particle pseudorapidity distributions in Au+Au collisions at sNN=62.4 GeV

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Halliwell, C.; Hamblen, J.; Hauer, M.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Seals, H.; Sedykh, I.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; Nieuwenhuizen, G. J. Van; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wysłouch, B.

2006-08-01

The charged-particle pseudorapidity density for Au+Au collisions at sNN=62.4 GeV has been measured over a wide range of impact parameters and compared to results obtained at other energies. As a function of collision energy, the pseudorapidity distribution grows systematically both in height and width. The midrapidity density is found to grow approximately logarithmically between BNL Alternating Gradient Synchrotron (AGS) energies and the top BNL Relativistic Heavy Ion Collider (RHIC) energy. There is also an approximate factorization of the centrality and energy dependence of the midrapidity yields. The new results at sNN=62.4 GeV confirm the previously observed phenomenon of “extended longitudinal scaling” in the pseudorapidity distributions when viewed in the rest frame of one of the colliding nuclei. It is also found that the evolution of the shape of the distribution with centrality is energy independent, when viewed in this reference frame. As a function of centrality, the total charged particle multiplicity scales linearly with the number of participant pairs as it was observed at other energies.

Self-diffusion in MgO--a density functional study.

PubMed

Runevall, Odd; Sandberg, Nils

2011-08-31

Density functional theory calculations have been performed to study self-diffusion in magnesium oxide, a model material for a wide range of ionic compounds. Formation energies and entropies of Schottky defects and divacancies were obtained by means of total energy and phonon calculations in supercell configurations. Transition state theory was used to estimate defect migration rates, with migration energies taken from static calculations, and the corresponding frequency factors estimated from the phonon spectrum. In all static calculations we corrected for image effects using either a multipole expansion or an extrapolation to the low concentration limit. It is shown that both methods give similar results. The results for self-diffusion of Mg and O confirm the previously established picture, namely that in materials of nominal purity, Mg diffuses extrinsically by a single vacancy mechanism, while O diffuses intrinsically by a divacancy mechanism. Quantitatively, the current results are in very good agreement with experiments concerning O diffusion, while for Mg the absolute diffusion rate is generally underestimated by a factor of 5-10. The reason for this discrepancy is discussed.

First-principles calculations of two cubic fluoropervskite compounds: RbFeF3 and RbNiF3

NASA Astrophysics Data System (ADS)

Mubarak, A. A.; Al-Omari, Saleh

2015-05-01

We present first-principles calculations of the structural, elastic, electronic, magnetic and optical properties for RbFeF3 and RbNiF3. The full-potential linear augmented plan wave (FP-LAPW) method within the density functional theory was utilized to perform the present calculations. We employed the generalized gradient approximation as exchange-correlation potential. It was found that the calculated analytical lattice parameters agree with previous studies. The analysis of elastic constants showed that the present compounds are elastically stable and anisotropic. Moreover, both compounds are classified as a ductile compound. The calculations of the band structure and density functional theory revealed that the RbFeF3 compound has a half-metallic behavior while the RbNiF3 compound has a semiconductor behavior with indirect (M-Γ) band gap. The ferromagnetic behavior was studied for both compounds. The optical properties were calculated for the radiation of up to 40 eV. A beneficial optics technology is predicted as revealed from the optical spectra.

Adsorption of rare gases on the C20 nanocage: a theoretical investigation

NASA Astrophysics Data System (ADS)

Rahimi, Rezvan; Kamalinahad, Saeedeh; Solimannejad, Mohammad

2018-03-01

The adsorption of rare gases (Rg) on the external surface of pristine and Sc-doped C20 (ScC19) nanocage is investigated using density functional theory (DFT). Also, time-dependent density functional theory (TD-DFT) and natural bond orbital (NBO) calculations are performed at the CAM-B3LYP/6-31G (d) level. The NBO analyses indicate that the adsorption of Rg molecules with studied nanocage significantly alters its electronic nature. Theoretical results have shown that Rg is weakly adsorbed on the pristine C20, so this nanocage cannot be a proper sensor for detecting and sensing rare gases. In order to improve properties of the nanocage as a promising sensor, Sc-doping process was investigated. The more negative adsorption energies (Eads) of Rg/ScC19 means that adsorption of Rg on the surface of ScC19 is energetically more favored than C20 and other nano-structures as reported in previous studies. It is expected that significant changes in the electronic properties caused by Rg may be used for designing new sensors for detection of rare gases.

Matrix isolation infrared spectroscopic studies and density functional theory calculations of the MNN, (MN)2 (M = Y and La), and Y3NN molecules.

PubMed

Teng, Yun-Lei; Xu, Qiang

2008-04-24

The reactions of yttrium and lanthanum with dinitrogen were reinvestigated. Laser-ablated yttrium and lanthanum atoms were co-deposited at 4 K with dinitrogen in excess argon, and the low-temperature reactions of Y and La with N2 in solid argon were studied using infrared spectroscopy. The reaction products YNN, (YN)2, LaNN, and (LaN)2 were formed in the present experiments and characterized on the basis of 14N/15N isotopic shifts, mixed isotope splitting patterns, stepwise annealing, change of reagent concentration and laser energy, and comparison with theoretical predictions. Some assignments were made based on a previous report. Density functional theory calculations were performed on these systems to identify possible reaction products. The agreement between experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts of the MNN and (MN)2 (M = Y and La) molecules supports the identification of these molecules from the matrix infrared spectra. Plausible reaction mechanisms were proposed for the formation of these molecules along with tentative identification of the Y3NN molecule.

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Malakkal, Linu; Szpunar, Barbara; Zuniga, Juan Carlos; Siripurapu, Ravi Kiran; Szpunar, Jerzy A.

2016-05-01

In this work, we have used Quantum ESPRESSO (QE), an open source first principles code, based on density-functional theory, plane waves, and pseudopotentials, along with quasi-harmonic approximation (QHA) to calculate the thermo-mechanical properties of thorium dioxide (ThO2). Using Python programming language, our group developed qe-nipy-advanced, an interface to QE, which can evaluate the structural and thermo-mechanical properties of materials. We predicted the phonon contribution to thermal conductivity (kL) using the Slack model. We performed the calculations within local density approximation (LDA) and generalized gradient approximation (GGA) with the recently proposed version for solids (PBEsol). We employed a Monkhorst-Pack 5 × 5 × 5 k-points mesh in reciprocal space with a plane wave cut-off energy of 150 Ry to obtain the convergence of the structure. We calculated the dynamical matrices of the lattice on a 4 × 4 × 4 mesh. We have predicted the heat capacity, thermal expansion and the phonon contribution to thermal conductivity, as a function of temperature up to 1400K, and compared them with the previous work and known experimental results.

DFMSPH14: A C-code for the double folding interaction potential of two spherical nuclei

NASA Astrophysics Data System (ADS)

Gontchar, I. I.; Chushnyakova, M. V.

2016-09-01

This is a new version of the DFMSPH code designed to obtain the nucleus-nucleus potential by using the double folding model (DFM) and in particular to find the Coulomb barrier. The new version uses the charge, proton, and neutron density distributions provided by the user. Also we added an option for fitting the DFM potential by the Gross-Kalinowski profile. The main functionalities of the original code (e.g. the nucleus-nucleus potential as a function of the distance between the centers of mass of colliding nuclei, the Coulomb barrier characteristics, etc.) have not been modified. Catalog identifier: AEFH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 7211 No. of bytes in distributed program, including test data, etc.: 114404 Distribution format: tar.gz Programming language: C Computer: PC and Mac Operation system: Windows XP and higher, MacOS, Unix/Linux Memory required to execute with typical data: below 10 Mbyte Classification: 17.9 Catalog identifier of previous version: AEFH_v1_0 Journal reference of previous version: Comp. Phys. Comm. 181 (2010) 168 Does the new version supersede the previous version?: Yes Nature of physical problem: The code calculates in a semimicroscopic way the bare interaction potential between two colliding spherical nuclei as a function of the center of mass distance. The height and the position of the Coulomb barrier are found. The calculated potential is approximated by an analytical profile (Woods-Saxon or Gross-Kalinowski) near the barrier. Dependence of the barrier parameters upon the characteristics of the effective NN forces (like, e.g. the range of the exchange part of the nuclear term) can be investigated. Method of solution: The nucleus-nucleus potential is calculated using the double folding model with the Coulomb and the effective M3Y NN interactions. For the direct parts of the Coulomb and the nuclear terms, the Fourier transform method is used. In order to calculate the exchange parts, the density matrix expansion method is applied. Typical running time: less than 1 minute. Reason for new version: Many users asked us how to implement their own density distributions in the DFMSPH. Now this option has been added. Also we found that the calculated Double-Folding Potential (DFP) is approximated more accurately by the Gross-Kalinowski (GK) profile. This option has been also added.

Active Space Dependence in Multiconfiguration Pair-Density Functional Theory.

PubMed

Sharma, Prachi; Truhlar, Donald G; Gagliardi, Laura

2018-02-13

In multiconfiguration pair-density functional theory (MC-PDFT), multiconfiguration self-consistent-field calculations and on-top density functionals are combined to describe both static and dynamic correlation. Here, we investigate how the MC-PDFT total energy and its components depend on the active space choice in the case of the H 2 and N 2 molecules. The active space dependence of the on-top pair density, the total density, the ratio of on-top pair density to half the square of the electron density, and the satisfaction of the virial theorem are also explored. We find that the density and on-top pair density do not change significantly with changes in the active space. However, the on-top ratio does change significantly with respect to active space change, and this affects the on-top energy. This study provides a foundation for designing on-top density functionals and automatizing the active space choice in MC-PDFT.

Negative relationships between population density and metabolic rates are not general.

PubMed

Yashchenko, Varvara; Fossen, Erlend Ignacio; Kielland, Øystein Nordeide; Einum, Sigurd

2016-07-01

Population density has recently been suggested to be an important factor influencing metabolic rates and to represent an important 'third axis' explaining variation beyond that explained by body mass and temperature. In situations where population density influences food consumption, the immediate effect on metabolism acting through specific dynamic action (SDA), and downregulation due to fasting over longer periods, is well understood. However, according to a recent review, previous studies suggest a more general effect of population density per se, even in the absence of such effects. It has been hypothesized that this results from animals performing anticipatory responses (i.e. reduced activity) to expected declines in food availability. Here, we test the generality of this finding by measuring density effects on metabolic rates in 10 clones from two different species of the zooplankton Daphnia (Daphnia pulex Leydig and D. magna Straus). Using fluorescence-based respirometry, we obtain high-precision measures of metabolism. We also identify additional studies on this topic that were not included in the previous review, compare the results and evaluate the potential for measurement bias in all previous studies. We demonstrate significant variation in mass-specific metabolism among clones within both species. However, we find no evidence for a negative relationship between population density and mass-specific metabolism. The previously reported pattern also disappeared when we extended the set of studies analysed. We discuss potential reasons for the discrepancy among studies, including two main sources of potential bias (microbial respiration and declining oxygen consumption due to reduced oxygen availability). Only one of the previous studies gives sufficient information to conclude the absence of such biases, and consistent with our results, no effect of density on metabolism was found. We conclude that population density per se does not have a general effect on mass-specific metabolic rate. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

NASA Astrophysics Data System (ADS)

Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

2008-12-01

This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

Relationships between brightness of nighttime lights and population density

NASA Astrophysics Data System (ADS)

Naizhuo, Z.

2012-12-01

Brightness of nighttime lights has been proven to be a good proxy for socioeconomic and demographic statistics. Moreover, the satellite nighttime lights data have been used to spatially disaggregate amounts of gross domestic product (GDP), fossil fuel carbon dioxide emission, and electric power consumption (Ghosh et al., 2010; Oda and Maksyutov, 2011; Zhao et al., 2012). Spatial disaggregations were performed in these previous studies based on assumed linear relationships between digital number (DN) value of pixels in the nighttime light images and socioeconomic data. However, reliability of the linear relationships was never tested due to lack of relative high-spatial-resolution (equal to or finer than 1 km × 1 km) statistical data. With the similar assumption that brightness linearly correlates to population, Bharti et al. (2011) used nighttime light data as a proxy for population density and then developed a model about seasonal fluctuations of measles in West Africa. The Oak Ridge National Laboratory used sub-national census population data and high spatial resolution remotely-sensed-images to produce LandScan population raster datasets. The LandScan population datasets have 1 km × 1 km spatial resolution which is consistent with the spatial resolution of the nighttime light images. Therefore, in this study I selected 2008 LandScan population data as baseline reference data and the contiguous United State as study area. Relationships between DN value of pixels in the 2008 Defense Meteorological Satellite Program's Operational Linescan System (DMSP-OLS) stable light image and population density were established. Results showed that an exponential function can more accurately reflect the relationship between luminosity and population density than a linear function. Additionally, a certain number of saturated pixels with DN value of 63 exist in urban core areas. If directly using the exponential function to estimate the population density for the whole brightly lit area, relatively large under-estimations would emerge in the urban core regions. Previous studies have shown that GDP, carbon dioxide emission, and electric power consumption strongly correlate to urban population (Ghosh et al., 2010; Sutton et al., 2007; Zhao et al., 2012). Thus, although this study only examined the relationships between brightness of nighttime lights and population density, the results can provide insight for the spatial disaggregations of socioeconomic data (e.g. GDP, carbon dioxide emission, and electric power consumption) using the satellite nighttime light image data. Simply distributing the socioeconomic data to each pixel in proportion to the DN value of the nighttime light images may generate relatively large errors. References Bharit N, Tatem AJ, Ferrari MJ, Grais RF, Djibo A, Grenfell BT, 2011. Science, 334:1424-1427. Ghosh T, Elvidge CD, Sutton PC, Baugh KE, Ziskin D, Tuttle BT, 2010. Energies, 3:1895-1913. Oda T, Maksyutov S, 2011. Atmospheric Chemistry and Physics, 11:543-556. Sutton PC, Elvidge CD, Ghosh T, 2007. International Journal of Ecological Economics and Statistics, 8:5-21. Zhao N, Ghosh T, Samson EL, 2012. International Journal of Remote sensing, 33:6304-6320.

Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

PubMed

McNamara, K B; Simmons, L W

2017-09-01

Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Effects of the unintentional background concentration, indium composition and defect density on the performance of InGaN p-i-n homojunction solar cells

NASA Astrophysics Data System (ADS)

Wu, Shudong; Cheng, Liwen; Wang, Qiang

2018-07-01

We theoretically investigate the effects of the unintentional background concentration, indium composition and defect density of intrinsic layer (i-layer) on the photovoltaic performance of InGaN p-i-n homojunction solar cells by solving the Poisson and steady-state continuity equations. The built-in electric field and carrier generation rate depend on the position within the i-layer. The collection efficiency, short circuit current density, open circuit voltage, fill factor, and conversion efficiency are found to depend strongly on the background concentration, thickness, indium composition, and defect density of the i-layer. With increasing the background concentration, the maximum thickness of field-bearing i-layer decreases, and the width of depletion region may become even too small to cover the whole i-layer, resulting in a serious decrease of the carrier collection. Some oscillations as a function of indium composition are found in the short circuit current density and conversion efficiency at high indium composition and low defect density due to the interference between the absorbance and the generation rate of carriers. The defect density degrades seriously the overall photovoltaic performance, and its effect on the photovoltaic performance is roughly seven orders of magnitude higher than the previously reported values [Feng et al., J. Appl. Phys. 108 (2010) 093118]. As a result, the high crystalline quality InGaN with high indium composition is a key factor in the device performance of III-nitride based solar cells.

Axially deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator basis (III) HFBTHO (v3.00): A new version of the program

NASA Astrophysics Data System (ADS)

Perez, R. Navarro; Schunck, N.; Lasseri, R.-D.; Zhang, C.; Sarich, J.

2017-11-01

We describe the new version 3.00 of the code HFBTHO that solves the nuclear Hartree-Fock (HF) or Hartree-Fock-Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle-hole and particle-particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scale mass table calculations. Program Files doi:http://dx.doi.org/10.17632/c5g2f92by3.1 Licensing provisions: GPL v3 Programming language: FORTRAN-95 Journal reference of previous version: M.V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, and S. Wild, Comput. Phys. Commun. 184 (2013). Does the new version supersede the previous one: Yes Summary of revisions: 1. the Gogny force in both particle-hole and particle-particle channels was implemented; 2. the nuclear collective inertia at the perturbative cranking approximation was implemented; 3. fission fragment charge, mass and deformations were implemented based on the determination of the position of the neck between nascent fragments; 4. the regularization method of zero-range pairing forces was implemented; 5. the localization functions of the HFB solution were implemented; 6. a MPI interface for large-scale mass table calculations was implemented. Nature of problem:HFBTHO is a physics computer code that is used to model the structure of the nucleus. It is an implementation of the energy density functional (EDF) approach to atomic nuclei, where the energy of the nucleus is obtained by integration over space of some phenomenological energy density, which is itself a functional of the neutron and proton intrinsic densities. In the present version of HFBTHO, the energy density derives either from the zero-range Skyrme or the finite-range Gogny effective two-body interaction between nucleons. Nuclear super-fluidity is treated at the Hartree-Fock-Bogolyubov (HFB) approximation. Constraints on the nuclear shape allows probing the potential energy surface of the nucleus as needed e.g., for the description of shape isomers or fission. The implementation of a local scale transformation of the single-particle basis in which the HFB solutions are expanded provide a tool to properly compute the structure of weakly-bound nuclei. Solution method: The program uses the axial Transformed Harmonic Oscillator (THO) single-particle basis to expand quasiparticle wave functions. It iteratively diagonalizes the Hartree-Fock-Bogolyubov Hamiltonian based on generalized Skyrme-like energy densities and zero-range pairing interactions or the finite-range Gogny force until a self-consistent solution is found. A previous version of the program was presented in M.V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, and S. Wild, Comput. Phys. Commun. 184 (2013) 1592-1604 with much of the formalism presented in the original paper M.V. Stoitsov, J. Dobaczewski, W. Nazarewicz, P. Ring, Comput. Phys. Commun. 167 (2005) 43-63. Additional comments: The user must have access to (i) the LAPACK subroutines DSYEEVR, DSYEVD, DSYTRF and DSYTRI, and their dependencies, which compute eigenvalues and eigenfunctions of real symmetric matrices, (ii) the LAPACK subroutines DGETRI and DGETRF, which invert arbitrary real matrices, and (iii) the BLAS routines DCOPY, DSCAL, DGEMM and DGEMV for double-precision linear algebra (or provide another set of subroutines that can perform such tasks). The BLAS and LAPACK subroutines can be obtained from the Netlib Repository at the University of Tennessee, Knoxville: http://netlib2.cs.utk.edu/.

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Multicomponent density functional theory embedding formulation

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

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

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 ismore » 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{sup −} 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.« less

Computed Tomography Density Change in the Thyroid Gland Before and After Radiation Therapy.

PubMed

Ishibashi, Naoya; Maebayashi, Toshiya; Aizawa, Takuya; Sakaguchi, Masakuni; Okada, Masahiro; Matsushita, Junichi

2018-01-01

Hypothyroidism is an established adverse effect of radiation therapy for head and neck cancer, and computed tomography (CT) density of the thyroid gland is lower in hypothyroid than euthyroid individuals. No previous studies have evaluated changes in CT densities of the thyroid gland caused by radiation therapy. The aim was to investigate the relationship between the change in CT density of the thyroid gland before and after radiation therapy for head and neck cancer and hypothyroidism. This retrospective study analyzed data of 24 patients treated by radiation therapy for head and neck cancers. After dosimetric analysis of received radiation therapy, a Picture Archiving and Communication System was used to manually contour the thyroid on pre-treatment CT images to enable determination of mean thyroid gland CT densities and received radiation doses. Pre- and post-treatment thyroid function was assessed on the basis of serum TSH concentrations. Multivariate and univariate analyses were used to determine what clinical factors are associated with post-radiation therapy decrease in CT density of the thyroid and Pearson's χ 2 test was used to assess correlations between these densities and TSH concentrations. Mean CT densities of the thyroid gland decreased from before to after radiation therapy in 73.9% of our patients (median decrease 16.8 HU). Serum TSH concentrations were significantly higher in patients with greater then median decreases in CT density than in those with lesser or no decreases. Post-radiation therapy hypothyroidism may be predicted by significant decreases in CT density of the thyroid gland. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

ORDEM 3.0 and the Risk of High-Density Debris

NASA Technical Reports Server (NTRS)

Matney, Mark; Anz-Meador, Philip

2014-01-01

NASA’s Orbital Debris Engineering Model was designed to calculate orbital debris fluxes on spacecraft in order to assess collision risk. The newest of these models, ORDEM 3.0, has a number of features not present in previous models. One of the most important is that the populations and fluxes are now broken out into material density groups. Previous models concentrated on debris size alone, but a particle’s mass and density also determine the amount of damage it can cause. ORDEM 3.0 includes a high-density component, primarily consisting of iron/steel particles that drive much of the risk to spacecraft. This paper will outline the methods that were used to separate and identify the different densities of debris, and how these new densities affect the overall debris flux and risk.

Ocean Turbulence V: Mesoscale Modeling in Level Coordinates. The Effect of Random Nature of Density

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Dubovikov, M. S.

1998-01-01

The main result of this paper is the derivation of a new expression for the tracer subgrid term in level coordinates S(l) to be employed in O-GCM. The novel feature is the proper account of the random nature of the density field which strongly affects the transformation from isopycnal to level coordinates of the variables of interest, velocity and tracer fields, their correlation functions and ultimately the subgrid terms. In deriving our result we made use of measured properties of vertical ocean turbulence. The major new results are: 1) the new subgrid expression is different from that of the heuristic GM model, 2) u++(tracer)=1/2u+(thickness), where u++ and u+ are the tracer and thickness bolus velocities. In previous models, u++ = u+, 2) the subgrid for a tracer tau is not the same as that for the density rho even when one accounts for the obvious absence of a diffusion term in the latter. The difference stems from a new treatment of the stochastic nature of the density, 3) the mesoscale diffusivity enters both locally and non-locally, as the integral over all z's from the bottom of the ocean to the level z.

The 5-10 keV AGN luminosity function at 0.01 < z < 4.0

NASA Astrophysics Data System (ADS)

Fotopoulou, S.; Buchner, J.; Georgantopoulos, I.; Hasinger, G.; Salvato, M.; Georgakakis, A.; Cappelluti, N.; Ranalli, P.; Hsu, L. T.; Brusa, M.; Comastri, A.; Miyaji, T.; Nandra, K.; Aird, J.; Paltani, S.

2016-03-01

The active galactic nuclei (AGN) X-ray luminosity function traces actively accreting supermassive black holes and is essential for the study of the properties of the AGN population, black hole evolution, and galaxy-black hole coevolution. Up to now, the AGN luminosity function has been estimated several times in soft (0.5-2 keV) and hard X-rays (2-10 keV). AGN selection in these energy ranges often suffers from identification and redshift incompleteness and, at the same time, photoelectric absorption can obscure a significant amount of the X-ray radiation. We estimate the evolution of the luminosity function in the 5-10 keV band, where we effectively avoid the absorbed part of the spectrum, rendering absorption corrections unnecessary up to NH ~ 1023 cm-2. Our dataset is a compilation of six wide, and deep fields: MAXI, HBSS, XMM-COSMOS, Lockman Hole, XMM-CDFS, AEGIS-XD, Chandra-COSMOS, and Chandra-CDFS. This extensive sample of ~1110 AGN (0.01 < z < 4.0, 41 < log Lx < 46) is 98% redshift complete with 68% spectroscopic redshifts. For sources lacking a spectroscopic redshift estimation we use the probability distribution function of photometric redshift estimation specifically tuned for AGN, and a flat probability distribution function for sources with no redshift information. We use Bayesian analysis to select the best parametric model from simple pure luminosity and pure density evolution to more complicated luminosity and density evolution and luminosity-dependent density evolution (LDDE). We estimate the model parameters that describe best our dataset separately for each survey and for the combined sample. We show that, according to Bayesian model selection, the preferred model for our dataset is the LDDE. Our estimation of the AGN luminosity function does not require any assumption on the AGN absorption and is in good agreement with previous works in the 2-10 keV energy band based on X-ray hardness ratios to model the absorption in AGN up to redshift three. Our sample does not show evidence of a rapid decline of the AGN luminosity function up to redshift four.

Long-Term Effects of Acute Stress on the Prefrontal-Limbic System in the Healthy Adult

PubMed Central

Wei, Dongtao; Du, Xue; Zhang, Qinglin; Liu, Guangyuan; Qiu, Jiang

2017-01-01

Most people are exposed to at least one traumatic event during the course of their lives, but large numbers of people do not develop posttraumatic stress disorders. Although previous studies have shown that repeated and chronic stress change the brain’s structure and function, few studies have focused on the long-term effects of acute stressful exposure in a nonclinical sample, especially the morphology and functional connectivity changes in brain regions implicated in emotional reactivity and emotion regulation. Forty-one months after the 5/12 Wenchuan earthquake, we investigated the effects of trauma exposure on the structure and functional connectivity of the brains of trauma-exposed healthy individuals compared with healthy controls matched for age, sex, and education. We then used machine-learning algorithms with the brain structural features to distinguish between the two groups at an individual level. In the trauma-exposed healthy individuals, our results showed greater gray matter density in prefrontal-limbic brain systems, including the dorsal anterior cingulate cortex, medial prefrontal cortex, amygdala and hippocampus, than in the controls. Further analysis showed stronger amygdala-hippocampus functional connectivity in the trauma-exposed healthy compared to the controls. Our findings revealed that survival of traumatic experiences, without developing PTSD, was associated with greater gray matter density in the prefrontal-limbic systems related to emotional regulation. PMID:28045980

Model of random center vortex lines in continuous 2 +1 -dimensional spacetime

NASA Astrophysics Data System (ADS)

Altarawneh, Derar; Engelhardt, Michael; Höllwieser, Roman

2016-12-01

A picture of confinement in QCD based on a condensate of thick vortices with fluxes in the center of the gauge group (center vortices) is studied. Previous concrete model realizations of this picture utilized a hypercubic space-time scaffolding, which, together with many advantages, also has some disadvantages, e.g., in the treatment of vortex topological charge. In the present work, we explore a center vortex model which does not rely on such a scaffolding. Vortices are represented by closed random lines in continuous 2 +1 -dimensional space-time. These random lines are modeled as being piecewise linear, and an ensemble is generated by Monte Carlo methods. The physical space in which the vortex lines are defined is a torus with periodic boundary conditions. Besides moving, growing, and shrinking of the vortex configurations, also reconnections are allowed. Our ensemble therefore contains not a fixed but a variable number of closed vortex lines. This is expected to be important for realizing the deconfining phase transition. We study both vortex percolation and the potential V (R ) between the quark and antiquark as a function of distance R at different vortex densities, vortex segment lengths, reconnection conditions, and at different temperatures. We find three deconfinement phase transitions, as a function of density, as a function of vortex segment length, and as a function of temperature.

High-resolution molybdenum K-edge X-ray absorption spectroscopy analyzed with time-dependent density functional theory.

PubMed

Lima, Frederico A; Bjornsson, Ragnar; Weyhermüller, Thomas; Chandrasekaran, Perumalreddy; Glatzel, Pieter; Neese, Frank; DeBeer, Serena

2013-12-28

X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.

Search for the First-Order Liquid-to-Liquid Phase Transition in Low-Temperature Confined Water by Neutron Scattering

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

Chen, Sow-Hsin; Wang, Zhe; Kolesnikov, Alexander I

2013-01-01

It has been conjectured that a 1st order liquid-to-liquid (L-L) phase transition (LLPT) between high density liquid (HDL) and low density liquid (LDL) in supercooled water may exist, as a thermodynamic extension to the liquid phase of the 1st order transition established between the two bulk solid phases of amorphous ice, the high density amorphous ice (HDA) and the low density amorphous ice (LDA). In this paper, we first recall our previous attempts to establish the existence of the 1st order L-L phase transition through the use of two neutron scattering techniques: a constant Q elastic diffraction study of isobaricmore » temperature scan of the D2O density, namely, the equation of state (EOS) measurements. A pronounced density hysteresis phenomenon in the temperature scan of the density above P = 1500 bar is observed which gives a plausible evidence of crossing the 1st order L-L phase transition line above this pressure; an incoherent quasi-elastic scattering measurements of temperature-dependence of the alpha-relaxation time of H2O at a series of pressures, namely, the study of the Fragile-to-Strong dynamic crossover (FSC) phenomenon as a function of pressure which we interpreted as the results of crossing the Widom line in the one-phase region. In this new experiment, we used incoherent inelastic neutron scattering (INS) to measure the density of states (DOS) of H atoms in H2O molecules in confined water as function of temperature and pressure, through which we may be able to follow the emergence of the LDL and HDL phases at supercooled temperature and high pressures. We here report for the first time the differences of librational and translational DOSs between the hypothetical HDL and LDL phases, which are similar to the corresponding differences between the well-established HDA and LDA ices. This is plausible evidence that the HDL and LDL phases are the thermodynamic extensions of the corresponding amorphous solid water HDA and LDA ices.« less

Search for the first-order liquid-to-liquid phase transition in low-temperature confined water by neutron scattering

NASA Astrophysics Data System (ADS)

Chen, Sow-Hsin; Wang, Zhe; Kolesnikov, Alexander I.; Zhang, Yang; Liu, Kao-Hsiang

2013-02-01

It has been conjectured that a 1st order liquid-to-liquid (L-L) phase transition (LLPT) between high density liquid (HDL) and low density liquid (LDL) in supercooled water may exist, as a thermodynamic extension to the liquid phase of the 1st order transition established between the two bulk solid phases of amorphous ice, the high density amorphous ice (HDA) and the low density amorphous ice (LDA). In this paper, we first recall our previous attempts to establish the existence of the 1st order L-L phase transition through the use of two neutron scattering techniques: a constant Q elastic diffraction study of isobaric temperature scan of the D2O density, namely, the equation of state (EOS) measurements. A pronounced density hysteresis phenomenon in the temperature scan of the density above P = 1500 bar is observed which gives a plausible evidence of crossing the 1st order L-L phase transition line above this pressure; an incoherent quasi-elastic scattering measurements of temperature-dependence of the α-relaxation time of H2O at a series of pressures, namely, the study of the Fragile-to-Strong dynamic crossover (FSC) phenomenon as a function of pressure which we interpreted as the results of crossing the Widom line in the one-phase region. In this new experiment, we used incoherent inelastic neutron scattering (INS) to measure the density of states (DOS) of H atoms in H2O molecules in confined water as function of temperature and pressure, through which we may be able to follow the emergence of the LDL and HDL phases at supercooled temperature and high pressures. We here report for the first time the differences of librational and translational DOSs between the hypothetical HDL and LDL phases, which are similar to the corresponding differences between the well-established HDA and LDA ices. This is plausible evidence that the HDL and LDL phases are the thermodynamic extensions of the corresponding amorphous solid water HDA and LDA ices.