Optical absorption in B{sub 13} cluster: A time-dependent density functional approach
Shinde, Ravindra; Tayade, Meenakshi
2013-02-05
The linear optical absorption spectra of three isomers of planar boron cluster B{sub 13} are calculated using time-dependent spin-polarized density functional approach. The geometries of these cluster are optimized at the B3LYP/6-311+G* level of theory. Even though the isomers are almost degenerate, the calculated spectra are quite different, indicating a strong structure-property relationship. Therefore, these computed spectra can be used in the photo-absorption experiments to distinguish between different isomers of a cluster.
NASA Astrophysics Data System (ADS)
Steinke, I.; Hoose, C.; Möhler, O.; Connolly, P.; Leisner, T.
2015-04-01
Deposition nucleation experiments with Arizona Test Dust (ATD) as a surrogate for mineral dusts were conducted at the AIDA cloud chamber at temperatures between 220 and 250 K. The influence of the aerosol size distribution and the cooling rate on the ice nucleation efficiencies was investigated. Ice nucleation active surface site (INAS) densities were calculated to quantify the ice nucleation efficiency as a function of temperature, humidity and the aerosol surface area concentration. Additionally, a contact angle parameterization according to classical nucleation theory was fitted to the experimental data in order to relate the ice nucleation efficiencies to contact angle distributions. From this study it can be concluded that the INAS density formulation is a very useful tool to describe the temperature- and humidity-dependent ice nucleation efficiency of ATD particles. Deposition nucleation on ATD particles can be described by a temperature- and relative-humidity-dependent INAS density function ns(T, Sice) with ns(xtherm) = 1.88 ×105 · exp(0.2659 · xtherm) [m-2] , (1) where the temperature- and saturation-dependent function xtherm is defined as xtherm = -(T-273.2)+(Sice-1) ×100, (2) with the saturation ratio with respect to ice Sice >1 and within a temperature range between 226 and 250 K. For lower temperatures, xtherm deviates from a linear behavior with temperature and relative humidity over ice. Also, two different approaches for describing the time dependence of deposition nucleation initiated by ATD particles are proposed. Box model estimates suggest that the time-dependent contribution is only relevant for small cooling rates and low number fractions of ice-active particles.
Size dependence of yield strength simulated by a dislocation-density function dynamics approach
NASA Astrophysics Data System (ADS)
Leung, P. S. S.; Leung, H. S.; Cheng, B.; Ngan, A. H. W.
2015-04-01
The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ?4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ?4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ?2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16?000b), according to the weakest-link concept.
A consumer-resource approach to the density-dependent population dynamics of mutualism
Holland, J. Nathaniel; DeAngelis, Donald L.
2010-01-01
Like predation and competition, mutualism is now recognized as a consumer resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant- mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.
Why Density Dependent Propulsion?
NASA Technical Reports Server (NTRS)
Robertson, Glen A.
2011-01-01
In 2004 Khoury and Weltman produced a density dependent cosmology theory they call the Chameleon, as at its nature, it is hidden within known physics. The Chameleon theory has implications to dark matter/energy with universe acceleration properties, which implies a new force mechanism with ties to the far and local density environment. In this paper, the Chameleon Density Model is discussed in terms of propulsion toward new propellant-less engineering methods.
Guido, Ciro A; Jacquemin, Denis; Adamo, Carlo; Mennucci, Benedetta
2015-12-01
We critically analyze the performances of continuum solvation models when coupled to time-dependent density functional theory (TD-DFT) to predict solvent effects on both absorption and emission energies of chromophores in solution. Different polarization schemes of the polarizable continuum model (PCM), such as linear response (LR) and three different state specific (SS) approaches, are considered and compared. We show the necessity of introducing a SS model in cases where large electron density rearrangements are involved in the excitations, such as charge-transfer transitions in both twisted and quadrupolar compounds, and underline the very delicate interplay between the selected polarization method and the chosen exchange-correlation functional. This interplay originates in the different descriptions of the transition and ground/excited state multipolar moments by the different functionals. As a result, the choice of both the DFT functional and the solvent polarization scheme has to be consistent with the nature of the studied electronic excitation. PMID:26642990
Ion Collisions with Water Molecules: A Time-Dependent Density Functional Theory Approach
NASA Astrophysics Data System (ADS)
Kirchner, Tom; Murakami, Mitsuko; Horbatscha, Marko; Lüddeb, Hans Jürgen
2013-06-01
Collisions of simple ions from water molecules in the energy range of 10-5000 keV/amu are considered within an independent electron model. The basis generator method applied in the past successfully to ion-atom collisions is adapted to deal with molecular targets. Cross sections for single- and multiple-electron processes (capture and transfer to the continuum) are obtained directly from solving time-dependent Kohn-Sham-type orbital equations and using a Slater determinant based analysis. Fragmentation yields are predicted on the basis of a semi-phenomenological model which uses the calculated cross sections as input. Comparison with experiment is made for proton and He+He+ impact collisions.
Zhang, Xing; Herbert, John M.
2015-02-14
We revisit the formalism for analytic derivative couplings between excited states in time-dependent density functional theory (TDDFT). We derive and implement these couplings using quadratic response theory, then numerically compare this response-theory formulation to couplings implemented previously based on a pseudo-wavefunction formalism and direct differentiation of the Kohn-Sham determinant. Numerical results, including comparison to full configuration interaction calculations, suggest that the two approaches perform equally well for many molecular systems, provided that the underlying DFT method affords accurate potential energy surfaces. The response contributions are found to be important for certain systems with high symmetry, but can be calculated with only a moderate increase in computational cost beyond what is required for the pseudo-wavefunction approach. In the case of spin-flip TDDFT, we provide a formal proof that the derivative couplings obtained using response theory are identical to those obtained from the pseudo-wavefunction formulation, which validates our previous implementation based on the latter formalism.
NASA Astrophysics Data System (ADS)
Irani, E.; Sadighi-Bonabi, R.; Anvari, A.
2014-06-01
Three dimensional calculations of electronic dynamics of CH4 in a strong laser field are presented with time-dependent density-functional theory. Time evolution of dipole moment and electron localization function is presented. The dependence of dissociation rate on the laser characters is shown and optimal effective parameters are evaluated. The optimum field leads to 76% dissociation probability for GAUSSIAN envelope and 40 fs (FWHM) at 1016 W cm-2. The dissociation probability is calculated by optimum convolution of dual short pulses. By combining of field assisted dissociation process and Ehrenfest molecular dynamics, time variation of bond length, velocity and orientation effect are investigated.
Sakko, Arto; Hakala, Mikko; Haemaelaeinen, Keijo; Rubio, Angel
2010-11-07
We apply time-dependent density functional theory to study the valence electron excitations of molecules and generalize the typically used time-propagation scheme and Casida's method to calculate the full wavevector dependent response function. This allows the computational study of dipole-forbidden valence electron transitions and the dispersion of spectral weight as a function of the wavevector. The method provides a novel analysis tool for spectroscopic methods such as inelastic x-ray scattering and electron energy loss spectroscopy. We present results for benzene and CF{sub 3}Cl and make a comparison with experimental results.
Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel
2015-12-15
The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715
Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel
2015-01-01
The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electronâ€“photon interactions in terms of effective Kohnâ€“Sham potentials. In this work, we numerically construct the exact electronâ€“photon Kohnâ€“Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical lightâ€“matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715
Evolution in population parameters: density-dependent selection or density-dependent fitness?
Travis, Joseph; Leips, Jeff; Rodd, F Helen
2013-05-01
Density-dependent selection is one of earliest topics of joint interest to both ecologists and evolutionary biologists and thus occupies an important position in the histories of these disciplines. This joint interest is driven by the fact that density-dependent selection is the simplest form of feedback between an ecological effect of an organism's own making (crowding due to sustained population growth) and the selective response to the resulting conditions. This makes density-dependent selection perhaps the simplest process through which we see the full reciprocity between ecology and evolution. In this article, we begin by tracing the history of studying the reciprocity between ecology and evolution, which we see as combining the questions of evolutionary ecology with the assumptions and approaches of ecological genetics. In particular, density-dependent fitness and density-dependent selection were critical concepts underlying ideas about adaptation to biotic selection pressures and the coadaptation of interacting species. However, theory points to a critical distinction between density-dependent fitness and density-dependent selection in their influences on complex evolutionary and ecological interactions among coexisting species. Although density-dependent fitness is manifestly evident in empirical studies, evidence of density-dependent selection is much less common. This leads to the larger question of how prevalent and important density-dependent selection might really be. Life-history variation in the least killifish Heterandria formosa appears to reflect the action of density-dependent selection, and yet compelling evidence is elusive, even in this well-studied system, which suggests some important challenges for understanding density-driven feedbacks between ecology and evolution. PMID:23598362
NASA Astrophysics Data System (ADS)
Tawfik, Sherif A.; El-Sheikh, S. M.; Salem, N. M.
2011-05-01
We introduce a new simplified method for computing the electron field emission current in short carbon nanotubes and graphene sheets using ab-initio computation in slab-periodic simulation cells. The evolution of the wave functions using Time-Dependent Density Functional Theory is computed by utilizing the Crank-Nicholson propagator and using the Octopus code (Castro et al., 2006 [1]), where we skip the wave function relaxation step elaborated by Han et al. (2002) [2], and apply a norm-conserving wave propagation method instead of the norm-nonconserving seventh-order Taylor Expansion method used by Araidai et al. (2004) [3]. Our method is mainly geared towards reducing the time it takes to compute the wave function propagation and enhancing the calculation precision. We found that in pristine carbon nanotubes, the emitted charge tends to emerge mostly from electrons that are concentrated at the nanotube tip region. The charge beam concentrates into specific channel structures, showing the utility of carbon nanotubes in precision emission applications.
Density-dependent covariant energy density functionals
Lalazissis, G. A.
2012-10-20
Relativistic nuclear energy density functionals are applied to the description of a variety of nuclear structure phenomena at and away fromstability line. Isoscalar monopole, isovector dipole and isoscalar quadrupole giant resonances are calculated using fully self-consistent relativistic quasiparticle randomphase approximation, based on the relativistic Hartree-Bogoliubovmodel. The impact of pairing correlations on the fission barriers in heavy and superheavy nuclei is examined. The role of pion in constructing desnity functionals is also investigated.
The dynamics of density dependent population models.
Guckenheimer, J; Oster, G; Ipaktchi, A
1977-05-23
The dynamics of density-dependent population models can be extraordinarily complex as numerous authors have displayed in numerical simulations. Here we commence a theoretical analysis of the mathematical mechanisms underlying this complexity from the viewpoint of modern dynamical systems theory. After discussing the chaotic behavior of one-dimensional difference equations we proceed to illustrate the general theory on a density-dependent Leslie model with two age classes. The pattern of bofurcations away from the equilibrium point is investigated and the existence of a "strange attractor" is demonstrated--i.e. an attracting limit set which is neither an equilibrium nor a limit cycle. Near the strange attractor the system exhibits essentially random behavior. An approach to the statical analysis of the dynamics in the chaotic regime is suggested. We then generalize our conclusions to higher dimensions and continuous models (e.g. the nonlinear von Foerster equation). PMID:886232
A density-dependent Leslie matrix model.
Allen, L J
1989-08-01
A density-dependent Leslie matrix model introduced in 1948 by Leslie is mathematically analyzed. It is shown that the behavior is similar to that of the constant Leslie matrix. In the primitive case, the density-dependent Leslie matrix model has an asymptotic distribution corresponding to the logistic equation. However, in the imprimitive case, the asymptotic distribution is periodic, with period depending on the imprimitivity index. PMID:2520184
Wohlgemuth, Matthias; Bonaci?-Koutecký, Vlasta; Mitri?, Roland
2011-08-01
We present a combination of time-dependent density functional theory with the quantum mechanical/molecular mechanical approach which can be applied to study nonadiabatic dynamical processes in molecular systems interacting with the environment. Our method is illustrated on the example of ultrafast excited state dynamics of indole in water. We compare the mechanisms of nonradiative relaxation and the electronic state lifetimes for isolated indole, indole in a sphere of classical water, and indole + 3H(2)O embedded in a classical water sphere. In the case of isolated indole, the initial excitation to the S(2) electronic state is followed by an ultrafast internal conversion to the S(1) state with a time constant of 17 fs. The S(1) state is long living (>30 ps) and deactivates to the ground state along the N-H stretching coordinate. This deactivation mechanism remains unchanged for indole in a classical water sphere. However, the lifetimes of the S(2) and S(1) electronic states are extended. The inclusion of three explicit water molecules opens a new relaxation channel which involves the electron transfer to the solvent, leading eventually to the formation of a solvated electron. The relaxation to the ground state takes place on a time scale of 60 fs and contributes to the lowering of the fluorescence quantum yield. Our simulations demonstrate the importance of including explicit water molecules in the theoretical treatment of solvated systems. PMID:21823688
Density-dependent adjustment of inducible defenses.
Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C; Laforsch, Christian; Kopp, Michael
2015-01-01
Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators' densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428
Density-dependent adjustment of inducible defenses
Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C.; Laforsch, Christian; Kopp, Michael
2015-01-01
Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predatorsâ€™ densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428
Fragment-Based Time-Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Mosquera, MartÃn A.; Jensen, Daniel; Wasserman, Adam
2013-07-01
Using the Runge-Gross theorem that establishes the foundation of time-dependent density functional theory, we prove that for a given electronic Hamiltonian, choice of initial state, and choice of fragmentation, there is a unique single-particle potential (dubbed time-dependent partition potential) which, when added to each of the preselected fragment potentials, forces the fragment densities to evolve in such a way that their sum equals the exact molecular density at all times. This uniqueness theorem suggests new ways of computing the time-dependent properties of electronic systems via fragment-time-dependent density functional theory calculations. We derive a formally exact relationship between the partition potential and the total density, and illustrate our approach on a simple model system for binary fragmentation in a laser field.
Local density dependent potential for compressible mesoparticles.
Faure, Gérôme; Maillet, Jean-Bernard; Stoltz, Gabriel
2014-03-21
This work proposes a coarse grained description of molecular systems based on mesoparticles representing several molecules, where interactions between mesoparticles are modelled by an interparticle potential of molecular type. Since strong non-equilibrium situations over a wide range of pressure and density are targeted, the internal compressibility of the mesoparticles has to be considered. This is done by introducing a dependence of the potential on the local environment of the mesoparticles. To define local densities, we resort to a three-dimensional Voronoi tessellation instead of standard local, spherical averages. As an example, a local density dependent potential is fitted to reproduce the Hugoniot curve of a model of nitromethane over a large range of pressures and densities. PMID:24655170
The cosmological dependence of cluster density profiles
NASA Technical Reports Server (NTRS)
Crone, Mary M.; Evrard, August E.; Richstone, Douglas O.
1994-01-01
We use N-body simulations to study the shape of mean cluster density and velocity profiles in the nonlinear regime formed via gravitational instability. The dependence of the final structure on both cosmology and initial density field is examined, using a grid of cosmologies and scale-free initial power spectra P(k) varies as k(exp n). Einstein-de Sitter, open (Omega(sub 0) = 0.2 and 0.1) and flat, low density (Omega(sub 0) = 0.2 lambda(sub 0) = 0.8) models are examined, with initial spectral indices n = -2, -1 and 0. For each model, we stack clusters in an appropriately scaled manner to define an average density profile in the nonlinear regime. The profiles are well fit by a power law rho(r) varies as r(exp -alpha) for radii whereat the local density contrast is between 100 and 3000. This covers 99% of the cluster volume. We find a clear trend toward steeper slopes (larger alphas) with both increasing n and decreasing Omega(sub 0). The Omega(sub 0) dependence is partially masked by the n dependence; there is degeneracy in the values of alpha between the Einstein-de Sitter and flat, low-density cosmologies. However, the profile slopes in the open models are consistently higher than the Omega = 1 values for the range of n examined. Cluster density profiles are thus potentially useful cosmological diagnostics. We find no evidence for a constant density core in any of the models, although the density profiles do tend to flatten at small radii. Much of the flattening is due to the force softening required by the simulations. An attempt is made to recover the unsoftened profiles assuming angular momentum invariance. The recovered profiles in Einstein-de Sitter cosmologies are consistent with a pure power law up to the highest density contrasts (10(exp 6)) accessible with our resolution. The low-density models show significant deviation from a power law above density contrasts approximately 10(exp 5). We interpret this curvature as reflecting the non-scale-invariant nature of the background cosmology in these models. These results are at the limit of our resolution and so should be tested in the future using simulations with larger numbers of particles. Such simulations will also provide insight on the broader problem of understanding, in a statistical sense, the full phase space structure of collapsed, cosmological halos.
Size-dependent density of zirconia nanoparticles
Opalinska, Agnieszka; Dzwolak, Wojciech; Chudoba, Tadeusz; Presz, Adam; Lojkowski, Witold
2015-01-01
Summary The correlation between density and specific surface area of ZrO2 nanoparticles (NPs) was studied. The NPs were produced using a hydrothermal process involving microwave heating. The material was annealed at 1100 °C which resulted in an increase in the average grain size of the ZrO2 NPs from 11 to 78 nm and a decrease in the specific surface area from 97 to 15 m2/g. At the same time, the density increased from 5.22 g/m3 to 5.87 g/m3. This effect was interpreted to be the result of the presence of a hydroxide monolayer on the NP surface. A smaller ZrO2 grain size was correlated with a larger contribution of the low density surface layer to the average density. To prove the existence of such a layer, the material was synthesized using 50% heavy water. Fourier transform infrared spectroscopy (FTIR) permitted the identification of the –OD groups created during synthesis. It was found that the –OD groups persisted on the ZrO2 surface even after annealing at 1100 °C. This hydroxide layer is responsible for the decrease in the average density of the NPs as their size decreases. This study of the correlation between particle size and density may be used to assess the quality of the NPs. In most cases, the technological aim is to avoid an amorphous layer and to obtain fully crystalline nanoparticles with the highest density possible. However, due to the effect of the surface layers, there is a maximum density which can be achieved for a given average NP diameter. The effect of the surface layer on the NP density becomes particularly evident for NPs smaller than 50 nm, and thus, the density of nanoparticles is size dependent. PMID:25671149
Kityk, A V
2014-07-15
A long-range-corrected time-dependent density functional theory (LC-TDDFT) in combination with polarizable continuum model (PCM) have been applied to study charge transfer (CT) optical absorption and fluorescence emission energies basing on parameterized LC-BLYP xc-potential. The molecule of 4-(9-acridyl)julolidine selected for this study represents typical CT donor-acceptor dye with strongly solvent dependent optical absorption and fluorescence emission spectra. The result of calculations are compared with experimental spectra reported in the literature to derive an optimal value of the model screening parameter ?. The first absorption band appears to be quite well predictable within DFT/TDDFT/PCM with the screening parameter ? to be solvent independent (? ? 0.245 Bohr(-1)) whereas the fluorescence emission exhibits a strong dependence on the range separation with ?-value varying on a rising solvent polarity from about 0.225 to 0.151 Bohr(-1). Dipolar properties of the initial state participating in the electronic transition have crucial impact on the effective screening. PMID:24682050
Evolution of density-dependent cooperation.
SeppÃ¤nen, Anne; Parvinen, Kalle
2014-12-01
Cooperation is surprisingly common in life despite of its vulnerability to selfish cheating, i.e. defecting. Defectors do not contribute to common resources but take the advantage of cooperators' investments. Therefore, the emergence and maintenance of cooperation have been considered irrational phenomena. In this study, we focus on plastic, quantitative cooperation behaviour, especially on its evolution. We assume that individuals are capable to sense the population density in their neighbourhood and adjust their real-valued investments on public goods based on that information. The ecological setting is described with stochastic demographic events, e.g. birth and death, occurring at individual level. Individuals form small populations, which further constitute a structured metapopulation. For evolutionary investigations, we apply the adaptive dynamics framework. The cost of cooperative investment is incorporated into the model in two ways, by decreasing the birth rate or by increasing the death rate. In the first case, density-dependent cooperation evolves to be a decreasing function of population size as expected. In the latter case, however, the density-dependent cooperative investment can have a qualitatively different form as it may evolve to be highest in intermediate-sized populations. Indeed, we emphasize that some details in modelling may have a significant impact on the results obtained. PMID:25213153
Density-dependent diversification in North American wood warblers.
Rabosky, Daniel L; Lovette, Irby J
2008-10-22
Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model. PMID:18611849
Sublinear scaling for time-dependent stochastic density functional theory
Gao, Yi; Neuhauser, Daniel; Baer, Roi; Rabani, Eran
2015-01-21
A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (â‰ˆ16) of such orbitals is enough to obtain meaningful results for absorption spectrum and the RPA correlation energy per electron. We implement the approach for silicon nanocrystals using real-space grids and find that the overall scaling of the algorithm is sublinear with computational time and memory.
Density-Dependent Cladogenesis in Birds
Phillimore, Albert B; Price, Trevor D
2008-01-01
A characteristic signature of adaptive radiation is a slowing of the rate of speciation toward the present. On the basis of molecular phylogenies, studies of single clades have frequently found evidence for a slowdown in diversification rate and have interpreted this as evidence for density dependent speciation. However, we demonstrated via simulation that large clades are expected to show stronger slowdowns than small clades, even if the probability of speciation and extinction remains constant through time. This is a consequence of exponential growth: clades, which, by chance, diversify at above the average rate early in their history, will tend to be large. They will also tend to regress back to the average diversification rate later on, and therefore show a slowdown. We conducted a meta-analysis of the distribution of speciation events through time, focusing on sequence-based phylogenies for 45 clades of birds. Thirteen of the 23 clades (57%) that include more than 20 species show significant slowdowns. The high frequency of slowdowns observed in large clades is even more extreme than expected under a purely stochastic constant-rate model, but is consistent with the adaptive radiation model. Taken together, our data strongly support a model of density-dependent speciation in birds, whereby speciation slows as ecological opportunities and geographical space place limits on clade growth. PMID:18366256
Variational minimization of orbital-density-dependent functionals
NASA Astrophysics Data System (ADS)
Borghi, Giovanni; Park, Cheol-Hwan; Nguyen, Ngoc Linh; Ferretti, Andrea; Marzari, Nicola
2015-04-01
Orbital-density-dependent functionals, such as the Perdew-Zunger or the Koopmans-compliant functionals, are used to remove unphysical self-interaction energies and to restore missing piece-wise linearity in approximate formulations of density-functional theory (DFT). At variance with functionals of the total density, orbital-density-dependent functionals are typically not invariant with respect to unitary transformations of the occupied states. Such additional degrees of freedom require an extension of established approaches for direct minimization that preserve their numerical robustness and efficiency, and make it possible to apply these advanced electronic-structure functionals to large or complex systems. In this work we adapt the ensemble-DFT algorithm [N. Marzari, D. Vanderbilt, and M. C. Payne, Phys. Rev. Lett. 79, 1337 (1997), 10.1103/PhysRevLett.79.1337] to the case of orbital-density-dependent functionals, partitioning the variational problem into a nested loop of (i) minimizations with respect to unitary transformations at a fixed orbital manifold, that lead to a projected, unitary-covariant functional of the orbitals only that enforces the Pederson condition and (ii) variational optimization of the orbital manifold for this projected functional. We discuss in detail both general and functional-dependent trends and suggest a procedure to efficiently exploit the combination of the different minimization strategies. The overall formulation allows for a stable, robust, and efficient algorithm, yielding great improvements over conventional techniques.
Selective fishing induces density-dependent growth
Svedäng, Henrik; Hornborg, Sara
2014-01-01
Over the last decades, views on fisheries management have oscillated between alarm and trust in management progress. The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort. Here we report a case study on how striving for higher yields from the Eastern Baltic cod stock by increasing selectivity has become exceedingly detrimental for its productivity. Although there is a successive increase in numbers of undersized fish, growth potential is severely reduced, and fishing mortality in fishable size has increased. Once density-dependent growth is introduced, the process is self-enforcing as long as the recruitment remains stable. Our findings suggest that policies focusing on maximum yield while targeting greater sizes are risky and should instead prioritize catch rates over yield. Disregarding the underlying population structure may jeopardize stock productivity, with dire consequences for the fishing industry and ecosystem structure and function. PMID:24920387
Selective fishing induces density-dependent growth.
Svedäng, Henrik; Hornborg, Sara
2014-01-01
Over the last decades, views on fisheries management have oscillated between alarm and trust in management progress. The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort. Here we report a case study on how striving for higher yields from the Eastern Baltic cod stock by increasing selectivity has become exceedingly detrimental for its productivity. Although there is a successive increase in numbers of undersized fish, growth potential is severely reduced, and fishing mortality in fishable size has increased. Once density-dependent growth is introduced, the process is self-enforcing as long as the recruitment remains stable. Our findings suggest that policies focusing on maximum yield while targeting greater sizes are risky and should instead prioritize catch rates over yield. Disregarding the underlying population structure may jeopardize stock productivity, with dire consequences for the fishing industry and ecosystem structure and function. PMID:24920387
Ohlberger, Jan; Rogers, Lauren A.; Stenseth, Nils Chr.
2014-01-01
A persistent debate in population ecology concerns the relative importance of environmental stochasticity and density dependence in determining variability in adult year-class strength, which contributes to future reproduction as well as potential yield in exploited populations. Apart from the strength of the processes, the timing of density regulation may affect how stochastic variation, for instance through climate, translates into changes in adult abundance. In this study, we develop a life-cycle model for the population dynamics of a large marine fish population, Northeast Arctic cod, to disentangle the effects of density-independent and density-dependent processes on early life-stages, and to quantify the strength of compensatory density dependence in the population. The model incorporates information from scientific surveys and commercial harvest, and dynamically links multiple effects of intrinsic and extrinsic factors on all life-stages, from eggs to spawners. Using a state-space approach we account for observation error and stochasticity in the population dynamics. Our findings highlight the importance of density-dependent survival in juveniles, indicating that this period of the life cycle largely determines the compensatory capacity of the population. Density regulation at the juvenile life-stage dampens the impact of stochastic processes operating earlier in life such as environmental impacts on the production of eggs and climate-dependent survival of larvae. The timing of stochastic versus regulatory processes thus plays a crucial role in determining variability in adult abundance. Quantifying the contribution of environmental stochasticity and compensatory mechanisms in determining population abundance is essential for assessing population responses to climate change and exploitation by humans. PMID:24893001
Density-Dependent Metabolic Heterogeneity in Human Mesenchymal Stem Cells.
Liu, Yijun; Muñoz, Nathalie; Bunnell, Bruce A; Logan, Timothy M; Ma, Teng
2015-11-01
Human mesenchymal stem cells (hMSCs) are intrinsically heterogeneous and comprise subpopulations that differ in their proliferation, multi-potency, and functional properties, which are commonly demonstrated by culturing hMSCs at different plating densities. The objective of this study was to investigate the metabolic profiles of different subpopulations of hMSC by testing the hypothesis that the clonogenic hMSC subpopulation, which is selectively enriched in clonal density (CD) and low density (LD) culture (10 and 100 cells per square centimeter, respectively), possesses a metabolic phenotype that differs from that of hMSC in medium- or high-density (MD: 1,000 and HD: 3,000 cells per square centimeter, respectively). Cells at CD and LD conditions exhibited elevated expression of CD146 and colony forming unit-fibroblast compared with cells at MD- or HD. Global metabolic profiles revealed by gas chromatography-mass spectrometry of cell extracts showed clear distinction between LD and HD cultures, and density-dependent differences in coupling of glycolysis to the TCA cycle. Metabolic inhibitors revealed density-dependent differences in glycolysis versus oxidative phosphorylation (OXPHOS) for ATP generation, in glutamine metabolism, in the dependence on the pentose phosphate pathway for maintaining cellular redox state, and sensitivity to exogenous reactive oxygen species. We also show that active OXPHOS is not required for proliferation in LD culture but that OXPHOS activity increases senescence in HD culture. Together, the results revealed heterogeneity in hMSC culture exists at the level of primary metabolism. The unique metabolic characteristics of the clonogenic subpopulation suggest a novel approach for optimizing in vitro expansion of hMSCs. Stem Cells 2015;33:3368-3381. PMID:26274841
Pernal, Katarzyna
2012-05-14
Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other excitations is in general much better than that offered by TD-DFT-LDA or TD-DMFT-BB approximations if the range-separation parameter is properly chosen. The latter remains an open problem. PMID:22583275
Simulating Density-Dependent Flows Using the Lattice Boltzmann Method
NASA Astrophysics Data System (ADS)
Bardsley, K. J.; Sukop, M. C.
2008-05-01
Seawater intrusion is a classic density-dependent problem in hydrogeology. It must be fully understood in order to be able to predict and prevent groundwater deterioration in coastal areas. Although there is extensive research on this topic, more tools are required to fully understand and predict the location and behavior of the freshwater/seawater boundary. Due to the difficulty of sampling, one widely used method to obtain this information is numerical modeling. Various software programs have been developed and are being used to model coupled fluid flow and solute transport for density-dependent applications. All of the current programs are either finite difference or finite element methods. Density-dependent flow problems are exceptionally challenging for conventional numerical methods due to inherent non-linearity; definitive solutions are often elusive and a completely different modeling approach may be advantageous. The lattice Boltzmann method represents such a radically different numerical tool because it is not based on discretization of a series of differential equations. Instead, its foundation lies in the kinetic theory of gasses as proposed by Boltzmann. Recent advances in lattice Boltzmann modeling permit simulation of large-scale density-dependent ground water flow and heat/solute transport. A key advantage of lattice Boltzmann method is that it has the ability to solve the Navier-Stokes equations in larger conduits and pores. Hence it allows for eddy diffusion brought on by inertial components of flow at higher Reynolds numbers, which may occur in some coastal aquifers. Simulation of these phenomena is not possible with traditional Darcy's law-based groundwater models. Some geologists and engineers have been able to successfully apply lattice Boltzmann methods to fluid flow and contaminant transport problems. There are only a handful of scientists attempting to apply lattice Boltzmann methods to density-dependent flows in general; even fewer have considered seawater intrusion. Almost all previous simulations were conducted in closed or periodic domains. We simulate temperature- or concentration-induced density-dependent flows in domains with boundary conditions such as constant flow and hydrostatic pressure that are relevant to real-world systems with lattice Boltzmann models and compare with other solutions.
Statistical approach to nuclear level density
Sen'kov, R. A.; Horoi, M.; Zelevinsky, V. G.
2014-10-15
We discuss the level density in a finite many-body system with strong interaction between the constituents. Our primary object of applications is the atomic nucleus but the same techniques can be applied to other mesoscopic systems. We calculate and compare nuclear level densities for given quantum numbers obtained by different methods, such as nuclear shell model (the most successful microscopic approach), our main instrument - moments method (statistical approach), and Fermi-gas model; the calculation with the moments method can use any shell-model Hamiltonian excluding the spurious states of the center-of-mass motion. Our goal is to investigate statistical properties of nuclear level density, define its phenomenological parameters, and offer an affordable and reliable way of calculation.
NASA Astrophysics Data System (ADS)
Iakovlev, Anton; Bedrov, Dmitry; MÃ¼ller, Marcus
2015-12-01
Motivated by growing interest in interfacial properties of liquid mercury we investigate by atomistic Molecular Dynamics simulation the ability of density-independent, empiric density-dependent, and recently proposed embedded-atom force fields to predict the surface tension and coexistence density of liquid mercury at room temperature, 293 K. The effect of the density dependence of the studied models on the liquid-vapor coexistence and surface tension is discussed in detail and our results are corroborated by Monte Carlo simulations and semi-analytic liquid-state theory. The latter approach is particularly useful to identify and rationalize artifacts that arise from an ad-hoc generalization of density-independent potentials by introducing density-dependent coefficients. In view of computational efficiency and thermodynamic robustness of density-independent model we optimize its functional form to obtain higher surface tension values in order to improve agreement with experiment.
Density dependence in Caenorhabditis larval starvation
Artyukhin, Alexander B.; Schroeder, Frank C.; Avery, Leon
2013-01-01
Availability of food is often a limiting factor in nature. Periods of food abundance are followed by times of famine, often in unpredictable patterns. Reliable information about the environment is a critical ingredient of successful survival strategy. One way to improve accuracy is to integrate information communicated by other organisms. To test whether such exchange of information may play a role in determining starvation survival strategies, we studied starvation of L1 larvae in C. elegans and other Caenorhabditis species. We found that some species in genus Caenorhabditis, including C. elegans, survive longer when starved at higher densities, while for others survival is independent of the density. The density effect is mediated by chemical signal(s) that worms release during starvation. This starvation survival signal is independent of ascarosides, a class of small molecules widely used in chemical communication of C. elegans and other nematodes. PMID:24071624
Simulating density-dependent flows using the lattice Boltzmann method
NASA Astrophysics Data System (ADS)
Bardsley, K. J.; Sukop, M. C.
2008-12-01
Seawater intrusion is a classic density-dependent problem in hydrogeology. It must be fully understood in order to be able to predict and prevent groundwater deterioration in coastal areas. All of the current programs used to study this issue are either finite difference or finite element methods. Density-dependent flow problems are exceptionally challenging for conventional numerical methods due to inherent non-linearity; definitive solutions are often elusive and a completely different modeling approach may be advantageous. The lattice Boltzmann method (LBM) represents such a numerical tool because it is not based on discretization of a series of differential equations. Instead, its foundation lies in the kinetic theory of gasses as proposed by Boltzmann. A key advantage of lattice Boltzmann method is that it has the ability to solve the Navier-Stokes equations in larger conduits and pores. Recent advances in lattice Boltzmann modeling permit simulation of large-scale density-dependent ground water flow and heat/solute transport. These simulations can be accomplished while retaining the advantages of 'regular' lattice Boltzmann methods, such as solute/heat transport at high Reynolds numbers. Hence it allows for eddy diffusion brought on by inertial components of flow at higher Reynolds numbers, which may occur in some coastal aquifers. This may prove to be an advantage for freshwater/seawater interface simulations especially given the highly macroporous nature of the aquifers underlying south Florida. Simulation of these phenomena is not possible with traditional Darcy's law-based groundwater models. Some geologists and engineers have been able to successfully apply LBM to fluid flow and contaminant transport problems. There are only a handful of scientists attempting to apply LBM to density-dependent flows in general; even fewer have considered seawater intrusion. We show how this method can be applied to density-dependent flows. We present two sets of results. The first are the results for the Horton-Rogers-Lapwood problem, where heat is the cause of varying density. The second are our results for a seawater intrusion simulation, a Henry-like problem.
THE DEPENDENCE OF STAR FORMATION EFFICIENCY ON GAS SURFACE DENSITY
Burkert, Andreas; Hartmann, Lee E-mail: lhartm@umich.edu
2013-08-10
Studies by Lada et al. and Heiderman et al. have suggested that star formation mostly occurs above a threshold in gas surface density {Sigma} of {Sigma}{sub c} {approx} 120 M{sub Sun} pc{sup -2} (A{sub K} {approx} 0.8). Heiderman et al. infer a threshold by combining low-mass star-forming regions, which show a steep increase in the star formation rate per unit area {Sigma}{sub SFR} with increasing {Sigma}, and massive cores forming luminous stars which show a linear relation. We argue that these observations do not require a particular density threshold. The steep dependence of {Sigma}{sub SFR}, approaching unity at protostellar core densities, is a natural result of the increasing importance of self-gravity at high densities along with the corresponding decrease in evolutionary timescales. The linear behavior of {Sigma}{sub SFR} versus {Sigma} in massive cores is consistent with probing dense gas in gravitational collapse, forming stars at a characteristic free-fall timescale given by the use of a particular molecular tracer. The low-mass and high-mass regions show different correlations between gas surface density and the area A spanned at that density, with A {approx} {Sigma}{sup -3} for low-mass regions and A {approx} {Sigma}{sup -1} for the massive cores; this difference, along with the use of differing techniques to measure gas surface density and star formation, suggests that connecting the low-mass regions with massive cores is problematic. We show that the approximately linear relationship between dense gas mass and stellar mass used by Lada et al. similarly does not demand a particular threshold for star formation and requires continuing formation of dense gas. Our results are consistent with molecular clouds forming by galactic hydrodynamic flows with subsequent gravitational collapse.
Elevational variation in density dependence in a subtropical forest
Xu, Meng; Yu, Shixiao
2014-01-01
Density-dependent mortality has been recognized as an important mechanism that underpins tree species diversity, especially in tropical forests. However, few studies have attempted to explore how density dependence varies with spatial scale and even fewer have attempted to identify why there is scale-dependent differentiation. In this study, we explore the elevational variation in density dependence. Three 1-ha permanent plots were established at low and high elevations in the Heishiding subtropical forest, southern China. Using data from 1200 1 m2 seedling quadrats, comprising of 200 1 m2 quadrats located in each 1-ha plot, we examined the variation in density dependence between elevations using a generalized linear mixed model with crossed random effects. A greenhouse experiment also investigated the potential effects of the soil biota on density-dependent differentiation. Our results demonstrated that density-dependent seedling mortality can vary between elevations in subtropical forests. Species found at a lower elevation suffered stronger negative density dependence than those found at a higher elevation. The greenhouse experiment indicated that two species that commonly occur at both elevations suffered more from soilborne pathogens during seed germination and seedling growth when they grew at the lower elevation, which implied that soil pathogens may play a crucial role in density-dependent spatial variation. PMID:25165522
Density-dependent growth in invasive Lionfish (Pterois volitans).
Benkwitt, Cassandra E
2013-01-01
Direct demographic density dependence is necessary for population regulation and is a central concept in ecology, yet has not been studied in many invasive species, including any invasive marine fish. The red lionfish (Pterois volitans) is an invasive predatory marine fish that is undergoing exponential population growth throughout the tropical western Atlantic. Invasive lionfish threaten coral-reef ecosystems, but there is currently no evidence of any natural population control. Therefore, a manipulative field experiment was conducted to test for density dependence in lionfish. Juvenile lionfish densities were adjusted on small reefs and several demographic rates (growth, recruitment, immigration, and loss) were measured throughout an 8-week period. Invasive lionfish exhibited direct density dependence in individual growth rates, as lionfish grew slower at higher densities throughout the study. Individual growth in length declined linearly with increasing lionfish density, while growth in mass declined exponentially with increasing density. There was no evidence, however, for density dependence in recruitment, immigration, or loss (mortality plus emigration) of invasive lionfish. The observed density-dependent growth rates may have implications for which native species are susceptible to lionfish predation, as the size and type of prey that lionfish consume is directly related to their body size. The absence of density-dependent loss, however, contrasts with many native coral-reef fish species and suggests that for the foreseeable future manual removals may be the only effective local control of this invasion. PMID:23825604
Density-Dependent Growth in Invasive Lionfish (Pterois volitans)
Benkwitt, Cassandra E.
2013-01-01
Direct demographic density dependence is necessary for population regulation and is a central concept in ecology, yet has not been studied in many invasive species, including any invasive marine fish. The red lionfish (Pterois volitans) is an invasive predatory marine fish that is undergoing exponential population growth throughout the tropical western Atlantic. Invasive lionfish threaten coral-reef ecosystems, but there is currently no evidence of any natural population control. Therefore, a manipulative field experiment was conducted to test for density dependence in lionfish. Juvenile lionfish densities were adjusted on small reefs and several demographic rates (growth, recruitment, immigration, and loss) were measured throughout an 8-week period. Invasive lionfish exhibited direct density dependence in individual growth rates, as lionfish grew slower at higher densities throughout the study. Individual growth in length declined linearly with increasing lionfish density, while growth in mass declined exponentially with increasing density. There was no evidence, however, for density dependence in recruitment, immigration, or loss (mortality plus emigration) of invasive lionfish. The observed density-dependent growth rates may have implications for which native species are susceptible to lionfish predation, as the size and type of prey that lionfish consume is directly related to their body size. The absence of density-dependent loss, however, contrasts with many native coral-reef fish species and suggests that for the foreseeable future manual removals may be the only effective local control of this invasion. PMID:23825604
Density dependence of the nuclear symmetry energy: A microscopic perspective
Vidana, Isaac; Providencia, Constanca; Polls, Artur; Rios, Arnau
2009-10-15
We perform a systematic analysis of the density dependence of nuclear symmetry energy within the microscopic Brueckner-Hartree-Fock (BHF) approach using the realistic Argonne V18 nucleon-nucleon potential plus a phenomenological three-body force of Urbana type. Our results are compared thoroughly with those arising from several Skyrme and relativistic effective models. The values of the parameters characterizing the BHF equation of state of isospin asymmetric nuclear matter fall within the trends predicted by those models and are compatible with recent constraints coming from heavy ion collisions, giant monopole resonances, or isobaric analog states. In particular we find a value of the slope parameter L=66.5 MeV, compatible with recent experimental constraints from isospin diffusion, L=88{+-}25 MeV. The correlation between the neutron skin thickness of neutron-rich isotopes and the slope L and curvature K{sub sym} parameters of the symmetry energy is studied. Our BHF results are in very good agreement with the correlations already predicted by other authors using nonrelativistic and relativistic effective models. The correlations of these two parameters and the neutron skin thickness with the transition density from nonuniform to {beta}-stable matter in neutron stars are also analyzed. Our results confirm that there is an inverse correlation between the neutron skin thickness and the transition density.
Information density and dependency length as complementary cognitive models.
Collins, Michael Xavier
2014-10-01
Certain English constructions permit two syntactic alternations. (1) a. I looked up the number. b. I looked the number up. (2) a. He is often at the office. b. He often is at the office. This study investigates the relationship between syntactic alternations and processing difficulty. What cognitive mechanisms are responsible for our attraction to some alternations and our aversion to others?This article reviews three psycholinguistic models of the relationship between syntactic alternations and processing: Maximum Per Word Surprisal (building on the ideas of Hale, in Proceedings of the 2nd Meeting of the North American chapter of the association for computational linguistics. Association for Computational Linguistics, Pittsburgh, PA, pp 159-166, 2001), Uniform Information Density (UID) (Levy and Jaeger in Adv Neural Inf Process Syst 19:849-856, 2007; inter alia), and Dependency Length Minimization (DLM) (Gildea and Temperley in Cognit Sci 34:286-310, 2010). Each theory makes predictions about which alternations native speakers should favor. Subjects were recruited using Amazon Mechanical Turk and asked to judge which of two competing syntactic alternations sounded more natural. Logistic regression analysis on the resulting data suggests that both UID and DLM are powerful predictors of human preferences. We conclude that alternations that approach uniform information density and minimize dependency length are easier to process than those that do not. PMID:24077911
Excitons in time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Ullrich, Carsten
2014-03-01
Excitons are the dominant feature in the optical spectra of insulators and semiconductors close to the absorption edge. They are collective excitations of the many-body system, but can often be discussed in a simplified picture as bound electron-hole pairs. To describe excitons in bulk materials with time-dependent density-functional theory (TDDFT), exchange-correlation functionals with a proper long-range behavior are required. The first part of this talk will present a TDDFT approach for directly calculating singlet and triplet exciton binding energies, which is based on an adaptation of the Casida formalism for periodic solids. Several exchange-correlation kernels have been tested for a variety of semiconductors and large-gap insulators. The second part of this talk will discuss a method to visualize exciton dynamics in large organic molecules in real time, based on the time-dependent transition density matrix. The method is applied to study the optical properties of intramolecular charge-transfer excitons in photoexcited molecular donor-acceptor systems that are of interest in organic photovoltaics. This work has been supported by NSF Grant DMR-1005651.
NASA Astrophysics Data System (ADS)
Kimura, Y.; Yoshimura, Y.; Nakahara, M.
1989-08-01
We studied the dimerization equilibrium of 2-methyl-2-nitrosopropane in argon at 25.0 °C from about 500 to 1200 kg m-3. It is clarified that in the simplest solvent, argon, there exists a definite difference in the density dependence of the equilibrium constant between the high and medium density regions. In the high density region, the equilibrium constant shows a sizable increase with the solvent density as in the liquid phase. Near the critical density, however, the equilibrium constant shows little density dependence.
Kobryn, Alexander E; Yamaguchi, Tsuyoshi; Hirata, Fumio
2005-05-01
We present results of the theoretical study and numerical calculation of the dynamics of molecular liquids based on the combination of the memory equation formalism and the reference interaction site model (RISM). Memory equations for the site-site intermediate scattering functions are studied in the mode-coupling approximation for the first-order memory kernels, while equilibrium properties such as site-site static structure factors are deduced from RISM. The results include the temperature-density (pressure) dependence of translational diffusion coefficients D and orientational relaxation times tau for acetonitrile in water, methanol in water, and methanol in acetonitrile--all in the limit of infinite dilution. Calculations are performed over the range of temperatures and densities employing the extended simple point charge model for water and optimized site-site potentials for acetonitrile and methanol. The theory is able to reproduce qualitatively all main features of temperature and density dependences of D and tau observed in real and computer experiments. In particular, anomalous behavior, i.e, the increase in mobility with density, is observed for D and tau of methanol in water, while acetonitrile in water and methanol in acetonitrile do not show deviations from the ordinary behavior. The variety exhibited by the different solute-solvent systems in the density dependence of the mobility is interpreted in terms of the two competing origins of friction, which interplay with each other as density increases: the collisional and dielectric frictions which, respectively, increase and decrease with increasing density. PMID:15918733
Density-dependent acoustic properties of PBX 9502
Brown, Geoffrey W; Thompson, Darla G; Deluca, Racci; Hartline, Ernest L; Hagelberg, Stephanie I
2009-07-31
We have measured the longitudinal and shear acoustic velocities of PBX 9502 as a function of density for die-pressed samples over the range 1.795 g/cc to 1.888 g/cc. The density dependence of the velocities is linear. Thermal cycling of PBX 9502 is known to induce irreversible volume growth. We have measured this volume growth dependence on density for a subset of the pressed parts and find that the most growth occurs for the samples with lowest initial density. The acoustic velocity changes due to the volume growth are significant and reflect damage in the samples.
Constraints on the density dependence of the symmetry energy.
Tsang, M B; Zhang, Yingxun; Danielewicz, P; Famiano, M; Li, Zhuxia; Lynch, W G; Steiner, A W
2009-03-27
Collisions involving 112Sn and 124Sn nuclei have been simulated with the improved quantum molecular dynamics transport model. The results of the calculations reproduce isospin diffusion data from two different observables and the ratios of neutron and proton spectra. By comparing these data to calculations performed over a range of symmetry energies at saturation density and different representations of the density dependence of the symmetry energy, constraints on the density dependence of the symmetry energy at subnormal density are obtained. The results from the present work are compared to constraints put forward in other recent analyses. PMID:19392271
Density dependence of reactor performance with thermal confinement scalings
Stotler, D.P.
1992-03-01
Energy confinement scalings for the thermal component of the plasma published thus far have a different dependence on plasma density and input power than do scalings for the total plasma energy. With such thermal scalings, reactor performance (measured by Q, the ratio of the fusion power to the sum of the ohmic and auxiliary input powers) worsens with increasing density. This dependence is the opposite of that found using scalings based on the total plasma energy, indicating that reactor operation concepts may need to be altered if this density dependence is confirmed in future research.
Time dependent density functional calculation of plasmon response in clusters
NASA Astrophysics Data System (ADS)
Wang, Feng; Zhang, Feng-Shou; Eric, Suraud
2003-02-01
We have introduced a theoretical scheme for the efficient description of the optical response of a cluster based on the time-dependent density functional theory. The practical implementation is done by means of the fully fledged time-dependent local density approximation scheme, which is solved directly in the time domain without any linearization. As an example we consider the simple Na2 cluster and compute its surface plasmon photoabsorption cross section, which is in good agreement with the experiments.
Dynamical instabilities in density-dependent hadronic relativistic models
Santos, A. M.; Brito, L.; Providencia, C.
2008-04-15
Unstable modes in asymmetric nuclear matter (ANM) at subsaturation densities are studied in the framework of relativistic mean-field density-dependent hadron models. The size of the instabilities that drive the system are calculated and a comparison with results obtained within the nonlinear Walecka model is presented. The distillation and antidistillation effects are discussed.
Walsh, Rachael K.; Aguilar, Cristobal L.; Facchinelli, Luca; Valerio, Laura; Ramsey, Janine M.; Scott, Thomas W.; Lloyd, Alun L.; Gould, Fred
2013-01-01
Transgenic strains of Aedes aegypti have been engineered to help control transmission of dengue virus. Although resources have been invested in developing the strains, we lack data on the ecology of mosquitoes that could impact the success of this approach. Although studies of intra-specific competition have been conducted using Ae. aegypti larvae, none of these studies examine mixed age cohorts at densities that occur in the field, with natural nutrient levels. Experiments were conducted in Mexico to determine the impact of direct and delayed density dependence on Ae. aegypti populations. Natural water, food, and larval densities were used to estimate the impacts of density dependence on larval survival, development, and adult body size. Direct and delayed density-dependent factors had a significant impact on larval survival, larval development, and adult body size. These results indicate that control methods attempting to reduce mosquito populations may be counteracted by density-dependent population regulation. PMID:23669230
Evolution of positive and negative density-dependent dispersal
Rodrigues, António M. M.; Johnstone, Rufus A.
2014-01-01
Understanding the evolution of density-dependent dispersal strategies has been a major challenge for evolutionary ecologists. Some existing models suggest that selection should favour positive and others negative density-dependence in dispersal. Here, we develop a general model that shows how and why selection may shift from positive to negative density-dependence in response to key ecological factors, in particular the temporal stability of the environment. We find that in temporally stable environments, particularly with low dispersal costs and large group sizes, habitat heterogeneity selects for negative density-dependent dispersal, whereas in temporally variable environments, particularly with high dispersal costs and small group sizes, habitat heterogeneity selects for positive density-dependent dispersal. This shift reflects the changing balance between the greater competition for breeding opportunities in more productive patches, versus the greater long-term value of offspring that establish themselves there, the latter being very sensitive to the temporal stability of the environment. In general, dispersal of individuals out of low-density patches is much more sensitive to habitat heterogeneity than is dispersal out of high-density patches. PMID:25100700
DSA planarization approach to solve pattern density issue
NASA Astrophysics Data System (ADS)
Pimenta Barros, P.; Gharbi, A.; Sarrazin, A.; Tiron, R.; Posseme, N.; Barnola, S.; Bos, S.; Tallaron, C.; Claveau, G.; Chevalier, X.; Argoud, M.; Servin, I.; Navarro, C.; Nicolet, C.; Lapeyre, C.; Monget, C.
2015-03-01
Directed Self-Assembly (DSA) of Block Copolymers (BCP) is one of the most promising solutions for sub-10 nm nodes. However, some challenges need to be addressed for a complete adoption of DSA in manufacturing such as achieving DSA-friendly design, low defectivity and accurate pattern placement. In this paper, we propose to discuss the DSA integration flows using graphoepitaxy for contact-hole patterning application. DSA process dependence on guiding pattern density has been studied and solved thanks to a new approach called "DSA planarization". The capabilities of this new approach have been evaluated in terms of defectivity, Critical Dimension (CD) control and uniformity before and after DSA etching transfer.
Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird
Dunn, Jenny C.; Hamer, Keith C.; Benton, Tim G.
2015-01-01
Land management intrinsically influences the distribution of animals and can consequently alter the potential for density-dependent processes to act within populations. For declining species, high densities of breeding territories are typically considered to represent productive populations. However, as density-dependent effects of food limitation or predator pressure may occur (especially when species are dependent upon separate nesting and foraging habitats), high territory density may limit per-capita productivity. Here, we use a declining but widespread European farmland bird, the yellowhammer Emberiza citrinella L., as a model system to test whether higher territory densities result in lower fledging success, parental provisioning rates or nestling growth rates compared to lower densities. Organic landscapes held higher territory densities, but nests on organic farms fledged fewer nestlings, translating to a 5 times higher rate of population shrinkage on organic farms compared to conventional. In addition, when parental provisioning behaviour was not restricted by predation risk (i.e., at times of low corvid activity), nestling provisioning rates were higher at lower territory densities, resulting in a much greater increase in nestling mass in low density areas, suggesting that food limitation occurred at high densities. These findings in turn suggest an ecological trap, whereby preferred nesting habitat does not provide sufficient food for rearing nestlings at high population density, creating a population sink. Habitat management for farmland birds should focus not simply on creating a high nesting density, but also on ensuring heterogeneous habitats to provide food resources in close proximity to nesting birds, even if this occurs through potentially restricting overall nest density but increasing population-level breeding success. PMID:26431173
An Infrastructureless Approach to Estimate Vehicular Density in Urban Environments
Sanguesa, Julio A.; Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J.; Cano, Juan-Carlos; Calafate, Carlos T.; Manzoni, Pietro
2013-01-01
In Vehicular Networks, communication success usually depends on the density of vehicles, since a higher density allows having shorter and more reliable wireless links. Thus, knowing the density of vehicles in a vehicular communications environment is important, as better opportunities for wireless communication can show up. However, vehicle density is highly variable in time and space. This paper deals with the importance of predicting the density of vehicles in vehicular environments to take decisions for enhancing the dissemination of warning messages between vehicles. We propose a novel mechanism to estimate the vehicular density in urban environments. Our mechanism uses as input parameters the number of beacons received per vehicle, and the topological characteristics of the environment where the vehicles are located. Simulation results indicate that, unlike previous proposals solely based on the number of beacons received, our approach is able to accurately estimate the vehicular density, and therefore it could support more efficient dissemination protocols for vehicular environments, as well as improve previously proposed schemes. PMID:23435054
Female elk contacts are neither frequency nor density dependent.
Cross, P C; Creech, T G; Ebinger, M R; Manlove, K; Irvine, K; Henningsen, J; Rogerson, J; Scurlock, B M; Creel, S
2013-09-01
Identifying drivers of contact rates among individuals is critical to understanding disease dynamics and implementing targeted control measures. We studied the interaction patterns of 149 female elk (Cervus canadensis) distributed across five different regions of western Wyoming over three years, defining a contact as an approach within one body length (-2 min). Using hierarchical models that account for correlations within individuals, pairs, and groups, we found that pairwise contact rates within a group declined by a factor of three as group sizes increased 33-fold. Per capita contact rates, however, increased with group size according to a power function, such that female elk contact rates fell in between the predictions of density- or frequency-dependent disease models. We found similar patterns for the duration of contacts. Our results suggest that larger elk groups are likely to play a disproportionate role in the disease dynamics of directly transmitted infections in elk. Supplemental feeding of elk had a limited impact on pairwise interaction rates and durations, but per capita rates were more than two times higher on feeding grounds. Our statistical approach decomposes the variation in contact rate into individual, dyadic, and environmental effects, and provides insight into factors that may be targeted by disease control programs. In particular, female elk contact patterns were driven more by environmental factors such as group size than by either individual or dyad effects. PMID:24279278
Female elk contacts are neither frequency nor density dependent
Cross, Paul C.; Creech, Tyler G.; Ebinger, Michael R.; Manlove, Kezia R.; Irvine, Kathryn M.; Henningsen, John C.; Rogerson, Jared D.; Scurlock, Brandon M.; Creely, Scott
2013-01-01
Identifying drivers of contact rates among individuals is critical to understanding disease dynamics and implementing targeted control measures. We studied the interaction patterns of 149 female elk (Cervus canadensis) distributed across five different regions of western Wyoming over three years, defining a contact as an approach within one body length (âˆ¼2 m). Using hierarchical models that account for correlations within individuals, pairs, and groups, we found that pairwise contact rates within a group declined by a factor of three as group sizes increased 33-fold. Per capita contact rates, however, increased with group size according to a power function, such that female elk contact rates fell in between the predictions of density- or frequency-dependent disease models. We found similar patterns for the duration of contacts. Our results suggest that larger elk groups are likely to play a disproportionate role in the disease dynamics of directly transmitted infections in elk. Supplemental feeding of elk had a limited impact on pairwise interaction rates and durations, but per capita rates were more than two times higher on feeding grounds. Our statistical approach decomposes the variation in contact rate into individual, dyadic, and environmental effects, and provides insight into factors that may be targeted by disease control programs. In particular, female elk contact patterns were driven more by environmental factors such as group size than by either individual or dyad effects.
Dependence of polar hole density on magnetic and solar conditions
NASA Technical Reports Server (NTRS)
Hoegy, W. R.; Grebowsky, J. M.
1991-01-01
Electron densities from the Langmuir probes on the Atmospheric Explorer C and Dynamics Explorer 2 are used for analyzing the behavior of the high-altitude night-side F region polar hole as a function of solar and magnetic activity and of universal time (UT). The polar region of invariant latitude from 70 deg to 80 deg and MLT from 22 to 03 hours is examined. The strongest dependencies are observed in F10.7 and UT; a strong hemispherical difference due to the offset of the magnetic poles from the earth's rotation axis is observed in the UT dependence of the ionization hole. A seasonal variation in the dependence of ion density on solar flux is indicated, and an overall asymmetry in the density level between hemispheres is revealed, with the winter-hole density about a factor of 10 greater in the north than in the south.
Transverse momentum dependent quark densities from Lattice QCD
Bernhard Musch,Philipp Hagler,John Negele,Andreas Schafer
2011-10-01
We study transverse momentum dependent parton distribution functions (TMDs) with non-local operators in lattice QCD, using MILC/LHPC lattices. We discuss the basic concepts of the method, including renormalization of the gauge link. Results obtained with a simplified operator geometry show visible dipole deformations of spin-dependent quark momentum densities.
Time-dependent density functional theory based Ehrenfest dynamics.
Wang, Fan; Yam, Chi Yung; Hu, LiHong; Chen, GuanHua
2011-07-28
Time-dependent density functional theory based Ehrenfest dynamics with atom-centered basis functions is developed in present work. The equation of motion for electrons is formulated in terms of first-order reduced density matrix and an additional term arises due to the time-dependence of basis functions through their dependence on nuclear coordinates. This time-dependence of basis functions together with the imaginary part of density matrix leads to an additional term for nuclear force. The effects of the two additional terms are examined by studying the dynamics of H(2) and C(2)H(4), and it is concluded that the inclusion of these two terms is essential for correct electronic and nuclear dynamics. PMID:21806109
p53 mediates density-dependent growth arrest.
Meerson, A; Milyavsky, M; Rotter, V
2004-02-13
While the stress-response-associated importance of the p53 tumor suppressor is well established, recent studies have also linked p53 with several basic parameters in the normal behavior of cells. Here, we present evidence that basal p53 expression in WI38 human embryonic lung fibroblasts restricts growth rate and mediates density-dependent inhibition of growth and the associated G1 phase arrest of the cell cycle by affecting the density-dependent regulation of p16/INK4a. Additionally, we show that prolonged culturing of hTert-immortalized WI38 cells leads to a loss of density-dependent growth inhibition that correlates with p27/KIP deregulation as well as the previously shown INK4a locus silencing, and to an onset of contact-induced, p53-dependent cell death. PMID:14960324
Transverse momentum dependent quark densities from Lattice QCD
Bernhard Musch,Philipp Hagler,John Negele,Andreas Schafer
2011-02-01
We study transverse momentum dependent parton distribution functions (TMDs) with non-local operators in lattice QCD, using MILC/LHPC lattices. Results obtained with a simpli?ed operator geometry show visible dipole de- formations of spin-dependent quark momentum densities. We discuss the basic concepts of the method, including renormalization of the gauge link, and an ex- tension to a more elaborate operator geometry that would allow us to analyze process-dependent TMDs such as the Sivers-function.
Action formalism of time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Mosquera, MartÃn A.
2013-08-01
The Runge-Gross [E. Runge and E. K. U. Gross, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.52.997 52, 997 (1984)] action functional of time-dependent density-functional theory leads to a well-known causality paradox; that is, a perturbation of the electronic density in the future affects the response of the system in the present. This paradox is known to be caused by an inconsistent application of the Dirac-Frenkel variational principle. In view of the recent solutions to this problem, the action functional employed by Runge and Gross in their formulation of time-dependent density-functional theory is analyzed in the context of the Keldysh contour technique. The time-dependent electronic density and the concept of causality are extended to the contour. We derive a variational equation that obeys causality and relates the exchange-correlation potential with its kernel and the functional derivative of the exchange-correlation action functional with respect to the density. It is shown that the adiabatic local-density approximation is a consistent solution of this equation and that the time-dependent optimized potential method can also be derived from it. The formalism presented here can be used to find new approximation methods for the exchange-correlation potential and to avoid the causality dilemma.
Density dependence of nuclear neutrino-pair production
Horowitz, C.J. )
1992-11-02
Nuclear decay via neutrino-pair production is found to have a large density dependence because of intermediate electromagnetic couplings to electrons. These are calculated in a relativistic random phase approximation. The decay rate for vector (Fermi) transitions producing electron type neutrino pairs can be enhanced by 10{sup 5} or more at densities relevant for stellar collapse. Axial-vector (Gamow-Teller) transitions are not enhanced.
Parity dependence of level densities in sup 49 V
York, B.W.
1991-01-01
In this research, we have studied {sup 48}Ti(p, p{sub 1}) and {sup 48}(p, p{sub 1}{gamma}) in an effort to determine the dependence of level densities on parity in the compound nucleus {sup 49}V. This nuclide was chosen because of the high level density of the {sup 49}V system (leading to good statistical accuracy) and because the target is zero spin (making the assignment of J easier). 5 refs., 3 figs.
Nonlinear Density Dependence of Singlet Fission Rate in Tetracene Films.
Zhang, Bo; Zhang, Chunfeng; Wang, Rui; Tan, Zhanao; Liu, Yunlong; Guo, Wei; Zhai, Xiaoling; Cao, Yi; Wang, Xiaoyong; Xiao, Min
2014-10-16
Singlet fission holds the potential to dramatically improve the efficiency of solar energy conversion by creating two triplet excitons from one photoexcited singlet exciton in organic semiconductors. It is generally assumed that the singlet-fission rate is linearly dependent on the exciton density. Here we experimentally show that the rate of singlet fission has a nonlinear dependence on the density of photoexcited singlet excitons in tetracene films with small crystalline grains. We disentangle the spectrotemporal features of singlet and triplet dynamics from ultrafast spectroscopic data with the algorithm of singular value decomposition. The correlation between their temporal dynamics indicates a superlinear dependence of fission rate on the density of singlet excitons, which may arise from excitonic interactions. PMID:26278594
Intercohort density dependence drives brown trout habitat selection
NASA Astrophysics Data System (ADS)
Ayllón, Daniel; Nicola, Graciela G.; Parra, Irene; Elvira, Benigno; Almodóvar, Ana
2013-01-01
Habitat selection can be viewed as an emergent property of the quality and availability of habitat but also of the number of individuals and the way they compete for its use. Consequently, habitat selection can change across years due to fluctuating resources or to changes in population numbers. However, habitat selection predictive models often do not account for ecological dynamics, especially density dependent processes. In stage-structured population, the strength of density dependent interactions between individuals of different age classes can exert a profound influence on population trajectories and evolutionary processes. In this study, we aimed to assess the effects of fluctuating densities of both older and younger competing life stages on the habitat selection patterns (described as univariate and multivariate resource selection functions) of young-of-the-year, juvenile and adult brown trout Salmo trutta. We observed all age classes were selective in habitat choice but changed their selection patterns across years consistently with variations in the densities of older but not of younger age classes. Trout of an age increased selectivity for positions highly selected by older individuals when their density decreased, but this pattern did not hold when the density of younger age classes varied. It suggests that younger individuals are dominated by older ones but can expand their range of selected habitats when density of competitors decreases, while older trout do not seem to consider the density of younger individuals when distributing themselves even though they can negatively affect their final performance. Since these results may entail critical implications for conservation and management practices based on habitat selection models, further research should involve a wider range of river typologies and/or longer time frames to fully understand the patterns of and the mechanisms underlying the operation of density dependence on brown trout habitat selection.
Time-dependent density functional theory on a lattice
NASA Astrophysics Data System (ADS)
Farzanehpour, M.; Tokatly, I. V.
2012-09-01
Time-dependent density functional theory (TDDFT) for quantum many-body systems on a lattice is formulated rigorously. We prove the uniqueness of the density-to-potential mapping and demonstrate that a given density is v representable if the initial many-body state and the density satisfy certain well-defined conditions. In particular, we show that for a system evolving from its ground state any density with a continuous second time derivative is locally in time v representable and therefore the lattice TDDFT is guaranteed to exist. The TDDFT existence and uniqueness theorem is valid for any connected lattice, independently of its size, geometry, and/or spatial dimensionality. General statements of the existence theorem are illustrated on a pedagogical exactly solvable example, which displays all the details and subtleties of the proof in a transparent form. In conclusion we briefly discuss remaining open problems and directions for future research.
Time-dependent density functional theory for quantum transport
NASA Astrophysics Data System (ADS)
Kwok, Yanho; Zhang, Yu; Chen, GuanHua
2014-12-01
The rapid miniaturization of electronic devices motivates research interests in quantum transport. Recently time-dependent quantum transport has become an important research topic. Here we review recent progresses in the development of time-dependent density-functional theory for quantum transport including the theoretical foundation and numerical algorithms. In particular, the reduced-single electron density matrix based hierarchical equation of motion, which can be derived from Liouville-von Neumann equation, is reviewed in details. The numerical implementation is discussed and simulation results of realistic devices will be given.
Ackerman, Joshua T.; Ringelman, KM; Eadie, J.M.
2012-01-01
When nest predation levels are very high or very low, the absolute range of observable nest success is constrained (a floor/ceiling effect), and it may be more difficult to detect density-dependent nest predation. Density-dependent nest predation may be more detectable in years with moderate predation rates, simply because there can be a greater absolute difference in nest success between sites. To test this, we replicated a predation experiment 10 years after the original study, using both natural and artificial nests, comparing a year when overall rates of nest predation were high (2000) to a year with moderate nest predation (2010). We found no evidence for density-dependent predation on artificial nests in either year, indicating that nest predation is not density-dependent at the spatial scale of our experimental replicates (1-ha patches). Using nearest-neighbor distances as a measure of nest dispersion, we also found little evidence for “dispersion-dependent” predation on artificial nests. However, when we tested for dispersion-dependent predation using natural nests, we found that nest survival increased with shorter nearest-neighbor distances, and that neighboring nests were more likely to share the same nest fate than non-adjacent nests. Thus, at small spatial scales, density-dependence appears to operate in the opposite direction as predicted: closer nearest neighbors are more likely to be successful. We suggest that local nest dispersion, rather than larger-scale measures of nest density per se, may play a more important role in density-dependent nest predation.
Ringelman, Kevin M; Eadie, John M; Ackerman, Joshua T
2012-07-01
When nest predation levels are very high or very low, the absolute range of observable nest success is constrained (a floor/ceiling effect), and it may be more difficult to detect density-dependent nest predation. Density-dependent nest predation may be more detectable in years with moderate predation rates, simply because there can be a greater absolute difference in nest success between sites. To test this, we replicated a predation experiment 10 years after the original study, using both natural and artificial nests, comparing a year when overall rates of nest predation were high (2000) to a year with moderate nest predation (2010). We found no evidence for density-dependent predation on artificial nests in either year, indicating that nest predation is not density-dependent at the spatial scale of our experimental replicates (1-ha patches). Using nearest-neighbor distances as a measure of nest dispersion, we also found little evidence for "dispersion-dependent" predation on artificial nests. However, when we tested for dispersion-dependent predation using natural nests, we found that nest survival increased with shorter nearest-neighbor distances, and that neighboring nests were more likely to share the same nest fate than non-adjacent nests. Thus, at small spatial scales, density-dependence appears to operate in the opposite direction as predicted: closer nearest neighbors are more likely to be successful. We suggest that local nest dispersion, rather than larger-scale measures of nest density per se, may play a more important role in density-dependent nest predation. PMID:22179311
Watching excitons move: the time-dependent transition density matrix
NASA Astrophysics Data System (ADS)
Ullrich, Carsten
2012-02-01
Time-dependent density-functional theory allows one to calculate excitation energies and the associated transition densities in principle exactly. The transition density matrix (TDM) provides additional information on electron-hole localization and coherence of specific excitations of the many-body system. We have extended the TDM concept into the real-time domain in order to visualize the excited-state dynamics in conjugated molecules. The time-dependent TDM is defined as an implicit density functional, and can be approximately obtained from the time-dependent Kohn-Sham orbitals. The quality of this approximation is assessed in simple model systems. A computational scheme for real molecular systems is presented: the time-dependent Kohn-Sham equations are solved with the OCTOPUS code and the time-dependent Kohn-Sham TDM is calculated using a spatial partitioning scheme. The method is applied to show in real time how locally created electron-hole pairs spread out over neighboring conjugated molecular chains. The coupling mechanism, electron-hole coherence, and the possibility of charge separation are discussed.
Density dependence and density independence during the early life stages of four marine fish stocks.
DingsÃ¸r, Gjert E; Ciannelli, Lorenzo; Chan, Kung-Sik; Ottersen, Geir; Stenseth, Nils Chr
2007-03-01
Recruitment variability caused by density-dependent and density-independent processes is an important area within the study of fish dynamics. These processes can exhibit nonlinearities and nonadditive properties that may have profound dynamic effects. We investigate the importance of population density (i.e., density dependence) and environmental forcing (i.e., density independence) on the age-0 and age-1 abundance of capelin (Mallotus villosus), northeast Arctic cod (Gadus morhua), northeast Arctic haddock (Melanogrammus aeglefinus), and Norwegian spring spawning herring (Clupea harengus) in the Barents Sea. We use statistical methods that explicitly account for nonlinearities and nonadditive interactions between internal and external variables in the abundance of these two pre-recruitment stages. Our results indicate that, during their first five months of life, cod, haddock, and herring experience higher density-dependent survival than capelin. The abundance of age-0 cod depends on the mean age and biomass of the spawning stock, a result which has implications for the management of the entire cod stock. Temperature is another important factor influencing the abundance at age-0 and age-1 of all four species, except herring at age-1. Between age-0 and age-1, there is an attenuation of density-dependent survival for cod and herring, while haddock and capelin experience density dependence at high and low temperatures, respectively. Predation by subadult cod is important for both capelin and cod at age-1. We found strong indications for interactions among the studied species, pointing to the importance of viewing the problem of species recruitment variability as a community, rather than as a population phenomenon. PMID:17503591
Approach of high density coal preparation method
Yang, Y.; Chen, Q.
1996-12-31
Density difference of aged anthracite coal of high density and discard is less than that of general coal and discard; conventional separation methods are difficult to be used. For the special coal, coal dry beneficiation technology with air-dense medium fluidized bed has obvious superiority over other separation methods.
Cuticular Antifungals in Spiders: Density- and Condition Dependence
GonzÃ¡lez-Tokman, Daniel; Ruch, Jasmin; Pulpitel, Tamara; Ponton, Fleur
2014-01-01
Animals living in groups face a high risk of disease contagion. In many arthropod species, cuticular antimicrobials constitute the first protective barrier that prevents infections. Here we report that group-living spiders produce cuticular chemicals which inhibit fungal growth. Given that cuticular antifungals may be costly to produce, we explored whether they can be modulated according to the risk of contagion (i.e. under high densities). For this purpose, we quantified cuticular antifungal activity in the subsocial crab spider Diaea ergandros in both natural nests and experimentally manipulated nests of varying density. We quantified the body-condition of spiders to test whether antifungal activity is condition dependent, as well as the effect of spider density on body-condition. We predicted cuticular antifungal activity to increase and body-condition to decrease with high spider densities, and that antifungal activity would be inversely related to body-condition. Contrary to our predictions, antifungal activity was neither density- nor condition-dependent. However, body-condition decreased with density in natural nests, but increased in experimental nests. We suggest that pathogen pressure is so important in nature that it maintains high levels of cuticular antifungal activity in spiders, impacting negatively on individual energetic condition. Future studies should identify the chemical structure of the isolated antifungal compounds in order to understand the physiological basis of a trade-off between disease prevention and energetic condition caused by group living, and its consequences in the evolution of sociality in spiders. PMID:24637563
Time-dependent Partition Density-functional Theory
NASA Astrophysics Data System (ADS)
Mosquera, Martin; Wasserman, Adam
2012-02-01
We present an extension of time-dependent density functional theory that allows to partition the time-dependent external potential in terms of localized molecular fragment potentials. As a consequence, localized time-dependent densities arise for each molecular fragment. To enforce the condition that the sum of fragments must add up to the exact total density, a new quantity termed ``time-dependent partition potential'' is introduced. The Runge-Gross theorem is employed to show that there is a quasi one-to-one correspondence between the partition potential and the electronic density. The corresponding quantum-mechanical actions are derived by using the van Leeuwen's action and are used to derive a decomposition of the partition potential which allows for practical approximations. Linear response formulas are deduced to obtain the transition energies, and an approximation is suggested to obtain localized excitations in large molecular systems. Finally, numerical illustration of our theory is shown for one-dimensional fermions under the influence of a laser field.
NASA Astrophysics Data System (ADS)
Ruggenthaler, Michael; Penz, Markus; van Leeuwen, Robert
2015-05-01
In this work we review the mapping from densities to potentials in quantum mechanics, which is the basic building block of time-dependent density-functional theory and the Kohn-Sham construction. We first present detailed conditions such that a mapping from potentials to densities is defined by solving the time-dependent SchrÃ¶dinger equation. We specifically discuss intricacies connected with the unboundedness of the Hamiltonian and derive the local-force equation. This equation is then used to set up an iterative sequence that determines a potential that generates a specified density via time propagation of an initial state. This fixed-point procedure needs the invertibility of a certain Sturm-Liouville problem, which we discuss for different situations. Based on these considerations we then present a discussion of the famous Runge-Gross theorem which provides a density-potential mapping for time-analytic potentials. Further we give conditions such that the general fixed-point approach is well-defined and converges under certain assumptions. Then the application of such a fixed-point procedure to lattice Hamiltonians is discussed and the numerical realization of the density-potential mapping is shown. We conclude by presenting an extension of the density-potential mapping to include vector-potentials and photons.
Both, Christiaan; Visser, Marcel E
2003-02-01
Species differ enormously in their territorial systems. Some species defend only small areas surrounded by undefended space, while others defend large contiguous territories. Using an optimization approach, we show that this variation can be explained from the density of two types of resources: divisible and nondivisible. We assume that benefits of territories are monotonously related to the defended amount of divisible resources (hereafter called food). In contrast, no benefits are obtained without a nondivisible resource (hereafter called nest site) in the territory, while more than one nest site does not further increase the benefits. The optimal territory size depends on the relative abundance of these resources. With a low density of nest sites, the optimal territory size is small and includes only the nest site. If the density of nest sites is relatively large, the optimal territory size is high, and territories are contiguous. Competition for these different resources yields contrasting patterns of how populations are regulated. If there is mainly competition for nest sites, we expect density-dependent exclusion through territoriality and no density-dependent reproduction. When competition is mainly for food, we expect density-dependent reproduction because optimal territory size will be compressed at higher densities, resulting in lower reproductive success. These predicted patterns indeed are observed in some well-studied passerine species for which both the territorial system and the occurrence of density dependence is known. PMID:12675376
NASA Astrophysics Data System (ADS)
Ferretti, Andrea; Dabo, Ismaila; Cococcioni, Matteo; Marzari, Nicola
2012-02-01
Energy functionals which depend explicitly on the orbital densities (ODD), instead of the total charge density, appear when applying self-interaction corrections to density-functional theory. In these cases (e.g. the Perdew-Zunger [1] and the non-Koopmans [2] approaches) the total energy loses invariance under unitary rotations of the orbitals, and the minimization of the functionals leads to orbital-dependent Hamiltonians. We show that it is possible to identify the orbital-dependency of densities and potentials with an effective and discretized frequency-dependency, in close analogy to the quasi-particle approximation of frequency-dependent self-energies and naturally oriented to interpret electronic spectroscopies [3]. Some of the existing ODD functionals are analyzed from this new perspective. Numerical results for the electronic structure of gas-phase molecules (within the Koopmans-corrected class of functionals) are computed and found in excellent agreement with photoemission (UPS) data. [1] J.-P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981). [2] I. Dabo, A. Ferretti, N. Poilvert, Y. Li, N. Marzari, M. Cococcioni, Phys. Rev. B 82, 115121 (2010). [3] M. Gatti, V. Olevano, L. Reining, I.-V. Tokatly, Phys. Rev. Lett. 99, 057401 (2007).
Saturating interactions in /sup 4/He with density dependence
Bloom, S.D.; Resler, D.A.; Moszkowski, S.A.
1989-05-03
With the advent of larger and faster computers, as well as modern shell model codes, nuclear structure calculations for the light nuclei (A<16) which include full 2/bar h/..omega.. model spaces are quite feasible. However, there can be serious problems in the mixing of 2/bar h/..omega.. and higher excitations into the low-lying spectra if the effective interaction is non-saturating. Furthermore, effective interactions which are both saturating and density dependent have not generally been used in previous nuclear structure calculations. Therefore, we have undertaken studies of /sup 4/He using two-body potential interactions which incorporate both saturation and density-dependence. Encouraging initial results in remedying the mixing of 0 and 2/bar h/..omega.. excitations have been obtained. We have also considered the effects of our interaction on the /sup 4/He compressibility and the centroid of the breathing mode strength. First indications are that a saturating effective interaction, with a short-range density dependent part and a long-range density independent part, comes close to matching crude predictions for the compressibility of /sup 4/He. 11 refs., 6 tabs.
Possible density dependent local variations in the IMF
NASA Astrophysics Data System (ADS)
Kavila, Indulekha; George, Babitha
2015-08-01
Variations in the IMF have been reported within open clusters (signifying mass segregation), between globular clusters, within galaxies and between galaxies. Most stars are considered to form in a clustered mode. However, the surface density of YSO's shows a wide range and it is also considered that stars form in the clustered mode only at the peaks of the surface density. The bound cluster formation efficiency in galaxies is observed to be correlated with the Star Formation Rate density which itself is seen to be correlated with the gas surface density by the Kennicutt Schmidt law.Observationally, dense cores in molecular clouds - which go on to produce stars - have a mass spectrum that is broadly consistent with a Salpeter slope of -1.35 at the high mass end. In simulations of clouds with Gaussian fluctuations it is seen that the mass spectrum of peaks which collapse are approximately log-normal, peaking roughly at the average Jeans' mass in the cloud. We explore a possible way in which the IMF could depend on the local gas density. The extent of the variations that can be caused by such a dependence is explored. The IMFs of the sample clusters that are generated are compared with the IMFs of observed clusters and also against radial trends reported in galaxies.
Energy dependence with the number of particles: Density and reduced density matrices functionals
NASA Astrophysics Data System (ADS)
Miranda-Quintana, RamÃ³n A.; Bochicchio, Roberto C.
2014-02-01
The energy of a physical domain within a molecular system considered as a quantum open system is analyzed as a functional of the electron distribution dependence with the number of particles. Our attention is focused upon the constrained-search functionals of the electron density, the 1- and 2-reduced density matrices (1-, 2-RDMs) for grand-canonical states. It is shown that functionals of the 2-RDM depend on the number of particles if the ground state energy is not a convex function of them.
Umbanhowar, James; Maron, John; Harrison, Susan
2003-09-01
Empirical studies of spatial heterogeneity in parasitism by insect parasitoids have focused largely on patterns, while the many possible underlying mechanisms have been little studied in the field. We conducted experimental and observational studies on Tachinomyia similis (Diptera: Tachinidae) attacking western tussock moths (Orgyia vetusta; Lepidoptera: Lymantriidae) on lupine bushes at Bodega Bay, Calif., USA. We examined several foraging behaviors that have been hypothesized to create density-dependent variation in parasitism rates, including spatial aggregation of parasitoids to high host density, mutual interference among searching parasitoids and decelerating functional responses of the parasitoid. At the spatial scale of individual bushes, we detected both aggregation to a high density and a decelerating functional response. The resulting spatial pattern of parasitism was best fit by two models; one included an effect of parasitoid aggregation and the other included an effect of aggregation and a decelerating functional response. Most of the variation in parasitism was not correlated with density of O. vetusta. PMID:12883984
Density Functional Theory Approach to Nuclear Fission
NASA Astrophysics Data System (ADS)
Schunck, N.
The Skyrme nuclear energy density functional theory (DFT) is used to model neutron-induced fission in actinides. This paper focuses on the numerical implementation of the theory. In particular, it reports recent advances in DFT code development on leadership class computers, and presents a detailed analysis of the numerical accuracy of DFT solvers for near-scission calculations.
Modelling interactions of toxicants and density dependence in wildlife populations
Schipper, Aafke M.; Hendriks, Harrie W.M.; Kauffman, Matthew J.; Hendriks, A. Jan; Huijbregts, Mark A.J.
2013-01-01
1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 ?g g?1 fresh weight for DDE and PBDEs, respectively. 5. Synthesis and applications. Our modelling results showed that particular life stages of a density-limited population may be relatively insensitive to toxicant impacts until a critical threshold is crossed. In our study population, toxicant-induced changes were observed in the equilibrium number of nonbreeding rather than breeding birds, suggesting that monitoring efforts including both life stages are needed to timely detect population declines. Further, by combining quantitative exposure–response relationships with a wildlife demographic model, we provided a method to quantify critical toxicant thresholds for wildlife population persistence.
The dependence of natural graphite anode performance on electrode density
Shim, Joongpyo; Striebel, Kathryn A.
2003-11-01
The effect of electrode density for lithium intercalation and irreversible capacity loss on the natural graphite anode in lithium ion batteries was studied by electrochemical methods. Both the first-cycle reversible and irreversible capacities of the natural graphite anode decreased with an increase in the anode density though compression. The reduction in reversible capacity was attributed to a reduction in the chemical diffusion coefficient for lithium though partially agglomerated particles with a larger stress. For the natural graphite in this study the potentials for Li (de)insertion shifted between the first and second formation cycles and the extent of this shift was dependent on electrode density. The relation between this peak shift and the irreversible capacity loss are probably both due to the decrease in graphite surface area with compression.
Density and Temperature Dependence of X-ray Thomson Scatteringjj
NASA Astrophysics Data System (ADS)
Mattern, B. A.; Seidler, G. T.; Rehr, J. J.
2013-03-01
X-ray Thomson Scattering (XRTS) provides a diagnostic tool for state-variable determination in the Warm Dense Matter (WDM) regime. We explore the density and temperature dependence of XRTS using a finite-temperature generalization of the real-space Green's function (RSGF) method. This method treats the interaction between the ionic cores and free/valence electrons non-perturbatively using full multiple-scattering theory[2]. Compared to perturbative treatments, we find a significantly modified density-dependence of XRTS. This modification, which is relevant for the extraction of state-variables from WDM experiments, remains when temperature is included. The effects of an exchange-correlation potential appropriate for WDM is also discussed. Funding provided by DOE Grant DE-SC0002194
Excitons in Time-Dependent Density-Functional Theory.
Ullrich, Carsten A; Yang, Zeng-hui
2016-01-01
This chapter gives an overview of the description of the optical and dielectric properties of bulk insulators and semiconductors in time-dependent density-functional theory (TDDFT), with an emphasis on excitons. We review the linear-response formalism for periodic solids, discuss excitonic exchange-correlation kernels, calculate exciton binding energies for various materials, and compare the treatment of excitons with TDDFT and with the Bethe-Salpeter equation. PMID:25805143
A phenomenological density-scaling approach to lamellipodial actin dynamics(†).
Lewalle, Alexandre; Fritzsche, Marco; Wilson, Kerry; Thorogate, Richard; Duke, Tom; Charras, Guillaume
2014-12-01
The integration of protein function studied in vitro in a dynamic system like the cell lamellipodium remains a significant challenge. One reason is the apparent contradictory effect that perturbations of some proteins can have on the overall lamellipodium dynamics, depending on exact conditions. Theoretical modelling offers one approach for understanding the balance between the mechanisms that drive and regulate actin network growth and decay. Most models use a 'bottom-up' approach, involving explicitly assembling biochemical components to simulate observable behaviour. Their correctness therefore relies on both the accurate characterization of all the components and the completeness of the relevant processes involved. To avoid potential pitfalls due to this uncertainty, we used an alternative 'top-down' approach, in which measurable features of lamellipodium behaviour, here observed in two different cell types (HL60 and B16-F1), directly inform the development of a simple phenomenological model of lamellipodium dynamics. We show that the kinetics of F-actin association and dissociation scales with the local F-actin density, with no explicit location dependence. This justifies the use of a simplified kinetic model of lamellipodium dynamics that yields predictions testable by pharmacological or genetic intervention. A length-scale parameter (the lamellipodium width) emerges from this analysis as an experimentally accessible probe of network regulatory processes. PMID:25485077
Cycles, stochasticity and density dependence in pink salmon population dynamics
KrkoÅ¡ek, Martin; Hilborn, Ray; Peterman, Randall M.; Quinn, Thomas P.
2011-01-01
Complex dynamics of animal populations often involve deterministic and stochastic components. A fascinating example is the variation in magnitude of 2-year cycles in abundances of pink salmon (Oncorhynchus gorbuscha) stocks along the North Pacific rim. Pink salmon have a 2-year anadromous and semelparous life cycle, resulting in odd- and even-year lineages that occupy the same habitats but are reproductively isolated in time. One lineage is often much more abundant than the other in a given river, and there are phase switches in dominance between odd- and even-year lines. In some regions, the weak line is absent and in others both lines are abundant. Our analysis of 33 stocks indicates that these patterns probably result from stochastic perturbations of damped oscillations owing to density-dependent mortality caused by interactions between lineages. Possible mechanisms are cannibalism, disease transmission, food depletion and habitat degradation by which one lineage affects the other, although no mechanism has been well-studied. Our results provide comprehensive empirical estimates of lagged density-dependent mortality in salmon populations and suggest that a combination of stochasticity and density dependence drives cyclical dynamics of pink salmon stocks. PMID:21147806
Cycles, stochasticity and density dependence in pink salmon population dynamics.
Krkosek, Martin; Hilborn, Ray; Peterman, Randall M; Quinn, Thomas P
2011-07-01
Complex dynamics of animal populations often involve deterministic and stochastic components. A fascinating example is the variation in magnitude of 2-year cycles in abundances of pink salmon (Oncorhynchus gorbuscha) stocks along the North Pacific rim. Pink salmon have a 2-year anadromous and semelparous life cycle, resulting in odd- and even-year lineages that occupy the same habitats but are reproductively isolated in time. One lineage is often much more abundant than the other in a given river, and there are phase switches in dominance between odd- and even-year lines. In some regions, the weak line is absent and in others both lines are abundant. Our analysis of 33 stocks indicates that these patterns probably result from stochastic perturbations of damped oscillations owing to density-dependent mortality caused by interactions between lineages. Possible mechanisms are cannibalism, disease transmission, food depletion and habitat degradation by which one lineage affects the other, although no mechanism has been well-studied. Our results provide comprehensive empirical estimates of lagged density-dependent mortality in salmon populations and suggest that a combination of stochasticity and density dependence drives cyclical dynamics of pink salmon stocks. PMID:21147806
Quark matter at high density based on an extended confined isospin-density-dependent mass model
NASA Astrophysics Data System (ADS)
Qauli, A. I.; Sulaksono, A.
2016-01-01
We investigate the effect of the inclusion of relativistic Coulomb terms in a confined-isospin-density-dependent-mass (CIDDM) model of strange quark matter (SQM). We found that if we include the Coulomb term in scalar density form, the SQM equation of state (EOS) at high densities is stiffer but if we include the Coulomb term in vector density form it is softer than that of the standard CIDDM model. We also investigate systematically the role of each term of the extended CIDDM model. Compared with what was reported by Chu and Chen [Astrophys. J. 780, 135 (2014)], we found the stiffness of SQM EOS is controlled by the interplay among the oscillator harmonic, isospin asymmetry and Coulomb contributions depending on the parameter's range of these terms. We have found that the absolute stable condition of SQM and the mass of 2 MâŠ™ pulsars can constrain the parameter of oscillator harmonic Îº1â‰ˆ0.53 in the case the Coulomb term is excluded. If the Coulomb term is included, for the models with their parameters are consistent with SQM absolute stability condition, the 2.0 MâŠ™ constraint more prefers the maximum mass prediction of the model with the scalar Coulomb term than that of the model with the vector Coulomb term. On the contrary, the high densities EOS predicted by the model with the vector Coulomb is more compatible with the recent perturbative quantum chromodynamics result [1] than that predicted by the model with the scalar Coulomb. Furthermore, we also observed the quark composition in a very high density region depends quite sensitively on the kind of Coulomb term used.
Density dependence and cooperation: theory and a test with bacteria.
Ross-Gillespie, Adin; Gardner, Andy; Buckling, Angus; West, Stuart A; Griffin, Ashleigh S
2009-09-01
Although cooperative systems can persist in nature despite the potential for exploitation by noncooperators, it is often observed that small changes in population demography can tip the balance of selective forces for or against cooperation. Here we consider the role of population density in the context of microbial cooperation. First, we account for conflicting results from recent studies by demonstrating theoretically that: (1) for public goods cooperation, higher densities are relatively unfavorable for cooperation; (2) in contrast, for self-restraint-type cooperation, higher densities can be either favorable or unfavorable for cooperation, depending on the details of the system. We then test our predictions concerning public goods cooperation using strains of the pathogenic bacterium Pseudomonas aeruginosa that produce variable levels of a public good-iron-scavenging siderophore molecules. As predicted, we found that the relative fitness of cheats (under-producers) was greatest at higher population densities. Furthermore, as assumed by theory, we show that this occurs because cheats are better able to exploit the cooperative siderophore production of other cells when they are physically closer to them. PMID:19453724
Density-dependent dispersal and spatial population dynamics
Ims, Rolf A; Andreassen, Harry P
2005-01-01
The synchronization of the dynamics of spatially subdivided populations is of both fundamental and applied interest in population biology. Based on theoretical studies, dispersal movements have been inferred to be one of the most general causes of population synchrony, yet no empirical study has mapped distance-dependent estimates of movement rates on the actual pattern of synchrony in species that are known to exhibit population synchrony. Northern vole and lemming species are particularly well-known for their spatially synchronized population dynamics. Here, we use results from an experimental study to demonstrate that tundra vole dispersal movements did not act to synchronize population dynamics in fragmented habitats. In contrast to the constant dispersal rate assumed in earlier theoretical studies, the tundra vole, and many other species, exhibit negative density-dependent dispersal. Simulations of a simple mathematical model, parametrized on the basis of our experimental data, verify the empirical results, namely that the observed negative density-dependent dispersal did not have a significant synchronizing effect. PMID:16024345
Exploration of a modified density dependence in the Skyrme functional
Erler, J.; Reinhard, P.-G.; Kluepfel, P.
2010-10-15
A variant of the basic Skyrme-Hartree-Fock functional is considered dealing with a new form of density dependence. It employs only integer powers and thus will allow a more sound basis for projection schemes (particle number, angular momentum). We optimize the new functional with exactly the same adjustment strategy as used in an earlier study with a standard Skyrme functional. This allows direct comparisons of the performance of the new functional relative to the standard one. We discuss various observables: bulk properties of finite nuclei, nuclear matter, giant resonances, superheavy elements, and energy systematics. The new functional performs at least as well as the standard one, but offers a wider range of applicability (e.g., for projection) and more flexibility in the regime of high densities.
Large area photonic crystal cavities: a local density approach.
Dobbelaar, M C F; Greveling, S; van Oosten, D
2015-03-23
Large area photonic crystal cavities are devices of interest for photovoltaics, optoelectronics, and solid-state lighting. However, depending on their dimensions they pose a large computational challenge. Here, we use a local density approach to avoid direct simulation of the device. We capture the effect of both ideal and distorted photonic crystals in an effective mass and an effective potential. We use these to map the problem of calculating the electromagnetic field modes to solving a simple time-independent Schrödinger equation. We show that, in the case that the hole radius varies quadratically as a function of position, the eigenmodes of the photonic crystals can be described by the corresponding eigenmodes of the quantum harmonic oscillator with typical agreements well above 90%. PMID:25837088
Effective local potentials for orbital-dependent density functionals
NASA Astrophysics Data System (ADS)
Staroverov, Viktor N.; Scuseria, Gustavo E.; Davidson, Ernest R.
2006-08-01
Practicality of the Kohn-Sham density functional scheme for orbital-dependent functionals hinges on the availability of an efficient procedure for constructing local exchange-correlation potentials in finite basis sets. We have shown recently that the optimized effective potential (OEP) method, commonly used for this purpose, is not free from difficulties. Here we propose a robust alternative to OEPs, termed effective local potentials (ELPs), based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart. The ELP method is applied to the exact-exchange-only problem and shown to be promising for overcoming troubles with OEPs.
Limits for density dependent time inhomogeneous Markov processes.
Smith, Andrew G
2015-10-01
A new functional law of large numbers to approximate a time inhomogeneous Markov process that is only density dependent in the limit as an index parameter goes to infinity is developed. This extends previous results by other authors to a broader class of Markov processes while relaxing some of the conditions required for those results to hold. This result is applied to a stochastic metapopulation model that accounts for spatial structure as well as within patch dynamics with the novel addition of time dependent dynamics. The resulting nonautonomous differential equation is analysed to provide conditions for extinction and persistence for a number of examples. This condition shows that the migration of a species will positively impact the reproduction in less populated areas while negatively impacting densely populated areas. PMID:26260102
NASA Astrophysics Data System (ADS)
Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.
2015-02-01
We perform an ab initio all-electron study of the subcycle structure, dynamics, and spectra of high harmonic generation (HHG) processes of Ar atoms in the presence of extreme ultraviolet (XUV) attosecond pulses and near-infrared (NIR) laser fields by means of the self-interaction-free time-dependent density functional theory (TDDFT). The TDDFT equations are solved accurately and efficiently via the time-dependent generalized pseudospectral (TDGPS) method. We focus on the subcycle (with respect to NIR field) temporal behavior of the level shift of the excited energy levels and related dynamics of harmonic photon emission. We observe and identify the subcycle shifts in the harmonic emission spectrum as a function of the time delay between the XUV and NIR pulses. In the region where the two pulses overlap, the photon emission peaks have an oscillatory structure with a period of Ëœ1.3 fs, which is half of the NIR laser optical cycle. We present and analyze the harmonic emission spectra from 3 s n p0,3 p0n s ,3 p1n d1,3 p1n p1,3 p0n d0,3 p0n p0 , and 3 p0n s excited states and the 3 p04 p0- virtual state as functions of the time delay. In addition, we explore the subcycle a.c. Stark shift phenomenon in NIR fields and its influence on the harmonic emission process. Our analysis reveals several features of the subcycle HHG dynamics and spectra as well as a temporal energy level shift.
Time-Dependent Electronic Populations in Fragment-Based Time-Dependent Density Functional Theory.
Mosquera, MartÃn A; Wasserman, Adam
2015-08-11
Conceiving a molecule as being composed of smaller molecular fragments, or subunits, is one of the pillars of the chemical and physical sciences and leads to productive methods in quantum chemistry. Using a fragmentation scheme, efficient algorithms can be proposed to address problems in the description of chemical bond formation and breaking. We present a formally exact time-dependent density functional theory for the electronic dynamics of molecular fragments with a variable number of electrons. This new formalism is an extension of previous work [Phys. Rev. Lett. 111, 023001 (2013)]. We also introduce a stable density-inversion method that is applicable to time-dependent and ground-state density functional theories and their extensions, including those discussed in this work. PMID:26574438
Current density partitioning in time-dependent current density functional theory
Mosquera, Martín A.; Wasserman, Adam; Department of Physics, Purdue University, West Lafayette, Indiana 47907
2014-05-14
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Current density partitioning in time-dependent current density functional theory
NASA Astrophysics Data System (ADS)
Mosquera, MartÃn A.; Wasserman, Adam
2014-05-01
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Leirs, H.; Stenseth, N.C.; Nichols, J.D.; Hines, J.E.; Verhagen, R.; Verheyen, W.
1997-01-01
Ecology has long been troubled by the controversy over how populations are regulated. Some ecologists focus on the role of environmental effects, whereas others argue that density-dependent feedback mechanisms are central. The relative importance of both processes is still hotly debated, but clear examples of both processes acting in the same population are rare. Keyfactor analysis (regression of population changes on possible causal factors) and time-series analysis are often used to investigate the presence of density dependence, but such approaches may be biased and provide no information on actual demographic rates. Here we report on both density-dependent and density-independent effects in a murid rodent pest species, the multimammate rat Mastomys natalensis (Smith, 1834), using statistical capture-recapture models. Both effects occur simultaneously, but we also demonstrate that they do not affect all demographic rates in the same way. We have incorporated the obtained estimates of demographic rates in a population dynamics model and show that the observed dynamics are affected by stabilizing nonlinear density-dependent components coupled with strong deterministic and stochastic seasonal components.
Time-dependent local density measurements in unsteady flows
NASA Technical Reports Server (NTRS)
Mckenzie, R. L.; Monson, D. J.; Exberger, R. J.
1979-01-01
A laser-induced fluorescence technique for measuring the relative time-dependent density fluctuations in unsteady or turbulent flows is demonstrated. Using a 1.5-W continuous-wave Kr(+) laser, measurements have been obtained in 0.1-mm diameter by 1-mm-long sampling volumes in a Mach 3 flow of N2 seeded with biacetyl vapor. A signal amplitude resolution of 2% was achieved for a detection frequency bandwidth of 10 kHz. The measurement uncertainty was found to be dominated by noise behaving as photon statistical noise. The practical limits of signal-to-noise ratios have been characterized for a wide range of detection frequency bandwidths that encompasses those of interest in supersonic turbulence measurements.
Time-dependent local density measurements in unsteady flows
NASA Technical Reports Server (NTRS)
Mckenzie, R. L.; Monson, D. J.; Exberger, R. J.
1979-01-01
A laser-induced fluorescence technique for measuring the relative time-dependent density fluctuations in unsteady or turbulent flows is demonstrated. Using a 1.5-W continuous-wave Kr(+) laser, measurements have been obtained in 0.1-mm-diameter by 1-mm-long sampling volumes in a Mach 3 flow of N2 seeded with biacetyl vapor. A signal amplitude resolution of 2% was achieved for a detection frequency bandwidth of 10 kHz. The measurement uncertainty was found to be dominated by noise behaving as photon statistical noise. The practical limits of signal-to-noise ratios have been characterized for a wide range of detection frequency bandwidths that encompasses those of interest in supersonic turbulence measurements.
Time-dependent density functional theory for open quantum systems
NASA Astrophysics Data System (ADS)
Tempel, David; Aspuru-Guzik, Alan
2012-02-01
We present the extension of time-dependent density functional theory (TDDFT) to the realm of open quantum systems (OQS). OQS-TDDFT allows a first principles description of electronic systems undergoing non-unitary dynamics due to coupling with a bath, such as that arising from molecular vibrations, solvent degrees of freedom or photon modes of the electromagnetic field. We first prove extensions of the Runge-Gross and van Leeuwen theorems to OQS-TDDFT, which rigorously establish it as a formally exact theory. We then discuss development of approximate OQS-TDDFT functionals, exact conditions on these functionals, as well as future challenges. Finally, we will discuss the application of OQS-TDDFT in obtaining broadened absorption spectra.
Density-dependent migratory waves in the marine pelagic ecosystem.
Fauchald, Per; Mauritzen, Mette; GjÃ¸saeter, Harald
2006-11-01
The migration of large aggregations of animals that sweep through the landscape is a phenomenon with large consequences in many ecosystems. It has been suggested that such migrations are mediated by resource depletion. Under this hypothesis it has been shown that simple foraging rules may generate density-dependent migratory waves (DDMW) in which the speed and amplitude increase with animal abundance. We tested these predictions on a 32-year data set of the spatial distribution of the two youngest age groups of a small pelagic schooling fish, the capelin (Mallotus villosus), by the end of their annual feeding migration in the Barents Sea. Our data suggest that the two age groups divided the Barents Sea by forming migratory waves that moved in opposite directions. The aggregation and spatial displacement of these waves increased with increasing age-specific abundance. However, possibly through social interactions, migratory pattern was modified by the abundance of the other age group. PMID:17168035
NASA Astrophysics Data System (ADS)
Zahn, Jochen
2015-11-01
In the framework of quantum electrodynamics (QED) in external potentials, we introduce a method to compute the time-dependence of the expectation value of the current density for time-dependent homogeneous external electric fields. We apply it to the so-called Sauter pulse. For late times, our results agree with the asymptotic value due to electron-positron pair production. We correct a general expression derived by Serber for the expectation value of the current, linearized in the external field, and compare with our results for the Sauter pulse. Based on the properties of the current density, we argue that the appearance of enhanced quasi-particle densities at intermediate times in slowly varying sub-critical potentials is generic. Also an alternative approach, which circumvents these difficulties, is sketched.
The dependence of ZnO photoluminescence efficiency on excitation conditions and defect densities
Simmons, Jay G.; Liu, Jie; Foreman, John V.; Everitt, Henry O.
2013-11-11
The quantum efficiencies of both the band edge and deep-level defect emission from annealed ZnO powders were measured as a function of excitation fluence and wavelength from a tunable sub-picosecond source. A simple model of excitonic decay reproduces the observed excitation dependence of rate constants and associated trap densities for all radiative and nonradiative processes. The analysis explores how phosphor performance deteriorates as excitation fluence and energy increase, provides an all-optical approach for estimating the number density of defects responsible for deep-level emission, and yields new insights for designing efficient ZnO-based phosphors.
Linear-response calculation in the time-dependent density functional theory
Nakatsukasa, Takashi; Inakura, Tsunenori; Avogadro, Paolo; Ebata, Shuichiro; Sato, Koichi; Yabana, Kazuhiro
2012-11-12
Linear response calculations based on the time-dependent density-functional theory are presented. Especially, we report results of the finite amplitude method which we have recently proposed as an alternative and feasible approach to the (quasiparticle-)random-phase approximation. Calculated properties of the giant resonances and low-energy E1 modes are discussed. We found a universal linear correlation between the low-energy E1 strength and the neutron skin thickness.
Host selection by an insect herbivore with spatially variable density dependence.
Wetzel, William C; Strong, Donald R
2015-11-01
Many species of phytophagous insects do not oviposit preferentially on plants that yield high offspring performance. One proposed explanation is that negatively density-dependent offspring performance would select for females that disperse eggs among plants to minimize competition. Recent work showing larval density dependence often varies substantially among plants suggests that ovipositing females should not only respond to the density of competitors but also to traits predictive of the strength of density dependence mediated by plants. In this study, we used field and greenhouse experiments to examine oviposition behavior in an insect herbivore that experiences density-dependent larval performance and variability in the strength of that density dependence among host-plant individuals. We found females moved readily among plants in the field and had strong preferences for plants that mediate weak offspring density dependence. Females, however, did not avoid plants with high densities of competitors, despite the fact that offspring performance declines steeply with density on most plants in natural populations. This means females minimize the effects of density dependence on their offspring by choosing plants that mediate only weak larval density dependence, not by choosing plants with low densities of competitors. Our results suggest that explaining the lack of positive preference-performance correlations in many systems may not be as simple as invoking density dependence. Resource selection behavior may depend not just on the presence or absence of density-dependent offspring performance but also on variation in the strength of offspring density dependence among sites within populations. PMID:26120095
From patterns to processes: phase and density dependencies in the Canadian lynx cycle.
Stenseth, N C; Falck, W; Chan, K S; Bjørnstad, O N; O'Donoghue, M; Tong, H; Boonstra, R; Boutin, S; Krebs, C J; Yoccoz, N G
1998-12-22
Across the boreal forest of North America, lynx populations undergo 10-year cycles. Analysis of 21 time series from 1821 to the present demonstrates that these fluctuations are generated by nonlinear processes with regulatory delays. Trophic interactions between lynx and hares cause delayed density-dependent regulation of lynx population growth. The nonlinearity, in contrast, appears to arise from phase dependencies in hunting success by lynx through the cycle. Using a combined approach of empirical, statistical, and mathematical modeling, we highlight how shifts in trophic interactions between the lynx and the hare generate the nonlinear process primarily by shifting functional response curves during the increase and the decrease phases. PMID:9860985
A discrete model with density dependent fast migration.
Bravo de la Parra, R; SÃ¡nchez, E; Arino, O; Auger, P
1999-03-15
The aim of this work is to develop an approximate aggregation method for certain non-linear discrete models. Approximate aggregation consists in describing the dynamics of a general system involving many coupled variables by means of the dynamics of a reduced system with a few global variables. We present discrete models with two different time scales, the slow one considered to be linear and the fast one non-linear because of its transition matrix depends on the global variables. In our discrete model the time unit is chosen to be the one associated to the slow dynamics, and then we approximate the effect of fast dynamics by using a sufficiently large power of its corresponding transition matrix. In a previous work the same system is treated in the case of fast dynamics considered to be linear, conservative in the global variables and inducing a stable frequency distribution of the state variables. A similar non-linear model has also been studied which uses as time unit the one associated to the fast dynamics and has the non-linearity in the slow part of the system. In the present work we transform the system to make the global variables explicit, and we justify the quick derivation of the aggregated system. The local asymptotic behaviour of the aggregated system entails that of the general system under certain conditions, for instance, if the aggregated system has a stable hyperbolic fixed point then the general system has one too. The method is applied to aggregate a multiregional Leslie model with density dependent migration rates. PMID:10194925
Global fixed-point proof of time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Ruggenthaler, M.; van Leeuwen, R.
2011-07-01
We reformulate the uniqueness and existence proofs of time-dependent density-functional theory. The central idea is to restate the fundamental one-to-one correspondence between densities and potentials as a global fixed-point question for potentials on a given time interval. We show that the unique fixed point, i.e. the unique potential generating a given density, is reached as the limiting point of an iterative procedure. The one-to-one correspondence between densities and potentials is a straightforward result provided that the response function of the divergence of the internal forces is bounded. The existence, i.e. the v-representability of a density, can be proven as well provided that the operator norms of the response functions of the members of the iterative sequence of potentials have an upper bound. The densities under consideration have second time-derivatives that are required to satisfy a condition slightly weaker than being square-integrable. This approach avoids the usual restrictions of Taylor-expandability in time of the uniqueness theorem by Runge and Gross (Phys. Rev. Lett., 52 (1984) 997) and of the existence theorem by van Leeuwen (Phys. Rev. Lett., 82 (1999) 3863). Owing to its generality, the proof not only answers basic questions in density-functional theory but also has potential implications in other fields of physics.
Pernal, Katarzyna; Giesbertz, Klaas J H
2016-01-01
Recent advances in reduced density matrix functional theory (RDMFT) and linear response time-dependent reduced density matrix functional theory (TD-RDMFT) are reviewed. In particular, we present various approaches to develop approximate density matrix functionals which have been employed in RDMFT. We discuss the properties and performance of most available density matrix functionals. Progress in the development of functionals has been paralleled by formulation of novel RDMFT-based methods for predicting properties of molecular systems and solids. We give an overview of these methods. The time-dependent extension, TD-RDMFT, is a relatively new theory still awaiting practical and generally useful functionals which would work within the adiabatic approximation. In this chapter we concentrate on the formulation of TD-RDMFT response equations and various adiabatic approximations. None of the adiabatic approximations is fully satisfactory, so we also discuss a phase-dependent extension to TD-RDMFT employing the concept of phase-including-natural-spinorbitals (PINOs). We focus on applications of the linear response formulations to two-electron systems, for which the (almost) exact functional is known. PMID:25971917
Time-dependent density functional theory quantum transport simulation in non-orthogonal basis
Kwok, Yan Ho; Xie, Hang; Yam, Chi Yung; Chen, Guan Hua; Zheng, Xiao
2013-12-14
Basing on the earlier works on the hierarchical equations of motion for quantum transport, we present in this paper a first principles scheme for time-dependent quantum transport by combining time-dependent density functional theory (TDDFT) and Keldysh's non-equilibrium Green's function formalism. This scheme is beyond the wide band limit approximation and is directly applicable to the case of non-orthogonal basis without the need of basis transformation. The overlap between the basis in the lead and the device region is treated properly by including it in the self-energy and it can be shown that this approach is equivalent to a lead-device orthogonalization. This scheme has been implemented at both TDDFT and density functional tight-binding level. Simulation results are presented to demonstrate our method and comparison with wide band limit approximation is made. Finally, the sparsity of the matrices and computational complexity of this method are analyzed.
Energy-density functional approach for non-spherical nuclei
NASA Astrophysics Data System (ADS)
Krömer, E.; Tolokonnikov, S. V.; Fayans, S. A.; Zawischa, D.
1995-02-01
The extension of the self-consistent energy-density functional method to non-spherical nuclei is briefly described. A comparison of the spherical and the non-spherical approach in lead nuclei is given and first results for the chain of strongly deformed dysprosium isotopes are presented.
A real-space stochastic density matrix approach for density functional electronic structure.
Beck, Thomas L
2015-12-21
The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches. PMID:25969148
Towards time-dependent current-density-functional theory in the non-linear regime.
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. PMID:25725723
Towards time-dependent current-density-functional theory in the non-linear regime
NASA Astrophysics Data System (ADS)
EscartÃn, 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
EscartÃn, J. M.; Vincendon, M.; Dinh, P. M.; Suraud, E.; Romaniello, P.; Reinhard, P.-G.
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 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.
Bartolino, Valerio; Ciannelli, Lorenzo; Bacheler, Nathan M; Chan, Kung-Sik
2011-01-01
The spatial dynamics of species are the result of complex interactions between density-independent and density-dependent sources of variability. Disentangling these two sources of variability has challenged ecologists working in both terrestrial and aquatic ecosystems. Using a novel spatially explicit statistical model, we tested for the presence of density-independent and density-dependent habitat selection in yellowfin sole (Limanda aspera) in the eastern Bering Sea. We found specificities in the density-dependent processes operating across ontogeny and particularly with gender. Density-dependent habitat expansion occurred primarily in females, and to a lesser degree in males. These patterns were especially evident in adult stages, while juvenile stages of both sexes exhibited a mix of different dynamics. Association of yellowfin sole with substrate type also varied by sex and to a lesser degree with size, with large females distributed over a wider range of substrates than males. Moreover, yellowfin sole expanded northward as cold subsurface waters retracted in summer, suggesting high sensitivity to arctic warming. Our findings illustrate how marginal habitats can play an important role in buffering density-dependent habitat expansion, with direct implications for resource management. Our spatially explicit modeling approach is effective in evaluating density-dependent spatial dynamics, and can easily be used to test similar hypotheses from a variety of aquatic and terrestrial ecosystems. PMID:21560689
Continuous Dependence on the Density for Stratified Steady Water Waves
NASA Astrophysics Data System (ADS)
Chen, Robin Ming; Walsh, Samuel
2016-02-01
There are two distinct regimes commonly used to model traveling waves in stratified water: continuous stratification, where the density is smooth throughout the fluid, and layer-wise continuous stratification, where the fluid consists of multiple immiscible strata. The former is the more physically accurate description, but the latter is frequently more amenable to analysis and computation. By the conservation of mass, the density is constant along the streamlines of the flow; the stratification can therefore be specified by prescribing the value of the density on each streamline. We call this the streamline density function. Our main result states that, for every smoothly stratified periodic traveling wave in a certain small-amplitude regime, there is an L âˆž neighborhood of its streamline density function such that, for any piecewise smooth streamline density function in that neighborhood, there is a corresponding traveling wave solution. Moreover, the mapping from streamline density function to wave is Lipschitz continuous in a certain function space framework. As this neighborhood includes piecewise smooth densities with arbitrarily many jump discontinues, this theorem provides a rigorous justification for the ubiquitous practice of approximating a smoothly stratified wave by a layered one. We also discuss some applications of this result to the study of the qualitative features of such waves.
The multi-configurational time-dependent Hartree approach revisited
NASA Astrophysics Data System (ADS)
Manthe, Uwe
2015-06-01
The multi-configurational time-dependent Hartree (MCTDH) approach facilitates accurate high-dimensional quantum dynamics simulations. In the approach, the wavefunction is expanded in a direct product of self-adapting time-dependent single-particle functions (SPFs). The equations of motion for the expansion coefficients and the SPFs are obtained via the Dirac-Frenkel variational principle. While this derivation yields well-defined differential equations for the motion of occupied SPFs, singularities in the working equations resulting from unoccupied SPFs have to be removed by a regularization procedure. Here, an alternative derivation of the MCTDH equations of motion is presented. It employs an analysis of the time-dependence of the single-particle density matrices up to second order. While the analysis of the first order terms yields the known equations of motion for the occupied SPFs, the analysis of the second order terms provides new equations which allow one to identify optimal choices for the unoccupied SPFs. The effect of the optimal choice of the unoccupied SPFs on the structure of the MCTDH equations of motion and their regularization is discussed. Generalized equations applicable in the multi-layer MCTDH framework are presented. Finally, the effects resulting from the initial choice of the unoccupied SPFs are illustrated by a simple numerical example.
The multi-configurational time-dependent Hartree approach revisited.
Manthe, Uwe
2015-06-28
The multi-configurational time-dependent Hartree (MCTDH) approach facilitates accurate high-dimensional quantum dynamics simulations. In the approach, the wavefunction is expanded in a direct product of self-adapting time-dependent single-particle functions (SPFs). The equations of motion for the expansion coefficients and the SPFs are obtained via the Dirac-Frenkel variational principle. While this derivation yields well-defined differential equations for the motion of occupied SPFs, singularities in the working equations resulting from unoccupied SPFs have to be removed by a regularization procedure. Here, an alternative derivation of the MCTDH equations of motion is presented. It employs an analysis of the time-dependence of the single-particle density matrices up to second order. While the analysis of the first order terms yields the known equations of motion for the occupied SPFs, the analysis of the second order terms provides new equations which allow one to identify optimal choices for the unoccupied SPFs. The effect of the optimal choice of the unoccupied SPFs on the structure of the MCTDH equations of motion and their regularization is discussed. Generalized equations applicable in the multi-layer MCTDH framework are presented. Finally, the effects resulting from the initial choice of the unoccupied SPFs are illustrated by a simple numerical example. PMID:26133412
The dependence of cylindrical resonator natural frequencies on the fluid density
NASA Astrophysics Data System (ADS)
Rudachenko, V.; Filushin, V.; Korotchenko, T.
2015-11-01
The article examines the dependence of cylindrical resonator natural frequencies (sensitive element) on the density (mass) of different fluids flowing through it. The cylindrical resonators are being widely applied in automatic control systems of technological processes as oscillating transducer density meter. The article presents the experimental results that prove the dependence of natural frequencies and vibration amplitude on the fluid density.
NASA Astrophysics Data System (ADS)
Petrenko, Taras; Kossmann, Simone; Neese, Frank
2011-02-01
In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ˜26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ˜27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ˜24 on 30 processors. The parallelization efficiency for the Coulomb terms can be somewhat smaller (speedup ˜15-25 for 30 processors), but their contribution to the total calculation time is small. Thus, the parallel program completes a Becke3-Lee-Yang-Parr energy and gradient calculation on the Ag-TB2-helicate in less than 4 h on 30 processors. We also present the necessary extension of the Lagrangian formalism, which enables the calculation of the TDDFT excited state properties in the frozen-core approximation. The algorithms described in this work are implemented into the ORCA electronic structure system.
Bollinger, Jonathan A; Jain, Avni; Truskett, Thomas M
2014-07-22
Molecular dynamics simulations and a stochastic method based on the Fokker-Planck equation are used to explore the consequences of inhomogeneous density profiles on the thermodynamic and dynamic properties of the hard-sphere fluid and supercooled liquid water. Effects of the inhomogeneity length scale are systematically considered via the imposition of sinusoidal density profiles of various wavelengths. For long-wavelength density profiles, bulk-like relationships between local structure, thermodynamics, and diffusivity are observed as expected. However, for both systems, a crossover in behavior occurs as a function of wavelength, with qualitatively different correlations between the local static and dynamic quantities emerging as density variations approach the scale of a particle diameter. Irrespective of the density variation wavelength, average diffusivities of hard-sphere fluids in the inhomogeneous and homogeneous directions are coupled and approximately correlate with the volume available for insertion of another particle. Unfortunately, a quantitatively reliable static predictor of position-dependent dynamics has yet to be identified for even the simplest of inhomogeneous fluids. PMID:24984592
Cell density-dependent reduction of dihydroceramide desaturase activity in neuroblastoma cells[S
Spassieva, Stefka D.; Rahmaniyan, Mehrdad; Bielawski, Jacek; Clarke, Christopher J.; Kraveka, Jacqueline M.; Obeid, Lina M.
2012-01-01
We applied a metabolic approach to investigate the role of sphingolipids in cell density-induced growth arrest in neuroblastoma cells. Our data revealed that sphingolipid metabolism in neuroblastoma cells significantly differs depending on the cells’ population context. At high cell density, cells exhibited G0/G1 cell-cycle arrest and reduced ceramide, monohexosylceramide, and sphingomyelin, whereas dihydroceramide was significantly increased. In addition, our metabolic-labeling experiments showed that neuroblastoma cells at high cell density preferentially synthesized very long chain (VLC) sphingolipids and dramatically decreased synthesis of sphingosine-1-phosphate (S1P). Moreover, densely populated neuroblastoma cells showed increased message levels of both anabolic and catabolic enzymes of the sphingolipid pathway. Notably, our metabolic-labeling experiments indicated reduced dihydroceramide desaturase activity at confluence, which was confirmed by direct measurement of dihydroceramide desaturase activity in situ and in vitro. Importantly, we could reduce dihydroceramide desaturase activity in low-density cells by applying conditional media from high-density cells, as well as by adding reducing agents, such as DTT and l-cysteine to the media. In conclusion, our data suggest a role of the sphingolipid pathway, dihydroceramides desaturase in particular, in confluence-induced growth arrest in neuroblastoma cells. PMID:22377532
Ion upflow dependence on ionospheric density and solar photoionization
NASA Astrophysics Data System (ADS)
Cohen, I. J.; Lessard, M. R.; Varney, R. H.; Oksavik, K.; Zettergren, M.; Lynch, K. A.
2015-11-01
Motivated by rocket observations showing a variety of different ionospheric responses to precipitation, this paper explores the influence of the background ionospheric density on upflow resulting from auroral precipitation. Simulations of upflow driven by auroral precipitation were conducted using a version of the Varney et al. (2014) model driven by precipitation characterized by observations made during the 2012 Magnetosphere-Ionosphere Coupling in the Alfvén resonator rocket mission and using a variety of different initial electron density profiles. The simulation results show that increased initial density before the onset of precipitation leads to smaller electron temperature increases, longer ionospheric heating timescales, weaker ambipolar electric fields, lower upflow speeds, and longer upflow timescales but larger upflow fluxes. The upflow flux can increase even when the ambipolar electric field strength decreases due to the larger number of ions that are accelerated. Long-term observations from the European Incoherent Scatter (EISCAT) Svalbard radar taken during the International Polar Year support the effects seen in the simulations. This correlation between ionospheric density and ion upflows emphasizes the important role of photoionization from solar ultraviolet radiation, which the EISCAT observations show can increase ionospheric density by as much as an order of magnitude during the summer months.
Density dependent stopping power and muon sticking in muon catalyzed D-T fusion
Rafelski, H.E.; Mueller, B.
1988-12-27
The origin of the experimentally observed (1) density dependence of the muon alpha sticking fraction ..omega../sub s/ in muon catalyzed deuterium- tritium fusion is investigated. We show that the reactivation probability depends sensitively on the target stopping power at low ion velocities. The density dependence of the stopping power for a singly charged projectile in liquid heavy hydrogen is parametrized to simulate possible screening effects and a density dependent effective ionization potential. We find that, in principle, a description of the measured density dependence is possible, but the required parameters appear too large. Also, the discrepancy with observed (He..mu..) X-ray data widens.
Density dependence, whitebark pine, and vital rates of grizzly bears
van Manen, Frank T.; Haroldson, Mark A.; Bjornlie, Daniel D; Ebinger, Michael R.; Thompson, Daniel J.; Costello, Cecily M; White, Gary C.
2016-01-01
Understanding factors influencing changes in population trajectory is important for effective wildlife management, particularly for populations of conservation concern. Annual population growth of the grizzly bear (Ursus arctos) population in the Greater Yellowstone Ecosystem, USA has slowed from 4.2â€“7.6% during 1983â€“2001 to 0.3â€“2.2% during 2002â€“2011. Substantial changes in availability of a key food source and bear population density have occurred. Whitebark pine (Pinus albicaulis), the seeds of which are a valuable but variable fall food for grizzly bears, has experienced substantial mortality primarily due to a mountain pine beetle (Dendroctonus ponderosae) outbreak that started in the early 2000s. Positive growth rates of grizzly bears have resulted in populations reaching high densities in some areas and have contributed to continued range expansion. We tested research hypotheses to examine if changes in vital rates detected during the past decade were more associated with whitebark pine decline or, alternatively, increasing grizzly bear density. We focused our assessment on known-fate data to estimate survival of cubs-of-the-year (cubs), yearlings, and independent bears (â‰¥2 yrs), and reproductive transition of females from having no offspring to having cubs. We used spatially and temporally explicit indices for grizzly bear density and whitebark pine mortality as individual covariates. Models indicated moderate support for an increase in survival of independent male bears over 1983â€“2012, whereas independent female survival did not change. Cub survival, yearling survival, and reproductive transition from no offspring to cubs all changed during the 30-year study period, with lower rates evident during the last 10â€“15 years. Cub survival and reproductive transition were negatively associated with an index of grizzly bear density, indicating greater declines where bear densities were higher. Our analyses did not support a similar relationship for the index of whitebark pine mortality. The results of our study support the interpretation that slowing of population growth during the last decade was associated more with increasing grizzly bear density than the decline in whitebark pine. Grizzly bear density and its potential effect on vital rates and population trajectory warrant consideration for management of the grizzly bear population in the Greater Yellowstone Ecosystem.
A density-based approach to node clustering in decentralized peer-to- peer networks
NASA Astrophysics Data System (ADS)
Shi, Qingwei; Zhao, Zheng; Bao, Hu
2007-09-01
Efficient organization of the nodes in decentralized peer-to-peer (P2P) networks is a challenging problem, especially in the absence of a global schema. Node clustering is an available way to optimize infrastructure and decrease traffic cost in P2P networks. This paper proposes a Density-based Distributed Node Clustering (DDNC) approach to discovering clusters in P2P networks. This approach is completely distributed, in which each node only depends on the knowledge of its neighbors for node clustering. Unlike other graph based algorithms, the DDNC approach utilizes density of node's neighbor for discovering clusters. For a given node, the DDNC determines its neighbor density by computing the link time with its neighbors, which not only considers the node connectivity but also connection quality. The DDNC scheme can also dynamically adapt its clusters according to the participation and departure of nodes. Experimental results have shown ours scheme's feasibility and efficiency.
Dependence of Type Ia Supernovae on Progenitor Central Density
NASA Astrophysics Data System (ADS)
Krueger, Brendan K.; Calder, A. C.; Townsley, D. M.; Jackson, A. P.; Brown, E. F.
2010-01-01
Recent observational studies of Type Ia supernovae (SNeIa) suggest correlations between the brightness of an event and properties of the host galaxy that may involve the age of the progenitor population. One way to influence the explosion systematically is through the ignition density, which is determined by both the mass of the white dwarf before the onset of accretion and the subsequent accretion history, and is therefore related to the age of the progenitor. We present the results of a suite of two-dimensional SNeIa simulations investigating how the central density of the progenitor white dwarf at flame ignition influences the production of Fe-group material, particularly the production of radioactive Ni-56 that powers the light curve. The simulation suite constitutes a theoretical population of events allowing a statistically well-controlled investigation into systematic trends (Townsley et al. 2009). The simulations indicate that with increased central density, more Fe-group material is produced but with less total Ni-56, which we attribute to a higher rate of neutronization occurring at higher density. Additionally, we compare our results with those of Roepke et al. (2006). This work was supported by NASA under grant No. NNX09AD19G and utilized resources at the New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory, which is supported by the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 and by the State of New York.
Excursion behaviour of female roe deer may depend on density.
Bocci, A; Aiello, V; Lovari, S
2013-07-01
The excursion behaviour of roe does was studied for two years in a low density population (ca. 6.5 ind./100 ha), in an Apennine-continental forest of Southern Italy, through satellite radiotracking. During the rutting period, our radiotagged does (N=6) moved well outside their summer ranges, with an average exploration area eight times greater than summer ranges. The median duration of excursions was 51 h (range: 10-99 h). One female stayed away for a total of 11 days. In order further to understand this behaviour, we reviewed all studies (N=6) dealing with excursion behaviour of roe does and carried out in areas where population density was assessed through the same method (i.e. drive counts). Out of five ecological parameters included in the analysis, excursion behaviour of roe does was found significantly and negatively associated only to population density: when density was low, the proportion of roaming does increased, probably because of the lower availability of "free" bucks during the short time of female oestrous. PMID:23567912
Relativistic Coulomb excitation within the time dependent superfluid local density approximation
Stetcu, I.; Bertulani, C. A.; Bulgac, A.; Magierski, P.; Roche, K. J.
2015-01-06
Within the framework of the unrestricted time-dependent density functional theory, we present for the first time an analysis of the relativistic Coulomb excitation of the heavy deformed open shell nucleus ^{238}U. The approach is based on the superfluid local density approximation formulated on a spatial lattice that can take into account coupling to the continuum, enabling self-consistent studies of superfluid dynamics of any nuclear shape. We compute the energy deposited in the target nucleus as a function of the impact parameter, finding it to be significantly larger than the estimate using the Goldhaber-Teller model. The isovector giant dipole resonance, the dipole pygmy resonance, and giant quadrupole modes are excited during the process. As a result, the one-body dissipation of collective dipole modes is shown to lead a damping width Î“â†“â‰ˆ0.4 MeV and the number of preequilibrium neutrons emitted has been quantified.
Relativistic Coulomb excitation within the time dependent superfluid local density approximation.
Stetcu, I; Bertulani, C A; Bulgac, A; Magierski, P; Roche, K J
2015-01-01
Within the framework of the unrestricted time-dependent density functional theory, we present for the first time an analysis of the relativistic Coulomb excitation of the heavy deformed open shell nucleus (238)U. The approach is based on the superfluid local density approximation formulated on a spatial lattice that can take into account coupling to the continuum, enabling self-consistent studies of superfluid dynamics of any nuclear shape. We compute the energy deposited in the target nucleus as a function of the impact parameter, finding it to be significantly larger than the estimate using the Goldhaber-Teller model. The isovector giant dipole resonance, the dipole pygmy resonance, and giant quadrupole modes are excited during the process. The one-body dissipation of collective dipole modes is shown to lead a damping width ?(?)?0.4??MeV and the number of preequilibrium neutrons emitted has been quantified. PMID:25615463
Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors
The interaction between density dependence (DD) and environmental stressors can result in a compensatory or synergistic response in population growth, and population models that use density-independent demographic rates or generic DD functions may be introducing bias into managem...
Wang, Fan; Yam, Chi Yung; Chen, GuanHua; Fan, Kangnian
2007-04-01
A density matrix based time-dependent density functional theory is extended in the present work. Chebyshev expansion is introduced to propagate the linear response of the reduced single-electron density matrix upon the application of a time-domain delta-type external potential. The Chebyshev expansion method is more efficient and accurate than the previous fourth-order Runge-Kutta method and removes a numerical divergence problem. The discrete Fourier transformation and filter diagonalization of the first-order dipole moment are implemented to determine the excited state energies. It is found that the filter diagonalization leads to highly accurate values for the excited state energies. Finally, the density matrix based time-dependent density functional is generalized to calculate the energies of singlet-triplet excitations. PMID:17430013
Einum, Sigurd; Robertsen, Grethe; Fleming, Ian A
2008-01-01
Theory suggests an important role for population density in shaping adaptive landscapes through density-dependent selection. Here, we identify five methodological approaches for studying such selection, review the existing empirical evidence for it, and ask whether current declines in abundance can be expected to trigger evolutionary responses in salmonid fishes. Across taxa we find substantial amounts of evidence for population density influencing the location of adaptive peaks for a range of traits, and, in the presence of frequency dependence, changing the shape of selection (stabilizing versus disruptive). For salmonids, biological and theoretical considerations suggest that the optimal value of a number of traits associated with juvenile competitive ability (e.g. egg size, timing of emergence from nests, dominance ability), may depend on population density. For adults, more direct experimental and comparative evidence suggest that secondary sexual traits can be subject to density-dependent selection. There is also evidence that density affects the frequency-dependent selection likely responsible for the expression of alternative male reproductive phenotypes in salmon. Less is known however about the role of density in maintaining genetic variation among juveniles. Further efforts are required to elucidate the indirect evolutionary effects of declining population abundances, both in salmonids and in other anthropogenically challenged organisms. PMID:25567629
Investigation of power dependence of electron density for various pressures
NASA Astrophysics Data System (ADS)
Kim, June Young; Kim, Dong-Hwan; Kim, Ju Ho; Jeon, Sang-Bum; Chung, Chin-Wook
2014-10-01
Experimental observation of the electron density variation in inductively coupled plasmas with the electron energy probability function was performed at various gas pressures at two RF input powers (25 W, 200 W). The measured electron energy probability functions (EEPFs) at high power discharges (200 W) showed a Maxwellian distribution, while evolution of the EEPFs from a bi-Maxwellian distribution to a Druyvesteyn-like distribution was observed at low RF powers (25 W) with increasing pressure. A discrepancy of the electron density variation between the two RF input powers was observed, and it was explained by the modified collisional loss and the Bohm velocity from the electron energy probability functions of the bi-Maxwellian distribution and the Druyvesteyn -like distribution.
Attarian Shandiz, M. Gauvin, R.
2014-10-28
The temperature and pressure dependency of the volume plasmon energy of solids was investigated by density functional theory calculations. The volume change of crystal is the major factor responsible for the variation of valence electron density and plasmon energy in the free electron model. Hence, to introduce the effect of temperature and pressure for the density functional theory calculations of plasmon energy, the temperature and pressure dependency of lattice parameter was used. Also, by combination of the free electron model and the equation of state based on the pseudo-spinodal approach, the temperature and pressure dependency of the plasmon energy was modeled. The suggested model is in good agreement with the results of density functional theory calculations and available experimental data for elements with the free electron behavior.
Broadcasting but not receiving: density dependence considerations for SETI signals
NASA Astrophysics Data System (ADS)
Smith, Reginald D.
2009-04-01
This paper develops a detailed quantitative model which uses the Drake equation and an assumption of an average maximum radio broadcasting distance by an communicative civilization. Using this basis, it estimates the minimum civilization density for contact between two civilizations to be probable in a given volume of space under certain conditions, the amount of time it would take for a first contact, and the question of whether reciprocal contact is possible.
How important is self-consistency for the dDsC density dependent dispersion correction?
BrÃ©mond, Ã‰ric; Corminboeuf, ClÃ©mence; Golubev, Nikolay; Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991 ; Steinmann, Stephan N.
2014-05-14
The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.
How important is self-consistency for the dDsC density dependent dispersion correction?
BrÃ©mond, Ã‰ric; Golubev, Nikolay; Steinmann, Stephan N; Corminboeuf, ClÃ©mence
2014-05-14
The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation. PMID:24832324
Invasion rate of deer ked depends on spatiotemporal variation in host density.
Meier, C M; Bonte, D; Kaitala, A; Ovaskainen, O
2014-06-01
Invasive parasites are of great global concern. Understanding the factors influencing the spread of invading pest species is a first step in developing effective countermeasures. Growing empirical evidence suggests that spread rates are essentially influenced by spatiotemporal dynamics of host-parasite interactions, yet approaches modelling spread rate have typically assumed static environmental conditions. We analysed invasion history of the deer ked (Lipoptena cervi) in Finland with a diffusion-reaction model, which assumed either the movement rate, the population growth rate, or both rates may depend on spatial and temporal distribution of moose (Alces alces), the main host of deer ked. We fitted the model to the data in a Bayesian framework, and used the Bayesian information criterion to show that accounting for the variation in local moose density improved the model's ability to describe the pattern of the invasion. The highest ranked model predicted higher movement rate and growth rate of deer ked with increasing moose density. Our results suggest that the historic increase in host density has facilitated the spread of the deer ked. Our approach illustrates how information about the ecology of an invasive species can be extracted from the spatial pattern of spread even with rather limited data. PMID:24521661
Using time-dependent density functional theory in real time for calculating electronic transport
NASA Astrophysics Data System (ADS)
Schaffhauser, Philipp; KÃ¼mmel, Stephan
2016-01-01
We present a scheme for calculating electronic transport within the propagation approach to time-dependent density functional theory. Our scheme is based on solving the time-dependent Kohn-Sham equations on grids in real space and real time for a finite system. We use absorbing and antiabsorbing boundaries for simulating the coupling to a source and a drain. The boundaries are designed to minimize the effects of quantum-mechanical reflections and electrical polarization build-up, which are the major obstacles when calculating transport by applying an external bias to a finite system. We show that the scheme can readily be applied to real molecules by calculating the current through a conjugated molecule as a function of time. By comparing to literature results for the conjugated molecule and to analytic results for a one-dimensional model system we demonstrate the reliability of the concept.
NASA Astrophysics Data System (ADS)
Showalter, Rachel Hodges
The nuclear symmetry energy, which is important for asymmetric nuclear systems including rare isotopes and neutron stars, has been studied through both experimental and theoretical approaches, spanning a range of densities from below and above normal nuclear matter density. In the past decade, significant constraints on the density dependence have been obtained in the subsaturation density region, from Heavy Ion Collision (HIC) experiments as well as experiments probing nuclear structure. On the other hand, very little has been determined about the symmetry energy at suprasaturation densities; experimentally, this density region is only accessible in HICs. It is therefore important to understand how to extract nuclear symmetry energy information from HIC at high energies where high density nuclear matter is created in a very brief instant. Symmetry energy constraints from HICs are determined by comparing experimental observables with those calculated using transport models. The goals of this dissertation are to identify the observables most sensitive to the symmetry energy strength, the effective mass splitting, and the in-medium nucleon-nucleon cross sections, sigmaNN, at the region just above saturation density which can be created with heavy ion beams available at NSCL. With better constraints in place, the predictive power of transport models will improve. Recent constraints from HIC experiments have relied on symmetric systems, which are predicted to be sensitive to both the density- and the momentum-dependence of the symmetry potentials. In the study of the nuclear equation of state, asymmetric systems have proven to be more effective at low energy in exploring sensitivities to nucleon-nucleon collisions, which is an important input to any transport model. In this work, particles that were emitted from Ca+Sn systems, with a 48Ca beam impinging on 112Sn or 124Sn targets are measured. The experimental data were compared to predictions from the Improved Molecular Dynamics model with Skyrme interactions (ImQMD-Sky). Four Skyrme parameter sets were chosen that span current constraints on the density dependence of the symmetry energy and on the nucleon effective mass splitting, m*n?m* p, which results from the momentum dependent interaction potentials. ImQMD-Sky calculations were repeated using an alternate form for sigma NN.. The yields and ratios of both free and coalescence invariant experimental spectra, constructed as a function of the transverse momentum, were contrasted to those simulated by ImQMD-Sky. To select the overlap region between beam and target nuclei, a mid-rapidity cut was taken in the analysis. The parameter sets included in this analysis did not show a significant sensitivity to the symmetry energy strength, but do suggest that the neutron-to-proton ratio bears a large sensitivity both to the nucleon effective mass splitting and the sigmaNN forms used in the calculations. Comparison to the measured coalescence invariant spectra suggests a better agreement with calculations employing effective masses that are greater for neutrons than for protons and a set of isospin-dependent sigma NN. The results in this analysis for the asymmetric Ca+Sn reaction are compared with previous results for a symmetric Sn+Sn reaction at 120 AMeV, which shows an opposite conclusion for low energy particles.
Dynamics of kaonic nuclei in an improved quark mass density-dependent model
NASA Astrophysics Data System (ADS)
Xu, R. L.; Wu, C.; Qian, W.-L.; Ren, Z. Z.
2015-02-01
The improved quark mass density-dependent model, which is able to provide a good description for the properties of both finite nuclei and bulk nuclear matter, is employed to investigate the properties of several possible light kaonic nuclei. The current approach is based on an extended version of the relativistic mean-field theory, where the kaon-nucleon and nucleon-nucleon interactions are treated on the same footing. In this work, the single K--nuclear states in the possible bubble nuclei are studied, with concentration on the experimentally accessible light nuclei. The K- binding energies, the decay widths, single-particle spectra, and nuclear and K- density distributions are evaluated. The calculations indicate that, when the K- meson is embedded in nuclei with speculated "bubble" structure, the depleted central nuclear density might be modified, and in certain cases, the bubble structure may even disappear. Furthermore, it is found that the properties of the kaonic nuclei are sensitive to the strength of the antikaon optical potential at saturation density.
Modeling density dependent flow in the sedimentary basin of Thuringia
NASA Astrophysics Data System (ADS)
Zech, A.; Zehner, B.; Fischer, T.; Kolditz, O.; Attinger, S.
2012-04-01
Salty groundwater reaching the surface or coming close to it is a phenomena that can be observed in many places of the Thuringian Basin. However, it is not obvious, why denser brine overlays lighter fresh water in this region. The hydrogeological processes which cause the rising of saltwater plumes from deeper geological layers to the surface are not yet fully understood. The goal of this modeling project is to investigate the mechanism of brine transport within the aquifers of sedimentary basins in general and of Thuringian Basin in particular. In this study we focus at investigating the fluid dynamics of the basin and how the fluid convection of the deep horizons interacts with groundwater flow near the surface. By gradually increasing the complexity of our model we analyze the major mechanism influencing the flow pattern: geology and hydraulic properties, fluid density differences caused by temperature and salt concentration gradients, fractures and faults as well as boundary conditions of the model, like inflow, outflow and groundwater recharge. For our numerical investigations we use a cross section of the Thuringian basin of approximately 80km length and maximal 800m height. The hydrogeological model is based on the major stratigraphical units from upper Perm (Zechstein) to upper Triassic (Keuper) with the lower Triassic (Bundsandstein) formations representing the main aquifer. The structural model as well as aquifer parameters are provided by geological partner groups of the University of Jena, Germany. To investigate hydrogeological scenarios we use the groundwater simulation program OpenGeoSys, which allows us to calculate thermally, hydrologically and chemically coupled processes. The challenge for us is to include density driven flow as a numerically very sensitive process on a grid that represents a large scale geologically realistic setting. With this work we contribute to the understanding of fluid convection processes influenced by density differences and local geological characteristics, especially for the local conditions in the sedimentary basin of Thuringia.
Volume dependence of two-dimensional large-N QCD with a nonzero density of baryons
Bringoltz, Barak
2009-05-15
We take a first step towards the solution of QCD in 1+1 dimensions at nonzero density. We regularize the theory in the UV by using a lattice and in the IR by putting the theory in a box of spatial size L. After fixing to axial gauge we use the coherent states approach to obtain the large-N classical Hamiltonian H that describes color neutral quark-antiquark pairs interacting with spatial Polyakov loops in the background of baryons. Minimizing H we get a regularized form of the 't Hooft equation that depends on the expectation values of the Polyakov loops. Analyzing the L dependence of this equation we show how volume independence, a la Eguchi and Kawai, emerges in the large-N limit, and how it depends on the expectation values of the Polyakov loops. We describe how this independence relies on the realization of translation symmetry, in particular, when the ground state contains a baryon crystal. Finally, we remark on the implications of our results on studying baryon density in large-N QCD within single-site lattice theories and on some general lessons concerning the way four-dimensional large-N QCD behaves in the presence of baryons.
Density-dependence of functional spiking networks in vitro
Ham, Michael I; Gintautuas, Vadas; Rodriguez, Marko A; Bettencourt, Luis M A; Bennett, Ryan; Santa Maria, Cara L
2008-01-01
During development, the mammalian brain differentiates into specialized regions with unique functional abilities. While many factors contribute to this functional specialization, we explore the effect neuronal density can have on neuronal interactions. Two types of networks, dense (50,000 neurons and glia support cells) and sparse (12,000 neurons and glia support cells), are studied. A competitive first response model is applied to construct activation graphs that represent pairwise neuronal interactions. By observing the evolution of these graphs during development in vitro we observe that dense networks form activation connections earlier than sparse networks, and that link-!llltropy analysis of the resulting dense activation graphs reveals that balanced directional connections dominate. Information theoretic measures reveal in addition that early functional information interactions (of order 3) are synergetic in both dense and sparse networks. However, during development in vitro, such interactions become redundant in dense, but not sparse networks. Large values of activation graph link-entropy correlate strongly with redundant ensembles observed in the dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue also in vivo.
Simulation of sprays using a Lagrangian filtered density function approach
NASA Astrophysics Data System (ADS)
Liu, Wanjiao; Garrick, Sean
2013-11-01
Sprays and atomization have wide applications in industry, including combustion/engines, pharmaceutics and agricultural spraying. Due to the complexity of the underlying processes, much of the underlying phenomena are not fully understood. Numerical simulation may provide ways to investigate atomization and spray dynamics. Large eddy simulation (LES) is a practical approach to flow simulation as it resolves only the large-scale structures while modeling the sub-grid scale (SGS) effects. We combine a filtered density function (FDF) based approach with a Lagrangian volume-of-fluid method to perform LES. This resulting methodology is advantageous in that it has no diffusive or dissipative numerical errors, and the highly non-linear surface tension force appears in closed form thus the modeling of the SGS surface tension is not needed when simulating turbulent, multiphase flows. We present the methodology and some results for the simulation of multiphase jets.
High temperature intensifies negative density dependence of fitness in red flour beetles
Halliday, William D; Thomas, Alison S; Blouin-Demers, Gabriel
2015-01-01
Competition for food, space, or other depletable resources has strong impacts on the fitness of organisms and can lead to a pattern known as negative density dependence, where fitness decreases as population density increases. Yet, many resources that have strong impacts on fitness are nondepletable (e.g., moisture or temperature). How do these nondepletable resources interact with depletable resources to modify negative density dependence? We tested the hypothesis that negative density dependence is modulated by temperature in red flour beetles and tested the prediction that the strength of negative density dependence should decrease as temperature decreases. We measured the number of eggs laid, offspring development time, and the number of offspring that reached maturity at three temperatures and two food treatment combinations as we simultaneously manipulated adult population density. We demonstrated that low temperatures weaken negative density dependence in the number of eggs laid; this pattern was most evident when food was abundant. Density had no effect on development time, but low temperatures increased development time. The percent of eggs that emerged as adults decreased with both density and temperature and increased with food. Temperature, an abiotic driver, can thus modulate density-dependent processes in ectotherms. Therefore, models of population growth for ectotherms should incorporate the effects of temperature. PMID:25798223
Density-Dependent Effects on Group Size Are Sex-Specific in a Gregarious Ungulate
Vander Wal, Eric; van Beest, Floris M.; Brook, Ryan K.
2013-01-01
Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km2 between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ?0.70 elk/km2 and we found evidence for a minimum group size at population density ?0.70 elk/km2. Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission. PMID:23326502
Position-dependent mass quantum Hamiltonians: general approach and duality
NASA Astrophysics Data System (ADS)
Rego-Monteiro, M. A.; Rodrigues, Ligia M. C. S.; Curado, E. M. F.
2016-03-01
We analyze a general family of position-dependent mass (PDM) quantum Hamiltonians which are not self-adjoint and include, as particular cases, some Hamiltonians obtained in phenomenological approaches to condensed matter physics. We build a general family of self-adjoint Hamiltonians which are quantum mechanically equivalent to the non-self-adjoint proposed ones. Inspired by the probability density of the problem, we construct an ansatz for the solutions of the family of self-adjoint Hamiltonians. We use this ansatz to map the solutions of the time independent SchrÃ¶dinger equations generated by the non-self-adjoint Hamiltonians into the Hilbert space of the solutions of the respective dual self-adjoint Hamiltonians. This mapping depends on both the PDM and on a function of position satisfying a condition that assures the existence of a consistent continuity equation. We identify the non-self-adjoint Hamiltonians here studied with a very general family of Hamiltonians proposed in a seminal article of Harrison (1961 Phys. Rev. 123 85) to describe varying band structures in different types of metals. Therefore, we have self-adjoint Hamiltonians that correspond to the non-self-adjoint ones found in Harrisonâ€™s article.
Approaches to 100 Gbit/sq. in. recording density
NASA Technical Reports Server (NTRS)
Kryder, Mark H.
1994-01-01
A recording density of 10 Gbit/sq. in. is being pursued by a number of companies and universities in the National Storage Industry Consortium. It is widely accepted that this goal will be achieved in the laboratory within a few years. In this paper approaches to achieving 100 Gbit/sq. in. storage densities are considered. A major obstacle to continued scaling of magnetic recording to higher densities is that as the bit size is reduced, the grain size in the magnetic media must be reduced in order that media noise does not become so large that the signal to noise ratio (SNR) degrades sufficiently to make detection impossible. At 100 Gbit/sq. in., the bit size is only 0.006 square micrometers, which, in order to achieve 30 dB SNR, requires a grain size of about 2.5 nm. Such small grains are subject to thermal instability, and the recorded information will degrade over time unless the magnetic anisotropy of the materials used is increased significantly, or the media thickness is made much larger than expected on the basis of scaling today's longitudinal media thickness.
Time-Dependent Density Functional Theory for Extreme Environments
NASA Astrophysics Data System (ADS)
Baczewski, Andrew; Magyar, Rudolph; Shulenburger, Luke
2013-10-01
In recent years, DFT-MD has been shown to be a powerful tool for calculating the equation of state and constitutive properties of warm dense matter (WDM). These studies are validated through a number of experiments, including recently developed X-Ray Thomson Scattering (XRTS) techniques. Here, electronic temperatures and densities of WDM are accessible through x-ray scattering data, which is related to the system's dynamic structure factor (DSF)-a quantity that is accessible through DFT-MD calculations. Previous studies predict the DSF within the Born-Oppenheimer approximation, with the electronic state computed using Mermin DFT. A capability for including more general coupled electron-ion dynamics is desirable, to study both the effect on XRTS observables and the broader problem of electron-ion energy transfer in extreme WDM conditions. Progress towards such a capability will be presented, in the form of an Ehrenfest MD framework using TDDFT. Computational challenges and open theoretical questions will be discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94AL85000.
Density-dependent life history and the dynamics of small populations.
Mugabo, Marianne; Perret, Samuel; Legendre, Stéphane; Le Galliard, Jean-François
2013-11-01
1. Small population dynamics depend importantly on the strength and shape of density dependence. Unfortunately, the lack of reliable life-history data often prevents to make accurate demographic predictions for populations regulated by density dependence. 2. We created a gradient from low to high densities in small experimental populations of common lizards (Zootoca vivipara) and investigated the shape and strength of the density dependence of life-history traits during a yearly cycle. We then analysed stochastic population dynamics using one-sex and two-sex age-structured matrix models. 3. Body growth and reproductive performances decreased with density, yearling and adult survival and body size at birth were density-independent, and juvenile survival increased with density. The density dependence of reproduction was partly explained by positive effects of body size on age at first reproduction and clutch size. 4. Parturition date decreased with density in sparse populations and then increased, providing one of the first empirical evidence of a component Allee effect in the phenology of reproduction. 5. Population growth rate (?) was most affected by variations in juvenile and yearling survival. However, density at equilibrium was most affected by juvenile access to reproduction and yearling clutch size. 6. Stochastic simulations revealed that negative density dependence buffers the effects of initial density on extinction probability, has positive effects on the persistence of sparse populations and interacts with sex ratio fluctuations to shape extinction dynamics. 7. This study demonstrates that negative density dependence modifies the dynamics of small populations and should be investigated together with Allee effects to predict extinction risks. PMID:23859253
Electron density dependence of impedance probe plasma potential measurements
NASA Astrophysics Data System (ADS)
Walker, D. N.; Blackwell, D. D.; Amatucci, W. E.
2015-08-01
In earlier works, we used spheres of various sizes as impedance probes in demonstrating a method of determining plasma potential, ?p, when the probe radius is much larger than the Debye length, ?D. The basis of the method in those works [Walker et al., Phys. Plasmas 13, 032108 (2006); ibid. 15, 123506 (2008); ibid. 17, 113503 (2010)] relies on applying a small amplitude signal of fixed frequency to a probe in a plasma and, through network analyzer-based measurements, determining the complex reflection coefficient, ?, for varying probe bias, Vb. The frequency range of the applied signal is restricted to avoid sheath resonant effects and ion contributions such that ?pi ? ? ? ?pe, where ?pi is the ion plasma frequency and ?pe is the electron plasma frequency. For a given frequency and applied bias, both Re(Zac) and Im(Zac) are available from ?. When Re(Zac) is plotted versus Vb, a minimum predicted by theory occurs at ?p [Walker et al., Phys. Plasmas 17, 113503 (2010)]. In addition, Im(Zac) appears at, or very near, a maximum at ?p. As ne decreases and the sheath expands, the minimum becomes harder to discern. The purpose of this work is to demonstrate that when using network analyzer-based measurements, ? itself and Im(Zac) and their derivatives are useful as accompanying indicators to Re(Zac) in these difficult cases. We note the difficulties encountered by the most commonly used plasma diagnostic, the Langmuir probe. Spherical probe data is mainly used in this work, although we present limited data for a cylinder and a disk. To demonstrate the effect of lowered density as a function of probe geometry, we compare the cylinder and disk using only the indicator Re(Zac).
Bassar, Ronald D; Lopez-Sepulcre, Andres; Reznick, David N; Travis, Joseph
2013-01-01
Recent study of feedbacks between ecological and evolutionary processes has renewed interest in population regulation and density-dependent selection because they represent black-box descriptions of these feedbacks. The roles of population regulation and density-dependent selection in life-history evolution have received a significant amount of theoretical attention, but there are few empirical examples demonstrating their importance. We address this challenge in natural populations of the Trinidadian guppy (Poecilia reticulata) that differ in their predation regimes. First, we tested whether natural populations of guppies are regulated by density dependence and quantified in which phases of the life cycle the effects of density are important. We found that guppies from low-predation (LP) environments are tightly regulated and that the density-dependent responses disproportionately affected some size classes. Second, we tested whether there are differences in density-dependent selection between guppies from LP or high-predation (HP) environments. We found that the fitness of HP guppies is more sensitive to the depressant effects of density than the fitness of LP guppies. Finally, we used an evolutionary invasion analysis to show that, depending on the effect of density on survival of the HP phenotype, this greater sensitivity of the HP phenotype to density can partially explain the evolution of the LP phenotype. We discuss the relevance of these findings to the study of feedbacks between ecology and evolution. PMID:23234843
Temperature and electron density dependence of spin relaxation in GaAs/AlGaAs quantum well
2011-01-01
Temperature and carrier density-dependent spin dynamics for GaAs/AlGaAs quantum wells (QWs) with different structural symmetries have been studied by using time-resolved Kerr rotation technique. The spin relaxation time is measured to be much longer for the symmetrically designed GaAs QW comparing with the asymmetrical one, indicating the strong influence of Rashba spin-orbit coupling on spin relaxation. D'yakonov-Perel' mechanism has been revealed to be the dominant contribution for spin relaxation in GaAs/AlGaAs QWs. The spin relaxation time exhibits non-monotonic-dependent behavior on both temperature and photo-excited carrier density, revealing the important role of non-monotonic temperature and density dependence of electron-electron Coulomb scattering. Our experimental observations demonstrate good agreement with recently developed spin relaxation theory based on microscopic kinetic spin Bloch equation approach. PMID:21711611
Temperature and electron density dependence of spin relaxation in GaAs/AlGaAs quantum well.
Han, Lifen; Zhu, Yonggang; Zhang, Xinhui; Tan, Pingheng; Ni, Haiqiao; Niu, Zhichuan
2011-01-01
Temperature and carrier density-dependent spin dynamics for GaAs/AlGaAs quantum wells (QWs) with different structural symmetries have been studied by using time-resolved Kerr rotation technique. The spin relaxation time is measured to be much longer for the symmetrically designed GaAs QW comparing with the asymmetrical one, indicating the strong influence of Rashba spin-orbit coupling on spin relaxation. D'yakonov-Perel' mechanism has been revealed to be the dominant contribution for spin relaxation in GaAs/AlGaAs QWs. The spin relaxation time exhibits non-monotonic-dependent behavior on both temperature and photo-excited carrier density, revealing the important role of non-monotonic temperature and density dependence of electron-electron Coulomb scattering. Our experimental observations demonstrate good agreement with recently developed spin relaxation theory based on microscopic kinetic spin Bloch equation approach. PMID:21711611
Magnetization Dynamics from Time-Dependent Noncollinear Spin Density Functional Theory Calculations.
Peralta, Juan E; Hod, Oded; Scuseria, Gustavo E
2015-08-11
A computational scheme, based on a time-dependent extension of noncollinear spin density functional theory, for the simultaneous simulation of charge and magnetization dynamics in molecular systems is presented. We employ a second-order Magnus propagator combined with an efficient predictor-corrector scheme that allows us to treat large molecular systems over long simulation periods. The method is benchmarked against the low-frequency dynamics of the H-He-H molecule where the magnetization dynamics can be modeled by the simple classical magnetization precession of a Heisenberg-Dirac-van Vleck Hamiltonian. Furthermore, the magnetic exchange couplings of the bimetallic complex [Cu(bpy)(H2O)(NO3)2(?-C2O4)] (BISDOW) are extracted from its low-frequency spin precession dynamics showing good agreement with the coupling obtained from ground state energy differences. Our approach opens the possibility to perform real-time simulation of spin-related phenomena using time-dependent density functional theory in realistic molecular systems. PMID:26574449
NASA Astrophysics Data System (ADS)
Nishimoto, Yoshio
2015-09-01
We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.
Roy, Justin; Yannic, Glenn; CÃ´tÃ©, Steeve D; Bernatchez, Louis
2012-03-01
Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432
Roy, Justin; Yannic, Glenn; CÃ´tÃ©, Steeve D; Bernatchez, Louis
2012-01-01
Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432
Negative density-dependent emigration of males in an increasing red deer population
Loe, Leif Egil; Mysterud, Atle; Veiberg, VebjÃ¸rn; Langvatn, Rolf
2009-01-01
In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deer Cervus elaphus marked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (37â€Škm) than at low density in 1977 (26â€Škm), possibly caused by increasing saturation of deer in areas surrounding the marking sites. Our study highlights that pattern of density dependence in dispersal rates may differ markedly between sexes in highly polygynous species. Contrasting patterns reported in small-scale studies are suggestive that spatial scale of density variation may affect the pattern of temporal density dependence in emigration rates and distances. PMID:19364736
Local bias approach to the clustering of discrete density peaks
NASA Astrophysics Data System (ADS)
Desjacques, Vincent
2013-02-01
Maxima of the linear density field form a point process that can be used to understand the spatial distribution of virialized halos that collapsed from initially overdense regions. However, owing to the peak constraint, clustering statistics of discrete density peaks are difficult to evaluate. For this reason, local bias schemes have received considerably more attention in the literature thus far. In this paper, we show that the two-point correlation function of maxima of a homogeneous and isotropic Gaussian random field can be thought of, up to second order at least, as arising from a local bias expansion formulated in terms of rotationally invariant variables. This expansion relies on a unique smoothing scale, which is the Lagrangian radius of dark matter halos. The great advantage of this local bias approach is that it circumvents the difficult computation of joint probability distributions. We demonstrate that the bias factors associated with these rotational invariants can be computed using a peak-background split argument, in which the background perturbation shifts the corresponding probability distribution functions. Consequently, the bias factors are orthogonal polynomials averaged over those spatial locations that satisfy the peak constraint. In particular, asphericity in the peak profile contributes to the clustering at quadratic and higher order, with bias factors given by generalized Laguerre polynomials. We speculate that our approach remains valid at all orders, and that it can be extended to describe clustering statistics of any point process of a Gaussian random field. Our results will be very useful to model the clustering of discrete tracers with more realistic collapse prescriptions involving the tidal shear for instance.
Electrostatics on particles: Phenomenological and orientational density functional theory approach
NASA Astrophysics Data System (ADS)
HaDuong, Tap; Phan, Sebastien; Marchi, Massimo; Borgis, Daniel
2002-07-01
In order to describe efficiently the solvation of complex solutes in computer simulations, we introduce several simple particle-based models with the requirement that they yield, on average, either an exact or approximate representation of the macroscopic laws of electrostatics. First, in a phenomenological approach, electrostatics of continuous media is formulated in terms of a polarization density free energy functional, which is projected on randomly distributed discrete Lennard-Jones pseudoparticles. The resulting model is that a polarizable fluid, in which the induced dipoles describe both orientational and electronic polarization. The problem of the connection between the macroscopic dielectric constant and the pseudoparticles polarizability is examined and important deviations with respect to the commonly accepted Clausius-Mossotti relation are found. Dipolar saturation effects can also be added to the model to yield a "nonlocal Langevin solvent model" and an approximate, numerically very efficient, "local Langevin solvent model." The two models are implemented in molecular dynamics simulations and their solvation properties are compared to continuous electrostatics for simple solutes such as spherical ions or ion pairs. Their computational efficiency is also discussed and compared to explicit microscopic solvent models. Then a statistical mechanics approach based on orientational density functional theory ideas is presented. Starting from a microscopic Hamiltonian describing a polar solvent, and for a given position of all the solvent molecules, a preliminary thermodynamic average over all the possible orientations of the molecules is performed. This can done by defining an orientational free-energy functional which, at a formal stage, is perfectly well-defined and exact. Minimization of the functional with respect the angular degrees of freedom yields an effective Hamiltonian acting on the translational degrees of freedom only which can be explored via molecular dynamics simulations. The simplest approximation for the orientational functional yields a version of the nonlocal Langevin solvent model mentioned above. More general approximations are suggested.
Physical Origin of Density Dependent Force of the Skyrme Type within the Quark Meson Coupling Model
Pierre Guichon; Hrayr Matevosyan; N. Sandulescu; Anthony Thomas
2006-03-17
A density dependent, effective nucleon-nucleon force of the Skyrme type is derived from the quark-meson coupling model--a self-consistent, relativistic quark level description of nuclear matter. This new formulation requires no assumption that the mean scalar field is small and hence constitutes a significant advance over earlier work. The similarity of the effective interaction to the widely used SkM* force encourages us to apply it to a wide range of nuclear problems, beginning with the binding energies and charge distributions of doubly magic nuclei. Finding impressive results in this conventional arena, we apply the same effective interaction, within the Hartree-Fock-Bogoliubov approach, to the properties of nuclei far from stability. The resulting two neutron drip lines and shell quenching are quite satisfactory. Finally, we apply the relativistic formulation to the properties of dense nuclear matter in anticipation of future application to the properties of neutron stars.
Density-dependent nucleon-nucleon interaction from three-nucleon forces
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.
2011-05-15
Microscopic calculations based on realistic nuclear Hamiltonians, while yielding accurate results for the energies of the ground and low-lying excited states of nuclei with A{<=}12, fail to reproduce the empirical equilibrium properties of nuclear matter, that are known to be significantly affected by three-nucleon forces. We discuss a scheme suitable to construct a density-dependent two-nucleon potential, in which the effects of n-particle interactions can be included by integrating out the degrees of freedom of (n-2) nucleons. Our approach, based on the formalism of correlated basis function and state-of-the-art models of the two- and three-nucleon potentials, leads to an effective interaction that can be easily employed in nuclear matter calculations, yielding results in good agreement with those obtained from the underlying three-body potential.
Density-dependent nucleon-nucleon interaction from three-nucleon forces
NASA Astrophysics Data System (ADS)
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.
2011-05-01
Microscopic calculations based on realistic nuclear Hamiltonians, while yielding accurate results for the energies of the ground and low-lying excited states of nuclei with A?12, fail to reproduce the empirical equilibrium properties of nuclear matter, that are known to be significantly affected by three-nucleon forces. We discuss a scheme suitable to construct a density-dependent two-nucleon potential, in which the effects of n-particle interactions can be included by integrating out the degrees of freedom of (n-2) nucleons. Our approach, based on the formalism of correlated basis function and state-of-the-art models of the two- and three-nucleon potentials, leads to an effective interaction that can be easily employed in nuclear matter calculations, yielding results in good agreement with those obtained from the underlying three-body potential.
Estimation of density-dependent mortality of juvenile bivalves in the Wadden Sea.
Andresen, Henrike; Strasser, Matthias; van der Meer, Jaap
2014-01-01
We investigated density-dependent mortality within the early months of life of the bivalves Macoma balthica (Baltic tellin) and Cerastoderma edule (common cockle) in the Wadden Sea. Mortality is thought to be density-dependent in juvenile bivalves, because there is no proportional relationship between the size of the reproductive adult stocks and the numbers of recruits for both species. It is not known however, when exactly density dependence in the pre-recruitment phase occurs and how prevalent it is. The magnitude of recruitment determines year class strength in bivalves. Thus, understanding pre-recruit mortality will improve the understanding of population dynamics. We analyzed count data from three years of temporal sampling during the first months after bivalve settlement at ten transects in the Sylt-Rømø-Bay in the northern German Wadden Sea. Analyses of density dependence are sensitive to bias through measurement error. Measurement error was estimated by bootstrapping, and residual deviances were adjusted by adding process error. With simulations the effect of these two types of error on the estimate of the density-dependent mortality coefficient was investigated. In three out of eight time intervals density dependence was detected for M. balthica, and in zero out of six time intervals for C. edule. Biological or environmental stochastic processes dominated over density dependence at the investigated scale. PMID:25105293
Estimation of Density-Dependent Mortality of Juvenile Bivalves in the Wadden Sea
Andresen, Henrike; Strasser, Matthias; van der Meer, Jaap
2014-01-01
We investigated density-dependent mortality within the early months of life of the bivalves Macoma balthica (Baltic tellin) and Cerastoderma edule (common cockle) in the Wadden Sea. Mortality is thought to be density-dependent in juvenile bivalves, because there is no proportional relationship between the size of the reproductive adult stocks and the numbers of recruits for both species. It is not known however, when exactly density dependence in the pre-recruitment phase occurs and how prevalent it is. The magnitude of recruitment determines year class strength in bivalves. Thus, understanding pre-recruit mortality will improve the understanding of population dynamics. We analyzed count data from three years of temporal sampling during the first months after bivalve settlement at ten transects in the Sylt-RÃ¸mÃ¸-Bay in the northern German Wadden Sea. Analyses of density dependence are sensitive to bias through measurement error. Measurement error was estimated by bootstrapping, and residual deviances were adjusted by adding process error. With simulations the effect of these two types of error on the estimate of the density-dependent mortality coefficient was investigated. In three out of eight time intervals density dependence was detected for M. balthica, and in zero out of six time intervals for C. edule. Biological or environmental stochastic processes dominated over density dependence at the investigated scale. PMID:25105293
NASA Astrophysics Data System (ADS)
Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A.; Oliveira, Micael J. T.; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G.; Aspuru-Guzik, AlÃ¡n; Rubio, Angel; Marques, Miguel A. L.
2012-06-01
Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.
A high-performance Fortran code to calculate spin- and parity-dependent nuclear level densities
NASA Astrophysics Data System (ADS)
Sen'kov, R. A.; Horoi, M.; Zelevinsky, V. G.
2013-01-01
A high-performance Fortran code is developed to calculate the spin- and parity-dependent shell model nuclear level densities. The algorithm is based on the extension of methods of statistical spectroscopy and implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The proton-neutron formalism is used. We have applied the method for calculating the level densities for a set of nuclei in the sd-, pf-, and pf+g- model spaces. Examples of the calculations for 28Si (in the sd-model space) and 64Ge (in the pf+g-model space) are presented. To illustrate the power of the method we estimate the ground state energy of 64Ge in the larger model space pf+g, which is not accessible to direct shell model diagonalization due to the prohibitively large dimension, by comparing with the nuclear level densities at low excitation energy calculated in the smaller model space pf. Program summaryProgram title: MM Catalogue identifier: AENM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 193181 No. of bytes in distributed program, including test data, etc.: 1298585 Distribution format: tar.gz Programming language: Fortran 90, MPI. Computer: Any architecture with a Fortran 90 compiler and MPI. Operating system: Linux. RAM: Proportional to the system size, in our examples, up to 75Mb Classification: 17.15. External routines: MPICH2 (http://www.mcs.anl.gov/research/projects/mpich2/) Nature of problem: Calculating of the spin- and parity-dependent nuclear level density. Solution method: The algorithm implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The code is parallelized using the Message Passing Interface and a master-slaves dynamical load-balancing approach. Restrictions: The program uses two-body interaction in a restricted single-level basis. For example, GXPF1A in the pf-valence space. Running time: Depends on the system size and the number of processors used (from 1 min to several hours).
Block, G L; Allen, L J
2000-03-01
Density-independent and density-dependent, stochastic and deterministic, discrete-time, structured models are formulated, analysed and numerically simulated. A special case of the deterministic, density-independent, structured model is the well-known Leslie age-structured model. The stochastic, density-independent model is a multitype branching process. A review of linear, density-independent models is given first, then nonlinear, density-dependent models are discussed. In the linear, density-independent structured models, transitions between states are independent of time and state. Population extinction is determined by the dominant eigenvalue lambda of the transition matrix. If lambda < or = 1, then extinction occurs with probability one in the stochastic and deterministic models. However, if lambda > 1, then the deterministic model has exponential growth, but in the stochastic model there is a positive probability of extinction which depends on the fixed point of the system of probability generating functions. The linear, density-independent, stochastic model is generalized to a nonlinear, density-dependent one. The dependence on state is in terms of a weighted total population size. It is shown for small initial population sizes that the density-dependent, stochastic model can be approximated by the density-independent, stochastic model and thus, the extinction behavior exhibited by the linear model occurs in the nonlinear model. In the deterministic models there is a unique stable equilibrium. Given the population does not go extinct, it is shown that the stochastic model has a quasi-stationary distribution with mean close to the stable equilibrium, provided the population size is sufficiently large. For small values of the population size, complete extinction can be observed in the simulations. However, the persistence time increases rapidly with the population size. PMID:10824427
Fronhofer, Emanuel A; Kropf, Tabea; Altermatt, Florian
2015-05-01
Movement and dispersal are critical processes for almost all organisms in natural populations. Understanding their causes and consequences is therefore of high interest. While both theoretical and empirical work suggest that dispersal, more exactly emigration, is plastic and may be a function of local population density, the functional relationship between the underlying movement strategies and population density has received less attention. We here present evidence for the shape of this reaction norm and are able to differentiate between three possible cues: the relative number of individuals, the presence of metabolites (chemical cues) and resource availability. We performed microcosm experiments with the ciliate model organism Tetrahymena in order to understand the plasticity of movement strategies with respect to local density while controlling for possible confounding effects mediated by the availability of different cues. In addition, we investigated how an Allee effect can influence movement and dispersal plasticity. Our findings suggest that movement strategies in Tetrahymena are plastic and density-dependent. The observed movement reaction norm was U-shaped. This may be due to an Allee effect which led to negative density dependence at low population densities and generally positive density dependence at high population densities due to local competition. This possibly adaptive density-dependent movement strategy was likely mediated by chemical cues. Our experimental work in highly controlled conditions indicates that both environmental cues as well as inherent population dynamics must be considered to understand movement and dispersal. PMID:25376344
Archer, Elizabeth K; Bennett, Nigel C; Faulkes, Chris G; Lutermann, Heike
2016-02-01
Due to the density-dependent nature of parasite transmission parasites are generally assumed to constrain the evolution of sociality. However, evidence for a correlation between group size and parasite burden is equivocal, particularly for mammals. Host contact rates may be modified by mobility of the host and parasite as well as social barriers. In the current study, we used the common mole-rat (Cryptomys hottentotus hottentotus), a social subterranean rodent, as a model system to investigate the effect of host density and frequency of contact rates on ectoparasite burdens. To address these factors we used a study species that naturally varies in population densities and intergroup contact rates across its geographic range. We found that ectoparasite prevalence, abundance and species richness decreased with increasing host density at a regional scale. At the same time, measures of parasite burden increased with intergroup contact rates. Ectoparasite burdens decreased with colony size at the group level possibly as a result of increased grooming rates. Equating group size with population density might be too simplistic an approach when assessing parasite distributions in social mammals. Our data suggest that frequency-dependent mechanisms may play a much greater role at a population level than density-dependent mechanisms in determining parasite distributions in social species. We suggest that future studies should explicitly consider behavioural mechanisms that may affect parasite distribution. PMID:26546084
NASA Astrophysics Data System (ADS)
Kestin, J.; Korfali, Ö.; Sengers, J. V.; Kamgar-Parsi, B.
1981-04-01
In this paper we present a detailed experimental study of the density dependence of the viscosity of He?Ne and Ne?Ar mixtures at various compositions. The data are analyzed in terms of a density expansion including a logarithmic contribution whose presence is predicted by the kinetic theory of gases. The composition dependence of the viscosity of the dense gas mixtures is compared with estimated values predicted on the basis of the Enskog-Thorne theory for dense mixtures of gases of hard spheres.
Density functional theory approach for calculation of dielectric properties of warm dense matter
NASA Astrophysics Data System (ADS)
Saitov, Ilnur
2015-06-01
The reflectivity of shocked xenon was measured in the experiments of Mintsev and Zaporoghets for wavelength 1064 nm. But there is no adequate theoretical explanation of these reflectivity results in the framework of the standard methods of nonideal plasma theory. The assumption of significant width to the shock front gives a good agreement with the experimental data. However, there are no evidences of this effect in the experiment. Reflectivity of shocked compressed xenon plasma is calculated in the framework of the density functional theory approach as in. Dependencies on the frequency of incident radiation and on the plasma density are analyzed. The Fresnel formula for the reflectivity is used. The longitudinal expression in the long wavelength limit is applied for the calculation of the imaginary part of the dielectric function. The real part of the dielectric function is calculated by means of the Kramers-Kronig transformation. The approach for the calculation of plasma frequency is developed.
Density-dependent nerve growth factor regulation of Gs-alpha RNA in pheochromocytoma 12 cells.
Tjaden, G; Aguanno, A; Kumar, R; Benincasa, D; Gubits, R M; Yu, H; Dolan, K P
1990-01-01
Nerve growth factor (NGF) affects levels of the alpha subunit of the stimulatory G protein (Gs-alpha) in pheochromocytoma 12 cells in a bidirectional, density-dependent manner. Cells grown at high density responded to NGF treatment with increased levels of Gs-alpha mRNA and protein. Conversely, in cells grown in low-density cultures, levels of this mRNA were lowered by NGF treatment. Images PMID:2160599
Rotella, J.J.; Link, W.A.; Nichols, J.D.; Hadley, G.L.; Garrott, R.A.; Proffitt, K.M.
2009-01-01
Much of the existing literature that evaluates the roles of density-dependent and density-independent factors on population dynamics has been called into question in recent years because measurement errors were not properly dealt with in analyses. Using state-space models to account for measurement errors, we evaluated a set of competing models for a 22-year time series of mark-resight estimates of abundance for a breeding population of female Weddell seals (Leptonychotes weddellii) studied in Erebus Bay, Antarctica. We tested for evidence of direct density dependence in growth rates and evaluated whether equilibrium population size was related to seasonal sea-ice extent and the Southern Oscillation Index (SOI). We found strong evidence of negative density dependence in annual growth rates for a population whose estimated size ranged from 438 to 623 females during the study. Based on Bayes factors, a density-dependence-only model was favored over models that also included en! vironmental covariates. According to the favored model, the population had a stationary distribution with a mean of 497 females (SD = 60.5), an expected growth rate of 1.10 (95% credible interval 1.08-1.15) when population size was 441 females, and a rate of 0.90 (95% credible interval 0.87-0.93) for a population of 553 females. A model including effects of SOI did receive some support and indicated a positive relationship between SOI and population size. However, effects of SOI were not large, and including the effect did not greatly reduce our estimate of process variation. We speculate that direct density dependence occurred because rates of adult survival, breeding, and temporary emigration were affected by limitations on per capita food resources and space for parturition and pup-rearing. To improve understanding of the relative roles of various demographic components and their associated vital rates to population growth rate, mark-recapture methods can be applied that incorporate both environmental covariates and the seal abundance estimates that were developed here. An improved understanding of why vital rates change with changing population abundance will only come as we develop a better understanding of the processes affecting marine food resources in the Southern Ocean.
Relativistic Coulomb excitation within the time dependent superfluid local density approximation
Stetcu, I.; Bertulani, C. A.; Bulgac, A.; Magierski, P.; Roche, K. J.
2015-01-06
Within the framework of the unrestricted time-dependent density functional theory, we present for the first time an analysis of the relativistic Coulomb excitation of the heavy deformed open shell nucleus 238U. The approach is based on the superfluid local density approximation formulated on a spatial lattice that can take into account coupling to the continuum, enabling self-consistent studies of superfluid dynamics of any nuclear shape. We compute the energy deposited in the target nucleus as a function of the impact parameter, finding it to be significantly larger than the estimate using the Goldhaber-Teller model. The isovector giant dipole resonance, themoreÂ Â» dipole pygmy resonance, and giant quadrupole modes are excited during the process. As a result, the one-body dissipation of collective dipole modes is shown to lead a damping width Î“â†“â‰ˆ0.4 MeV and the number of preequilibrium neutrons emitted has been quantified.Â«Â less
Influence of field dependent critical current density on flux profiles in high Tc superconductors
NASA Technical Reports Server (NTRS)
Takacs, S.
1990-01-01
The field distribution for superconducting cylinders and slabs with field dependent critical current densities in combined DC and AC magnetic fields and the corresponding magnetic fluxes are calculated. It is shown that all features of experimental magnetic-field profile measurements can be explained in the framework of field dependent critical current density. Even the quantitative agreement between the experimental and theoretical results using Kim's model is very good.
NASA Astrophysics Data System (ADS)
Ducomet, Bernard; Ne?asová, Šárka; Vasseur, Alexis
2010-06-01
We consider the Cauchy problem for the equations of selfgravitating motions of a barotropic gas with density-dependent viscosities ?( ?), and ?( ?) satisfying the Bresch-Desjardins condition, when the pressure P( ?) is not necessarily a monotone function of the density. We prove that this problem admits a global weak solution provided that the adiabatic exponent ? associated with P( ?) satisfies {? > 4/3}.
Field tests of density-and frequency-dependent selection in Erigeron annuus (Compositae).
Bennington, C; Stratton, D
1998-04-01
Selection may maintain genetic diversity in natural populations if the physical or biotic environment is variable over space and-or time. Because density and genotype frequencies can be heterogeneous, and because genotypes may differ in competitive ability, both density-and frequency-dependent selection have been considered to be potentially important evolutionary processes. To address the possibility that intraspecific interactions among plants are a source of fitness variation in Erigeron annuus, we conducted field experiments over 2 yr that were designed to examine the potential of population density, genotype frequency, and their interaction to act as selective agents. In both experiments, apomictic genotypes of Erigeron were paired. Seedlings were planted into plots that differed in density and the identity of minority and majority genotype. There was evidence for a differential effect of density among genotypes for only one year's experiment, suggesting that density-dependent selection is either weak or temporally variable. Genotype frequency had no effect on fitness in either year, and thus there was no evidence for frequency-dependent selection. In addition, the lack of a frequency ;ts density interaction demonstrates that resource partitioning, one mechanism for frequency dependence, is not strong among Erigeron genotypes. If frequency-dependent selection does occur in this species, it is either too weak to detect even in large field experiments, or occurs only in the presence of a selective agent (e.g., pathogens) that was lacking in our experiments. PMID:21684937
An Experimental Field Study of Delayed Density Dependence in Natural Populations of Aedes albopictus
Walsh, Rachael K.; Bradley, Caitlin; Apperson, Charles S.; Gould, Fred
2012-01-01
Aedes albopictus, a species known to transmit dengue and chikungunya viruses, is primarily a container-inhabiting mosquito. The potential for pathogen transmission by Ae. albopictus has increased our need to understand its ecology and population dynamics. Two parameters that we know little about are the impact of direct density-dependence and delayed density-dependence in the larval stage. The present study uses a manipulative experimental design, under field conditions, to understand the impact of delayed density dependence in a natural population of Ae. albopictus in Raleigh, North Carolina. Twenty liter buckets, divided in half prior to experimentation, placed in the field accumulated rainwater and detritus, providing oviposition and larval production sites for natural populations of Ae. albopictus. Two treatments, a larvae present and larvae absent treatment, were produced in each bucket. After five weeks all larvae were removed from both treatments and the buckets were covered with fine mesh cloth. Equal numbers of first instars were added to both treatments in every bucket. Pupae were collected daily and adults were frozen as they emerged. We found a significant impact of delayed density-dependence on larval survival, development time and adult body size in containers with high larval densities. Our results indicate that delayed density-dependence will have negative impacts on the mosquito population when larval densities are high enough to deplete accessible nutrients faster than the rate of natural food accumulation. PMID:22563428
Size selectivity of predation by brown bears depends on the density of their sockeye salmon prey.
Cunningham, Curry J; Ruggerone, Gregory T; Quinn, Thomas P
2013-05-01
Can variation in prey density drive changes in the intensity or direction of selective predation in natural systems? Despite ample evidence of density-dependent selection, the influence of prey density on predatory selection patterns has seldom been investigated empirically. We used 20 years of field data on brown bears (Ursus arctos) foraging on sockeye salmon (Oncorhynchus nerka) in Alaska, to test the hypothesis that salmon density affects the strength of size-selective predation. Measurements from 41,240 individual salmon were used to calculate variance-standardized selection differentials describing the direction and magnitude of selection. Across the time series, the intensity of predatory selection was inversely correlated with salmon density; greater selection for smaller salmon occurred at low salmon densities as bears' tendency to kill larger-than-average salmon was magnified. This novel connection between density dependence and selective predation runs contrary to some aspects of optimal foraging theory and differs from many observations of density-dependent selection because (1) the direction of selection remains constant while its magnitude changes as a function of density and (2) stronger selection is observed at low abundance. These findings indicate that sockeye salmon may be subject to fishery-induced size selection from both direct mechanisms and latent effects of altered predatory selection patterns on the spawning grounds, resulting from reduced salmon abundance. PMID:23594549
Dependence of the density limit on the toroidal magnetic field on FTU
NASA Astrophysics Data System (ADS)
Pucella, G.; Tudisco, O.; Apicella, M. L.; Apruzzese, G.; Artaserse, G.; Belli, F.; Bin, W.; Boncagni, L.; Botrugno, A.; Buratti, P.; Calabrò, G.; Castaldo, C.; Cianfarani, C.; Cocilovo, V.; Dimatteo, L.; Esposito, B.; Frigione, D.; Gabellieri, L.; Giovannozzi, E.; Granucci, G.; Marinucci, M.; Marocco, D.; Martines, E.; Mazzitelli, G.; Mazzotta, C.; Nowak, S.; Ramogida, G.; Romano, A.; Tuccillo, A. A.; Zeng, L.; Zuin, M.
2013-02-01
The capability of predicting the density limit of a magnetically confined burning plasma is of crucial importance to establish the ultimate performance of a fusion power plant. The Greenwald density limit, commonly used as an empirical scaling law, predicts that the maximum achievable central line-averaged density is given by the relation \\bar{n}_G = k \\bar{J} , where \\bar{J} is the average plasma current density and k is the plasma elongation. However, several experiments have pointed out that such a limit can be overcome in the presence of peaked density profiles. This paper proposes a new empirical scaling law for a limiter tokamak operating in the low-energy confinement mode (L-mode) concerning the case of peaked density profiles associated with the presence of multifaceted asymmetric radiation from the edges. This result is based on dedicated experiments performed on the Frascati Tokamak Upgrade (FTU) under extremely clean machine conditions (Zeff = 1.0-1.5), in which the high-density domain is explored in a wide range of values of plasma current (Ip = 500-900 kA) and toroidal magnetic field (BT = 4-8 T). It is found that the maximum achievable central line-averaged density essentially depends on the toroidal magnetic field only and does not depend on the average plasma current density: the behaviour is explained in terms of density profile peaking in the high-density domain. As a confirmation that the limit is an edge limit, it is also shown that a Greenwald-like scaling (i.e. depending on the current density) actually holds for the edge line-averaged density (at r/a ? 4/5).
NASA Astrophysics Data System (ADS)
Magrakvelidze, Maia; Madjet, Mohamed El-Amine; Dixit, Gopal; Ivanov, Misha; Chakraborty, Himadri S.
2015-06-01
We determine and analyze the quantum phases and time delays in photoionization and photorecombination of valence 3 p and 3 s electrons of argon using the Kohn-Sham local-density-functional approach. The time-dependent local-density approximation is used to account for the electron correlation. Resulting attosecond Wigner-Smith time delays show very good agreement with the recent experiment on argon that measured the delay in 3 p photorecombination [S. B. Schoun et al., Phys. Rev. Lett. 112, 153002 (2014), 10.1103/PhysRevLett.112.153002].
Demographic variability and density-dependent dynamics of a free-ranging rhesus macaque population
Hernández-Pacheco, Raisa; Rawlins, Richard G.; Kessler, Matthew J.; Williams, Lawrence E.; Ruiz-Maldonado, Tagrid M.; González-Martínez, Janis; Ruiz-Lambides, Angelina V.; Sabat, Alberto M.
2014-01-01
Density-dependence is hypothesized as the major mechanism of population regulation. However, the lack of long-term demographic data has hampered the use of density-dependent models in nonhuman primates. In this study, we make use of the long-term demographic data from Cayo Santiago’s rhesus macaques to parameterize and analyze both a density-independent and a density-dependent population matrix model, and compare their projections with the observed population changes. We also employ a retrospective analysis to determine how variance in vital rates, and covariance among them, contributed to the observed variation in long-term fitness across different levels of population density. The population exhibited negative density-dependence in fertility and the model incorporating this relationship accounted for 98% of the observed population dynamics. Variation in survival and fertility of sexually active individuals contributed the most to the variation in long-term fitness, while vital rates displaying high temporal variability exhibited lower sensitivities. Our findings are novel in describing density-dependent dynamics in a provisioned primate population, and in suggesting that selection is acting to lower the variance in the population growth rate by minimizing the variation in adult survival at high density. Because density-dependent mechanisms may become stronger in wild primate populations due to increasing habitat loss and food scarcity, our study demonstrates it is important to incorporate variation in population size, as well as demographic variability into population viability analyses for a better understanding of the mechanisms regulating the growth of primate populations. PMID:23847126
Sexual segregation in North American elk: the role of density dependence
Stewart, Kelley M; Walsh, Danielle R; Kie, John G; Dick, Brian L; Bowyer, R Terry
2015-01-01
We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 1999â€“2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20Â elk/km2, and a low-density population at 4Â elk/km2 to test hypotheses relative to timing and duration of sexual segregation and variation in selection of resources. We used multi-response permutation procedures to investigate patterns of sexual segregation, and resource selection functions to document differences in selection of resources by individuals in high- and low-density populations during sexual segregation and aggregation. The duration of sexual segregation was 2Â months longer in the high-density population and likely was influenced by individuals in poorer nutritional condition, which corresponded with later conception and parturition, than at low density. Males and females in the high-density population overlapped in selection of resources to a greater extent than in the low-density population, probably resulting from density-dependent effects of increased intraspecific competition and lower availability of resources. PMID:25691992
Sexual segregation in North American elk: the role of density dependence.
Stewart, Kelley M; Walsh, Danielle R; Kie, John G; Dick, Brian L; Bowyer, R Terry
2015-02-01
We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 1999-2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20 elk/km(2), and a low-density population at 4 elk/km(2) to test hypotheses relative to timing and duration of sexual segregation and variation in selection of resources. We used multi-response permutation procedures to investigate patterns of sexual segregation, and resource selection functions to document differences in selection of resources by individuals in high- and low-density populations during sexual segregation and aggregation. The duration of sexual segregation was 2 months longer in the high-density population and likely was influenced by individuals in poorer nutritional condition, which corresponded with later conception and parturition, than at low density. Males and females in the high-density population overlapped in selection of resources to a greater extent than in the low-density population, probably resulting from density-dependent effects of increased intraspecific competition and lower availability of resources. PMID:25691992
Lall, Upmanu; Devineni, Naresh; Kaheil, Yasir
2016-01-01
Multivariate simulations of a set of random variables are often needed for risk analysis. Given a historical data set, the goal is to develop simulations that reproduce the dependence structure in that data set so that the risk of potentially correlated factors can be evaluated. A nonparametric, copula-based simulation approach is developed and exemplified. It can be applied to multiple variables or to spatial fields with arbitrary dependence structures and marginal densities. The nonparametric simulator uses logspline density estimation in the univariate setting, together with a sampling strategy to reproduce dependence across variables or spatial instances, through a nonparametric numerical approximation of the underlying copula function. The multivariate data vectors are assumed to be independent and identically distributed. A synthetic example is provided to illustrate the method, followed by an application to the risk of livestock losses in Mongolia. PMID:26177987
Spatial, Temporal, and Density-Dependent Components of Habitat Quality for a Desert Owl
Flesch, Aaron D.; Hutto, Richard L.; van Leeuwen, Willem J. D.; Hartfield, Kyle; Jacobs, Sky
2015-01-01
Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches that consider habitat resources, stochastic factors, and conspecifics are necessary to accurately assess habitat quality. PMID:25786257
Spatial, temporal, and density-dependent components of habitat quality for a desert owl.
Flesch, Aaron D; Hutto, Richard L; van Leeuwen, Willem J D; Hartfield, Kyle; Jacobs, Sky
2015-01-01
Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches that consider habitat resources, stochastic factors, and conspecifics are necessary to accurately assess habitat quality. PMID:25786257
Role of prey and intraspecific density dependence on the population growth of an avian top predator
NASA Astrophysics Data System (ADS)
Fernandez-de-Simon, Javier; Díaz-Ruiz, Francisco; Cirilli, Francesca; Tortosa, Francisco S.; Villafuerte, Rafael; Ferreras, Pablo
2014-10-01
Exploring predator-prey systems in diverse ecosystems increases our knowledge about ecological processes. Predator population growth may be positive when conspecific density is low but predators also need areas with prey availability, associated with competition, which increases the risk of suffering losses but stabilises populations. We studied relationships between European rabbits Oryctolagus cuniculus (prey) and adult eagle owls Bubo bubo (predators) in south-western Europe. We assessed models explaining the predator population growth and stability. We estimated the abundance of rabbits and adult eagle owls during three years in eight localities of central-southern Spain. We explored models including rabbit and adult eagle owl abundance, accounting for yearly variations and including the locality as a random variable. We found that population growth of adult eagle owls was positive in situations with low conspecific abundance and tended to be negative but approaching equilibrium in situations of higher conspecific abundance. Population growth was also positively related to previous summer rabbit density when taking into account eagle owl conspecific abundance, possibly indicating that rabbits may support recruitment. Furthermore, abundance stability of adult eagle owls was positively related to previous winter-spring rabbit density, which could suggest predator population stabilisation through quick territory occupation in high-quality areas. These results exemplify the trade-off between prey availability and abundance of adult predators related to population growth and abundance stability in the eagle owl-rabbit system in south-western Europe. Despite rabbits have greatly declined during the last decades and eagle owls locally specialise on them, eagle owls currently have a favourable conservation status. As eagle owls are the only nocturnal raptor with such dependence on rabbits, this could point out that predators may overcome prey decreases in areas with favourable climate and prey in the absence of superior competitors with similar foraging mode.
Density and temperature dependence of spectral moments in depolarized light scattering by rare gases
NASA Astrophysics Data System (ADS)
Ladanyi, Branka M.; Barreau, Alain; Dumon, Bernard
We present an extensive study of the first three even moments M2n of depolarized light scattering (DLS) spectra of rare gases argon and xenon. Most of our results were obtained by molecular dynamics and Monte Carlo computer simulation methods, which were used to calculate the moments for pairwise-additive intermolecular pair potential and interaction-induced polarizability models over a wide density range and at two temperatures, one above and one below the critical point. Simulation was used to determine the dependence of the moments on the pair polarizability anisotropy ?(r) by comparing the results for the first order dipole-induced dipole (DID) model with those obtained for a semiempirical model of ?(r), recently proposed by Meinander, Tabisz and Zoppi (MTZ), which includes electron overlap, dispersion and second order DID interaction contributions. Comparison with experiment indicates that the MTZ model for ?(r) is clearly superior. Moments of increasing order are found to be increasingly more sensitive to the functional form of ?(r), pointing to the importance of short range interactions for the spectral line shape. By contrast, the cancellation effects due to short range ordering at high densities become less pronounced as the order of the moment increases. In the case of argon, simulation results were obtained for Lennard-Jones and Aziz-Slaman pair potential models. Their comparison revealed a weak dependence of the moments on the details of the intermolecular potential. The Kirkwood superposition approximation approach to estimating the contributions of 3 and 4 molecule correlations to M0 and M2 was generalized to a non-DID model of ?(r). The limits of accuracy of this approximation and of the lattice-gas model estimates of multiparticle correlation contributions to M2n are critically examined.
Time-Dependent Density-Functional Theory for Nonadiabatic Electronic Dynamics
NASA Astrophysics Data System (ADS)
Krishna, Vinod
2009-02-01
We show that the time-dependent single electron, nuclear density matrix of an interacting electronic system coupled to nuclear degrees of freedom can be exactly reproduced by that of an electronic system with arbitrarily specified electron-electron interactions coupled to the same nuclear degrees of freedom, given the initial density matrix of the interacting system. This formalism enables the construction of rigorous time-dependent density-functional theories to study nonadiabatic electronic dynamics. We obtain the Runge-Gross and van Leeuwen theorems as special cases in the adiabatic limit.
Modeling the doubly excited state with time-dependent Hartree-Fock and density functional theories
NASA Astrophysics Data System (ADS)
Isborn, Christine M.; Li, Xiaosong
2008-11-01
Multielectron excited states have become a hot topic in many cutting-edge research fields, such as the photophysics of polyenes and in the possibility of multiexciton generation in quantum dots for the purpose of increasing solar cell efficiency. However, obtaining multielectron excited states has been a major obstacle as it is often done with multiconfigurational methods, which involve formidable computational cost for large systems. Although they are computationally much cheaper than multiconfigurational wave function based methods, linear response adiabatic time-dependent Hartree-Fock (TDHF) and density functional theory (TDDFT) are generally considered incapable of obtaining multielectron excited states. We have developed a real-time TDHF and adiabatic TDDFT approach that is beyond the perturbative regime. We show that TDHF/TDDFT is able to simultaneously excite two electrons from the ground state to the doubly excited state and that the real-time TDHF/TDDFT implicitly includes double excitation within a superposition state. We also present a multireference linear response theory to show that the real-time electron density response corresponds to a superposition of perturbative linear responses of the S0 and S2 states. As a result, the energy of the two-electron doubly excited state can be obtained with several different approaches. This is done within the adiabatic approximation of TDDFT, a realm in which the doubly excited state has been deemed missing. We report results on simple two-electron systems, including the energies and dipole moments for the two-electron excited states of H2 and HeH+. These results are compared to those obtained with the full configuration interaction method.
Modeling the doubly excited state with time-dependent Hartree-Fock and density functional theories.
Isborn, Christine M; Li, Xiaosong
2008-11-28
Multielectron excited states have become a hot topic in many cutting-edge research fields, such as the photophysics of polyenes and in the possibility of multiexciton generation in quantum dots for the purpose of increasing solar cell efficiency. However, obtaining multielectron excited states has been a major obstacle as it is often done with multiconfigurational methods, which involve formidable computational cost for large systems. Although they are computationally much cheaper than multiconfigurational wave function based methods, linear response adiabatic time-dependent Hartree-Fock (TDHF) and density functional theory (TDDFT) are generally considered incapable of obtaining multielectron excited states. We have developed a real-time TDHF and adiabatic TDDFT approach that is beyond the perturbative regime. We show that TDHF/TDDFT is able to simultaneously excite two electrons from the ground state to the doubly excited state and that the real-time TDHF/TDDFT implicitly includes double excitation within a superposition state. We also present a multireference linear response theory to show that the real-time electron density response corresponds to a superposition of perturbative linear responses of the S(0) and S(2) states. As a result, the energy of the two-electron doubly excited state can be obtained with several different approaches. This is done within the adiabatic approximation of TDDFT, a realm in which the doubly excited state has been deemed missing. We report results on simple two-electron systems, including the energies and dipole moments for the two-electron excited states of H(2) and HeH(+). These results are compared to those obtained with the full configuration interaction method. PMID:19045852
Density-dependent habitat selection by brown-headed cowbirds (Molothrus ater) in tallgrass prairie
Jensen, W.E.; Cully, J.F., Jr.
2005-01-01
Local distributions of avian brood parasites among their host habitats may depend upon conspecific parasite density. We used isodar analysis to test for density-dependent habitat selection in brown-headed cowbirds (Molothrus ater) among tallgrass prairie adjacent to wooded edges, and prairie interior habitat (>100 m from wooded edges) with and without experimental perches. Eight study sites containing these three habitat treatments were established along a geographical gradient in cowbird abundance within the Flint Hills region of Eastern Kansas and Oklahoma, USA. The focal host species of our study, the dickcissel (Spiza americana), is the most abundant and preferred cowbird host in the prairie of this region. Cowbird relative abundance and cowbird:host abundance ratios were used as estimates of female cowbird density, whereas cowbird egg density was measured as parasitism frequency (percent of dickcissel nests parasitized), and parasitism intensity (number of cowbird eggs per parasitized nest). Geographical variation in cowbird abundance was independent of host abundance. Within study sites, host abundance was highest in wooded edge plots, intermediate in the experimental perch plots, and lowest in prairie interior. Cowbirds exhibited a pattern of density-dependent selection of prairie edge versus experimental perch and interior habitats. On sites where measures of cowbird density were lowest, all cowbird density estimates (female cowbirds and their eggs) were highest near (???100 m) wooded edges, where host and perch availability are highest. However, as overall cowbird density increased geographically, these density estimates increased more rapidly in experimental perch plots and prairie interiors. Variation in cowbird abundance and cowbird:host ratios suggested density-dependent cowbird selection of experimental perch over prairie interior habitat, but parasitism levels on dickcissel nests were similar among these two habitats at all levels of local cowbird parasitism. The density-dependent pattern of cowbird distribution among prairie edge and interior suggested that density effects on perceived cowbird fitness are greatest at wooded edges. A positive relationship between daily nest mortality rates of parasitized nests during the nestling period with parasitism intensity levels per nest suggested a density-dependent effect on cowbird reproductive success. However, this relationship was similar among habitats, such that all habitats should have been perceived as being equally suitable to cowbirds at all densities. Other unmeasured effects on cowbird habitat suitability (e.g., reduced cowbird success in edge-dwelling host nests, cowbird despotism at edges) might have affected cowbird habitat selection. Managers attempting to minimize cowbird parasitism on sensitive cowbird hosts should consider that hosts in otherwise less-preferred cowbird habitats (e.g., habitat interiors) are at greater risk of being parasitized where cowbirds become particularly abundant. ?? Springer-Verlag 2004.
Time-dependent density functional methods for Raman spectra in open-shell systems.
Aquino, Fredy W; Schatz, George C
2014-01-16
We present an implementation of a time-dependent density functional theory (TD-DFT) linear response module in NWChem for unrestricted DFT calculations and apply it to the calculation of resonant Raman spectra in open-shell molecular systems using the short-time approximation. The new source code was validated and applied to simulate Raman spectra on several doublet organic radicals (e.g., benzyl, benzosemiquinone, TMPD, trans-stilbene anion and cation, and methyl viologen) and the metal complex copper phthalocyanine. We also introduce a divide-and-conquer approach for the evaluation of polarizabilities in relatively large systems (e.g., copper phthalocyanine). The implemented tool gives comparisons with experiment that are similar to what is commonly found for closed-shell systems, with good agreement for most features except for small frequency shifts, and occasionally large deviations for some modes that depend on the molecular system studied, experimental conditions not being accounted in the modeling such as solvation effects and extra solvent-based peaks, and approximations in the underlying theory. The approximations used in the quantum chemical modeling include (i) choice of exchange-correlation functional and basis set; (ii) harmonic approximation used in the frequency analysis to determine vibrational normal modes; and (iii) short-time approximation (omission of nuclear motion effects) used in calculating resonant Raman spectra. PMID:24380604
Time-Dependent Density Functional Calculations for Optical Excitations in Nanoscale Materials.
NASA Astrophysics Data System (ADS)
Vasiliev, Igor
2006-03-01
Optical properties play a crucial role in our understanding of the electronic structure of nanoscale materials. Despite significant progress in the development of computational methodologies, first principles calculations for optical excitations in nanomaterials remain extremely difficult. While the ground-state electronic structure formalism is relatively well established, calculations for excited states present major challenges to theoretical methods traditionally employed by condensed matter physics and quantum chemistry. This talk focuses on recent advances in a computational technique based on time-dependent density functional theory (TDDFT). Within the TDDFT method, electronic transition energies and oscillator strengths are obtained in the framework of linear response theory by solving a frequency-dependent equation for the dynamic polarizability. The linear-response TDDFT formalism is applied to compute the excitation energies and absorption spectra for a variety of nanoscale systems, including molecules, atomic clusters, semiconductor quantum dots, functionalized carbon nanotubes, and nanotube-polymer composites. The TDDFT approach is compared to other first principles computational methods for excited states and discussed in terms of accuracy, efficiency, and computational cost.
Ross, Beth E; Hooten, Mevin B; DeVink, Jean-Michel; Koons, David N
2015-09-01
An understanding of species relationships is critical in the management and conservation of populations facing climate change, yet few studies address how climate alters species interactions and other population drivers. We use a long-term, broad-scale data set of relative abundance to examine the influence of climate, predators, and density dependence on the population dynamics of declining scaup (Aythya) species within the core of their breeding range. The state-space modeling approach we use applies to a wide range of wildlife species, especially populations monitored over broad spatiotemporal extents. Using this approach, we found that immediate snow cover extent in the preceding winter and spring had the strongest effects, with increases in mean snow cover extent having a positive effect on the local surveyed abundance of scaup. The direct effects of mesopredator abundance on scaup population dynamics were weaker, but the results still indicated a potentil interactive process between climate and food web dynamics (mesopredators, alternative prey, and scaup). By considering climate variables and other potential effects on population dynamics, and using a rigorous estimation framework, we provide insight into complex ecological processes for guiding. conservation and policy actions aimed at mitigating and reversing the decline of scaup. PMID:26552268
Density dependent growth in adult brown frogs Rana arvalis and Rana temporaria - A field experiment
NASA Astrophysics Data System (ADS)
Loman, Jon; Lardner, Björn
2009-11-01
In species with complex life cycles, density regulation can operate on any of the stages. In frogs there are almost no studies of density effects on the performance of adult frogs in the terrestrial habitat. We therefore studied the effect of summer density on the growth rate of adult frogs during four years. Four 30 by 30 m plots in a moist meadow were used. In early summer, when settled after post-breeding migration, frogs ( Rana arvalis and Rana temporaria that have a very similar ecology and potentially compete) were enclosed by erecting a fence around the plots. Frogs were captured, measured, marked and partly relocated to create two high density and two low density plots. In early autumn the frogs were again captured and their individual summer growth determined. Growth effects were evaluated in relation to two density measures: density by design (high/low manipulation), and actual (numerical) density. R. arvalis in plots with low density by design grew faster than those in high density plots. No such effect was found for R. temporaria. For none of the species was growth related to actual summer density, determined by the Lincoln index and including the density manipulation. The result suggests that R. arvalis initially settled according to an ideal free distribution and that density had a regulatory effect (mediated through growth). The fact that there were no density effects on R. temporaria (and a significant difference in its response to that of R. arvalis) suggests it is a superior competitor to R. arvalis during the terrestrial phase. There were no density effects on frog condition index, suggesting that the growth rate modifications may actually be an adaptive trait of R. arvalis. The study demonstrates that density regulation may be dependent on resources in frogs' summer habitat.
Density-dependent immune responses against the gastrointestinal nematode Strongyloides ratti
Bleay, Colin; Wilkes, Clare P.; Paterson, Steve; Viney, Mark E.
2007-01-01
Negative density-dependent effects on the fitness of parasite populations are an important force in their population dynamics. For the parasitic nematode Strongyloides ratti, density-dependent fitness effects require the rat host immune response. By analysis of both measurements of components of parasite fitness and of the host immune response to different doses of S. ratti infection, we have identified specific parts of the host immune response underlying the negative density-dependent effects on the fitness of S. ratti. The host immune response changes both qualitatively from an inflammatory Th1- to a Th2-type immune profile and the Th2-type response increases quantitatively, as the density of S. ratti infection increases. Parasite survivorship was significantly negatively related to the concentration of parasite-specific IgG1 and IgA, whereas parasite fecundity was significantly negatively related to the concentration of IgA only. PMID:17597133
A coarse-grain force field for RDX: Density dependent and energy conserving
NASA Astrophysics Data System (ADS)
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; LÃsal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Tussupbayev, Samat; Govind, Niranjan; Lopata, Kenneth A.; Cramer, Christopher J.
2015-03-10
We assess the performance of real-time time-dependent density functional theory (RT-TDDFT) for the calculation of absorption spectra of 12 organic dye molecules relevant to photovoltaics and dye sensitized solar cells with 8 exchange-correlation functionals (3 traditional, 3 global hybrids, and 2 range-separated hybrids). We compare the calculations with traditional linear-response (LR) TDDFT. In addition, we demonstrate the efficacy of the RT-TDDFT approach to calculate wide absorption spectra of two large chromophores relevant to photovoltaics and molecular switches.
Cascading effects of belowground predators on plant communities are density-dependent.
Thakur, Madhav Prakash; Herrmann, Martina; Steinauer, Katja; Rennoch, Saskia; Cesarz, Simone; Eisenhauer, Nico
2015-10-01
Soil food webs comprise a multitude of trophic interactions that can affect the composition and productivity of plant communities. Belowground predators feeding on microbial grazers like Collembola could decelerate nutrient mineralization by reducing microbial turnover in the soil, which in turn could negatively influence plant growth. However, empirical evidences for the ecological significance of belowground predators on nutrient cycling and plant communities are scarce. Here, we manipulated predator density (Hypoaspis aculeifer: predatory mite) with equal densities of three Collembola species as a prey in four functionally dissimilar plant communities in experimental microcosms: grass monoculture (Poa pratensis), herb monoculture (Rumex acetosa), legume monoculture (Trifolium pratense), and all three species as a mixed plant community. Density manipulation of predators allowed us to test for density-mediated effects of belowground predators on Collembola and lower trophic groups. We hypothesized that predator density will reduce Collembola population causing a decrease in nutrient mineralization and hence detrimentally affect plant growth. First, we found a density-dependent population change in predators, that is, an increase in low-density treatments, but a decrease in high-density treatments. Second, prey suppression was lower at high predator density, which caused a shift in the soil microbial community by increasing the fungal: bacterial biomass ratio, and an increase of nitrification rates, particularly in legume monocultures. Despite the increase in nutrient mineralization, legume monocultures performed worse at high predator density. Further, individual grass shoot biomass decreased in monocultures, while it increased in mixed plant communities with increasing predator density, which coincided with elevated soil N uptake by grasses. As a consequence, high predator density significantly increased plant complementarity effects indicating a decrease in interspecific plant competition. These results highlight that belowground predators can relax interspecific plant competition by increasing nutrient mineralization through their density-dependent cascading effects on detritivore and soil microbial communities. PMID:26664680
Representing the thermal state in time-dependent density functional theory.
Modine, N A; Hatcher, R M
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble. PMID:26026438
Representing the thermal state in time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Modine, N. A.; Hatcher, R. M.
2015-05-01
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble.
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble.
A comprehensive approach for the assessment of in-situ pavement density using GPR technique
NASA Astrophysics Data System (ADS)
Plati, Christina; Georgiou, Panos; Loizos, Andreas
2013-04-01
Proper construction of the asphalt pavement is a prerequisite to developing a long lasting roadway that does not require extensive future maintenance. This goal is achieved by verifying that design specifications are met through the use of quality assurance (QA) practices. The in-situ density is regarded as one of the most important controls used to ensure that a pavement being placed is of high quality because it is a good indicator of future performance. In-situ density is frequently assessed utilizing one or more of the following three methods: cores, nuclear density gauge measurements or non-nuclear density gauge measurements. Each of the above mentioned methods, however, have their distinct disadvantages. Cores, for example, are generally considered to be the most accurate means of measuring in-situ density, however, they are a time consuming and destructive test that introduces a defect into asphalt pavements. Because of the destructive nature associated with coring, contractors and agencies have alternatively used non-destructive nuclear and non-nuclear density gauges for quality control purposes. These instruments allow for a more rapid assessment of the in-situ density, allowing measurements to be taken even during the pavement's construction. The disadvantage of these gauges are that they provide density readings only at discrete locations of the asphalt pavement mat, while no consensus exists among pavement researchers on the proper correlation between the gauges and core density. In recent years, numerous alternative methods have been introduced for the assessment of in-situ density, both during asphalt pavement construction and afterwards. These methods include, amongst others, intelligent compaction, thermal imaging and ground penetrating radar (GPR). Among these methods, GPR has been defined as both a technically feasible and promising method for the nondestructive, rapid, and continuous evaluation of in-situ asphalt pavement density based on electromagnetic mixing (EM) theory, through the utilization of proper models. These models enable the prediction of asphalt mixture density dependent on its bulk dielectric constant as measured by the GPR, the dielectric properties of the asphalt mix materials, as well as other material information. The goal of the present study is to attempt to verify the prediction performance of various density models. To accomplish this goal GPR surveys were carried out in the field during asphalt pavement construction to evaluate the density results due to different compaction modes. The GPR data was analyzed to calculate the appropriate asphalt mix dielectric properties needed for the activation of the considered density prediction models. Predicted densities were compared with densities of the field cores extracted from the as-built asphalt pavement prior to trafficking. It was found that the predicted density values were significantly lower when compared to the ground truth data. A further investigation of the effect of temperature on GPR readings showed that GPR seems to overestimate the in-situ density. However, this approach could be used effectively to evaluate the performance of different compaction methods and set up the compaction pattern that is needed to achieve the desired asphalt pavement density.
Investigations of turbulent scalar fields using probability density function approach
NASA Technical Reports Server (NTRS)
Gao, Feng
1991-01-01
Scalar fields undergoing random advection have attracted much attention from researchers in both the theoretical and practical sectors. Research interest spans from the study of the small scale structures of turbulent scalar fields to the modeling and simulations of turbulent reacting flows. The probability density function (PDF) method is an effective tool in the study of turbulent scalar fields, especially for those which involve chemical reactions. It has been argued that a one-point, joint PDF approach is the one to choose from among many simulation and closure methods for turbulent combustion and chemically reacting flows based on its practical feasibility in the foreseeable future for multiple reactants. Instead of the multi-point PDF, the joint PDF of a scalar and its gradient which represents the roles of both scalar and scalar diffusion is introduced. A proper closure model for the molecular diffusion term in the PDF equation is investigated. Another direction in this research is to study the mapping closure method that has been recently proposed to deal with the PDF's in turbulent fields. This method seems to have captured the physics correctly when applied to diffusion problems. However, if the turbulent stretching is included, the amplitude mapping has to be supplemented by either adjusting the parameters representing turbulent stretching at each time step or by introducing the coordinate mapping. This technique is still under development and seems to be quite promising. The final objective of this project is to understand some fundamental properties of the turbulent scalar fields and to develop practical numerical schemes that are capable of handling turbulent reacting flows.
A New Approach of Designing Superalloys for Low Density
NASA Technical Reports Server (NTRS)
MacKay, Rebecca A.; Gabb, Timothy P.; Smialek, James L.; Nathal, Michael V.
2010-01-01
New low-density single-crystal (LDS) alloy, have bee. developed for turbine blade applications, which have the potential for significant improvements in the thrust-to-weight ratio over current production superalloys. An innovative alloying strategy was wed to achieve alloy density reductions, high-temperature creep resistance, microstructural stability, and cyclic oxidation resistance. The alloy design relies on molybdenum as a potent. lower-density solid-solution strengthener in the nickel-based superalloy. Low alloy density was also achieved with modest rhenium levels tmd the absence of tungsten. Microstructural, physical mechanical, and environmental testing demonstrated the feasibility of this new LDS superalloy design.
Negative density dependence of seed dispersal and seedling recruitment in a neotropical palm.
Jansen, Patrick A; Visser, Marco D; Joseph Wright, S; Rutten, Gemma; Muller-Landau, Helene C
2014-09-01
Negative density dependence (NDD) of recruitment is pervasive in tropical tree species. We tested the hypotheses that seed dispersal is NDD, due to intraspecific competition for dispersers, and that this contributes to NDD of recruitment. We compared dispersal in the palm Attalea butyracea across a wide range of population density on Barro Colorado Island in Panama and assessed its consequences for seed distributions. We found that frugivore visitation, seed removal and dispersal distance all declined with population density of A. butyracea, demonstrating NDD of seed dispersal due to competition for dispersers. Furthermore, as population density increased, the distances of seeds from the nearest adult decreased, conspecific seed crowding increased and seedling recruitment success decreased, all patterns expected under poorer dispersal. Unexpectedly, however, our analyses showed that NDD of dispersal did not contribute substantially to these changes in the quality of the seed distribution; patterns with population density were dominated by effects due solely to increasing adult and seed density. PMID:25039608
Universal time dependence of nighttime F region densities at high latitudes
NASA Technical Reports Server (NTRS)
De La Beaujardiere, O.; Wickwar, V. B.; Caudal, G.; Holt, J. M.; Craven, J. D.; Frank, L. A.; Brace, L. H.
1985-01-01
Coincident auroral-zone experiments using three incoherent-scatter radars at widely spaced longitudes are reported. The observational results demonstrate that, during the night, the F layer electron density is strongly dependent on the longitude of the observing site. Ionization patches were observed in the nighttime F region from the Chatanika and EISCAT radars, while densities observed from the Millstone radar were substantially smaller. The electron density within these maxima is larger at EISCAT than at Chatanika. When observed in the midnight sector auroral zone, these densities had a peak density at a high altitude of 360-475 km. The density was maximum when EISCAT was in the midnight sector and minimum when Millstone was in the midnight sector. A minimum in insolation in the auroral zone occurs at the UT when Millstone is in the midnight sector.
NASA Astrophysics Data System (ADS)
Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung
2015-04-01
Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.
Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung
2015-04-14
Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.
Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung
2015-04-14
Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene. PMID:25877567
Dependence of SOL Widths on Plasma Current and Density in NSTX H-mode Plasmas
Ahn, J W; Maingi, Rajesh; Boedo, J.; Soukhanovskii, V. A.
2009-01-01
The dependence of various SOL widths on the line-averaged density ((n) over bar (e)) and plasma current (I(p)) for the quiescent H-mode plasmas with Type-V ELMs in the National Spherical Torus Experiment (NSTX) was investigated. It is found that the heat flux SOL width (lambda(q)), measured by the IR camera, is virtually insensitive to (n) over bar (e) and has a strong negative dependence on I(p). This insensitivity of lambda(q) to (n) over bare is consistent with the scaling law from JET H-mode plasmas that shows a very weak dependence on the upstream density. The electron temperature, ion saturation current density, electron density, and electron pressure decay lengths (lambda(Te), lambda(jsat), lambda(ne), and lambda(pe), respectively) measured by the probe showed that lambda(Te) and lambda(jsat) have strong negative dependence on I(p), whereas lambda(ne) and lambda(pe) revealed only a little or no dependence. The dependence of lambda(Te) on I(p) is consistent with the scaling law in the literature, while lambda(ne) and lambda(pe) dependence shows a different trend. (C) 2009 Elsevier B.V. All rights reserved.
Dependence of various SOL widths on plasma current and density in NSTX H-mode plasmas
Ahn, J; Maingi, R; Boedo, J; Soukhanovskii, V A
2009-02-12
The dependence of various SOL widths on the line-averaged density ({ovr n}{sub e}) and plasma current (l{sub p}) for the quiescent H-mode plasmas with Type-V ELMs in the National Spherical Torus Experiment (NSTX) was investigated. It is found that the heat flux SOL width ({lambda}{sub q}), measured by the IR camera, is virtually insensitive to {ovr n}{sub e} and has a strong negative dependence on l{sub p}. This insensitivity of {lambda}{sub q} to {ovr n}{sub e} is consistent with the scaling law from JET H-mode plasmas that shows a very weak dependence on the upstream density. The electron temperature, ion saturation current density, electron density, and electron pressure decay lengths ({lambda}{sub Te}, {lambda}{sub jsat}, {lambda}{sub ne}, and {lambda}{sub pe}, respectively) measured by the probe showed that {lambda}{sub Te} and {lambda}{sub jsat} have strong negative dependence on l{sub p}, whereas {lambda}{sub ne} and {lambda}{sub pe} revealed only a little or no dependence. The dependence of {lambda}{sub Te} on l{sub p} is consistent with the scaling law in the literature while {lambda}{sub ne} and {lambda}{sub pe} dependence shows a different trend.
Cubaynes, Sarah; MacNulty, Daniel R; Stahler, Daniel R; Quimby, Kira A; Smith, Douglas W; Coulson, Tim
2014-11-01
Understanding the population dynamics of top-predators is essential to assess their impact on ecosystems and to guide their management. Key to this understanding is identifying the mechanisms regulating vital rates. Determining the influence of density on survival is necessary to understand the extent to which human-caused mortality is compensatory or additive. In wolves (Canis lupus), empirical evidence for density-dependent survival is lacking. Dispersal is considered the principal way in which wolves adjust their numbers to prey supply or compensate for human exploitation. However, studies to date have primarily focused on exploited wolf populations, in which density-dependent mechanisms are likely weak due to artificially low wolf densities. Using 13 years of data on 280 collared wolves in Yellowstone National Park, we assessed the effect of wolf density, prey abundance and population structure, as well as winter severity, on age-specific survival in two areas (prey-rich vs. prey-poor) of the national park. We further analysed cause-specific mortality and explored the factors driving intraspecific aggression in the prey-rich northern area of the park. Overall, survival rates decreased during the study. In northern Yellowstone, density dependence regulated adult survival through an increase in intraspecific aggression, independent of prey availability. In the interior of the park, adult survival was less variable and density-independent, despite reduced prey availability. There was no effect of prey population structure in northern Yellowstone, or of winter severity in either area. Survival was similar among yearlings and adults, but lower for adults older than 6 years. Our results indicate that density-dependent intraspecific aggression is a major driver of adult wolf survival in northern Yellowstone, suggesting intrinsic density-dependent mechanisms have the potential to regulate wolf populations at high ungulate densities. When low prey availability or high removal rates maintain wolves at lower densities, limited inter-pack interactions may prevent density-dependent survival, consistent with our findings in the interior of the park. PMID:24749694
Tussupbayev, Samat; Govind, Niranjan; Lopata, Kenneth; Cramer, Christopher J
2015-03-10
We assess the performance of real-time time-dependent density functional theory (RT-TDDFT) for the calculation of absorption spectra of 12 organic dye molecules relevant to photovoltaics and dye-sensitized solar cells with 8 exchange-correlation functionals (3 traditional, 3 global hybrids, and 2 range-separated hybrids). We compare the calculations with traditional linear-response (LR) TDDFT and experimental spectra. In addition, we demonstrate the efficacy of the RT-TDDFT approach to calculate wide absorption spectra of two large chromophores relevant to photovoltaics and molecular switches. RT-TDDFT generally requires longer simulation times, compared to LR-TDDFT, for absorption spectra of small systems. However, it becomes more effective for the calculation of wide absorption spectra of large molecular complexes and systems with very high densities of states. PMID:26579760
Adaptive nest clustering and density-dependent nest survival in dabbling ducks
Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.
2014-01-01
Density-dependent population regulation is observed in many taxa, and understanding the mechanisms that generate density dependence is especially important for the conservation of heavily-managed species. In one such system, North American waterfowl, density dependence is often observed at continental scales, and nest predation has long been implicated as a key factor driving this pattern. However, despite extensive research on this topic, it remains unclear if and how nest density influences predation rates. Part of this confusion may have arisen because previous studies have studied density-dependent predation at relatively large spatial and temporal scales. Because the spatial distribution of nests changes throughout the season, which potentially influences predator behavior, nest survival may vary through time at relatively small spatial scales. As such, density-dependent nest predation might be more detectable at a spatially- and temporally-refined scale and this may provide new insights into nest site selection and predator foraging behavior. Here, we used three years of data on nest survival of two species of waterfowl, mallards and gadwall, to more fully explore the relationship between local nest clustering and nest survival. Throughout the season, we found that the distribution of nests was consistently clustered at small spatial scales (Ëœ50â€“400 m), especially for mallard nests, and that this pattern was robust to yearly variation in nest density and the intensity of predation. We demonstrated further that local nest clustering had positive fitness consequences â€“ nests with closer nearest neighbors were more likely to be successful, a result that is counter to the general assumption that nest predation rates increase with nest density.
Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach
Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...
Density-dependent habitat selection and partitioning between two sympatric ungulates.
van Beest, Floris M; McLoughlin, Philip D; Vander Wal, Eric; Brook, Ryan K
2014-08-01
Theory on density-dependent habitat selection predicts that as population density of a species increases, use of higher quality (primary) habitat by individuals declines while use of lower quality (secondary) habitat rises. Habitat partitioning is often considered the primary mechanism for coexistence between similar species, but how this process evolves with changes in population density remains to be empirically tested for free-ranging ungulates. We used resource-selection functions to quantify density effects on landscape-scale habitat selection of two sympatric species of ungulates [moose (Alces alces) and elk (Cervus canadensis manitobensis)] in Riding Mountain National Park, Manitoba, Canada (2000-2011). The density of elk was actively reduced from 1.2 to 0.4 elk km(-2) through increased hunting effort during the period of study, while moose density decreased without additional human influence from 1.6-0.7 moose km(-2). Patterns of habitat selection during winter by both species changed in accordance to expectations from density-dependent habitat-selection theory. At low intraspecific density, moose and elk did not partition habitat, as both species selected strongly for mixed forest (primary habitat providing both food and cover), but did so in different areas segregated across an elevational gradient. As intraspecific density increased, selection for primary habitat by both species decreased, while selection for secondary, lower quality habitat such as agricultural fields (for elk) and built-up areas (for moose) increased. We show that habitat-selection strategies during winter for moose and elk, and subsequent effects on habitat partitioning, depend heavily on the position in state space (density) of both species. PMID:24913777
Yang Heping; Magilnick, Nathaniel; Xia Meng; Lu, Shelly C.
2008-01-15
Hepatocyte growth factor (HGF) is a potent hepatocyte mitogen that exerts opposing effects depending on cell density. Glutathione (GSH) is the main non-protein thiol in mammalian cells that modulates growth and apoptosis. We previously showed that GSH level is inversely related to cell density of hepatocytes and is positively related to growth. Our current work examined whether HGF can modulate GSH synthesis in a cell density-dependent manner and how GSH in turn influence HGF's effects. We found HGF treatment of H4IIE cells increased cell GSH levels only under subconfluent density. The increase in cell GSH under low density was due to increased transcription of GSH synthetic enzymes. This correlated with increased protein levels and nuclear binding activities of c-Jun, c-Fos, p65, p50, Nrf1 and Nrf2 to the promoter region of these genes. HGF acts as a mitogen in H4IIE cells under low cell density and protects against tumor necrosis factor {alpha} (TNF{alpha})-induced apoptosis by limiting JNK activation. However, HGF is pro-apoptotic under high cell density and exacerbates TNF{alpha}-induced apoptosis by potentiating JNK activation. The increase in cell GSH under low cell density allows HGF to exert its full mitogenic effect but is not necessary for its anti-apoptotic effect.
Time-dependent first-principles approaches to PV materials
Miyamoto, Yoshiyuki
2013-12-10
Computational scheme for designing photovoltaic (PV) materials is presented. First-principles electron dynamics of photo-excitation and subsequent electron-hole splitting is performed based on the time-dependent density functional theory. Photo-induced enhancement of dipole moment was observed in a polar crystal and a donor-acceptor molecular pair. These experiences will pave a way to design PV material from first-principles simulations.
Nowicki, Piotr; Bonelli, Simona; Barbero, Francesca; Balletto, Emilio
2009-08-01
The relative contribution of density-dependent regulation and environmental stochasticity to the temporal dynamics of animal populations is one of the central issues of ecology. In insects, the primary role of the latter factor, typically represented by weather patterns, is widely accepted. We have evaluated the impact of density dependence as well as density-independent factors, including weather and mowing regime, on annual fluctuations of butterfly populations. As model species, we used Maculinea alcon and M. teleius living in sympatry and, consequently, we also analysed the effect of their potential competition. Density dependence alone explained 62 and 42% of the variation in the year-to-year trends of M. alcon and M. teleius, respectively. The cumulative Akaike weight of models with density dependence, which can be interpreted as the probability that this factor should be contained in the most appropriate population dynamics model, exceeded 0.97 for both species. In contrast, the impacts of inter-specific competition, mowing regime and weather were much weaker, with their cumulative weights being in the range of 0.08-0.21; in addition, each of these factors explained only 2-5% of additional variation in Maculinea population trends. Our results provide strong evidence for density-dependent regulation in Maculinea, while the influence of environmental stochasticity is rather minor. In the light of several recent studies on other butterflies that detected significant density-dependent effects, it would appear that density-dependent regulation may be more widespread in this group than previously thought, while the role of environmental stochasticity has probably been overestimated. We suggest that this misconception is the result of deficiencies in the design of most butterfly population studies in the past, including (1) a strong focus on adults and a neglect of the larval stage in which density-dependent effects are most likely to occur; (2) an almost exclusive reliance on transect count results that may confound the impact of environmental stochasticity on butterfly numbers with its impact on adult longevity. PMID:19484269
Stochastic models of classical particle pumps : Density dependence of directed current
NASA Astrophysics Data System (ADS)
Chaudhuri, Debasish
2015-09-01
We present and compare different versions of a simple particle pump-model that describes average directed current of repulsively interacting particles in a narrow channel, due to time-varying local potentials. We analyze the model on discrete lattice with particle exclusion, using three choices of potential-dependent hopping rates that obey microscopic reversibility. Treating the strength of the external potential as a small parameter with respect to thermal energy, we present a perturbative calculation to obtain the expression for average directed current. This depends on driving frequency, phase, and particle density. The directed current vanishes as density goes to zero or close packing. For two choices of hopping rates, it reaches maximum at intermediate densities, while for a third choice, it shows a curious current reversal with increasing density. This can be interpreted in terms of a particle-hole symmetry. Stochastic simulations of the model show good agreement with our analytic predictions.
The dependence of Islamic and conventional stocks: A copula approach
NASA Astrophysics Data System (ADS)
Razak, Ruzanna Ab; Ismail, Noriszura
2015-09-01
Recent studies have found that Islamic stocks are dependent on conventional stocks and they appear to be more risky. In Asia, particularly in Islamic countries, research on dependence involving Islamic and non-Islamic stock markets is limited. The objective of this study is to investigate the dependence between financial times stock exchange Hijrah Shariah index and conventional stocks (EMAS and KLCI indices). Using the copula approach and a time series model for each marginal distribution function, the copula parameters were estimated. The Elliptical copula was selected to present the dependence structure of each pairing of the Islamic stock and conventional stock. Specifically, the Islamic versus conventional stocks (Shariah-EMAS and Shariah-KLCI) had lower dependence compared to conventional versus conventional stocks (EMAS-KLCI). These findings suggest that the occurrence of shocks in a conventional stock will not have strong impact on the Islamic stock.
Exposing extinction risk analysis to pathogens: Is disease just another form of density dependence?
Gerber, L.R.; McCallum, H.; Lafferty, K.D.; Sabo, J.L.; Dobson, A.
2005-01-01
In the United States and several other countries, the development of population viability analyses (PVA) is a legal requirement of any species survival plan developed for threatened and endangered species. Despite the importance of pathogens in natural populations, little attention has been given to host-pathogen dynamics in PVA. To study the effect of infectious pathogens on extinction risk estimates generated from PVA, we review and synthesize the relevance of host-pathogen dynamics in analyses of extinction risk. We then develop a stochastic, density-dependent host-parasite model to investigate the effects of disease on the persistence of endangered populations. We show that this model converges on a Ricker model of density dependence under a suite of limiting assumptions, including a high probability that epidemics will arrive and occur. Using this modeling framework, we then quantify: (1) dynamic differences between time series generated by disease and Ricker processes with the same parameters; (2) observed probabilities of quasi-extinction for populations exposed to disease or self-limitation; and (3) bias in probabilities of quasi-extinction estimated by density-independent PVAs when populations experience either form of density dependence. Our results suggest two generalities about the relationships among disease, PVA, and the management of endangered species. First, disease more strongly increases variability in host abundance and, thus, the probability of quasi-extinction, than does self-limitation. This result stems from the fact that the effects and the probability of occurrence of disease are both density dependent. Second, estimates of quasi-extinction are more often overly optimistic for populations experiencing disease than for those subject to self-limitation. Thus, although the results of density-independent PVAs may be relatively robust to some particular assumptions about density dependence, they are less robust when endangered populations are known to be susceptible to disease. If potential management actions involve manipulating pathogens, then it may be useful to model disease explicitly. ?? 2005 by the Ecological Society of America.
A Geometric Approach to Dislocation Densities in Semiconductors
NASA Astrophysics Data System (ADS)
Bakke, Knut; Moraes, Fernando
2015-10-01
Dislocation densities threading semiconductor crystals are a problem for device developers. Among the issues presented by the defect density is the appearance of the so called shallow levels. In this work we introduce a geometric model to explain the origin of the observed shallow levels. We show that a uniform distribution of screw dislocations acts as an effective uniform magnetic field which yields electronic bound states even in the presence of a repulsive Coulomb-like potential. This introduces energy levels within the band gap, increasing the carrier concentration in the region threaded by the dislocation density and adding additional recombination paths other than the near band-edge recombination. Our results suggest that one might use a magnetic field to destroy the dislocation density bound states and therefore minimize its effects on the charge carriers.
Structural Implications of Reciprocal Exchange: A Power-Dependence Approach
ERIC Educational Resources Information Center
Bonacich, Phillip; Bienenstock, Elisa Jayne
2009-01-01
This paper presents and tests a general model to predict emergent exchange patterns and power differences in reciprocal exchange networks when individual actors follow the norm of reciprocity. With an interesting qualification, the experimental results reported here support the power-dependence approach (Emerson 1972a, b): those who acquire theâ€¦
A novel approach to evaluating breast density using ultrasound tomography
NASA Astrophysics Data System (ADS)
Glide, Carri K.
2007-12-01
Women with high mammographic breast density have a 4- to 5-fold increased breast cancer risk compared to women with fatty breasts. Current breast density estimation involves mammography, although a mammogram is a 2-D projection which does not provide an accurate volumetric density estimate due to breast thickness not being taken into account. Presumably, breast cancer risk would have a stronger relationship to the volume of dense tissue as opposed to projected area. The purpose of this work was to investigate the feasibility of assessing breast density with ultrasound tomography. First, we evaluated a breast-mimicking phantom, and sound speed measurements were well-correlated with mass density and CT number of the phantom material. Approximately 40 m/s difference in sound speed was observed between fatty and fibroglandular components, a critical result for breast density characterization. Next, we investigated the extension of our results in vivo for a sample of ˜100 patients. We observed significant differences in global sound speed between every BI-RADS compositional category, showing that our technique was consistent with the current standard of care. A strong, positive association was revealed between breast sound speed and quantitative mammographic percent density (MPD). We also assessed volumetric ultrasound percent density (USPD) using sound speed tomograms. The USPD results were also consistent with BI-RADS Categories. Further, an increase in USPD was observed with increased MPD for both mammographic views. Next, we introduced texture analysis, and moderate negative associations between sound speed skewness and MPD, and fractal dimension and MPD, were observed. This work suggests that non-invasive and non-ionizing evaluation of breast density is achievable, and global sound speed and USPD appear to be the most promising indicators of breast density. These applications may play an integral role in monitoring treatment, tracking chemoprevention response, and identifying high-risk patients. Overall, potential benefits of quantifying a relationship between acoustical properties and breast density introduce a novel application of clinical ultrasound, one that be significant in breast cancer risk assessment.
Lonely hearts or sex in the city? Density-dependent effects in mating systems
Kokko, Hanna; Rankin, Daniel J
2006-01-01
Two very basic ideas in sexual selection are heavily influenced by numbers of potential mates: the evolution of anisogamy, leading to sex role differentiation, and the frequency dependence of reproductive success that tends to equalize primary sex ratios. However, being explicit about the numbers of potential mates is not typical to most evolutionary theory of sexual selection. Here, we argue that this may prevent us from finding the appropriate ecological equilibria that determine the evolutionary endpoints of selection. We review both theoretical and empirical advances on how population density may influence aspects of mating systems such as intrasexual competition, female choice or resistance, and parental care. Density can have strong effects on selective pressures, whether or not there is phenotypic plasticity in individual strategies with respect to density. Mating skew may either increase or decrease with density, which may be aided or counteracted by changes in female behaviour. Switchpoints between alternative mating strategies can be density dependent, and mate encounter rates may influence mate choice (including mutual mate choice), multiple mating, female resistance to male mating attempts, mate searching, mate guarding, parental care, and the probability of divorce. Considering density-dependent selection may be essential for understanding how populations can persist at all despite sexual conflict, but simple models seem to fail to predict the diversity of observed responses in nature. This highlights the importance of considering the interaction between mating systems and population dynamics, and we strongly encourage further work in this area. PMID:16612890
Coping with crowds: Density-dependent disease resistance in desert locusts
Wilson, Kenneth; Thomas, Matthew B.; Blanford, Simon; Doggett, Matthew; Simpson, Stephen J.; Moore, Sarah L.
2002-01-01
Parasite transmission generally exhibits some form of positive density dependence. Thus, as population density increases, so too does the per capita risk of becoming infected. Under such circumstances, natural selection should favor individuals that use cues associated with population density to determine the optimal allocation of resources to disease resistance mechanisms. As a consequence, individuals experiencing crowded conditions are predicted to be more resistant to parasites and pathogens than those experiencing low-density conditions. This phenomenon (termed “density-dependent prophylaxis”) [Wilson, K. & Reeson, A. F. (1998) Ecol. Entomol. 23, 100–101] is predicted to be particularly prevalent in outbreak pest species and in species exhibiting density-dependent phase polyphenism, such as the desert locust, Schistocerca gregaria. Here we show that, as predicted, desert locusts reared under crowded conditions are significantly more resistant than solitary locusts to the entomopathogenic fungus, Metarhizium anisopliae var. acridum, a key natural disease of acridids and an important agent in locust and grasshopper biocontrol. Moreover, enhanced pathogen resistance in crowded locusts is associated with elevated antimicrobial activity, but not with any difference in thermal preferences or behavioral fever response. These results have implications for understanding the development and biocontrol of locust plagues. PMID:11960003
Zubillaga, MarÃa; Skewes, Oscar; Soto, NicolÃ¡s; Rabinovich, Jorge E.; Colchero, Fernando
2014-01-01
Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation. PMID:25514510
Gluon density and F2 functions from BK equation with impact parameter dependence
NASA Astrophysics Data System (ADS)
Bondarenko, S.
2008-07-01
The LO BK equation for unintegrated gluon density with impact parameter dependence is considered. The form of initial condition for the equation is determined, which is similar to the form of fenomenological GBW ansatz. The gluon density function and F2 function are calculated and compared with the results for the gluon density and F2 functions from the GRV parameterization for different values of Q2. It is shown, that the results for F2 structure function of the considered model are in the good accordance with the results obtained from the GRV parameterization of parton densities. Therefore, obtained initial conditions for unintegrated gluon density could be used for the calculation of proton-proton scattering process as well, [S. Bondarenko, L. Motyka, in preparation].
Kang, Hongyan; Fan, Yubo; Sun, Anqiang; Deng, Xiaoyan
2011-07-01
We hypothesized that diminished endothelial glycocalyx (GCX) at atherosclerotic lesion-prone sites accelerates flow-dependent concentration polarization of low-density lipoproteins (LDLs) at the luminal surface, and in turn contributes to vulnerability of these sites to atherosclerosis. A parallel plate flow chamber was applied to expose cultured endothelial monolayers to three different levels of shear stress (3, 12, 20 dyn/cm(2)). Heparinase III (Hep.III) was employed to degrade heparan sulfate proteoglycans selectively and 3-(N-morpholino) propanesulfonic acid-buffered physiological salt solutions (MOPS-PSS) were used at either normal ionic strength (Normal-MOPS), low ionic strength (LO-MOPS) or high ionic strength (HI-MOPS) to modify the effective charge density of the endothelial GCX. Water filtration velocity (V(w)) across the endothelial monolayer, the luminal concentration of LDLs (C(w)) and the uptake of LDLs by endothelial cells were measured and compared among the following five groups of cells: (1) Control; (2) Hep.III treatment; (3) LO-MOPS; (4) Normal-MOPS; and (5) HI-MOPS. The results obtained substantiated the aforementioned hypothesis and demonstrated that compositional or charge density modification of the endothelial GCX facilitated water filtration across the endothelium, enhanced the accumulation of LDLs on the luminal surface and increased the uptake of LDLs by endothelial cells, therefore contributing to atherogenesis. PMID:21659384
Density-dependent speciation alters the structure and dynamics of neutral communities.
Wang, Shaopeng; Chen, Anping; Pacala, Stephen W; Fang, Jingyun
2015-05-01
The neutral theory of biodiversity (NTB) provides an individual-based modeling framework to study eco-evolutionary dynamics. Previous NTB models usually assumed the same per capita rate of speciation across lineages. However, population dynamics may induce macroevolutionary feedbacks that can result in variable per capita speciation rates across lineages. In this paper, with analytical and simulation approaches, we explore how different scenarios of density-dependent speciation may impact the diversity and phylogenetic patterns of neutral communities, and compare the results to predictions of the original NTB model with an invariant speciation rate. Our results show that positive per capita speciation rate-abundance relationships could result in higher species richness and evenness, enhanced stability (evidenced by higher post-disturbance recovery rates and lower temporal variability in species diversity), and higher imbalance in phylogenetic trees. The opposite patterns are predicted when per capita speciation rates decrease with abundance. Particularly, strong negative speciation rate-abundance relationships can generate a positive correlation between phylogenetic age and abundance, which has been observed in Panamanian tree species. Our findings demonstrate the importance of eco-evolutionary feedbacks for understanding long-term diversity and phylogenetic patterns in ecological communities. PMID:25701450
Linear-scaling time-dependent density-functional theory in the linear response formalism.
Zuehlsdorff, T J; Hine, N D M; Spencer, J S; Harrison, N M; Riley, D J; Haynes, P D
2013-08-14
We present an implementation of time-dependent density-functional theory (TDDFT) in the linear response formalism enabling the calculation of low energy optical absorption spectra for large molecules and nanostructures. The method avoids any explicit reference to canonical representations of either occupied or virtual Kohn-Sham states and thus achieves linear-scaling computational effort with system size. In contrast to conventional localised orbital formulations, where a single set of localised functions is used to span the occupied and unoccupied state manifold, we make use of two sets of in situ optimised localised orbitals, one for the occupied and one for the unoccupied space. This double representation approach avoids known problems of spanning the space of unoccupied Kohn-Sham states with a minimal set of localised orbitals optimised for the occupied space, while the in situ optimisation procedure allows for efficient calculations with a minimal number of functions. The method is applied to a number of medium sized organic molecules and a good agreement with traditional TDDFT methods is observed. Furthermore, linear scaling of computational cost with system size is demonstrated on (10,0) carbon nanotubes of different lengths. PMID:23947840
NASA Astrophysics Data System (ADS)
Franco de Carvalho, F.; Tavernelli, I.
2015-12-01
In this work, we derive a method to perform trajectory-based nonadiabatic dynamics that is able to describe both nonadiabatic transitions and intersystem crossing events (transitions between states of different spin-multiplicity) at the same level of theory, namely, time-dependent density functional theory (TDDFT). To this end, we combined our previously developed TDDFT-based trajectory surface hopping scheme with an accurate and efficient algorithm for the calculation of the spin-orbit coupling (SOC) matrix elements. More specifically, we designed two algorithms for the calculation of intersystem crossing transitions, one based on an extended Tully's surface hopping scheme including SOC and the second based on a Landau-Zener approximation applied to the spin sector of the electronic Hilbert space. This development allows for the design of an efficient on-the-fly nonadiabatic approach that can handle, on an equal footing, nonadiabatic and intersystem crossing transitions. The method is applied to the study of the photophysics of sulfur dioxide (SO2) in gas and liquid phases.
NASA Technical Reports Server (NTRS)
Chen, A.-B.; Weisz, G.; Sher, A.
1972-01-01
A model calculation of the temperature dependence of the electronic density of states and the electrical conductivity of disordered binary alloys, based on the coherent-potential approximation is made by introducing thermal disorder in the single-band model (Velicky and others). Thermal disorder is found to broaden and smear the static-alloy density of states. The electrical resistivity in weak-scattering alloys always increases with temperature. However, in the strong-scattering case, the temperature coefficient of resistivity can be positive, zero, or negative, depending on the location of the Fermi energy.-
Jiang Weizhou
2010-04-15
Effects of the density dependence of the nuclear symmetry energy on ground-state properties of superheavy nuclei are studied in the relativistic mean-field theory. It is found that the softening of the symmetry energy plays an important role in the empirical shift [Phys. Rev. C 67, 024309 (2003)] of spherical orbitals in superheavy nuclei. The calculation based on the relativistic mean-field models NL3 and FSUGold supports the double shell closure in {sup 292}120 with the softening of the symmetry energy. In addition, the significant effect of the density dependence of the symmetry energy on the neutron skin thickness in superheavy nuclei is investigated.
Density-dependent nucleon-nucleon interaction from Urbana UIX three-nucleon force
NASA Astrophysics Data System (ADS)
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu; Schmidt, Kevin E.
2011-12-01
A density-dependent two-nucleon potential has been derived within the formalism of correlated basis function. The effects of three-particle interactions has been included by integrating out the degrees of freedom of the third nucleon. The potential can be easily employed in nuclear matter calculations. It yields results in agreement with those obtained from the underlying three-body potential. Using the density dependent potential, we have carried out a study of the effects of three-nucleon interactions in symmetric nuclear matter within the Auxiliary Field Diffusion Monte Carlo (AFDMC) computational scheme.
Density-dependent survival and fecundity of hemlock woolly adelgid (Hemiptera: Adelgidae).
Sussky, Elizabeth M; Elkinton, Joseph S
2014-10-01
The hemlock woolly adelgid (Adelges tsugae Annand) has decimated eastern hemlocks (Tsuga canadensis Carrière) in forests throughout the eastern United Sates, but its densities in central New England appear to have stabilized. To find out why, we infested 64 eastern hemlocks with varying densities of adelgid ovisacs in a typical eastern hemlock forest in western Massachusetts. We subsequently documented adelgid density, fecundity, and the amount of new growth on experimental trees over two consecutive years. We used a 2 by 2 randomized block design using previously and newly infested hemlocks that were either 1-m tall saplings or branches of mature trees. There was a density-dependent decline in the survival and fecundity of adelgid in both the spring and winter generations. This response was a function of both previous infestation by adelgid and current year's crawler density in the spring generation. Additionally, the production of sexuparae in the spring generation played a key role in the overall density-dependent survival of adelgid, suggesting that sexuparae production is strongly linked to developing crawler density. PMID:25203223
Density dependence in group dynamics of a highly social mongoose, Suricata suricatta.
Bateman, Andrew W; Ozgul, Arpat; Coulson, Tim; Clutton-Brock, Tim H
2012-05-01
1.?For social species, the link between individual behaviour and population dynamics is mediated by group-level demography. 2.?Populations of obligate cooperative breeders are structured into social groups, which may be subject to inverse density dependence (Allee effects) that result from a dependence on conspecific helpers, but evidence for population-wide Allee effects is rare. 3.?We use field data from a long-term study of cooperative meerkats (Suricata suricatta; Schreber, 1776) - a species for which local Allee effects are not reflected in population-level dynamics - to empirically model interannual group dynamics. 4.?Using phenomenological population models, modified to incorporate environmental conditions and potential Allee effects, we first investigate overall patterns of group dynamics and find support only for conventional density dependence that increases after years of low rainfall. 5.?To explain the observed patterns, we examine specific demographic rates and assess their contributions to overall group dynamics. Although per-capita meerkat mortality is subject to a component Allee effect, it contributes relatively little to observed variation in group dynamics, and other (conventionally density dependent) demographic rates - especially emigration - govern group dynamics. 6.?Our findings highlight the need to consider demographic processes and density dependence in subpopulations before drawing conclusions about how behaviour affects population processes in socially complex systems. PMID:22117843
NASA Astrophysics Data System (ADS)
Chizhov, Anton V.; Graham, Lyle J.
2007-01-01
We propose a macroscopic approach toward realistic simulations of the population activity of hippocampal pyramidal neurons, based on the known refractory density equation with a different hazard function and on a different single-neuron threshold model. The threshold model is a conductance-based model taking into account adaptation-providing currents, which is reduced by omitting the fast sodium current and instead using an explicit threshold criterion for action potential events. Compared to the full pyramidal neuron model, the threshold model well approximates spike-time moments, postspike refractory states, and postsynaptic current integration. The dynamics of a neural population continuum are described by a set of one-dimensional partial differential equations in terms of the distributions of the refractory density (where the refractory state is defined by the time elapsed since the last action potential), the membrane potential, and the gating variables of the voltage-dependent channels, across the entire population. As the source term in the density equation, the probability density of firing, or hazard function, is derived from the Fokker-Planck (FP) equation, assuming that a single neuron is governed by a deterministic average-across-population input and a noise term. A self-similar solution of the FP equation in the subthreshold regime is obtained. Responses of the ensemble to stimulation by a current step and oscillating current are simulated and compared with individual neuron simulations. An example of interictal-like activity of a population of all-to-all connected excitatory neurons is presented.
NASA Astrophysics Data System (ADS)
Davari, Nazanin; Ã…strand, Per-Olof; Unge, Mikael
2015-02-01
A recent method based on constrained density functional theory (CDFT) has been used to calculate the field-dependent ionization potential by determining the dissociation barrier for the interaction between a cation and an electron in an electric field. In the CDFT model, we rely on that the barrier is located somewhere outside the cation, which has limited the applicability for polyaromatic molecules where the barrier is located closer to the cation than for other molecules. Different density functionals, basis sets and choices of constraints in the CDFT calculations are tested for benzene as a case study. The field-dependent ionization potential calculated by constraining the charge with the B3LYP functional and the cc-pVDZ basis set shows a good agreement with our previous work and has a low computational cost for the larger aromatic molecules included here. In addition, field-dependent excitation energies are investigated using time-dependent DFT.
Density-Dependent Natal Dispersal Patterns in a Leopard Population Recovering from Over-Harvest
Fattebert, Julien; Balme, Guy; Dickerson, Tristan; Slotow, Rob; Hunter, Luke
2015-01-01
Natal dispersal enables population connectivity, gene flow and metapopulation dynamics. In polygynous mammals, dispersal is typically male-biased. Classically, the â€˜mate competitionâ€™, â€˜resource competitionâ€™ and â€˜resident fitnessâ€™ hypotheses predict density-dependent dispersal patterns, while the â€˜inbreeding avoidanceâ€™ hypothesis posits density-independent dispersal. In a leopard (Panthera pardus) population recovering from over-harvest, we investigated the effect of sex, population density and prey biomass, on age of natal dispersal, distance dispersed, probability of emigration and dispersal success. Over an 11-year period, we tracked 35 subadult leopards using VHF and GPS telemetry. Subadult leopards initiated dispersal at 13.6 Â± 0.4 months. Age at commencement of dispersal was positively density-dependent. Although males (11.0 Â± 2.5 km) generally dispersed further than females (2.7 Â± 0.4 km), some males exhibited opportunistic philopatry when the population was below capacity. All 13 females were philopatric, while 12 of 22 males emigrated. Male dispersal distance and emigration probability followed a quadratic relationship with population density, whereas female dispersal distance was inversely density-dependent. Eight of 12 known-fate females and 5 of 12 known-fate male leopards were successful in settling. Dispersal success did not vary with population density, prey biomass, and for males, neither between dispersal strategies (philopatry vs. emigration). Females formed matrilineal kin clusters, supporting the resident fitness hypothesis. Conversely, mate competition appeared the main driver for male leopard dispersal. We demonstrate that dispersal patterns changed over time, i.e. as the leopard population density increased. We conclude that conservation interventions that facilitated local demographic recovery in the study area also restored dispersal patterns disrupted by unsustainable harvesting, and that this indirectly improved connectivity among leopard populations over a larger landscape. PMID:25875293
An information theory approach to the density of the earth
NASA Technical Reports Server (NTRS)
Graber, M. A.
1977-01-01
Information theory can develop a technique which takes experimentally determined numbers and produces a uniquely specified best density model satisfying those numbers. A model was generated using five numerical parameters: the mass of the earth, its moment of inertia, three zero-node torsional normal modes (L = 2, 8, 26). In order to determine the stability of the solution, six additional densities were generated, in each of which the period of one of the three normal modes was increased or decreased by one standard deviation. The superposition of the seven models is shown. It indicates that current knowledge of the torsional modes is sufficient to specify the density in the upper mantle but that the lower mantle and core will require smaller standard deviations before they can be accurately specified.
Equation of state of dense matter from a density dependent relativistic mean field model
NASA Astrophysics Data System (ADS)
Shen, G.; Horowitz, C. J.; Teige, S.
2010-07-01
We calculate the equation of state (EOS) of dense matter using a relativistic mean field (RMF) model with a density dependent coupling that is a slightly modified form of the original NL3 interaction. For nonuniform nuclear matter we approximate the unit lattice as a spherical Wigner-Seitz cell, wherein the meson mean fields and nucleon Dirac wave functions are solved fully self-consistently. We also calculate uniform nuclear matter for a wide range of temperatures, densities, and proton fractions, and match them to nonuniform matter as the density decreases. The calculations took over 6000 CPU days in Indiana Universityâ€™s supercomputer clusters. We tabulate the resulting EOS at over 107,000 grid points in the proton fraction range YP=0 to 0.56. For the temperature range T=0.16 to 15.8 MeV, we cover the density range nB=10-4 to 1.6 fm-3; and for the higher temperature range T=15.8 to 80 MeV, we cover the larger density range nB=10-8 to 1.6 fm-3. In the future we plan to study low density, low temperature (T<15.8 MeV), nuclear matter using a Virial expansion, and we will match the low-density and high-density results to generate a complete EOS table for use in astrophysical simulations of supernova and neutron star mergers.
Equation of state of dense matter from a density dependent relativistic mean field model
Shen, G.; Horowitz, C. J.; Teige, S.
2010-07-15
We calculate the equation of state (EOS) of dense matter using a relativistic mean field (RMF) model with a density dependent coupling that is a slightly modified form of the original NL3 interaction. For nonuniform nuclear matter we approximate the unit lattice as a spherical Wigner-Seitz cell, wherein the meson mean fields and nucleon Dirac wave functions are solved fully self-consistently. We also calculate uniform nuclear matter for a wide range of temperatures, densities, and proton fractions, and match them to nonuniform matter as the density decreases. The calculations took over 6000 CPU days in Indiana University's supercomputer clusters. We tabulate the resulting EOS at over 107,000 grid points in the proton fraction range Y{sub P}=0 to 0.56. For the temperature range T=0.16 to 15.8 MeV, we cover the density range n{sub B}=10{sup -4} to 1.6 fm{sup -3}; and for the higher temperature range T=15.8 to 80 MeV, we cover the larger density range n{sub B}=10{sup -8} to 1.6 fm{sup -3}. In the future we plan to study low density, low temperature (T<15.8 MeV), nuclear matter using a Virial expansion, and we will match the low-density and high-density results to generate a complete EOS table for use in astrophysical simulations of supernova and neutron star mergers.
Schrader, Matthew; Jarrett, Benjamin J M; Kilner, Rebecca M
2015-04-01
Studies of siblings have focused mainly on their competitive interactions and to a lesser extent on their cooperation. However, competition and cooperation are at opposite ends on a continuum of possible interactions and the nature of these interactions may be flexible with ecological factors tipping the balance toward competition in some environments and cooperation in others. Here we show that the presence of parental care and the density of larvae on the breeding carcass change the outcome of sibling interactions in burying beetle broods. With full parental care there was a strong negative relationship between larval density and larval mass, consistent with sibling competition for resources. In the absence of care, initial increases in larval density had beneficial effects on larval mass but further increases in larval density reduced larval mass. This likely reflects a density-dependent shift between cooperation and competition. In a second experiment, we manipulated larval density and removed parental care. We found that the ability of larvae to penetrate the breeding carcass increased with larval density and that feeding within the carcass resulted in heavier larvae than feeding outside the carcass. However, larval density did not influence carcass decay. PMID:25648525
Schrader, Matthew; Jarrett, Benjamin J M; Kilner, Rebecca M
2015-01-01
Studies of siblings have focused mainly on their competitive interactions and to a lesser extent on their cooperation. However, competition and cooperation are at opposite ends on a continuum of possible interactions and the nature of these interactions may be flexible with ecological factors tipping the balance toward competition in some environments and cooperation in others. Here we show that the presence of parental care and the density of larvae on the breeding carcass change the outcome of sibling interactions in burying beetle broods. With full parental care there was a strong negative relationship between larval density and larval mass, consistent with sibling competition for resources. In the absence of care, initial increases in larval density had beneficial effects on larval mass but further increases in larval density reduced larval mass. This likely reflects a density-dependent shift between cooperation and competition. In a second experiment, we manipulated larval density and removed parental care. We found that the ability of larvae to penetrate the breeding carcass increased with larval density and that feeding within the carcass resulted in heavier larvae than feeding outside the carcass. However, larval density did not influence carcass decay. PMID:25648525
SchÃ¶nrogge, Karsten; Begg, Tracey; Stone, Graham N.
2013-01-01
Revealing the interactions between alien species and native communities is central to understanding the ecological consequences of range expansion. Much has been learned through study of the communities developing around invading herbivorous insects. Much less, however, is known about the significance of such aliens for native vertebrate predators for which invaders may represent a novel food source. We quantified spatial patterns in native bird predation of invading gall-inducing Andricus wasps associated with introduced Turkey oak (Quercus cerris) at eight sites across the UK. These gallwasps are available at high density before the emergence of caterpillars that are the principle spring food of native insectivorous birds. Native birds showed positive spatial density dependence in gall attack rates at two sites in southern England, foraging most extensively on trees with highest gall densities. In a subsequent study at one of these sites, positive spatial density dependence persisted through four of five sequential week-long periods of data collection. Both patterns imply that invading galls are a significant resource for at least some native bird populations. Density dependence was strongest in southern UK bird populations that have had longest exposure to the invading gallwasps. We hypothesise that this pattern results from the time taken for native bird populations to learn how to exploit this novel resource. PMID:23342048
Koons, David N; Colchero, Fernando; Hersey, Kent; Gimenez, Olivier
2015-06-01
Understanding the relative effects of climate, harvest, and density dependence on population dynamics is critical for guiding sound population management, especially for ungulates in arid and semiarid environments experiencing climate change. To address these issues for bison in southern Utah, USA, we applied a Bayesian state-space model to a 72-yr time series of abundance counts. While accounting for known harvest (as well as live removal) from the population, we found that the bison population in southern Utah exhibited a strong potential to grow from low density (?0 = 0.26; Bayesian credible interval based on 95% of the highest posterior density [BCI] = 0.19-0.33), and weak but statistically significant density dependence (?1 = -0.02, BCI = -0.04 to -0.004). Early spring temperatures also had strong positive effects on population growth (Pfat1 = 0.09, BCI = 0.04-0.14), much more so than precipitation and other temperature-related variables (model weight > three times more than that for other climate variables). Although we hypothesized that harvest is the primary driving force of bison population dynamics in southern Utah, our elasticity analysis indicated that changes in early spring temperature could have a greater relative effect on equilibrium abundance than either harvest or. the strength of density dependence. Our findings highlight the utility of incorporating elasticity analyses into state-space population models, and the need to include climatic processes in wildlife management policies and planning. PMID:26465036
Le Galliard, J-F; Paquet, M; Mugabo, M
2015-05-01
Temperament traits are seen in many animal species, and recent evolutionary models predict that they could be maintained by heterogeneous selection. We tested this prediction by examining density-dependent selection in juvenile common lizards Zootoca vivipara scored for activity, boldness and sociability at birth and at the age of 1 year. We measured three key life-history traits (juvenile survival, body growth rate and reproduction) and quantified selection in experimental populations at five density levels ranging from low to high values. We observed consistent individual differences for all behaviours on the short term, but only for activity and one boldness measure across the first year of life. At low density, growth selection favoured more sociable lizards, whereas viability selection favoured less active individuals. A significant negative correlational selection on activity and boldness existed for body growth rate irrespective of density. Thus, behavioural traits were characterized by limited ontogenic consistency, and natural selection was heterogeneous between density treatments and fitness traits. This confirms that density-dependent selection plays an important role in the maintenance of individual differences in exploration-activity and sociability. PMID:25865798
Time-dependent stochastic Bethe-Salpeter approach
NASA Astrophysics Data System (ADS)
Rabani, Eran; Baer, Roi; Neuhauser, Daniel
2015-06-01
A time-dependent formulation for electron-hole excitations in extended finite systems, based on the Bethe-Salpeter equation (BSE), is developed using a stochastic wave function approach. The time-dependent formulation builds on the connection between time-dependent Hartree-Fock (TDHF) theory and the configuration-interaction with single substitution (CIS) method. This results in a time-dependent Schrödinger-like equation for the quasiparticle orbital dynamics based on an effective Hamiltonian containing direct Hartree
The nutrient density approach to healthy eating: challenges and opportunities
Technology Transfer Automated Retrieval System (TEKTRAN)
The term 'nutrient density' for foods/beverages has been used loosely to promote the Dietary Guidelines for Americans. The 2010 Dietary Guidelines for Americans defined 'all vegetables, fruits, whole grains, fat-free or low-fat milk and milk products, seafood, lean meats and poultry, eggs, beans and...
Density dependent state space model for population abundance data with unequal time intervals
Dennis, Brian; Ponciano, JosÃ© Miguel
2014-01-01
The Gompertz state-space (GSS) model is a stochastic model for analyzing time series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise and observation error. PMID:25230459
Density dependence of the symmetry energy from neutron skin thickness in finite nuclei
Vinas, X.; Centelles, M.; Roca-Maza, X.; Warda, M.
2012-10-20
The density dependence of the symmetry energy, characterized by the parameter L, is studied using information provided by the neutron skin thickness in finite nuclei. An estimate of L is obtained from experimental data of antiprotonic atoms. We also discuss the ability of parity violating electron scatering to obtain information about the neutron skin thickness in {sup 208}Pb.
Density-dependent demographic variation determines extinction rate of experimental populations.
Drake, John M
2005-07-01
Understanding population extinctions is a chief goal of ecological theory. While stochastic theories of population growth are commonly used to forecast extinction, models used for prediction have not been adequately tested with experimental data. In a previously published experiment, variation in available food was experimentally manipulated in 281 laboratory populations of Daphnia magna to test hypothesized effects of environmental variation on population persistence. Here, half of those data were used to select and fit a stochastic model of population growth to predict extinctions of populations in the other half. When density-dependent demographic stochasticity was detected and incorporated in simple stochastic models, rates of population extinction were accurately predicted or only slightly biased. However, when density-dependent demographic stochasticity was not accounted for, as is usual when forecasting extinction of threatened and endangered species, predicted extinction rates were severely biased. Thus, an experimental demonstration shows that reliable estimates of extinction risk may be obtained for populations in variable environments if high-quality data are available for model selection and if density-dependent demographic stochasticity is accounted for. These results suggest that further consideration of density-dependent demographic stochasticity is required if predicted extinction rates are to be relied upon for conservation planning. PMID:15934788
DENSITY-DEPENDENT FLOW IN ONE-DIMENSIONAL VARIABLY-SATURATED MEDIA
A one-dimensional finite element is developed to simulate density-dependent flow of saltwater in variably saturated media. The flow and solute equations were solved in a coupled mode (iterative), in a partially coupled mode (non-iterative), and in a completely decoupled mode. P...
DENSITY-DEPENDENT RESPONSES OF GRAY-TAILED VOLES TO MOWING
Voles (Microtus spp.) commonly inhabit forage crops and may cause excessive damage to these crops. owever, cover removal by mowing or haying may cause vole populations to decline. o determine if gray-tailed voles responded to mowing of alfalfa in a density-dependent manner, the a...
2012-01-01
We have shown that it is possible to tune, up to complete suppression, the photoluminescence superlinear dependence on the excitation density in quantum dot samples at high temperatures by annealing treatments. The effect has been attributed to the reduction of the defectivity of the material induced by annealing. PMID:23033918
Demonstrating the Temperature Dependence of Density via Construction of a Galilean Thermometer
ERIC Educational Resources Information Center
Priest, Marie A.; Padgett, Lea W.; Padgett, Clifford W.
2011-01-01
A method for the construction of a Galilean thermometer out of common chemistry glassware is described. Students in a first-semester physical chemistry (thermodynamics) class can construct the Galilean thermometer as an investigation of the thermal expansivity of liquids and the temperature dependence of density. This is an excellent firstâ€¦
Density-dependent state-space model for population-abundance data with unequal time intervals.
Dennis, Brian; Ponciano, José Miguel
2014-08-01
The Gompertz state-space (GSS) model is a stochastic model for analyzing time-series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise, and observation error. PMID:25230459
Demonstrating the Temperature Dependence of Density via Construction of a Galilean Thermometer
ERIC Educational Resources Information Center
Priest, Marie A.; Padgett, Lea W.; Padgett, Clifford W.
2011-01-01
A method for the construction of a Galilean thermometer out of common chemistry glassware is described. Students in a first-semester physical chemistry (thermodynamics) class can construct the Galilean thermometer as an investigation of the thermal expansivity of liquids and the temperature dependence of density. This is an excellent first…
Ferris, H
1985-04-01
Nematode multiplication rates Pf/Pi and overwinter survivorship (Pi2/Pfl) for Meloidogyne incognita were both adequately described by negative exponential models, indicating density dependence in each case. Density dependence of the multiplication rates is mediated by resource limitation and host damage; in survivorship rates it may be mediated by limitation of stored reserves or prevalence of antagonists. Parameters of multiplication rate models were crop specific and varied with host status and environmental suitability. Maximum multiplication rates (a) of nearly 1,000 were measured for tomatoes. Equilibrium densities were sensitive to tolerance of the nematode by the crop. Overwinter survival rates varied among locations where cultural practices and length of infestation time differed. PMID:19294065
NASA Astrophysics Data System (ADS)
Yamilov, A.; Petrenko, S.; Sarma, R.; Cao, H.
2016-03-01
The universal bimodal distribution of transmission eigenvalues in lossless diffusive systems underpins such celebrated phenomena as universal conductance fluctuations, quantum shot noise in condensed matter physics, and enhanced transmission in optics and acoustics. Here, we show that in the presence of absorption, the density of the transmission eigenvalues depends on the confinement geometry of the scattering media. Furthermore, in an asymmetric waveguide, the densities of the reflection and absorption eigenvalues also depend on the side from which the waves are incident. With increasing absorption, the density of absorption eigenvalues transforms from a single-peak to a double-peak function. Our findings open an additional avenue for coherent control of wave transmission, reflection, and absorption in random media.
NASA Astrophysics Data System (ADS)
Zalewski, M.; Olbratowski, P.; Satu?a, W.
Calculations for infinite nuclear matter with realistic nucleon-nucleon interactions suggest that the isoscalar effective mass (IEM) of a nucleon at the saturation density equals m*/m 0.8 ± 0.1, at variance with empirical data on the nuclear level density in finite nuclei which are consistent with m*/m ? 1. This contradicting results might be reconciled by enriching the radial dependence of IEM. In this work four new terms are introduced into the Skyrme-force inspired local energy-density functional: ?(??)2, ? {{d? }}/{{dr}}, ?2 and ???. The aim is to investigate how they influence the radial dependence of IEM and, in turn, the single-particle spectra.
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wave functions are fixed by the initial state in TDDFT. Two key questions involve (1) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (2) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble. In Section II, we will address these questions by first demonstrating that thermodynamic expectations can be evaluated by averaging over certain many-body pure states, which we will call thermal states, and then constructing TDDFT states that approximate these thermal states. In Section III, we will present some numerical tests of the resulting theory, and in Section IV, we will summarize our main results and discuss some possible future directions for this work.
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state bymoreÂ Â» a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wave functions are fixed by the initial state in TDDFT. Two key questions involve (1) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (2) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble. In Section II, we will address these questions by first demonstrating that thermodynamic expectations can be evaluated by averaging over certain many-body pure states, which we will call thermal states, and then constructing TDDFT states that approximate these thermal states. In Section III, we will present some numerical tests of the resulting theory, and in Section IV, we will summarize our main results and discuss some possible future directions for this work.Â«Â less
Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout
Bassar, Ronald D.; Letcher, Benjamin H.; Nislow, Keith H.; Whiteley, Andrew R.
2016-01-01
Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) versus density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change.
Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout.
Bassar, Ronald D; Letcher, Benjamin H; Nislow, Keith H; Whiteley, Andrew R
2016-02-01
Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) vs. density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type, and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change. PMID:26490737
UC/MALDI-MS analysis of HDL; evidence for density-dependent post-translational modifications
Johnson, Jeffery D.; Henriquez, Ronald R.; Tichy, Shane E.; Russell, David H.; McNeal, Catherine J.; Macfarlane, Ronald D.
2007-01-01
The purpose of this study is to determine whether the nature of the post-translational modifications of the major apolipoproteins of HDL is different for density-distinct subclasses. These subclasses were separated by ultracentrifugation using a novel density-forming solute to yield a high-resolution separation. The serum of two subjects, a control with a normolipidemic profile and a subject with diagnosed cardiovascular disease, was studied. Aliquots of three HDL subclasses were analyzed by MALDI and considerable differences were seen when comparing density-distinct subclasses and also when comparing the two subjects. A detailed analysis of the post-translational modification pattern of apoA-1 shows evidence of considerable protease activity, particularly in the more dense fractions. We conclude that part of the heterogeneity of the population of HDL particles is due to density-dependent protease activity. PMID:19050741
Tight-binding approach to strain-dependent DNA electronics
NASA Astrophysics Data System (ADS)
Malakooti, Sadeq; Hedin, Eric; Joe, Yong
2013-07-01
Small mechanical strain perturbations are considered in calculations of the poly(G)-poly(C) DNA molecular electronic structure, using a tight-binding framework in conjunction with the theories of Slater-Koster and linear elasticity. Results reveal a strain-induced band gap for DNA which is linearly dependent on the induced strain. Local density of states calculations expose that the contribution of the guanine-cytosine base pairs in the charge transport mechanism is significantly enhanced relative to the backbones when DNA is compressed. Transport investigations also disclose a strain-induced metal-semiconductor transition for the DNA molecule, which suggests possible potential uses for sensing applications.
Mitric, Roland; Werner, Ute; Bonacic-Koutecky, Vlasta
2008-10-28
We present a theoretical approach for the nonadiabatic dynamics 'on the fly' based on the combination of the time-dependent density functional theory (TDDFT) with Tully's stochastic surface hopping method. Our formulation is based on localized Gaussian basis sets and is suitable for the simulation of ultrafast processes in complex molecular systems including all degrees of freedom. Our approach is used for the simulation of time resolved photoelectron spectra in the framework of the Wigner distribution approach. In order to illustrate the scope of the method, we study the ultrafast photoswitching dynamics of the prototype Schiff base benzylideneaniline (BAN). The nonradiative lifetime of the S{sub 1} state of BAN is determined to be {approx}200 fs. The mechanism of the photoisomerization has been investigated and a connection between the time resolved photoelectron signal and the underlying nonadiabatic processes has been established.
Density-dependent responses of fawn cohort body mass in two contrasting roe deer populations.
Kjellander, Petter; Gaillard, Jean-Michel; Hewison, A J Mark
2006-01-01
We investigated the influence of population density on juvenile body mass in two contrasting roe deer populations, in Sweden (Bogesund) and France (Chizé), in which density was monitored for >or=15 years. We investigated the effect of population density and climatic conditions on cohort performance. We predicted that: (1) body mass of growing fawns should be sensitive to environmental changes, showing marked between-year variation (i.e., cohort effects), (2) fawns in the less productive (weakly seasonal, weakly predictable summer weather) habitat of Chizé should show stronger density-dependent responses due to more severe food competition during summer than fawns in the more productive (markedly seasonal, moderately predictable summer weather) habitat of Bogesund, and (3) fawns at Bogesund should be heavier both in absolute terms and relative to their size than their conspecifics in Chizé due to a higher degree of fat accumulation in northern environments. In both study sites we found marked cohort variation and clear effects of density, with body mass varying by as much as 29% over years. While neither summer nor winter climate influenced fawn body mass at Bogesund, fawns tended to be lighter after summers with high temperatures at Chizé. In addition, fawns were heavier after acorn mast years experienced in utero at Bogesund. As expected, the strength of the density-dependent response of fawn body mass was greater at Chizé than at Bogesund. For a given density, male fawns were consistently heavier than females in both sites. Lastly, both sexes at Bogesund had higher absolute body mass and were larger for a given body size than in Chizé. Our results clearly demonstrate that absolute density is a poor predictor of roe deer performance and supports the view that habitat quality has an overwhelming importance for determining fawn body mass in roe deer populations. PMID:16341553
Density-dependent patterns of thiamine and pigment production in the diatom Nitzschia microcephala.
Pinto, Ernani; Van Nieuwerburgh, Lies; Paes de Barros, Marcelo; Pedersén, Marianne; Colepicolo, Pio; Snoeijs, Pauli
2003-05-01
In the present study we investigate how intraspecific (density-dependent) competition for nutrients by the diatom Nitzschia microcephala affects the level of oxidative stress in the algal cells as well as their production of pigments and thiamine. N. microcephala was grown in three different densities until the stationary growth phase was reached. Throughout the experiment, growth rate was negatively related to cell density. Superoxide dismutase activity, protein thiol, and diatoxanthin concentrations indicated increasing oxidative stress with increasing cell density, which was most probably caused by nutrient depletion of the medium. Pigment contents per cell (except for diatoxanthin) decreased with increasing cell density. N. microcephala was able to synthesize thiamine and its thiamine content per cell increased in concert with cell density. In comparison, the dinoflagellate Amphidinium carterae was unable to synthesize thiamine. These results suggest that cells of N. microcephala subjected to higher competition and lower growth rates have a lower carotenoid content and a higher thiamine content. If such responses would occur in nature as well, eutrophication (higher cell densities) may alter the quality of microalgae as food items for higher trophic levels not only by species shifts in the phytoplankton, but also by changes in the cellular nutritional value within species. PMID:12711136
Density- and Size-Dependent Winter Mortality and Growth of Late Chaoborus flavicans Larvae
SchrÃ¶der, Arne
2013-01-01
Winter processes such as overwinter survival and growth of individuals can have wide-ranging consequences for population dynamics and communities within and across seasons. In freshwater organisms winter processes have been mainly studied in fish despite that invertebrates also have substantial impacts on lake and pond food webs. One of the major invertebrate consumers in lake and ponds is the planktonic larvae of the dipteran insect Chaoborus spec. However, while much is known about Chaoborus feeding ecology, behaviour and structuring role in food webs, its winter ecology and how it affects its populations are poorly understood. Here size- and density-dependent winter mortality and body growth of late Chaoborus flavicans larvae were quantified over naturally occurring size and density ranges in autumn and under natural winter conditions using two field enclosure experiments. Winter mortality increased with autumn density but decreased with autumn body size while winter growth rates decreased with autumn density and body sizes. There was also a density- and size-independent background mortality component. The proportion of pupae found in spring decreased strongly and exponentially with autumn density. These results may explain the commonly observed univoltine life cycle and multi-annual density fluctuations in northern Chaoborus populations. They further demonstrate the relevance of winter processes and conditions for freshwater invertebrates and ecosystems. PMID:24124517
Progression of Plasmodium berghei through Anopheles stephensi Is Density-Dependent
Sinden, Robert E; Dawes, Emma J; Alavi, Yasmene; Waldock, Joanna; Finney, Olivia; Mendoza, Jacqui; Butcher, Geoff A; Andrews, Laura; Hill, Adrian V; Gilbert, Sarah C; Basáñez, María-Gloria
2007-01-01
It is well documented that the density of Plasmodium in its vertebrate host modulates the physiological response induced; this in turn regulates parasite survival and transmission. It is less clear that parasite density in the mosquito regulates survival and transmission of this important pathogen. Numerous studies have described conversion rates of Plasmodium from one life stage to the next within the mosquito, yet few have considered that these rates might vary with parasite density. Here we establish infections with defined numbers of the rodent malaria parasite Plasmodium berghei to examine how parasite density at each stage of development (gametocytes; ookinetes; oocysts and sporozoites) influences development to the ensuing stage in Anopheles stephensi, and thus the delivery of infectious sporozoites to the vertebrate host. We show that every developmental transition exhibits strong density dependence, with numbers of the ensuing stages saturating at high density. We further show that when fed ookinetes at very low densities, oocyst development is facilitated by increasing ookinete number (i.e., the efficiency of ookinete–oocyst transformation follows a sigmoid relationship). We discuss how observations on this model system generate important hypotheses for the understanding of malaria biology, and how these might guide the rational analysis of interventions against the transmission of the malaria parasites of humans by their diverse vector species. PMID:18166078
Latitudinal Density Dependence of Magnetic Field Lines Inferred from Polar Plasma Wave Data
NASA Technical Reports Server (NTRS)
Goldstein, J.; Denton, R. E.; Hudson, M. K.; Miftakhova, E. G.; Menietti, J. D.; Gallagher, D. L.
2000-01-01
Using observations of the electron density, n(sub e), based on measurement of the upper hybrid resonance frequency by the Polar spacecraft Plasma Wave Instrument, we have examined the radial density dependence along field lines in the outer plasmasphere and the near plasmatrough. Sampled L values range from 2.5 to 6.6. Our technique depends on the fact that Polar crosses particular L values at two different points with different radial distance R. In our plasmaspheric data set (n(sub e) > 100/cm3), we find that on average n(sub e) is flat along field lines from the equator up to the latitudes sampled by Polar (R approximately equal to or > 2.0). In the plasmatrough data set (n(sub e) < 100/cm-3), there is on average a mild radial dependence n(sub e) varies as R(exp -1.7).
The nutrient density approach to healthy eating: challenges and opportunities.
Nicklas, Theresa A; Drewnowski, Adam; O'Neil, Carol E
2014-12-01
The term 'nutrient density' for foods/beverages has been used loosely to promote the Dietary Guidelines for Americans. The 2010 Dietary Guidelines for Americans defined 'all vegetables, fruits, whole grains, fat-free or low-fat milk and milk products, seafood, lean meats and poultry, eggs, beans and peas (legumes), and nuts and seeds that are prepared without added solid fats, added sugars, and sodium' as nutrient dense. The 2010 Dietary Guidelines for Americans further states that nutrient-dense foods and beverages provide vitamins, minerals and other substances that may have positive health effects with relatively few (kilo)calories or kilojoules. Finally, the definition states nutrients and other beneficial substances have not been 'diluted' by the addition of energy from added solid fats, added sugars or by the solid fats naturally present in the food. However, the Dietary Guidelines Advisory Committee and other scientists have failed to clearly define 'nutrient density' or to provide criteria or indices that specify cut-offs for foods that are nutrient dense. Today, 'nutrient density' is a ubiquitous term used in the scientific literature, policy documents, marketing strategies and consumer messaging. However, the term remains ambiguous without a definitive or universal definition. Classifying or ranking foods according to their nutritional content is known as nutrient profiling. The goal of the present commentary is to address the research gaps that still exist before there can be a consensus on how best to define nutrient density, highlight the situation in the USA and relate this to wider, international efforts in nutrient profiling. PMID:25166614
NASA Astrophysics Data System (ADS)
Faghei, Kazem
2014-06-01
The purpose of this paper is to explore the influences of cooling timescale on fragmentation of self-gravitating protoplanetary disks. We assume the cooling timescale, expressed in terms of the dynamical timescale ? tcool, has a power-law dependence on temperature and density, ? tcool ? ?-aT-b, where a and b are constants. We use this cooling timescale in a simple prescription for the cooling rate, du/dt = -u/tcool, where u is the internal energy. We perform our simulations using the smoothed particle hydrodynamics method. The simulations demonstrate that the disk is very sensitive to the cooling timescale, which depends on density and temperature. Under such a cooling timescale, the disk becomes gravitationally unstable and clumps form in the disk. This property even occurs for cooling timescales which are much longer than the critical cooling timescale, ? tcool ? 7. We show that by adding the dependence of a cooling timescale on temperature and density, the number of clumps increases and the clumps can also form at smaller radii. The simulations imply that the sensitivity of a cooling timescale to density is more than to temperature, because even for a small dependence of the cooling timescale on density, clumps can still form in the disk. However, when the cooling timescale has a large dependence on temperature, clumps form in the disk. We also consider the effects of artificial viscosity parameters on fragmentation conditions. This consideration is performed in two cases, where ? tcool is a constant and ? tcool is a function of density and temperature. The simulations consider both cases, and results show the artificial viscosity parameters have rather similar effects. For example, using too small of values for linear and quadratic terms in artificial viscosity can suppress the gravitational instability and consequently the efficiency of the clump formation process decreases. This property is consistent with recent simulations of self-gravitating disks. We perform simulations with and without the Balsara form of artificial viscosity. We find that in the cooling and self-gravitating disks without the Balsara switch, the clumps can form more easily than those with the Balsara switch. Moreover, in both cases where the Balsara switch is present or absent, the simulations show that the cooling timescale strongly depends on density and temperature.
A Concept for Airborne Precision Spacing for Dependent Parallel Approaches
NASA Technical Reports Server (NTRS)
Barmore, Bryan E.; Baxley, Brian T.; Abbott, Terence S.; Capron, William R.; Smith, Colin L.; Shay, Richard F.; Hubbs, Clay
2012-01-01
The Airborne Precision Spacing concept of operations has been previously developed to support the precise delivery of aircraft landing successively on the same runway. The high-precision and consistent delivery of inter-aircraft spacing allows for increased runway throughput and the use of energy-efficient arrivals routes such as Continuous Descent Arrivals and Optimized Profile Descents. This paper describes an extension to the Airborne Precision Spacing concept to enable dependent parallel approach operations where the spacing aircraft must manage their in-trail spacing from a leading aircraft on approach to the same runway and spacing from an aircraft on approach to a parallel runway. Functionality for supporting automation is discussed as well as procedures for pilots and controllers. An analysis is performed to identify the required information and a new ADS-B report is proposed to support these information needs. Finally, several scenarios are described in detail.
A coarse-grain force field for RDX: Density dependent and energy conserving.
Moore, Joshua D; Barnes, Brian C; Izvekov, Sergei; LÃsal, Martin; Sellers, Michael S; Taylor, DeCarlos E; Brennan, John K
2016-03-14
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions. PMID:26979691
Density-dependent electron transport and precise modeling of GaN high electron mobility transistors
NASA Astrophysics Data System (ADS)
Bajaj, Sanyam; Shoron, Omor F.; Park, Pil Sung; Krishnamoorthy, Sriram; Akyol, Fatih; Hung, Ting-Hsiang; Reza, Shahed; Chumbes, Eduardo M.; Khurgin, Jacob; Rajan, Siddharth
2015-10-01
We report on the direct measurement of two-dimensional sheet charge density dependence of electron transport in AlGaN/GaN high electron mobility transistors (HEMTs). Pulsed IV measurements established increasing electron velocities with decreasing sheet charge densities, resulting in saturation velocity of 1.9 Ã— 107 cm/s at a low sheet charge density of 7.8 Ã— 1011 cm-2. An optical phonon emission-based electron velocity model for GaN is also presented. It accommodates stimulated longitudinal optical (LO) phonon emission which clamps the electron velocity with strong electron-phonon interaction and long LO phonon lifetime in GaN. A comparison with the measured density-dependent saturation velocity shows that it captures the dependence rather well. Finally, the experimental result is applied in TCAD-based device simulator to predict DC and small signal characteristics of a reported GaN HEMT. Good agreement between the simulated and reported experimental results validated the measurement presented in this report and established accurate modeling of GaN HEMTs.
Density matrix expansion for the isospin- and momentum-dependent MDI interaction
Xu Jun; Ko Che Ming
2010-10-15
By assuming that the isospin- and momentum-dependent MDI interaction has a form similar to the Gogny-like effective two-body interaction with a Yukawa finite-range term and the momentum dependence originates only from the finite-range exchange interaction, we determine its parameters by comparing the predicted potential energy density functional in uniform nuclear matter with what has been usually given and used extensively in transport models for studying isospin effects in intermediate-energy heavy-ion collisions as well as in investigating the properties of hot asymmetric nuclear matter and neutron star matter. We then use the density matrix expansion to derive from the resulting finite-range exchange interaction an effective Skyrme-like zero-range interaction with density-dependent parameters. As an application, we study the transition density and pressure at the inner edge of neutron star crusts using the stability conditions derived from the linearized Vlasov equation for the neutron star matter.
Density-dependent settlement and mortality structure the earliest life phases of a coral population.
Vermeij, Mark J A; Sandin, Stuart A
2008-07-01
The local densities of heterospecifics and conspecifics are known to have profound effects on the dynamics of many benthic species, including rates of settlement and early post-settlement survivorship. We described the early life history of the Caribbean coral, Siderastrea radians by tracking the population dynamics from recently settled planulae to juveniles. Through three years of observation, settlement correlated with the abundance of other benthic organisms, principally turf algae (negatively) and crustose coralline algae (positively). In addition, adult density showed independent effects on coral settlement and early post-settlement survivorship. Settlement rates increased across low levels of adult cover and saturated at a maximum around 10% cover. Early post-settlement survivorship decreased with adult cover, revealing structuring density dependence in coral settlers. The earliest life stages of corals are defined by low survivorship, with survivorship increasing appreciably with colony size. However, recent settlers (one-polyp individuals, < 1-year-old) are more likely to grow into two-polyp juveniles than older single polyps (> 1-year-old) that were delayed in their development. The early benthic phase of corals is defined by a severe demographic bottleneck for S. radians, with appreciable density-dependent and density-independent effects on survivorship. For effective management and restoration of globally imperiled coral reefs, we must focus more attention on this little studied, but dynamic, early life history period of corals. PMID:18705385
Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System
Fellous, Simon; Duncan, Alison; Coulon, Aurélie; Kaltz, Oliver
2012-01-01
Many organisms use cues to decide whether to disperse or not, especially those related to the composition of their environment. Dispersal hence sometimes depends on population density, which can be important for the dynamics and evolution of sub-divided populations. But very little is known about the factors that organisms use to inform their dispersal decision. We investigated the cues underlying density-dependent dispersal in inter-connected microcosms of the freshwater protozoan Paramecium caudatum. In two experiments, we manipulated (i) the number of cells per microcosm and (ii) the origin of their culture medium (supernatant from high- or low-density populations). We found a negative relationship between population density and rates of dispersal, suggesting the use of physical cues. There was no significant effect of culture medium origin on dispersal and thus no support for chemical cues usage. These results suggest that the perception of density – and as a result, the decision to disperse – in this organism can be based on physical factors. This type of quorum sensing may be an adaptation optimizing small scale monitoring of the environment and swarm formation in open water. PMID:23144882
Experimental excursions on adaptive landscapes: density-dependent selection on egg size.
Svensson, E; Sinervo, B
2000-08-01
Theories of density-dependent natural selection suggest that intraspecific competition will favor juveniles of high competitive ability. Empirical evidence has been provided from laboratory selection experiments, but field studies are lacking due to the logistical difficulties of experimentally manipulating population densities in natural settings. Here, we present data from a decade-long experimental field study of side-blotched lizards, Uta stansburiana that overcomes these difficulties. We tested the hypothesis that density-dependent natural selection causes egg size to increase from early to late clutches in this and many other species. Using a novel combination of environmental manipulations of hatchling density and phenotypic manipulations of egg size, we demonstrate that the nature of selection on egg size changes dramatically in the absence of older competitors. The strength of selection on egg size among later-clutch hatchlings released in areas without competitors from early clutches became almost doubled in magnitude, compared to that among hatchlings released in the presence of older competitors. These experimental findings demonstrate density-dependent natural selection on egg size; however, they contradict the classical idea that egg size increases during the reproductive season because of competition between early and late hatchlings. The results indicate that competitive age or size asymmetries between early and late hatchlings can override within-cohort asymmetries due to egg size. We suggest that competition could be an important mediator of oscillating selection pressures in this and other systems. Finally, we discuss the utility of "double-level," simultaneous experimental manipulation of both phenotypic traits that are targets of selection (e.g., egg size) as well the environmental agents of selection (e.g., population density). PMID:11005305
Dispersal, density dependence, and population dynamics of a fungal microbe on leaf surfaces.
Woody, Scott T; Ives, Anthony R; Nordheim, Erik V; Andrews, John H
2007-06-01
Despite the ubiquity and importance of microbes in nature, little is known about their natural population dynamics, especially for those that occupy terrestrial habitats. Here we investigate the dynamics of the yeast-like fungus Aureobasidium pullulans (Ap) on apple leaves in an orchard. We asked three questions. (1) Is variation in fungal population density among leaves caused by variation in leaf carrying capacities and strong density-dependent population growth that maintains densities near carrying capacity? (2) Do resident populations have competitive advantages over immigrant cells? (3) Do Ap dynamics differ at different times during the growing season? To address these questions, we performed two experiments at different times in the growing season. Both experiments used a 2 x 2 factorial design: treatment 1 removed fungal cells from leaves to reveal density-dependent population growth, and treatment 2 inoculated leaves with an Ap strain engineered to express green fluorescent protein (GFP), which made it possible to track the fate of immigrant cells. The experiments showed that natural populations of Ap vary greatly in density due to sustained differences in carrying capacities among leaves. The maintenance of populations close to carrying capacities indicates strong density-dependent processes. Furthermore, resident populations are strongly competitive against immigrants, while immigrants have little impact on residents. Finally, statistical models showed high population growth rates of resident cells in one experiment but not in the other, suggesting that Ap experiences relatively "good" and "bad" periods for population growth. This picture of Ap dynamics conforms to commonly held, but rarely demonstrated, expectations of microbe dynamics in nature. It also highlights the importance of local processes, as opposed to immigration, in determining the abundance and dynamics of microbes on surfaces in terrestrial systems. PMID:17601143
Jackson, Aaron P.; Calder, Alan C.; Townsley, Dean M.; Chamulak, David A.; Brown, Edward F.; Timmes, F. X.
2010-09-01
We explore the effects of the deflagration to detonation transition (DDT) density on the production of {sup 56}Ni in thermonuclear supernova (SN) explosions (Type Ia supernovae). Within the DDT paradigm, the transition density sets the amount of expansion during the deflagration phase of the explosion and therefore the amount of nuclear statistical equilibrium (NSE) material produced. We employ a theoretical framework for a well-controlled statistical study of two-dimensional simulations of thermonuclear SNe with randomized initial conditions that can, with a particular choice of transition density, produce a similar average and range of {sup 56}Ni masses to those inferred from observations. Within this framework, we utilize a more realistic 'simmered' white dwarf progenitor model with a flame model and energetics scheme to calculate the amount of {sup 56}Ni and NSE material synthesized for a suite of simulated explosions in which the transition density is varied in the range (1-3) x10{sup 7} g cm{sup -3}. We find a quadratic dependence of the NSE yield on the log of the transition density, which is determined by the competition between plume rise and stellar expansion. By considering the effect of metallicity on the transition density, we find the NSE yield decreases by 0.055 {+-} 0.004 M {sub sun} for a 1 Z{sub sun} increase in metallicity evaluated about solar metallicity. For the same change in metallicity, this result translates to a 0.067 {+-} 0.004 M{sub sun} decrease in the {sup 56}Ni yield, slightly stronger than that due to the variation in electron fraction from the initial composition. Observations testing the dependence of the yield on metallicity remain somewhat ambiguous, but the dependence we find is comparable to that inferred from some studies.
Jackson, A. P.; Calder, A. C.; Townsley, D. M.; Chamulak, D. A.; Brown, E. F.; Timmes, F. X.
2010-09-01
We explore the effects of the deflagration to detonation transition (DDT) density on the production of {sup 56}Ni in thermonuclear supernova (SN) explosions (Type Ia supernovae). Within the DDT paradigm, the transition density sets the amount of expansion during the deflagration phase of the explosion and therefore the amount of nuclear statistical equilibrium (NSE) material produced. We employ a theoretical framework for a well-controlled statistical study of two-dimensional simulations of thermonuclear SNe with randomized initial conditions that can, with a particular choice of transition density, produce a similar average and range of {sup 56}Ni masses to those inferred from observations. Within this framework, we utilize a more realistic 'simmered' white dwarf progenitor model with a flame model and energetics scheme to calculate the amount of {sup 56}Ni and NSE material synthesized for a suite of simulated explosions in which the transition density is varied in the range (1-3) x 10{sup 7} g cm{sup -3}. We find a quadratic dependence of the NSE yield on the log of the transition density, which is determined by the competition between plume rise and stellar expansion. By considering the effect of metallicity on the transition density, we find the NSE yield decreases by 0.055 {+-} 0.004 M {circle_dot} for a 1 Z {circle_dot} increase in metallicity evaluated about solar metallicity. For the same change in metallicity, this result translates to a 0.067 {+-} 0.004 M {circle_dot} decrease in the {sup 56}Ni yield, slightly stronger than that due to the variation in electron fraction from the initial composition. Observations testing the dependence of the yield on metallicity remain somewhat ambiguous, but the dependence we find is comparable to that inferred from some studies.
NASA Astrophysics Data System (ADS)
Rebolini, Elisa; Toulouse, Julien
2016-03-01
We present a range-separated linear-response time-dependent density-functional theory (TDDFT) which combines a density-functional approximation for the short-range response kernel and a frequency-dependent second-order Bethe-Salpeter approximation for the long-range response kernel. This approach goes beyond the adiabatic approximation usually used in linear-response TDDFT and aims at improving the accuracy of calculations of electronic excitation energies of molecular systems. A detailed derivation of the frequency-dependent second-order Bethe-Salpeter correlation kernel is given using many-body Green-function theory. Preliminary tests of this range-separated TDDFT method are presented for the calculation of excitation energies of the He and Be atoms and small molecules (H2, N2, CO2, H2CO, and C2H4). The results suggest that the addition of the long-range second-order Bethe-Salpeter correlation kernel overall slightly improves the excitation energies.
Nuclear clustering in the energy density functional approach
NASA Astrophysics Data System (ADS)
Ebran, J.-P.; Khan, E.; Nikši?, T.; Vretenar, D.
2015-10-01
Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.
Quantum Well Width Dependence of Threshold Current Density in InGaN Lasers
Amano, H.; Chow, W.W.; Han, J.; Takeuchi, T.
1999-03-16
The quantum confined Stark effect was found to result in a strong quantum well width dependence of threshold current density in strained group-III nitride quantum well lasers. For an In{sub 0.2}Ga{sub 0.8}N/GaN structure with quantum well width in the neighborhood of 3.5nm, our analysis shows that the reduction in spontaneous emission loss by the electron-hole spatial separation outweighs the corresponding reduction in gain to produce a threshold current density minimum.
Lengthscale-Dependent Solvation and Density Fluctuations in n-Octane.
Wu, Eugene; Garde, Shekhar
2015-07-23
Much attention has been focused on the solvation and density fluctuations in water over the past decade. These studies have brought to light interesting physical features of solvation in condensed media, especially the dependence of solvation on the solute lengthscale, which may be general to many fluids. Here, we focus on the lengthscale-dependent solvation and density fluctuations in n-octane, a simple organic liquid. Using extensive molecular simulations, we show a crossover in the solvation of solvophobic solutes with increasing size in n-octane, with the specifics of the crossover depending on the shape of the solute. Large lengthscale solvation, which is dominated by interface formation, emerges over subnanoscopic lengthscales. The crossover in n-octane occurs at smaller lengthscales than that in water. We connect the lengthscale of crossover to the range of attractive interactions in the fluid. The onset of the crossover is accompanied by the emergence of non-Gaussian tails in density fluctuations in solute shaped observation volumes. Simulations over a range of temperatures highlight a corresponding thermodynamic crossover in solvation. Qualitative similarities between lengthscale-dependent solvation in water, n-octane, and Lennard-Jones fluids highlight the generality of the underlying physics of solvation. PMID:25402732
Sum rules and properties in time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Qian, Zhixin; Sahni, Viraht
2001-04-01
Time-dependent quantal density-functional theory (Q-DFT) is a description of the s-system of noninteracting fermions with electronic density equivalent to that of Schrödinger theory, in terms of fields whose sources are quantum-mechanical expectations of Hermitian operators. The theory delineates and defines the contribution of each type of electron correlation to the local electron-interaction potential ?ee(r,t) of the s system. These correlations are due to the Pauli exclusion principle, Coulomb repulsion, correlation-kinetic, and correlation-current-density effects, the latter two resulting, respectively, from the difference in kinetic energy and current density between the interacting Schrödinger and noninteracting systems. We employ Q-DFT to prove the following sum rules and properties of the s system: (i) the components of the potential due to these correlations separately exert no net force on the system; (ii) the torque of the potential is finite and due solely to correlation-current-density effects; (iii) two sum rules involving the curl of the dynamic electron-interaction kernel defined as the functional derivative of ?ee(r,t) are derived and shown to depend on the frequency dependent correlation-current-density effect. Furthermore, via adiabatic coupling constant (?) perturbation theory, we prove: (iv) the exchange potential ?x(r,t) is the work done in a conservative field representative of Pauli correlations and lowest-order O(?) correlation-kinetic and correlation-current-density effects; (v) the correlation potential ?c(r,t) commences in O(?2), and, at each order, it is the work done in a conservative field representative of Coulomb correlations and correlation-kinetic and correlation-current-density effects; (vi) we derive the integral virial theorem relating ?ee(r,t) to the electron-interaction and correlation-kinetic energy for arbitrary coupling constant strength ?, and show there are no explicit correlation-current-density contributions to the energy. From this integral virial theorem we (vii) obtain the fully interacting (?=1) and exchange-only (?=0) integral virial theorems as special cases, the latter showing there is no explicit correlation-kinetic contribution to the exchange energy; and (viii) write expressions for the electron-interaction and correlation-kinetic actions for arbitrary coupling constant ? in terms of the corresponding fields.
KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES*
Speyer, Gil; Kiefer, Jeff; Dhruv, Harshil; Berens, Michael; Kim, Seungchan
2015-01-01
We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies. The method constructs gene dependency networks from bootstrapped samples in one condition and computes the divergence between distributions of network likelihood scores from different conditions. It was shown to be capable of sensitive and specific identification of pathways with phenotype-specific dysregulation, i.e., rewiring of dependencies between genes in different conditions. We now present an extension of the method by incorporating prior knowledge into the inference of networks. The degree of prior knowledge incorporation has substantial effect on the sensitivity of the method, as the data is the source of condition specificity while prior knowledge incorporation can provide additional support for dependencies that are only partially supported by the data. Use of prior knowledge also significantly improved the interpretability of the results. Further analysis of topological characteristics of gene differential dependency networks provides a new approach to identify genes that could play important roles in biological signaling in a specific condition, hence, promising targets customized to a specific condition. Through analysis of TCGA glioblastoma multiforme data, we demonstrate the method can identify not only potentially promising targets but also underlying biology for new targets. PMID:26776171
Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus)
Vas, Judit; Andersen, Inger Lise
2015-01-01
Very little is known about the spacing behaviour in social groups of domestic goats (Capra hircus) in the farm environment. In this experiment, we studied interindividual distances, movement patterns and activity budgets in pregnant goats housed at three different densities. Norwegian dairy goats were kept in stable social groups of six animals throughout pregnancy at 1, 2 or 3 m2 per individual and their spacing behaviours (i.e. distance travelled, nearest and furthest neighbour distance) and activity budgets (e.g. resting, feeding, social activities) were monitored. Observations were made in the first, second and last thirds of pregnancy in the mornings, at noon and in the afternoons of each of these phases (4.5 hours per observation period). The findings show that goats held at animal densities of 2 and 3 m2 moved longer distances when they had more space per animal and kept larger nearest and furthest neighbour distances when compared to the 1 m2 per animal density. Less feeding activity was observed at the high animal density compared to the medium and low density treatments. The phase of gestation also had an impact on almost all behavioural variables. Closer to parturition, animals moved further distances and the increase in nearest and furthest neighbour distance was more pronounced at the lower animal densities. During the last period of gestation, goats spent less time feeding and more on resting, social behaviours and engaging in other various activities. Our data suggest that more space per goat is needed for goats closer to parturition than in the early gestation phase. We concluded that in goats spacing behaviour is density-dependent and changes with stages of pregnancy and activities. Finally, the lower density allowed animals to express individual preferences regarding spacing behaviour which is important in ensuring good welfare in a farming situation. PMID:26657240
Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus).
Vas, Judit; Andersen, Inger Lise
2015-01-01
Very little is known about the spacing behaviour in social groups of domestic goats (Capra hircus) in the farm environment. In this experiment, we studied interindividual distances, movement patterns and activity budgets in pregnant goats housed at three different densities. Norwegian dairy goats were kept in stable social groups of six animals throughout pregnancy at 1, 2 or 3 m2 per individual and their spacing behaviours (i.e. distance travelled, nearest and furthest neighbour distance) and activity budgets (e.g. resting, feeding, social activities) were monitored. Observations were made in the first, second and last thirds of pregnancy in the mornings, at noon and in the afternoons of each of these phases (4.5 hours per observation period). The findings show that goats held at animal densities of 2 and 3 m2 moved longer distances when they had more space per animal and kept larger nearest and furthest neighbour distances when compared to the 1 m2 per animal density. Less feeding activity was observed at the high animal density compared to the medium and low density treatments. The phase of gestation also had an impact on almost all behavioural variables. Closer to parturition, animals moved further distances and the increase in nearest and furthest neighbour distance was more pronounced at the lower animal densities. During the last period of gestation, goats spent less time feeding and more on resting, social behaviours and engaging in other various activities. Our data suggest that more space per goat is needed for goats closer to parturition than in the early gestation phase. We concluded that in goats spacing behaviour is density-dependent and changes with stages of pregnancy and activities. Finally, the lower density allowed animals to express individual preferences regarding spacing behaviour which is important in ensuring good welfare in a farming situation. PMID:26657240
Breed, Greg A; Don Bowen, W; Leonard, Marty L
2013-01-01
In populations of colony-breeding marine animals, foraging around colonies can lead to intraspecific competition. This competition affects individual foraging behavior and can cause density-dependent population growth. Where behavioral data are available, it may be possible to infer the mechanism of intraspecific competition. If these mechanics are understood, they can be used to predict the population-level functional response resulting from the competition. Using satellite relocation and dive data, we studied the use of space and foraging behavior of juvenile and adult gray seals (Halichoerus grypus) from a large (over 200,000) and growing population breeding at Sable Island, Nova Scotia (44.0 oN 60.0 oW). These data were first analyzed using a behaviorally switching state-space model to infer foraging areas followed by randomization analysis of foraging region overlap of competing age classes. Patterns of habitat use and behavioral time budgets indicate that young-of-year juveniles (YOY) were likely displaced from foraging areas near (<10 km) the breeding colony by adult females. This displacement was most pronounced in the summer. Additionally, our data suggest that YOY are less capable divers than adults and this limits the habitat available to them. However, other segregating mechanisms cannot be ruled out, and we discuss several alternate hypotheses. Mark–resight data indicate juveniles born between 1998 and 2002 have much reduced survivorship compared with cohorts born in the late 1980s, while adult survivorship has remained steady. Combined with behavioral observations, our data suggest YOY are losing an intraspecific competition between adults and juveniles, resulting in the currently observed decelerating logistic population growth. Competition theory predicts that intraspecific competition resulting in a clear losing competitor should cause compensatory population regulation. This functional response produces a smooth logistic growth curve as carrying capacity is approached, and is consistent with census data collected from this population over the past 50 years. The competitive mechanism causing compensatory regulation likely stems from the capital-breeding life-history strategy employed by gray seals. This strategy decouples reproductive success from resources available around breeding colonies and prevents females from competing with each other while young are dependent. PMID:24198943
Energy density and stress: A new approach to teaching electromagnetism
NASA Astrophysics Data System (ADS)
Herrmann, F.
1989-08-01
By introducing the electromagnetic field in the customary way, ideas are promoted that do not correspond to those of contemporary physics: on the one hand, ideas that stem from pre-Maxwellian times when interactions were still conceived as actions at a distance and, on the other hand, ideas that can be understood only from the point of view that the electromagnetic field is carried by a medium. A part of a course in electromagnetism is sketched in which, from the beginning, the electromagnetic field is presented as a system in its own right and the local quantities energy density and stress are put into the foreground. In this way, justice is done to the views of modern physics and, moreover, the field becomes conceptually simpler.
PTPN14 is required for the density-dependent control of YAP1
Wang, Wenqi; Huang, Jun; Wang, Xin; Yuan, Jingsong; Li, Xu; Feng, Lin; Park, Jae-Il; Chen, Junjie
2012-01-01
Through an shRNA-mediated loss-of-function screen, we identified PTPN14 as a potential tumor suppressor. PTPN14 interacts with yes-associated protein 1 (YAP1), a member of the hippo signaling pathway. We showed that PTPN14 promotes the nucleus-to-cytoplasm translocation of YAP1 during contact inhibition and thus inhibits YAP1 transactivation activity. Interestingly, PTPN14 protein stability was positively controlled by cell density. We identified the CRL2LRR1 (cullin2 RING ubiquitin ligase complex/leucine-rich repeat protein 1) complex as the E3 ligase that targets PTPN14 for degradation at low cell density. Collectively, these data suggest that PTPN14 acts to suppress cell proliferation by promoting cell density-dependent cytoplasmic translocation of YAP1. PMID:22948661
Temperature and concentration dependences of density and refraction of aqueous duloxetine solutions
NASA Astrophysics Data System (ADS)
Deosarkar, S. D.; Deoraye, S. M.; Kalyankar, T. M.
2014-07-01
Present paper reports the measured densities (Ï) and refractive indices ( n D) of aqueous solutions of Duloxetine drug in wide range of molal concentrations ( m = 0.0101-0.1031 mol kg-1) and at different temperatures (297.15, 302.15, and 307.15 K). Apparent molar volumes (Ï†v) of drug were calculated from density data and fitted to Masson's relation and partial molar volumes (Ï†{v/0}) were evaluated at different temperatures. Concentration dependence of refractive index ( n D = Kc + n {D/0}) at experimental temperature has been studied. Density and refractive index data has been used for the calculation of specific refractions ( R D). Experimental (Ï and n D) and calculated (Ï†v, Ï†{v/0}, and R D) properties have been interpreted in terms of concentration and temperature effects on structural fittings and drug-water interactions.
Laboratory calibration of density-dependent lines in the extreme ultraviolet spectral region
NASA Astrophysics Data System (ADS)
Lepson, J. K.; Beiersdorfer, P.; Gu, M. F.; Desai, P.; Bitter, M.; Roquemore, L.; Reinke, M. L.
2012-05-01
We have been making spectral measurements in the extreme ultraviolet (EUV) from different laboratory sources in order to investigate the electron density dependence of various astrophysically important emission lines and to test the atomic models underlying the diagnostic line ratios. The measurement are being performed at the Livermore EBIT-I electron beam ion trap, the National Spherical Torus Experiment (NSTX) at Princeton, and the Alcator C-Mod tokamak at the Massachusetts Institute of Technology, which together span an electron density of four orders of magnitude and which allow us to test the various models at high and low density limits. Here we present measurements of Fe XXII and Ar XIV, which include new data from an ultra high resolution (?/?? >4000) spectrometer at the EBIT-I facility. We found good agreement between the measurements and modeling calculations for Fe XXII, but poorer agreement for Ar XIV.
Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation
KÃ¼hn, Michael; Weigend, Florian
2015-01-21
We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. KÃ¼hn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy){sub 3} (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its â€œspin-forbiddenâ€ triplet-singlet transition.
Minter, Ewan J. A.; Watts, Phillip C.; Lowe, Chris D.; Brockhurst, Michael A.
2015-01-01
Natural populations of free-living protists often exhibit high-levels of intraspecific diversity, yet this is puzzling as classic evolutionary theory predicts dominance by genotypes with high fitness, particularly in large populations where selection is efficient. Here, we test whether negative frequency-dependent selection (NFDS) plays a role in the maintenance of diversity in the marine flagellate Oxyrrhis marina using competition experiments between multiple pairs of strains. We observed strain-specific responses to frequency and density, but an overall signature of NFDS that was intensified at higher population densities. Because our strains were not selected a priori on the basis of particular traits expected to exhibit NFDS, these data represent a relatively unbiased estimate of the role for NFDS in maintaining diversity in protist populations. These findings could help to explain how bloom-forming plankton, which periodically achieve exceptionally high population densities, maintain substantial intraspecific diversity. PMID:26063750
Towards a description of the Kondo effect using time-dependent density-functional theory.
Stefanucci, G; Kurth, S
2011-11-18
We demonstrate that the zero-temperature conductance of the Anderson model can be calculated within the Landauer formalism combined with static density-functional theory. The proposed approximate functional is based on finite-temperature density-functional theory and yields the exact Kohn-Sham potential at the particle-hole symmetric point. Furthermore, in the limit of zero temperature it correctly exhibits a derivative discontinuity which is shown to be essential to reproduce the conductance plateau. On the other hand, at the Kondo temperature the exact Kohn-Sham conductance overestimates the real one by an order of magnitude. To understand the failure of density-functional theory, we resort to its time-dependent version and conclude that the suppression of the Kondo resonance must be attributed to dynamical exchange-correlation corrections. PMID:22181899
Subspace formulation of time-dependent density functional theory for large-scale calculations.
Zhang, Xu; Lu, Gang
2015-08-14
A subspace formulation of time-dependent density functional theory (TDDFT) is proposed for large-scale calculations based on density functional perturbation theory. The formulation is implemented in conjunction with projector augmented-wave method and plane-wave basis set. A key bottleneck of conventional TDDFT method is circumvented by projecting the time-dependent Kohn-Sham eigenvalue equations from a full Hilbert space to a substantially reduced sub-Hilbert space. As a result, both excitation energies and ionic forces can be calculated accurately within the reduced subspace. The method is validated for several model systems and exhibits the similar accuracy as the conventional TDDFT method but at a computational cost of the ground state calculation. The Born-Oppenheimer molecular dynamics can be successfully performed for excited states in C60 and T12 molecules, opening doors for many applications involving excited state dynamics. PMID:26277130
Energy density dependence of hydrogen combustion efficiency in atmospheric pressure microwave plasma
Yoshida, T.; Ezumi, N.; Sawada, K.; Tanaka, Y.; Tanaka, M.; Nishimura, K.
2015-03-15
The recovery of tritium in nuclear fusion plants is a key issue for safety. So far, the oxidation procedure using an atmospheric pressure plasma is expected to be part of the recovery method. In this study, in order to clarify the mechanism of hydrogen oxidation by plasma chemistry, we have investigated the dependence of hydrogen combustion efficiency on gas flow rate and input power in the atmospheric pressure microwave plasma. It has been found that the combustion efficiency depends on energy density of absorbed microwave power. Hence, the energy density is considered as a key parameter for combustion processes. Also neutral gas temperatures inside and outside the plasma were measured by an optical emission spectroscopy method and thermocouple. The result shows that the neutral gas temperature in the plasma is much higher than the outside temperature of plasma. The high neutral gas temperature may affect the combustion reaction. (authors)
Dependence of the LR-115 radon detector calibration factor on track density.
De Cicco, F; Pugliese, M; Roca, V; Sabbarese, C
2013-08-01
The reliability and accuracy of the methodology based on using LR-115 track detectors for radon measurements have been studied by determining the dependence of their calibration factors on radon exposure at levels reaching 13 MBq m(-3) h. This factor results not constant and demonstrated a decreasing exponential trend vs. exposure that has been explained in terms of the saturation effect and verified using a numerical simulation. This dependence does not affect the parameter that normalizes track density vs. film thickness. This parameter results constant and equal to - 0.30±0.02 cm(-2)/µm in the 300-8000 kBq h m(-3) exposure range. PMID:23694685
Time-dependent Density Functional Results for the Dynamic Hyperpolarizability of C{sub 60}
van Gisbergen, S.; Snijders, J.; Baerends, E.
1997-04-01
The experimental, as well as theoretical, values for the frequency-dependent hyperpolarizability of C{sub 60} differ by orders of magnitude. We present the first density functional calculation of a molecular frequency-dependent hyperpolarizability. Our implementation is very economical, enabling the treatment of molecules of this size, in a potentially much more accurate way than can be obtained with alternative methods. Our results strongly support the recent results by Geng and Wright, who report much lower experimental values than previous authors. {copyright} {ital 1997} {ital The American Physical Society}
Density-dependent prophylaxis in the coral-eating crown-of-thorns sea star, Acanthaster planci
NASA Astrophysics Data System (ADS)
Mills, S. C.
2012-06-01
The density-dependent prophylaxis hypothesis predicts that individuals at high density will invest more resources into immune defence than individuals at lower densities as a counter-measure to density-dependent pathogen transmission rates. Evidence has been found for this hypothesis in insects, but not in a non-arthropod taxon. To investigate this hypothesis in the coral-eating crown-of-thorns sea star, Acanthaster planci, density treatments were set up over 21 days, and pathogen infection was simulated with bacterial injection. Five immune responses: amoebocyte count, amoebocyte viability, lysosomal membrane integrity, respiratory burst and peroxidase activity were all upregulated at high density. These results demonstrate that immune investment shows phenotypic plasticity with adult population density in agreement with the density-dependent prophylaxis hypothesis. Here I show that the density-dependent prophylaxis hypothesis is neither dependent on larval density nor restricted to insects, and hence may potentially have important consequences on disease dynamics in any species with widely fluctuating population densities. This is the first demonstration of the density-dependent prophylaxis hypothesis outside arthropods.
NASA Astrophysics Data System (ADS)
Kuraptsev, A. S.
2015-03-01
On the basis of general theoretical results developed in our group previously [Sokolov I M et al 2011 J. Exp. Theor. Phys. 112 246], the transition spectrum of a single atom inside cold atomic ensemble is analyzed under conditions when the averaged interatomic separation is less than or comparable with the wavelength of resonant radiation. Density-dependent shifts of resonance as well as distortion of the spectral shape of the atomic transition are investigated.
Trenkel, V M; Lorance, P; Fässler, S M M; Høines, Å S
2015-10-01
Blue whiting Micromesistius poutassou mean total length at age in the north-east Atlantic Ocean was found to vary by around ±6% during the period 2004-2011 and mean mass at age by ±22% during the years 1981-2013. Linear modelling provided strong evidence that these phenotypic growth variations can be explained by trophic conditions, mainly negative density dependence and also food availability, and a negative long-term temperature effect on asymptotic size. PMID:26376856
Ignition of the beam-plasma-discharge and its dependence on electron density. Memorandum report
Walker, D.N.; Szuszczewicz, E.P.; Lin, C.S.
1981-07-23
A cold electron beam, propagating through a weakly ionized plasma will, under proper conditions, produce a modified beam-plasma state known as the Beam-Plasma-Discharge (BDP). As the subject of a continuing series of experiments in a large facility chamber it was previously determined that the BPD had an abrupt ignition threshold as the beam current I sub B was increased at fixed beam energy. While a specific empirical relationship was established among the controlling parameters of beam current, energy and length as well as ambient pressure and magnetic field, a dependence of the BPD on plasma density of the from, omega sub p approximates omega sub c, was suggested. We have since conducted a survey of various beam-plasma conditions covering beam currents from 8 to 85 ma, beam energies from 0.8 to 2.0 keV and magnetic fields at 0.9 and 1.5 gauss. This survey includes full determinations of radial profiles of electron density for each of the selected conditions extending from a low-density pre-BDP state to a strong BPD condition. At BPD threshold N sub e max was determined and omega sub p calculated as the density dependent threshold condition for BPD. The experimental results are shown to compare favorably with a developing theoretical model that considers BPD to be triggered by electron plasma wave excitation of a beam-plasma instability.
Multi-configuration time-dependent density-functional theory based on range separation.
Fromager, Emmanuel; Knecht, Stefan; Jensen, Hans Jørgen Aa
2013-02-28
Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration-Self-Consistent Field (MCSCF) treatment with an adiabatic short-range density-functional (DFT) description, is then considered. The resulting time-dependent multi-configuration short-range DFT (TD-MC-srDFT) model is applied to the calculation of singlet excitation energies in H2, Be, and ferrocene, considering both short-range local density (srLDA) and generalized gradient (srGGA) approximations. As expected, when modeling long-range interactions with the MCSCF model instead of the adiabatic Buijse-Baerends density-matrix functional as recently proposed by Pernal [J. Chem. Phys. 136, 184105 (2012)], the description of both the 1(1)D doubly-excited state in Be and the 1(1)?u(+) state in the stretched H2 molecule are improved, although the latter is still significantly underestimated. Exploratory TD-MC-srDFT/GGA calculations for ferrocene yield in general excitation energies at least as good as TD-DFT using the Coulomb attenuated method based on the three-parameter Becke-Lee-Yang-Parr functional (TD-DFT/CAM-B3LYP), and superior to wave-function (TD-MCSCF, symmetry adapted cluster-configuration interaction) and TD-DFT results based on LDA, GGA, and hybrid functionals. PMID:23464134
Single-electron approach for time-dependent electron transport
NASA Astrophysics Data System (ADS)
Gurvitz, Shmuel
2015-10-01
We developed a new approach to electron transport in mesoscopic systems by using a particular single-particle basis. Although this basis generates redundant many-particle amplitudes, it greatly simplifies the treatment. By using our method for transport of non-interacting electrons, we generalize the Landauer formula for transient currents and time-dependent potentials. The result has a very simple form and clear physical interpretation. As an example, we apply it to resonant tunneling through a quantum dot where the tunneling barriers are oscillating in time. We obtain an analytical expression for the time-dependent (ac) resonant current. However, in the adiabatic limit this expression displays the dc current for zero bias (electron pumping).
Density-dependent prey mortality is determined by the spatial scale of predator foraging.
McCarthy, Erin K; White, J Wilson
2016-02-01
Foraging theory predicts which prey patches predators should target. However, in most habitats, what constitutes a 'patch' and how prey density is calculated are subjective concepts and depend on the spatial scale at which the predator (or scientist) is observing. Moreover, the predator's 'foraging scale' affects prey population dynamics: predators should produce directly density-dependent (DDD) prey mortality at the foraging scale, but inversely density-dependent (IDD) mortality (safety-in-numbers) at smaller scales. We performed the first experimental test of these predictions using behavioral assays with guppies (Poecilia reticulata) feeding on bloodworm 'prey' patches. The guppy's foraging scale had already been estimated in a prior study. Our experimental results confirmed theoretical predictions: predation was IDD when prey were aggregated at a scale smaller than the foraging scale, but not when prey were aggregated at larger scales. These results could be used to predict outcomes of predator-prey interactions in continuous, non-discrete habitats in the field. PMID:26116266
A Dynamic Approach to Modeling Dependence Between Human Failure Events
Boring, Ronald Laurids
2015-09-01
In practice, most HRA methods use direct dependence from THERPâ€”the notion that error be- gets error, and one human failure event (HFE) may increase the likelihood of subsequent HFEs. In this paper, we approach dependence from a simulation perspective in which the effects of human errors are dynamically modeled. There are three key concepts that play into this modeling: (1) Errors are driven by performance shaping factors (PSFs). In this context, the error propagation is not a result of the presence of an HFE yielding overall increases in subsequent HFEs. Rather, it is shared PSFs that cause dependence. (2) PSFs have qualities of lag and latency. These two qualities are not currently considered in HRA methods that use PSFs. Yet, to model the effects of PSFs, it is not simply a matter of identifying the discrete effects of a particular PSF on performance. The effects of PSFs must be considered temporally, as the PSFs will have a range of effects across the event sequence. (3) Finally, there is the concept of error spilling. When PSFs are activated, they not only have temporal effects but also lateral effects on other PSFs, leading to emergent errors. This paper presents the framework for tying together these dynamic dependence concepts.
NASA Astrophysics Data System (ADS)
Cambré, Sofie; Muyshondt, Pieter; Federicci, Remi; Wenseleers, Wim
2015-11-01
Density gradient ultracentrifugation (DGU) becomes increasingly important for the sorting of nanomaterials according to the particles' density, hence structure and dimensions, which determine their unique properties, but the further development of this separation technique is hindered by the limited precision with which the densities could be characterized. In this work, we determine these densities by position-dependent 2D wavelength-dependent IR fluorescence-excitation and resonant Raman spectroscopy measured directly in the density gradient after ultracentrifugation. We apply this method to study the diameter and chirality-dependent sorting of empty and water-filled single-walled carbon nanotubes coated with two different surfactants, sodium cholate (SC) and sodium deoxycholate (DOC). The results elucidate the long standing contradiction that SC would provide better diameter sorting, while DOC is the most efficient surfactant to solubilise the nanotubes. A more predictable separation is obtained for empty DOC-coated nanotubes since their density is found to vary very smoothly with diameter. The accurate and chirality-dependent densities furthermore provide information on the surfactant coating, which is also important for other separation techniques, and allow to determine the mass percentage of water encapsulated inside the nanotubes.Density gradient ultracentrifugation (DGU) becomes increasingly important for the sorting of nanomaterials according to the particles' density, hence structure and dimensions, which determine their unique properties, but the further development of this separation technique is hindered by the limited precision with which the densities could be characterized. In this work, we determine these densities by position-dependent 2D wavelength-dependent IR fluorescence-excitation and resonant Raman spectroscopy measured directly in the density gradient after ultracentrifugation. We apply this method to study the diameter and chirality-dependent sorting of empty and water-filled single-walled carbon nanotubes coated with two different surfactants, sodium cholate (SC) and sodium deoxycholate (DOC). The results elucidate the long standing contradiction that SC would provide better diameter sorting, while DOC is the most efficient surfactant to solubilise the nanotubes. A more predictable separation is obtained for empty DOC-coated nanotubes since their density is found to vary very smoothly with diameter. The accurate and chirality-dependent densities furthermore provide information on the surfactant coating, which is also important for other separation techniques, and allow to determine the mass percentage of water encapsulated inside the nanotubes. Electronic supplementary information (ESI) available: (1) Density calibration, (2) fraction selection and reproducibility, (3) diffusion of the SWCNTs and (4) experimental RRS spectra and fits at various excitation wavelengths. See DOI: 10.1039/c5nr06020f
Time-dependent Kohn-Sham approach to quantum electrodynamics
Ruggenthaler, M.; Mackenroth, F.; Bauer, D.
2011-10-15
We prove a generalization of the van Leeuwen theorem toward quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. We circumvent the symmetry-causality problems associated with the action-functional approach to Kohn-Sham systems. We show that the effective external four-potential and four-current of the Kohn-Sham system are uniquely defined and that the effective four-current takes a very simple form. Further we rederive the Runge-Gross theorem for quantum electrodynamics.
Time-dependent Kohn-Sham approach to quantum electrodynamics
NASA Astrophysics Data System (ADS)
Ruggenthaler, M.; Mackenroth, F.; Bauer, D.
2011-10-01
We prove a generalization of the van Leeuwen theorem toward quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. We circumvent the symmetry-causality problems associated with the action-functional approach to Kohn-Sham systems. We show that the effective external four-potential and four-current of the Kohn-Sham system are uniquely defined and that the effective four-current takes a very simple form. Further we rederive the Runge-Gross theorem for quantum electrodynamics.
De Giovannini, Umberto; Brunetto, Gustavo; Castro, Alberto; Walkenhorst, Jessica; Rubio, Angel
2013-05-10
Molecular absorption and photoelectron spectra can be efficiently predicted with real-time time-dependent density functional theory. We show herein how these techniques can be easily extended to study time-resolved pump-probe experiments, in which a system response (absorption or electron emission) to a probe pulse is measured in an excited state. This simulation tool helps with the interpretation of fast-evolving attosecond time-resolved spectroscopic experiments, in which electronic motion must be followed at its natural timescale. We show how the extra degrees of freedom (pump-pulse duration, intensity, frequency, and time delay), which are absent in a conventional steady-state experiment, provide additional information about electronic structure and dynamics that improve characterization of a system. As an extension of this approach, time-dependent 2D spectroscopy can also be simulated, in principle, for large-scale structures and extended systems. PMID:23520148
Melzak, Kathryn A; Yu, Kai; Bo, Deng; Kizhakkedathu, Jayachandran N; Toca-Herrera, JosÃ© L
2015-06-16
Poly(N,N-dimethylacrylamide) (PDMA) brushes with different grafting density and chain length were grown from an ester group-containing initiator using surface-initiated polymerization. Hydrolysis of the PDMA chains from the surface was monitored by measuring thickness of the polymer layer by ellipsometry and extension length by atomic force microscopy. It was found that the initial rate of cleavage of one end-tethered PDMA chains was dependent on the grafting density and chain length; the hydrolysis rate was faster for high grafting density brushes and brushes with higher molecular weights. Additionally, the rate of cleavage of polymer chains during a given experiment changed by up to 1 order of magnitude as the reaction progressed, with a distinct transition to a lower rate as the grafting density decreased. Also, polymer chains undergo selective cleavage, with longer chains in a polydisperse brush being preferentially cleaved at one stage of the hydrolysis reaction. We suggest that the enhanced initial hydrolysis rates seen at high grafting densities and high chain lengths are due to mechanical activation of the ester bond connecting the polymer chains to the surface in association with high lateral pressure within the brush. These results have implications for the preparation of polymers brushes, their stability under harsh conditions, and the analysis of polymer brushes from partial hydrolysates. PMID:26010390
Tri-trophic interactions affect density dependence of seed fate in a tropical forest palm.
Visser, Marco D; Muller-Landau, Helene C; Wright, S Joseph; Rutten, Gemma; Jansen, Patrick A
2011-11-01
Natural enemies, especially host-specific enemies, are hypothesised to facilitate the coexistence of plant species by disproportionately inflicting more damage at increasing host abundance. However, few studies have assessed such Janzen-Connell mechanisms on a scale relevant for coexistence and no study has evaluated potential top-down influences on the specialized pests. We quantified seed predation by specialist invertebrates and generalist vertebrates, as well as larval predation on these invertebrates, for the Neotropical palm Attalea butyracea across ten 4-ha plots spanning 20-fold variation in palm density. As palm density increased, seed attack by bruchid beetles increased, whereas seed predation by rodents held constant. But because rodent predation on bruchid larvae increased disproportionately with increasing palm density, bruchid emergence rates and total seed predation by rodents and bruchids combined were both density-independent. Our results demonstrate that top-down effects can limit the potential of host-specific insects to induce negative-density dependence in plant populations. PMID:21899693
Density-dependent fitness benefits in quorum-sensing bacterial populations.
Darch, Sophie E; West, Stuart A; Winzer, Klaus; Diggle, Stephen P
2012-05-22
It has been argued that bacteria communicate using small diffusible signal molecules to coordinate, among other things, the production of factors that are secreted outside of the cells in a process known as quorum sensing (QS). The underlying assumption made to explain QS is that the secretion of these extracellular factors is more beneficial at higher cell densities. However, this fundamental assumption has never been tested experimentally. Here, we directly test this by independently manipulating population density and the induction and response to the QS signal, using the opportunistic pathogen Pseudomonas aeruginosa as a model organism. We found that the benefit of QS was relatively greater at higher population densities, and that this was because of more efficient use of QS-dependent extracellular "public goods." In contrast, the benefit of producing "private goods," which are retained within the cell, does not vary with cell density. Overall, these results support the idea that QS is used to coordinate the switching on of social behaviors at high densities when such behaviors are more efficient and will provide the greatest benefit. PMID:22566647
The ecological–evolutionary interplay: density-dependent sexual selection in a migratory songbird
Ryder, Thomas B; Fleischer, Robert C; Shriver, W Greg; Marra, Peter P
2012-01-01
Little is understood about how environmental heterogeneity influences the spatial dynamics of sexual selection. Within human-dominated systems, habitat modification creates environmental heterogeneity that could influence the adaptive value of individual phenotypes. Here, we used the gray catbird to examine if the ecological conditions experienced in the suburban matrix (SM) and embedded suburban parks (SP) influence reproductive strategies and the strength of sexual selection. Our results show that these habitats varied in a key ecological factor, breeding density. Moreover, this ecological factor was closely tied to reproductive strategies such that local breeding density predicted the probability that a nest would contain extra-pair offspring. Partitioning reproductive variance showed that while within-pair success was more important in both habitats, extra-pair success increased the opportunity for sexual selection by 39% at higher breeding densities. Body size was a strong predictor of relative reproductive success and was under directional selection in both habitats. Importantly, our results show that the strength of sexual selection did not differ among habitats at the landscape scale but rather that fine-scale variation in an ecological factor, breeding density, influenced sexual selection on male phenotypes. Here, we document density-dependent sexual selection in a migratory bird and hypothesize that coarse-scale environmental heterogeneity, in this case generated by anthropogenic habitat modification, changed the fine-scale ecological conditions that drove the spatial dynamics of sexual selection. PMID:22837842
Gotham, Steven; Song, Hojun
2013-11-01
Locusts are well known for exhibiting an extreme form of density-dependent phenotypic plasticity known as locust phase polyphenism. At low density, locust nymphs are cryptically colored and shy, but at high density they transform into conspicuously colored and gregarious individuals. Most of what we know about locust phase polyphenism come from the study of the desert locust Schistocerca gregaria (Forskål), which is a devastating pest species affecting many countries in North Africa and the Middle East. The desert locust belongs to the grasshopper genus Schistocerca Stål, which includes mostly non-swarming, sedentary species. Recent phylogenetic studies suggest that the desert locust is the earliest branching lineage within Schistocerca, which raises a possibility that the presence of density-dependent phenotypic plasticity may be a plesiomorphic trait for the whole genus. In order to test this idea, we have quantified the effect of rearing density in terms of the resulting behavior, color, and morphology in two non-swarming Schistocerca species native to Florida. When reared in both isolated and crowded conditions, the two non-swarming species, Schistocerca americana (Drury) and Schistocerca serialis cubense (Saussure) clearly exhibited plastic reaction norms in all traits measured, which were reminiscent of the desert locust. Specifically, we found that both species were more active and more attracted to each other when reared in a crowded condition than in isolation. They were mainly bright green in color when isolated, but developed strong black patterns and conspicuous background colors when crowded. We found a strong effect of rearing density in terms of size. There were also more mechanoreceptor hairs on the outer face of the hind femora in the crowded nymphs in both species. Although both species responded similarly, there were some clear species-specific differences in terms of color and behavior. Furthermore, we compare and contrast our findings with those on the desert locust and other relevant studies. We attribute the presence of density-dependent phenotypic plasticity in the non-swarming Schistocerca species to phylogenetic conservatism, but there may be a possible role of local adaptation in further shaping the ultimate expressions of plasticity. PMID:24035748
Zhang, Yachao
2014-12-07
A first-principles study of critical temperatures (T{sub c}) of spin crossover (SCO) materials requires accurate description of the strongly correlated 3d electrons as well as much computational effort. This task is still a challenge for the widely used local density or generalized gradient approximations (LDA/GGA) and hybrid functionals. One remedy, termed density functional theory plus U (DFT+U) approach, introduces a Hubbard U term to deal with the localized electrons at marginal computational cost, while treats the delocalized electrons with LDA/GGA. Here, we employ the DFT+U approach to investigate the T{sub c} of a pair of iron(II) SCO molecular crystals (? and ? phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ?E{sub HL} and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (?H and ?S), and finally extract T{sub c} by exploiting the ?H/T ? T and ?S ? T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the ? phase is slightly weakened by the H-bondings involving the ligand atoms and the specific crystal packing style. We find that this effect is largely responsible for the difference in T{sub c} of the two phases. This study shows the applicability of the DFT+U approach for predicting T{sub c} of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior.
Gradient single-crystal plasticity with free energy dependent on dislocation densities
NASA Astrophysics Data System (ADS)
Gurtin, Morton E.; Anand, Lallit; Lele, Suvrat P.
2007-09-01
This study develops a small-deformation theory of strain-gradient plasticity for single crystals. The theory is based on: (i) a kinematical notion of a continuous distribution of edge and screw dislocations; (ii) a system of microscopic stresses consistent with a system of microscopic force balances, one balance for each slip system; (iii) a mechanical version of the second law that includes, via the microscopic stresses, work performed during viscoplastic flow; and (iv) a constitutive theory that allows: the free energy to depend on densities of edge and screw dislocations and hence on gradients of (plastic) slip; the microscopic stresses to depend on slip-rate gradients. The microscopic force balances when augmented by constitutive relations for the microscopic stresses results in a system of nonlocal flow rules in the form of second-order partial differential equations for the slips. When the free energy depends on the dislocation densities the microscopic stresses are partially energetic, and this, in turn, leads to backstresses in the flow rules; on the other hand, a dependence of these stresses on slip-rate gradients leads to a strengthening. The flow rules, being nonlocal, require microscopic boundary conditions; as an aid to numerical solutions a weak (virtual power) formulation of the flow rule is derived.
Arthaud, Laury; Rokia-Mille, Selim Ben; Raad, Hussein; Dombrovsky, Aviv; Prevost, Nicolas
2011-01-01
Behaviors in insects are partly highly efficient Bayesian processes that fulfill exploratory tasks ending with the colonization of new ecological niches. The foraging (for) gene in Drosophila encodes a cGMP-dependent protein kinase (PKG). It has been extensively described as a frequency-dependent gene and its transcripts are differentially expressed between individuals, reflecting the population density context. Some for transcripts, when expressed in a population at high density for many generations, concomitantly trigger strong dispersive behavior associated with foraging activity. Moreover, genotype-by-environment interaction (GEI) analysis has highlighted a dormant role of for in energetic metabolism in a food deprivation context. In our current report, we show that alleles of for encoding different cGMP-dependent kinase isoforms influence the oxidation of aldehyde groups of aromatic molecules emitted by plants via Aldh-III and a phosphorylatable adaptor. The enhanced efficiency of oxidation of aldehyde odorants into carboxyl groups by the action of for lessens their action and toxicity, which should facilitate exploration and guidance in a complex odor environment. Our present data provide evidence that optimal foraging performance requires the fast metabolism of volatile compounds emitted by plants to avoid neurosensory saturation and that the frequency-dependent genes that trigger dispersion influence these processes. PMID:21625551
Flockhart, D. T. Tyler; Martin, Tara G.; Norris, D. Ryan
2012-01-01
A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism. PMID:22984614
Flockhart, D T Tyler; Martin, Tara G; Norris, D Ryan
2012-01-01
A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism. PMID:22984614
Space-dependent color gamut mapping: a variational approach.
Kimmel, Ron; Shaked, Doron; Elad, Michael; Sobel, Irwin
2005-06-01
Gamut mapping deals with the need to adjust a color image to fit into the constrained color gamut of a given rendering medium. A typical use for this tool is the reproduction of a color image prior to its printing, such that it exploits best the given printer/medium color gamut, namely the colors the printer can produce on the given medium. Most of the classical gamut mapping methods involve a pixel-by-pixel mapping and ignore the spatial color configuration. Recently proposed spatial-dependent approaches for gamut mapping are either based on heuristic assumptions or involve a high computational cost. In this paper, we present a new variational approach for space-dependent gamut mapping. Our treatment starts with the presentation of a new measure for the problem, closely related to a recent measure proposed for Retinex. We also link our method to recent measures that attempt to couple spectral and spatial perceptual measures. It is shown that the gamut mapping problem leads to a quadratic programming formulation, guaranteed to have a unique solution if the gamut of the target device is convex. An efficient numerical solution is proposed with promising results. PMID:15971778
Resampling method for applying density-dependent habitat selection theory to wildlife surveys.
Tardy, Olivia; Massé, Ariane; Pelletier, Fanie; Fortin, Daniel
2015-01-01
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents. PMID:26042998
Resampling Method for Applying Density-Dependent Habitat Selection Theory to Wildlife Surveys
Tardy, Olivia; MassÃ©, Ariane; Pelletier, Fanie; Fortin, Daniel
2015-01-01
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents. PMID:26042998
Native defects in oxide semiconductors: a density functional approach.
Oba, Fumiyasu; Choi, Minseok; Togo, Atsushi; Seko, Atsuto; Tanaka, Isao
2010-09-29
We report a semilocal and hybrid Hartree-Fock density functional study of native defects in three oxide semiconductors: ZnO, SrTiO(3), and SnO. The defect that is responsible for the n-type conductivity of ZnO has been debated, in which the O vacancy, Zn interstitial, their complexes, and residual H impurity are considered candidates. Our results indicate that the O vacancy induces a deep and localized in-gap state, whereas the Zn interstitial is a shallow donor and hence can be a source of the carriers. In view of the formation energies, the O vacancy is likely to form with a substantial concentration under O-poor conditions, but the Zn interstitial is unlikely. We thus propose that the O vacancy is relevant to the nonstoichiometry of ZnO and that a source other than the native defects, such as the H impurity, needs to be considered for the n-type conductivity. For SrTiO(3), the O vacancy and its complexes have been regarded as the origins of some of the remarkable electrical and optical properties. We suggest significant roles of the Ti antisite for a new insight into the defect-induced properties. Two types of Ti antisite, both of which are off-centered from the Sr site but toward different directions, exhibit low formation energies under Ti-rich conditions as does the O vacancy. They can explain optical properties such as visible-light emission, deep-level absorption, and the ferroelectricity observed in reduced SrTiO(3). As an example of p-type conductors, SnO has been investigated with a focus on the acceptor-like native defects. Under O-rich conditions, the Sn vacancy and O interstitial are found to be energetically favorable. The Sn vacancy induces shallow acceptor levels and can therefore be a source of carriers. The O interstitial shows no in-gap levels and hence it is inactive in terms of the carrier generation and compensation. However, this defect is a key to the understanding of the structures of intermediate compounds between SnO and SnO(2). PMID:21386545
Native defects in oxide semiconductors: a density functional approach
NASA Astrophysics Data System (ADS)
Oba, Fumiyasu; Choi, Minseok; Togo, Atsushi; Seko, Atsuto; Tanaka, Isao
2010-09-01
We report a semilocal and hybrid Hartree-Fock density functional study of native defects in three oxide semiconductors: ZnO, SrTiO3, and SnO. The defect that is responsible for the n-type conductivity of ZnO has been debated, in which the O vacancy, Zn interstitial, their complexes, and residual H impurity are considered candidates. Our results indicate that the O vacancy induces a deep and localized in-gap state, whereas the Zn interstitial is a shallow donor and hence can be a source of the carriers. In view of the formation energies, the O vacancy is likely to form with a substantial concentration under O-poor conditions, but the Zn interstitial is unlikely. We thus propose that the O vacancy is relevant to the nonstoichiometry of ZnO and that a source other than the native defects, such as the H impurity, needs to be considered for the n-type conductivity. For SrTiO3, the O vacancy and its complexes have been regarded as the origins of some of the remarkable electrical and optical properties. We suggest significant roles of the Ti antisite for a new insight into the defect-induced properties. Two types of Ti antisite, both of which are off-centered from the Sr site but toward different directions, exhibit low formation energies under Ti-rich conditions as does the O vacancy. They can explain optical properties such as visible-light emission, deep-level absorption, and the ferroelectricity observed in reduced SrTiO3. As an example of p-type conductors, SnO has been investigated with a focus on the acceptor-like native defects. Under O-rich conditions, the Sn vacancy and O interstitial are found to be energetically favorable. The Sn vacancy induces shallow acceptor levels and can therefore be a source of carriers. The O interstitial shows no in-gap levels and hence it is inactive in terms of the carrier generation and compensation. However, this defect is a key to the understanding of the structures of intermediate compounds between SnO and SnO2.
NASA Astrophysics Data System (ADS)
Heidtkamp, Christian; Lassen, Sabine; Schneider, Marcus; Reuter, Dirk; Versen, Martin; Wieck, Andreas D.
2000-07-01
Differently prepared mesas of the same wafer yield different longitudinal resistances ? xx(B) in the quantum Hall regime. The ratio of two neighboring spin-split maxima is constant for one sample, but varies from sample to sample. We assume an exponential law for the short-range elastic edge channel scattering rate 1/? eln,n+1? exp(- const·?n 2 Dl depl) where ? is spin-dependent, l depl the depletion length and n 2 D the electron density. Different depletion lengths can explain the measurements mentioned above. Furthermore, experiments with in-plane gates defined with focussed ion beam writing or mechanical scratching verify this dependence. Measurements under illumination confirm the dependence on l depl and n 2 D.
Adapting approximate-memory potentials for time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Kurzweil, Yair; Baer, Roi
2008-02-01
Frequency dependent exchange-correlation kernels for time-dependent density functional theory can be used to construct approximate exchange-correlation potentials. The resulting potentials are usually not translationally covariant nor do they obey the so-called zero-force condition. These two basic symmetry requirements are essential for using the potentials in actual applications (even in the linear regime). We provide two pragmatic methods for fully imposing these conditions for both linear and nonlinear regimes. As an example, we take the Gross and Kohn frequency dependent XC functional [Phys. Rev. Lett. 55, 2850 (1985)], correct it, and numerically test it on a sodium metal cluster. Violation of the basic symmetries causes instabilities or spurious low frequency modes.
Rao, Rekha R.; Mondy, Lisa Ann; Noble, David R.; Brunini, Victor; Roberts, Christine Cardinal; Long, Kevin Nicholas; Soehnel, Melissa Marie; Celina, Mathias C.; Wyatt, Nicholas B.; Thompson, Kyle R.; Tinsley, James
2015-09-01
We are studying PMDI polyurethane with a fast catalyst, such that filling and polymerization occur simultaneously. The foam is over-packed to tw ice or more of its free rise density to reach the density of interest. Our approach is to co mbine model development closely with experiments to discover new physics, to parameterize models and to validate the models once they have been developed. The model must be able to repres ent the expansion, filling, curing, and final foam properties. PMDI is chemically blown foam, wh ere carbon dioxide is pr oduced via the reaction of water and isocyanate. The isocyanate also re acts with polyol in a competing reaction, which produces the polymer. A new kinetic model is developed and implemented, which follows a simplified mathematical formalism that decouple s these two reactions. The model predicts the polymerization reaction via condensation chemis try, where vitrification and glass transition temperature evolution must be included to correctly predict this quantity. The foam gas generation kinetics are determined by tracking the molar concentration of both water and carbon dioxide. Understanding the therma l history and loads on the foam due to exothermicity and oven heating is very important to the results, since the kinetics and ma terial properties are all very sensitive to temperature. The conservation eq uations, including the e quations of motion, an energy balance, and thr ee rate equations are solved via a stabilized finite element method. We assume generalized-Newtonian rheology that is dependent on the cure, gas fraction, and temperature. The conservation equations are comb ined with a level set method to determine the location of the free surface over time. Results from the model are compared to experimental flow visualization data and post-te st CT data for the density. Seve ral geometries are investigated including a mock encapsulation part, two configur ations of a mock stru ctural part, and a bar geometry to specifically test the density model. We have found that the model predicts both average density and filling profiles well. However, it under predicts density gradients, especially in the gravity direction. Thoughts on m odel improvements are also discussed.
Pharmacological approaches to methamphetamine dependence: a focused review
Karila, Laurent; Weinstein, Aviv; Aubin, Henri-Jean; Benyamina, Amine; Reynaud, Michel; Batki, Steven L
2010-01-01
Methamphetamine dependence is a serious worldwide public health problem with major medical, psychiatric, socioeconomic and legal consequences. Various neuronal mechanisms implicated in methamphetamine dependence have suggested several pharmacological approaches. A literature search from a range of electronic databases (PubMed, EMBASE, PsycInfo, the NIDA research monograph index and the reference list of clinicaltrials.gov) was conducted for the period from January 1985 to October 2009. There were no restrictions on the identification or inclusion of studies in terms of publication status, language and design type. A variety of medications have failed to show efficacy in clinical trials, including a dopamine partial agonist (aripiprazole), GABAergic agents (gabapentin) and serotonergic agents (SSRI, ondansetron, mirtazapine). Three double-blind placebo-controlled trials using modafinil, bupropion and naltrexone have shown positive results in reducing amphetamine or methamphetamine use. Two studies employing agonist replacement medications, one with d-amphetamine and the other with methylphenidate, have also shown promise. Despite the lack of success in most studies to date, increasing efforts are being made to develop medications for the treatment of methamphetamine dependence and several promising agents are targets of further research. PMID:20565449
Stocking density affects the growth performance of broilers in a sex-dependent fashion.
Zuowei, S; Yan, L; Yuan, L; Jiao, H; Song, Z; Guo, Y; Lin, H
2011-07-01
The effects of stocking density, sex, and dietary ME concentration on live performance, footpad burns, and leg weakness of broilers were investigated. A total of 876 male and 1,020 female 1-d-old chicks were placed in 24 pens to simulate final stocking density treatments of 26 kg (LSD; 10 males or 12 females/m(2)) and 42 kg (HSD; 16 males or 18 females/m(2)) of BW/m(2) floor space. Two series of experimental diets with a 150 kcal/kg difference in ME concentration (2,800, 2,900, and 3,000 or 2,950, 3,050, and 3,150 kcal of ME/kg) were compared in a 3-phase feeding program. The HSD treatment significantly decreased BW gain and feed conversion ratio (FCR). The HSD chickens consumed less feed by 35 d of age; thereafter, the reverse was true. Male chickens had significantly higher feed intake (FI), BW gain, and FCR compared with females. A significant interaction was found of stocking density and age for FI, BW gain, and FCR. Compared with LSD treatment, HSD broilers had a higher FI and a lower FCR from 36 to 42 d of age. Stocking density, sex, and age had a significant interaction for BW gain and FCR. Female broilers had worse BW gain and FCR when stocked at high density from 36 to 42 d of age. Stocking density had no significant influence on breast, thigh, or abdominal fat yield. Female broilers had significantly higher breast yield and abdominal fat. Male broilers and HSD treatment had high footpad burn and gait scores. A low ME diet increased footpad burn score but had no effect on gait score. The result indicated that stocking density had a more severe effect on the growth of male broilers before 35 d of age. Female broilers need more space than males at similar BW per square meter near marketing age. The incidence and severity of leg weakness are associated with sex, diet, and stocking density. This result suggests that the deteriorated effect of high stocking density is sex and age dependent. PMID:21673155
BMP-2 Dependent Increase of Soft Tissue Density in Arthrofibrotic TKA
Pfitzner, Tilman; Röhner, Eric; Krenn, Veit; Perka, Carsten; Matziolis, Georg
2012-01-01
Arthrofibrosis after total knee arthroplasty (TKA) is difficult to treat, as its aetiology remains unclear. In a previous study, we established a connection between the BMP-2 concentration in the synovial fluid and arthrofibrosis after TKA. The hypothesis of the present study was, therefore, that the limited range of motion in arthrofibrosis is caused by BMP-2 induced heterotopic ossifications, the quantity of which is dependent on the BMP-2 concentration in the synovial fluid. Eight patients with arthrofibrosis after TKA were included. The concentration of BMP-2 in the synovial fluid from each patient was determined by ELISA. Radiologically, digital radiographs were evaluated and the grey scale values were determined as a measure of the tissue density of defined areas. Apart from air, cutis, subcutis and muscle, the soft-tissue density in the area of the capsule of the suprapatellar pouch was determined. The connection between the BMP-2 concentration and the soft-tissue density was then investigated. The average BMP-2 concentration in the synovial fluid was 24.3 ± 6.9 pg/ml. The density of the anterior knee capsule was on average 136 ± 35 grey scale values. A linear correlation was shown between the BMP-2 concentration in the synovial fluid and the radiological density of the anterior joint capsule (R=0.84, p = 0.009). We were able to show that there is a connection between BMP-2 concentration and soft-tissue density in arthrofibrosis after TKA. This opens up the possibility of conducting a prophylaxis against arthrofibrosis in risk patients by influencing the BMP-2 pathway. PMID:22629292
NASA Astrophysics Data System (ADS)
Jackson, Aaron P.; Calder, A. C.; Townsley, D. M.; Chamulak, D. A.; Brown, E. F.; Timmes, F. X.
2010-01-01
We explore the effects of the deflagration to detonation transition density on the production of 56Ni in thermonuclear supernova explosions (type Ia supernovae). The transition density indirectly sets the amount of expansion during the deflagration phase of the explosion and therefore the amount of Fe-group material produced. A fraction of the Fe-group material will be radioactive 56Ni that powers the supernova lightcurve. We employ a theoretical framework for a well-controlled statistical study of two-dimensional simulations of thermonuclear supernovae with randomized initial conditions that produce 56Ni masses with a similar average and range to those inferred from observations (Townsley et al. 2009) for a fiducial transition density of 107 g cm-3. Within this framework, we utilize a realistic 'simmered' white dwarf progenitor model and a detailed flame model and energetics scheme to calculate the amount of Fe-group material synthesized for a suite of simulated explosions in which the transition density is varied. Understanding the effect of transition density on the amount of Fe-group material produced in combination with the effect of 22Ne (and metallicity) on transition density allows us to construct the functional dependence of the amount of Fe-group material and 56Ni mass synthesized in the explosion on metallicity through the 22Ne content. This work was supported by NASA under grant No. NNX09AD19G and utilized resources at the New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory, which is supported by the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 and by the State of New York.
Time-dependent density-functional theory for electronic excitations in materials
NASA Astrophysics Data System (ADS)
Ullrich, Carsten A.
2009-03-01
There is currently an intense effort underway to study the optical properties of bulk and nanostructured materials using time-dependent density-functional theory (TDDFT). This talk will discuss challenges and recent advances of TDDFT in this area, and present some new applications to excitonic effects in bulk insulators and to collective charge- and spin-density excitations in doped quantum wells. A TDDFT version of the semiconductor Bloch equations is presented, which describes ultrafast electron dynamics, including excitonic effects, in insulators and semiconductors. From this, an excitonic Wannier equation is derived featuring a nonlocal effective electron-hole interaction determined by long-range exchange-correlation effects. Excitonic binding energies are calculated for several direct-gap insulators. The spin Coulomb drag (SCD), which constitutes an intrinsic source of dissipation for spin currents in metals and semiconductors, originates as a dynamical exchange-correlation effect in time-dependent current-DFT. We develop a linear-response description of collective spin-density excitations in quantum wells including SCD as well as Rashba and Dresselhaus spin-orbit coupling, and show that spin plasmon line widths in quantum wells allow a purely optical, quantitative measurement of the SCD effect.
NASA Astrophysics Data System (ADS)
England, S. M.; Stevens, G. T.
2008-05-01
Aquifer Storage and Recovery (ASR) is the storage of fresh water in an aquifer via injection during times when water is available, and recovery of the water from the same aquifer via pumping during times when it is needed. ASR is one of the proposed alternatives recommended by the Comprehensive Everglades Restoration Plan (CERP) to help with water supply, storage, and distribution of water in South Florida. To evaluate the numerous design considerations and the variation in aquifer response resulting from CERP ASR, regional density- dependent numerical modeling of the Floridan Aquifer System (FAS) in the southern half of Florida is in progress. This modeling incorporates use of two density-dependent numerical codes, SEAWAT and WASH123D, and the synthesis of regional knowledge of the FAS in terms of geologic parameters, groundwater flow patterns, and salinity influences. Several challenges have been discovered in replicating the existing regional groundwater flow patterns, most notably, that in south-central Florida the simulated heads are considerably lower than observed values. Recent model studies of several factors that could affect south Florida regional flow patterns indicate that the inclusion of preferential flow as well as the effects of temperature on groundwater density yield results that are more consistent with observed values. Future work will focus on the investigation of field data to support the application of preferential flow and the addition of groundwater injection and withdrawal including existing and proposed ASR projects.
Lateral density variations in elastic Earth models from an extended minimum energy approach
NASA Technical Reports Server (NTRS)
Sanchez, B. V.
1980-01-01
Kaula's minimum energy approach was extended to include the nonhydrostatic gravitational potential energy and the density perturbation field was obtained to degree and order eight. The depth profiles for the density perturbation show a stratification with density excesses and deficiencies alternating with depth. The addition of the gravitational potential energy in the minimization process does not change significantly the conclusions based on results for the minimum shear strain energy case, concerning the inability of the mantle to withstand the lateral loading elastically.
White, J Wilson; Samhouri, Jameal F; Stier, Adrian C; Wormald, Clare L; Hamilton, Scott L; Sandin, Stuart A
2010-07-01
Coral and rocky reef fish populations are widely used as model systems for the experimental exploration of density-dependent vital rates, but patterns of density-dependent mortality in these systems are not yet fully understood. In particular, the paradigm for strong, directly density-dependent (DDD) postsettlement mortality stands in contrast to recent evidence for inversely density-dependent (IDD) mortality. We review the processes responsible for DDD and IDD per capita mortality in reef fishes, noting that the pattern observed depends on predator and prey behavior, the spatial configuration of the reef habitat, and the spatial and temporal scales of observation. Specifically, predators tend to produce DDD prey mortality at their characteristic spatial scale of foraging, but prey mortality is IDD at smaller spatial scales due to attack-abatement effects (e.g., risk dilution). As a result, DDD mortality may be more common than IDD mortality on patch reefs, which tend to constrain predator foraging to the same scale as prey aggregation, eliminating attack-abatement effects. Additionally, adjacent groups of prey on continuous reefs may share a subset of refuges, increasing per capita refuge availability and relaxing DDD mortality relative to prey on patch reefs, where the patch edge could prevent such refuge sharing. These hypotheses lead to a synthetic framework to predict expected mortality patterns for a variety of scenarios. For nonsocial, nonaggregating species and species that aggregate in order to take advantage of spatially clumped refuges, IDD mortality is possible but likely superseded by DDD refuge competition, especially on patch reefs. By contrast, for species that aggregate socially, mortality should be IDD at the scale of individual aggregations but DDD at larger scales. The results of nearly all prior reef fish studies fit within this framework, although additional work is needed to test many of the predicted outcomes. This synthesis reconciles some apparent contradictions in the recent reef fish literature and suggests the importance of accounting for the scale-sensitive details of predator and prey behavior in any study system. PMID:20715614
NASA Astrophysics Data System (ADS)
Farzanehpour, Mehdi; Tokatly, Ilya; Nano-Bio Spectroscopy Group; ETSF Scientific Development Centre Team
2015-03-01
We present a rigorous formulation of the time-dependent density functional theory for interacting lattice electrons strongly coupled to cavity photons. We start with an example of one particle on a Hubbard dimer coupled to a single photonic mode, which is equivalent to the single mode spin-boson model or the quantum Rabi model. For this system we prove that the electron-photon wave function is a unique functional of the electronic density and the expectation value of the photonic coordinate, provided the initial state and the density satisfy a set of well defined conditions. Then we generalize the formalism to many interacting electrons on a lattice coupled to multiple photonic modes and prove the general mapping theorem. We also show that for a system evolving from the ground state of a lattice Hamiltonian any density with a continuous second time derivative is locally v-representable. Spanish Ministry of Economy and Competitiveness (Grant No. FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13), COST Actions CM1204 (XLIC) and MP1306 (EUSpec).
Temperature-Dependent Maximum Density of 1D Excitons in Carbon Nanotubes
NASA Astrophysics Data System (ADS)
Searles, Thomas; Walsh, Ian; Nosaka, Takayuki; Rice, William; Kono, Junichiro
2011-03-01
Previous studies have shown that an upper limit exists on the density of 1D excitons in single-walled carbon nanotubes (SWNTs) due to very efficient exciton-exciton annihilation (EEA). A recent theoretical study based on a dark-bright two-band exciton model predicts that there is a temperature at which the achievable exciton density will be maximized, surpassing the room-temperature upper limit. Therefore, we performed temperature-dependent (300 K to 11 K) photoluminescence (PL) on HiPco SWNTs embedded in an i-carrageenan matrix under high resonant excitation. To achieve high densities, we used pump fluences up to ~ 1014 photons/cm2 , utilizing intense fs pulses from a wavelength-tunable optical parametric amplifier. We found that for each temperature the PL intensity saturates as a function of pump fluence and the saturation intensity increases from 300 K to a moderate temperature around 100-150 K. Below that critical temperature, the PL intensity decreases with decreasing temperature. Within the framework of diffusion-limited EEA, we successfully estimated the upper limit of the density of 1D excitons in SWNTs as a function of temperature and chirality
Density-Dependent Effects of an Invasive Ant on a Ground-Dwelling Arthropod Community.
Cooling, M; Sim, D A; Lester, P J
2015-02-01
It is frequently assumed that an invasive species that is ecologically or economically damaging in one region, will typically be so in other environments. The Argentine ant Linepithema humile (Mayr) is listed among the world's worst invaders. It commonly displaces resident ant species where it occurs at high population densities, and may also reduce densities of other ground-dwelling arthropods. We investigated the effect of varying Argentine ant abundance on resident ant and nonant arthropod species richness and abundance in seven cities across its range in New Zealand. Pitfall traps were used to compare an invaded and uninvaded site in each city. Invaded sites were selected based on natural varying abundance of Argentine ant populations. Argentine ant density had a significant negative effect on epigaeic ant abundance and species richness, but hypogaeic ant abundance and species richness was unaffected. We observed a significant decrease in Diplopoda abundance with increasing Argentine ant abundance, while Coleoptera abundance increased. The effect on Amphipoda and Isopoda depended strongly on climate. The severity of the impact on negatively affected taxa was reduced in areas where Argentine ant densities were low. Surprisingly, Argentine ants had no effect on the abundance of the other arthropod taxa examined. Morphospecies richness for all nonant arthropod taxa was unaffected by Argentine ant abundance. Species that are established as invasive in one location therefore cannot be assumed to be invasive in other locations based on presence alone. Appropriate management decisions should reflect this knowledge. PMID:26308805
NASA Astrophysics Data System (ADS)
Puhakka, P. H.; Ylärinne, J. H.; Lammi, M. J.; Saarakkala, S.; Tiitu, V.; Kröger, H.; Virén, T.; Jurvelin, J. S.; Töyräs, J.
2014-11-01
Optical coherence tomography (OCT) has been applied for high resolution imaging of articular cartilage. However, the contribution of individual structural elements of cartilage on OCT signal has not been thoroughly studied. We hypothesize that both collagen and chondrocytes, essential structural components of cartilage, act as important light scatterers and that variation in their concentrations can be detected by OCT through changes in backscattering and attenuation. To evaluate this hypothesis, we established a controlled model system using agarose scaffolds embedded with variable collagen concentrations and chondrocyte densities. Using OCT, we measured the backscattering coefficient (µb) and total attenuation coefficient (µt) in these scaffolds. Along our hypothesis, light backscattering and attenuation in agarose were dependent on collagen concentration and chondrocyte density. Significant correlations were found between µt and chondrocyte density (? = 0.853, p < 0.001) and between µt and collagen concentration (? = 0.694, p < 0.001). µb correlated significantly with chondrocyte density (? = 0.504, p < 0.001) but not with collagen concentration (? = 0.103, p = 0.422) of the scaffold. Thus, quantitation of light backscattering and, especially, attenuation could be valuable when evaluating the integrity of soft tissues, such as articular cartilage with OCT.
Albuquerque, PatrÃcia; Nicola, AndrÃ© M.; Nieves, Edward; Paes, Hugo Costa; Williamson, Peter R.; Silva-Pereira, Ildinete; Casadevall, Arturo
2013-01-01
ABSTRACT Quorum sensing (QS) is a cell density-dependent mechanism of communication between microorganisms, characterized by the release of signaling molecules that affect microbial metabolism and gene expression in a synchronized way. In this study, we investigated cell density-dependent behaviors mediated by conditioned medium (CM) in the pathogenic encapsulated fungus Cryptococcus neoformans. CM produced dose-dependent increases in the growth of planktonic and biofilm cells, glucuronoxylomannan release, and melanin synthesis, important virulence attributes of this organism. Mass spectrometry revealed the presence of pantothenic acid (PA) in our samples, and commercial PA was able to increase growth and melanization, although not to the same extent as CM. Additionally, we found four mutants that were either unable to produce active CM or failed to respond with increased growth in the presence of wild-type CM, providing genetic evidence for the existence of intercellular communication in C.Â neoformans. C.Â neoformans CM also increased the growth of Cryptococcus albidus, Candida albicans, and Saccharomyces cerevisiae. Conversely, CM from Cryptococcus albidus, C.Â albicans, S. cerevisiae, and Sporothrix schenckii increased C.Â neoformans growth. In summary, we report the existence of a new QS system regulating the growth and virulence factor expression of C.Â neoformans in vitro and, possibly, also able to regulate growth in other fungi. PMID:24381301
NASA Astrophysics Data System (ADS)
Petrovici, M.; Berceanu, I.; Pop, A.; Andrei, C.; Herghelegiu, A.
2013-02-01
As far as details on the "Relativistic Heavy Ion Collisions - Expectations, Experimental Facts and Future Plans" lecture could be found on the Summer School web site, the present contribution will summarize the results considered to be of general interest, i.e. the energy scaling of centrality dependence of mid-rapidity charged particles density in relativistic heavy ion collisions, presented in the second part of the lecture, in the section dedicated to the global observables. The comparison of charged particle multiplicity in heavy ion central collisions and e+e- as a function of ?s, including the latest results obtained at LHC in Pb+Pb collisions at 2.76 is followed by the energy scaling of the pseudo-rapidity charged particle density in central rapidity as a function of centrality.
Density dependent hadronic models and the relation between neutron stars and neutron skin thickness
Avancini, S. S.; Marinelli, J. R.; Menezes, D. P.; Moraes, M. M. W.; Providencia, C.
2007-05-15
In the present work, we investigate the main differences in the lead neutron skin thickness, binding energy, surface energy, and density profiles obtained with two different density dependent hadron models. Our results are calculated within the Thomas-Fermi approximation with two different numerical prescriptions and compared with results obtained with a common parametrization of the nonlinear Walecka model. The neutron skin thickness is a reflex of the equation of state properties. Hence, a direct correlation is found between the neutron skin thickness and the slope of the symmetry energy. We show that within the present approximations, the asymmetry parameter for low momentum transfer polarized electron scattering is not sensitive to the model differences.
Time-dependent density functional theory study of correlation in proton-helium collisions
NASA Astrophysics Data System (ADS)
Baxter, Matthew; Kirchner, Tom
2014-05-01
A recent model to describe electron correlations in time-dependent density functional theory (TDDFT) studies of antiproton-helium collisions is extended to deal with positively charged projectiles. The main complication is that a positively-charged projectile can capture electrons in addition to ionizing them to the continuum. As a consequence, within the TDDFT framework one needs to consider three, instead of just one, correlation integrals (Ics) when formally expressing the probabilities for the occurring one- and two-electron processes in terms of the density. We discuss possible extensions of an adiabatic model for Ic to deal with this situation and present results for few keV to few MeV proton-helium collisions obtained from basis-generator-method calculations with microscopic response effects included. This work is supported by NSERC, Canada.
Density-dependent cooperation as a mechanism for persistence and coexistence.
Lampert, Adam; Tlusty, Tsvi
2011-10-01
To overcome stress, such as resource limitation, an organism often needs to successfully mediate competition with other members of its own species. This may favor the evolution of defective traits that are harmful to the species population as a whole, and that may lead to its dilution or even to its extinction (the tragedy of the commons). Here, we show that this phenomenon can be circumvented by cooperation plasticity, in which an individual decides, based on environmental conditions, whether to cooperate or to defect. Specifically, we analyze the evolution of density-dependent cooperation. In our model, the population is spatially subdivided, periodically remixed, and comprises several species. We find that evolution pushes individuals to be more cooperative when their own species is at lower densities, and we show that not only could this cooperation prevent the tragedy of the commons, but it could also facilitate coexistence between many species that compete for the same resource. PMID:21967418
Guido, Ciro A. Cortona, Pietro; Adamo, Carlo; Institut Universitaire de France, 103 Bd Saint-Michel, F-75005 Paris
2014-03-14
We extend our previous definition of the metric Î”r for electronic excitations in the framework of the time-dependent density functional theory [C. A. Guido, P. Cortona, B. Mennucci, and C. Adamo, J. Chem. Theory Comput. 9, 3118 (2013)], by including a measure of the difference of electronic position variances in passing from occupied to virtual orbitals. This new definition, called Î“, permits applications in those situations where the Î”r-index is not helpful: transitions in centrosymmetric systems and Rydberg excitations. The Î“-metric is then extended by using the Natural Transition Orbitals, thus providing an intuitive picture of how locally the electron density changes during the electronic transitions. Furthermore, the Î“ values give insight about the functional performances in reproducing different type of transitions, and allow one to define a â€œconfidence radiusâ€ for GGA and hybrid functionals.
Density-dependent recruitment of the bloater (Coregonus hoyi) in Lake Michigan
Brown, Edward H., Jr.; Eck, Gary W.
1992-01-01
Density-dependent recruitment of the bloater (Coregonus hoyi) in Lake Michigan during and after recovery of the population in about 1977-1983 was best reflected in the fit of the Beverton-Holt recruitment function to age -1 and -2 recruits and estimated eggs of parents surveyed with trawls. A lower growth rate and lower lipid content of bloaters at higher population densities and no evidence of cannibalism supported the conclusion that recruitment is resource limited when alewife (Alosa pseudoharengus) abundance is low. Predation on larvae by alewives was indicated in earlier studies as the probable cause of depressed recruitment of bloaters before their recovery, which coincided with declining alewife abundance. This negative interaction masked any bloater stock-recruitment relation in the earlier period.
NASA Astrophysics Data System (ADS)
Banerjee, Arup; Chakrabarti, Aparna; Ghanty, Tapan K.
We employ all-electron ab initio time-dependent density functional theory (DFT)-based method to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) C6 of potassium atom clusters (Kn) containing even number of atoms, n ranging from 2 to 20. The dispersion coefficients are obtained via Casimir-Polder relation. The calculations are carried out with the asymptotically correct statistical average of orbital potential and compared with the results obtained using Vosko-Wilk-Nusair representation of exchange-correlation potential within local density approximation. We report the dispersion coefficients between clusters of sodium and potassium atoms as well. The present results have been compared with the available jellium-based model and other DFT results in the literature. We also study the relationship between volume of the cluster and the C6 for K clusters. It is observed that the C6 scales as square of the volume.
Dependence of the cosmic microwave background lensing power spectrum on the matter density
NASA Astrophysics Data System (ADS)
Pan, Z.; Knox, L.; White, M.
2014-12-01
The anisotropies in the cosmic microwave background (CMB) provide our best laboratory for testing models of the formation and evolution of large-scale structure. The rich features in the CMB anisotropy spectrum, in combination with highly precise observations and theoretical predictions, also allow us to simultaneously constrain a number of cosmological parameters. As observations have progressed, measurements at smaller angular scales have provided increasing leverage. These smaller angular scales provide sensitive measures of the matter density through the effect of gravitational lensing. In this work, we provide an analytic explanation of the manner in which the lensing of CMB anisotropies depends on the matter density, finding that the dominant effect comes from the shape of the matter power spectrum set by the decay of small-scale potentials between horizon crossing and matter-radiation equality.
Size-dependent error of the density functional theory ionization potential in vacuum and solution.
Sosa Vazquez, Xochitl A; Isborn, Christine M
2015-12-28
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potential for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. In vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional. PMID:26723649
Turbo charging time-dependent density-functional theory with Lanczos chains.
Rocca, Dario; Gebauer, Ralph; Saad, Yousef; Baroni, Stefano
2008-04-21
We introduce a new implementation of time-dependent density-functional theory which allows the entire spectrum of a molecule or extended system to be computed with a numerical effort comparable to that of a single standard ground-state calculation. This method is particularly well suited for large systems and/or large basis sets, such as plane waves or real-space grids. By using a superoperator formulation of linearized time-dependent density-functional theory, we first represent the dynamical polarizability of an interacting-electron system as an off-diagonal matrix element of the resolvent of the Liouvillian superoperator. One-electron operators and density matrices are treated using a representation borrowed from time-independent density-functional perturbation theory, which permits us to avoid the calculation of unoccupied Kohn-Sham orbitals. The resolvent of the Liouvillian is evaluated through a newly developed algorithm based on the nonsymmetric Lanczos method. Each step of the Lanczos recursion essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn-Sham Hamiltonian. Suitable extrapolation of the Lanczos coefficients allows for a dramatic reduction of the number of Lanczos steps necessary to obtain well converged spectra, bringing such number down to hundreds (or a few thousands, at worst) in typical plane-wave pseudopotential applications. The resulting numerical workload is only a few times larger than that needed by a ground-state Kohn-Sham calculation for a same system. Our method is demonstrated with the calculation of the spectra of benzene, C(60) fullerene, and of chlorophyll a. PMID:18433188
Size-dependent error of the density functional theory ionization potential in vacuum and solution
Sosa Vazquez, Xochitl A.; Isborn, Christine M.
2015-12-22
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potentialmoreÂ Â» for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. As a result, in vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.Â«Â less
Size-dependent error of the density functional theory ionization potential in vacuum and solution
NASA Astrophysics Data System (ADS)
Sosa Vazquez, Xochitl A.; Isborn, Christine M.
2015-12-01
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potential for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. In vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.
Size-dependent error of the density functional theory ionization potential in vacuum and solution
Sosa Vazquez, Xochitl A.; Isborn, Christine M.
2015-12-22
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potential for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. As a result, in vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.
Cambré, Sofie; Muyshondt, Pieter; Federicci, Remi; Wenseleers, Wim
2015-12-21
Density gradient ultracentrifugation (DGU) becomes increasingly important for the sorting of nanomaterials according to the particles' density, hence structure and dimensions, which determine their unique properties, but the further development of this separation technique is hindered by the limited precision with which the densities could be characterized. In this work, we determine these densities by position-dependent 2D wavelength-dependent IR fluorescence-excitation and resonant Raman spectroscopy measured directly in the density gradient after ultracentrifugation. We apply this method to study the diameter and chirality-dependent sorting of empty and water-filled single-walled carbon nanotubes coated with two different surfactants, sodium cholate (SC) and sodium deoxycholate (DOC). The results elucidate the long standing contradiction that SC would provide better diameter sorting, while DOC is the most efficient surfactant to solubilise the nanotubes. A more predictable separation is obtained for empty DOC-coated nanotubes since their density is found to vary very smoothly with diameter. The accurate and chirality-dependent densities furthermore provide information on the surfactant coating, which is also important for other separation techniques, and allow to determine the mass percentage of water encapsulated inside the nanotubes. PMID:26565985
Monte Carlo study of voxel S factor dependence on tissue density and atomic composition
NASA Astrophysics Data System (ADS)
Amato, Ernesto; Italiano, Antonio; Baldari, Sergio
2013-11-01
Voxel dosimetry is a common approach to the internal dosimetry of non-uniform activity distributions in nuclear medicine therapies with radiopharmaceuticals and in the estimation of the radiation hazard due to internal contamination of radionuclides. Aim of the present work is to extend our analytical approach for the calculation of voxel S factors to materials different from the soft tissue. We used a Monte Carlo simulation in GEANT4 of a voxelized region of each material in which the source of monoenergetic electrons or photons was uniformly distributed within the central voxel, and the energy deposition was scored over the surrounding 11Ã—11Ã—11 voxels. Voxel S factors were obtained for the following standard ICRP materials: Adipose tissue, Bone cortical, Brain, Lung, Muscle skeletal and Tissue soft with 1 g cm-3 density. Moreover, we considered the standard ICRU materials: Bone compact and Muscle striated. Voxel S factors were represented as a function of the â€œnormalized radiusâ€, defined as the ratio between the source-target voxel distance and the voxel side. We found that voxel S factors and related analytical fit functions are mainly affected by the tissue density, while the material composition gives only a slight contribution to the difference between data series, which is negligible for practical purposes. Our results can help in broadening the dosimetric three-dimensional approach based on voxel S factors to other tissues where diagnostic and therapeutic radionuclides can be taken up and radiation can propagate.
Optical response of C60 fullerene from a time dependent Thomas Fermi approach
NASA Astrophysics Data System (ADS)
Palade, D. I.; Baran, V.
2015-09-01
We study the collective electron dynamics in C60 clusters within the time dependent Thomas Fermi method in the frame of jellium model. The results regarding the optical spectrum are in good agreement with the experimental data, our simulations being able to reproduce both resonances from 20 {eV} and 40 {eV}. We compare also, the results with those from other theoretical approaches and investigate the implications of quantum effects including exchange-correlation corrections, or gradient corrections from a Weizsacker term. The nature of the second resonance is studied using transition densities.
Variational approach to the time-dependent Schrödinger-Newton equations
NASA Astrophysics Data System (ADS)
Manfredi, Giovanni; Hervieux, Paul-Antoine; Haas, Fernando
2013-04-01
Using a variational approach based on a Lagrangian formulation and Gaussian trial functions, we derive a simple dynamical system that captures the main features of the time-dependent Schrödinger-Newton equations. With little analytical or numerical effort, the model furnishes information on the ground-state density and energy eigenvalue, the linear frequencies, as well as the nonlinear long-time behaviour. Our results are in good agreement with those obtained through analytical estimates or numerical simulations of the full Schrödinger-Newton equations.
Mukamel, Shaul
2005-02-01
Time-ordered superoperators are used to develop a unified description of nonlinear density response and spontaneous fluctuations of many-electron systems. The pth-order density response functions are decomposed into 2{sup p+1} non-causal Liouville space pathways. Individual pathways are symmetric to the interchange of their space, time, and superoperator indices and can thus be calculated as functional derivatives. Other combinations of these pathways represent spontaneous density fluctuations and the response of such fluctuations to an external field. The resolution of the causality paradox of time-dependent density-functional theory (TDDFT) is shown to be intimately connected with the nonretarded nature of fluctuations.
Density dependence and risk of extinction in a small population of sea otters
Gerber, L.R.; Buenau, K.E.; VanBlaricom, G.
2004-01-01
Sea otters (Enhydra lutris (L.)) were hunted to extinction off the coast of Washington State early in the 20th century. A new population was established by translocations from Alaska in 1969 and 1970. The population, currently numbering at least 550 animals, A major threat to the population is the ongoing risk of majour oil spills in sea otter habitat. We apply population models to census and demographic data in order to evaluate the status of the population. We fit several density dependent models to test for density dependence and determine plausible values for the carrying capacity (K) by comparing model goodness of fit to an exponential model. Model fits were compared using Akaike Information Criterion (AIC). A significant negative relationship was found between the population growth rate and population size (r2=0.27, F=5.57, df=16, p<0.05), suggesting density dependence in Washington state sea otters. Information criterion statistics suggest that the model is the most parsimonious, followed closely by the logistic Beverton-Holt model. Values of K ranged from 612 to 759 with best-fit parameter estimates for the Beverton-Holt model including 0.26 for r and 612 for K. The latest (2001) population index count (555) puts the population at 87-92% of the estimated carrying capacity, above the suggested range for optimum sustainable population (OSP). Elasticity analysis was conducted to examine the effects of proportional changes in vital rates on the population growth rate (??). The elasticity values indicate the population is most sensitive to changes in survival rates (particularly adult survival).
NASA Astrophysics Data System (ADS)
Fadjie-Djomkam, A. B.; Ababou-Girard, S.; Hiremath, R.; Herrier, C.; Fabre, B.; Solal, F.; Godet, C.
2011-10-01
Electrical transport in ultrathin Metal-insulator-semiconductor (MIS) tunnel junctions is analyzed using the temperature dependence of current density and admittance characteristics, as illustrated by Hg//C12H25 - n Si junctions incorporating n-alkyl molecular layers (1.45 nm thick) covalently bonded to Si(111). The voltage partition is obtained from J(V, T) characteristics, over eight decades in current. In the low forward bias regime (0.2-0.4 V) governed by thermionic emission, the observed linear T-dependence of the effective barrier height, q?EFF(T)=q?B+(kT)?0dT, provides the tunnel barrier attenuation, exp(-?0dT), with ?0= 0.93 Å-1 and the thermionic emission barrier height, ?B=0.53 eV. In the high-forward-bias regime (0.5-2.0 V), the bias dependence of the tunnel barrier transparency, approximated by a modified Simmons model for a rectangular tunnel barrier, provides the tunnel barrier height, ?T=0.5 eV; the fitted prefactor value, G0 = 10-10 ?-1, is four decades smaller than the theoretical Simmons prefactor for MIM structures. The density distribution of defects localized at the C12H25 - n Si interface is deduced from admittance data (low-high frequency method) and from a simulation of the response time ?R(V) using Gomila's model for a non equilibrium tunnel junction. The low density of electrically active defects near mid-gap (DS < 2 × 1011 eV-1.cm-2) indicates a good passivation of dangling bonds at the dodecyl - n Si (111) interface.
Sex modulates approach systems and impulsivity in substance dependence
Perry, Robert I.; Krmpotich, Theodore; Thompson, Laetitia L.; Mikulich-Gilbertson, Susan K.; Banich, Marie T.; Tanabe, Jody
2013-01-01
Background Personality traits such as pathological engagement in approach behaviors, high levels of impulsivity and heightened negative affect are consistently observed in substance dependent individuals (SDI). The clinical course of addiction has been shown to differ between sexes. For example, women increase their rates of consumption of some drugs of abuse more quickly than men. Despite the potential influence of personality and sex on features of addiction, few studies have investigated the interaction of these factors in substance dependence. Methods Fifty-one SDI (26 male, 25 female) and 66 controls (41 male, 25 female) completed the Behavioral Inhibition/Behavioral Activation System (BIS/BAS) Scales, the Barratt Impulsiveness Scale, and the Positive and Negative Affect Schedule (PANAS-X). Data were analyzed with 2Ã—2 ANCOVAs testing for main effects of group, sex and group by sex interactions, adjusting for education level. Results Significant group by sex interactions were observed for BAS scores [F(1,116)=7.03, p<.01] and Barratt Motor Impulsiveness [F(1,116)=6.11, p<.02] with female SDI showing the highest approach tendencies and impulsivity followed by male SDI, male controls, and finally female controls. SDI scored higher on negative affect [F(1,116)=25.23, p<.001] than controls. Behavioral Inhibition System scores were higher in women than men [F(1,116)=14.03, p< .001]. Conclusion Higher BAS and motor impulsivity in SDI women relative to SDI men and control women suggest that personality traits that have been previously associated with drug use may be modulated by sex. These factors may contribute to differences in the disease course observed in male compared to female drug users. PMID:23725607
A note on benchmarking of numerical models for density dependent flow in porous media
NASA Astrophysics Data System (ADS)
Ataie-Ashtiani, B.; Aghayi, M. M.
2006-12-01
Verification of numerical models for density dependent flow in porous media (DDFPM) by the means of appropriate benchmark problems is a very important step in developing and using these models. Recently, Infinite Horizontal Box (IHB) problem was suggested as a possible benchmark problem for verification of DDFPM codes. IHB is based on Horton-Rogers-Lapwood (HRL) problem. Suitability of this problem for the benchmarking purpose has been investigated in this paper. It is shown that the wavelength of instabilities fails to be a proper criterion to be considered for this problem. However, the threshold of instability formation has been found to be appropriate for benchmarking purpose.
Pressure Dependence of the Charge-Density-Wave Gap in Rare-Earth Tri-Tellurides
Sacchetti, A.; Arcangeletti, E.; Perucchi, A.; Baldassarre, L.; Postorino, P.; Lupi, S.; Ru, N.; Fisher, I.R.; Degiorgi, L.; /Zurich, ETH
2009-12-14
We investigate the pressure dependence of the optical properties of CeTe{sub 3}, which exhibits an incommensurate charge-density-wave (CDW) state already at 300 K. Our data are collected in the mid-infrared spectral range at room temperature and at pressures between 0 and 9 GPa. The energy for the single particle excitation across the CDW gap decreases upon increasing the applied pressure, similarly to the chemical pressure by rare-earth substitution. The broadening of the bands upon lattice compression removes the perfect nesting condition of the Fermi surface and therefore diminishes the impact of the CDW transition on the electronic properties of RTe{sub 3}.
Excitons in Organics Using Time-Dependent Density Functional Theory: PPV, Pentacene, and Picene.
Sharma, S; Dewhurst, J K; Shallcross, S; Madjarova, G K; Gross, E K U
2015-04-14
We apply the bootstrap kernel within time-dependent density functional theory to study the one-dimensional chain of polymer polyphenylenevinylene and molecular crystals of picene and pentacene. The absorption spectra of poly(p-phenylenevinylene) has a bound excitonic peak that is well-reproduced. Pentacene and picene, electronically similar materials, have remarkably different excitonic physics, and this difference is also well captured. We show that the inclusion of local-field effects dramatically changes the spectra of both picene and pentacene but not for poly(p-phenylenevinylene). PMID:26574381
Charge transfer in time-dependent density-functional theory via spin-symmetry breaking
Fuks, Johanna I.; Maitra, Neepa T.
2011-04-15
Long-range charge-transfer excitations pose a major challenge for time-dependent density-functional approximations. We show that spin-symmetry breaking offers a simple solution for molecules composed of open-shell fragments, yielding accurate excitations at large separations when the acceptor effectively contains one active electron. Unrestricted exact-exchange and self-interaction-corrected functionals are performed on one-dimensional models and on the real LiH molecule within the pseudopotential approximation to demonstrate our results.
Barabash, O.M.; Santella, M.; Barabash, R.I.; Ice, G.E.; Tischler, J.
2011-12-14
The indentation-induced elastic-plastic zone in an IN 740 Ni-based superalloy was studied by three-dimensional (3-D) x-ray microdiffraction and electron back scattering diffraction (EBSD). Large lattice reorientations and the formation of geometrically necessary dislocations are observed in the area with a radius of {approx}75 {mu}m. A residual compression zone is found close to the indent edge. An elastic-plastic transition is observed at {approx}20 {mu}m from the indent edge. Depth dependent dislocation densities are determined at different distances from the indent edge.
Sarri, G.; Kar, S.; Kourakis, I.; Borghesi, M.; Romagnani, L.; Bulanov, S. V.; Cecchetti, C. A.; Gizzi, L. A.; Galimberti, M.; Heathcote, R.; Jung, R.; Osterholz, J.; Willi, O.; Schiavi, A.
2011-08-15
The experimental evidence of the correlation between the initial electron density of the plasma and electromagnetic soliton excitation at the wake of an intense (10{sup 19} W/cm{sup 2}) and short (1 ps) laser pulse is presented. The spatial distribution of the solitons, together with their late time evolution into post-solitons, is found to be dependent upon the background plasma parameters, in agreement with published analytical and numerical findings. The measured temporal evolution and electrostatic field distribution of the structures are consistent with their late time evolution and the occurrence of multiple merging of neighboring post-solitons.
Density determination of nano-layers depending to the thickness by non-destructive method
Gacem, A.; Doghmane, A.; Hadjoub, Z.
2013-12-16
Non-destructive tests used to characterize and observe the state of the solids near the surface or at depth, without damaging them or damaging them. Density is frequently used to follow the variations of the physical structure of the samples, as well as in the calculation of quantity of material required to fill a given volume, and it is also used to determine the homogeneity of a sample. However, the measurement of the acoustic properties (density, elastic constants,â€¦) of a thin film whose thickness is smaller than several atomic layers is not easy to perform. For that reason, we expose in this work the effects of the thicknesses of thin films on the evolution of the density, where several samples are analyzed. The samples selected structures are thin films deposited on substrates, these coatings have thicknesses varying from a few atomic layers to ten or so micrometers and can change the properties of the substrate on which they are deposited. To do so, we considered a great number of layers (Cr, Al, SiO{sub 2}, ZnO, Cu, AlN, Si{sub 3}N{sub 4}, SiC) deposited on different substrates (Al{sub 2}O{sub 3}, Cu and Quartz). It is first shown that the density exhibits a dispersive behaviour. Such a behaviour is characterized by an initial increase (or decrease) followed by a saturated region. Further investigations of these dependences led to the determination of a semi-empirical universal relations, Ï=f(h/Î»{sub T}), for all the investigated layer/substrate combination. Such expression could be of great importance in the density prediction of even layers thicknesses.
NASA Astrophysics Data System (ADS)
Lipatov, A. V.; Zotov, N. P.
2014-11-01
We study the associated production of real (isolated) or virtual photons (with their subsequent leptonic decay) and hadronic jets in proton-proton collisions at the LHC using the kT-factorization approach of QCD. The consideration is based on the off-shell quark-gluon QCD Compton scattering subprocesses. In the case of virtual photon production, the contributions from Z boson exchange as well as ?*-Z interference with the full spin correlations are included. The transversemomentum-dependent (TMD) quark and gluon densities in a proton are determined from the Kimber-Martin-Ryskin prescription or Catani-Ciafoloni-Fiorani-Marchesini (CCFM) equation. In the latter, we restrict to the case where the gluon-to-quark splitting occurs at the last evolution step and calculate the sea quark density as a convolution of the CCFM-evolved gluon distribution and the TMD gluon-to-quark splitting function. Our numerical predictions are compared with the recent experimental data taken by the ATLAS Collaboration. We discuss the theoretical uncertainties of our calculations and argue that further studies are capable of constraining the TMD parton densities in the proton.
Evolution of flowering decisions in a stochastic, density-dependent environment
Metcalf, C. J. E.; Rose, K. E.; Childs, D. Z.; Sheppard, A. W.; Grubb, P. J.; Rees, M.
2008-01-01
Demography is central to both ecology and evolution, and characterizing the feedback between ecology and evolution is critical for understanding organisms' life histories and how these might evolve through time. Here, we show how, by combining a range of theoretical approaches with the statistical analysis of individually structured databases, accurate prediction of life history decisions is possible in natural density-regulated populations undergoing large fluctuations in demographic rates from year to year. Our predictions are remarkably accurate and statistically well defined. In addition, we show that the predicted trait values are evolutionarily and convergence stable and that protected polymorphisms are possible. PMID:18641119
Nalmefene: a new approach to the treatment of alcohol dependence
Paille, François; Martini, Hervé
2014-01-01
Reduction of alcohol consumption is not yet a widely accepted treatment objective for alcohol-dependent patients, as abstinence is often considered to be the only possible objective in this situation. However, various studies have demonstrated the value of proposing these two options to such patients. Firstly, reduction of alcohol consumption very significantly reduces the risk of alcohol-related damage, and also modifies the patient’s and the doctor’s perception of the disease, resulting in improved access to care and better patient adherence with the proposed treatment objective and consequently better clinical results. Recent studies have shown that some medicinal products can help patients reduce their alcohol consumption. One such product, nalmefene, has been granted European marketing authorization and is now being released onto the market in various countries. The ESENSE 1 and 2 studies in alcohol-dependent patients showed that, in combination with BRENDA, a psychosocial intervention focusing on reinforcement of motivation and treatment adherence, nalmefene significantly reduced the number of heavy drinking days and mean daily total alcohol consumption versus placebo. This reduction was more marked in the marketing authorization target population, ie, patients with a high or very high drinking risk level according to World Health Organization criteria. Another original feature of this molecule is that it can be used as needed if the patient perceives a risk of drinking, which is a more flexible approach and more likely to ensure the patient’s active involvement in the treatment of his/her disease. This molecule opens up interesting and original therapeutic prospects in the treatment of alcohol dependence. PMID:25187751
Inverse density dependence of parity rates in the onchocerciasis vector Simulium damnosum s.l.
Cheke, R A; Young, S; Garms, R
2016-03-01
A correlation between parity rates and an index of adult numbers of Simulium damnosum s.l. (Diptera: Simuliidae) indicates an association, but does not prove causality or show the direction of any causal relationship. The question of whether adult numbers affect parity rates or vice versa is reminiscent of the age-old query of which of the chicken and the egg came first. A method for resolving such issues based on analyses of pairs of time series was proposed by Granger in 1969. When Granger's method was applied to monthly numbers of adult female S. damnosum s.l. caught attempting to bite humans at Asubende, Ghana, and their parity rates, a significant relationship (P = 0.005) emerged, clearly showing that parity rates were dependent on adult numbers. Implications of this inverse density dependence and the results of analyses of other similar time series are presented and discussed. PMID:26477539
Field Dependence of the Spin Density Wave Transition Temperature in (TMTSF)_2PF_6
NASA Astrophysics Data System (ADS)
Leone, M. J.; Lee, I. J.; Hope, A. P.; Naughton, M. J.
1997-03-01
The magnetic field dependence of the Spin Density Wave transition in (TMTSF)_2PF6 has been studied at ambient pressure to 17 Tesla using cantilever magnetometry. Simultaneous resistance and torque magnetization measurements have been conducted on a single crystal (Hallelc^*+20^o). Above the spin flop field, we find both measurements yield a linear relationship between T_SDW and the applied field, with slope 0.036 K/T. This appears to be inconsistent with theoretical works by Montambaux(G. Montambaux, Phys. Rev. B 38), 4788 (1988), Bjelis and Maki(A. Bjelis and K. Maki, Phys. Rev. B 45), 12887 (1992), which predict a quadratic dependence at low field followed by saturation at high field. Investigations to higher fields will be reported. ^* Supported by NSF DMR-9258579
Ionic thermal effects on photo-electron emission within time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Gao, Cong-Zhang; Dinh, Phuong Mai; Reinhard, Paul-Gerhard; Suraud, Eric
2016-02-01
We study the impact of thermal fluctuations of cluster/molecule shape on photo-electron spectra (PES) and photo-electron angular distributions (PAD) using a detailed time-dependent simulation of the emission dynamics and thermal ionic motion. Basis of the description is time-dependent density-functional theory (TDDFT) coupled to molecular dynamics for ionic motion. Test cases are small Na clusters and the C3 molecule. For Na clusters, we find that PES signals are rather robust for one-photon processes while large smearing of the pattern are observed at lower frequencies in multi-photon processes. This effect can be related to the typical spectral response of the metal clusters. PAD are generally much more robust than PES. The C3 molecule produces a greater variety of thermal response. This happens because this molecule has eigenmodes with much different softness.
Rotochemical heating with a density-dependent superfluid energy gap in neutron stars
Gonzalez-Jimenez, Nicolas; Petrovich, Cristobal; Reisenegger, Andreas
2010-08-04
When a rotating neutron star loses angular momentum, the reduction of the centrifugal force makes it contract. This perturbs each fluid element, raising the local pressure and originating deviations from beta equilibrium, inducing reactions that release heat (rotochemical heating). This effect has previously been studied by Fernandez and Reisenegger for neutron stars of non-superfluid matter and by Petrovich and Reisenegger for superfluid matter, finding that the system in both cases reaches a quasi-steady state, corresponding to a partial equilibration between compression, due to the loss of angular momentum, and reactions that try to restore the equilibrium. However, Petrovich and Reisenegger assumes a constant value of the superfluid energy gap, whereas theoretical models predict density-dependent gap amplitudes, and therefore gaps that depend on the location in the star. In this work, we try to discriminate between several proposed gap models, comparing predicted surface temperatures to the value measured for the nearest millisecond pulsar, J0437-4715.
Time-dependent approach to electron pumping in open quantum systems
NASA Astrophysics Data System (ADS)
Stefanucci, G.; Kurth, S.; Rubio, A.; Gross, E. K. U.
2008-02-01
We use a recently proposed time-dependent approach to investigate the motion of electrons in quantum pump device configurations. The occupied one-particle states are propagated in real time and employed to calculate the local electron density and current. The approach can also be embedded in the framework of time-dependent density functional theory to include electron-electron interactions. An advantage of the present computational scheme is that the same computational effort is required to simulate monochromatic, polychromatic, and nonperiodic drivings. Furthermore, initial-state dependence and history effects are naturally accounted for. We present results for one-dimensional devices exposed to a traveling potential wave. (i) We show that for pumping across a single potential barrier, electrons are transported in pockets and the transport mechanism resembles pumping of water with the Archimedean screw; (ii) we propose a simple model to study pumping through semiconductor nanostructures and we address the phenomenon of the current flowing in the opposite direction to the field propagation; (iii) we present the first numerical evidence of long-lived superimposed oscillations as induced by the presence of bound states and discuss the dependence of their lifetime on the frequency and amplitude of the driving field. By combining Floquet theory with nonequilibrium Green’s functions, we also obtain a general expression for the pumped current in terms of inelastic transmission probabilities. This latter result is used for benchmarking our propagation scheme in the long-time limit. Finally, we discuss the limitations of Floquet-based algorithms and suggest our approach as a possible way to go beyond them.
A DENSITY DEPENDENCE FOR PROTOSTELLAR LUMINOSITY IN CLASS I SOURCES: COLLABORATIVE ACCRETION
Elmegreen, Bruce G.; Hurst, Rachel; Koenig, Xavier
2014-02-10
Class I protostars in three high-mass star-forming regions are found to have correlations among the local projected density of other Class I protostars, the summed flux from these other protostars, and the protostellar luminosity in the WISE 22 Î¼m band. Brighter Class I sources form in higher-density and higher-flux regions, while low luminosity sources form anywhere. These correlations depend slightly on the number of neighbors considered (from 2 to 20) and could include a size-of-sample effect from the initial mass function (i.e., larger numbers include rarer and more massive stars). Luminosities seem to vary by neighborhood with nearby protostars having values proportional to each other and higher density regions having higher values. If Class I luminosity is partially related to the accretion rate, then this luminosity correlation is consistent with the competitive accretion model, although it is more collaborative than competitive. The correlation is also consistent with primordial mass segregation and could explain why the stellar initial mass function resembles the dense core mass function even when cores form multiple stars.
Spin- and Parity-Dependent Level Densities in Exotic Calcium Isotopes?
NASA Astrophysics Data System (ADS)
Usman, I. T.; Carter, J.; Sideras-Haddad, E.; Jingo, M.; Kureba, C. O.; Donaldson, L.; Latif, M.; Neveling, R.; Smit, F. D.; Swartz, C.; Nemulodi, F.; von Neumann-Cosel, P.; Richter, A.; Fearick, R. W.; Fujita, H.; Fulita, Y.; Tamii, A.
2015-11-01
Level densities of 2+ and 1- states in 40Ca have been extracted from high energy-resolution (p,p') experiments performed using the K600 magnetic spectrometer at iThemba LABS, South Africa. The success of the method depends on the accurate determination of various background components underneath the giant resonance. It was found that using the nearly model-independent method of Discrete Wavelet Transform (DWT) background determination using bi-orthogonal wavelets of high order of vanishing moments proved sufficient for the extraction of level density in the excitation energy region of the Isoscalar Giant Quadrupole Resonance (ISGQR) and Isovector Giant Dipole Resonance (IVGDR). Comparison of the experimentally extracted 2+ and 1- level densities with Back-Shifted Fermi Gas Model (BSFG), Hartree-Fock Bogoliubov (HFB) and Hartree-Fock-Bardeen-Cooper Schriffer (HF-BCS) theoretical model predictions were made. Future interests in the use of radioactive-ion beams of different intensities will provide opportunities in elucidating this important property experimentally for more exotic calcium isotopes.
Young-Wolff, Kelly C.; Henriksen, Lisa; Delucchi, Kevin
2014-01-01
Objectives. We examined the density and proximity of tobacco retailers and associations with smoking behavior and mental health in a diverse sample of 1061 smokers with serious mental illness (SMI) residing in the San Francisco Bay Area of California. Methods. Participantsâ€™ addresses were geocoded and linked with retailer licensing data to determine the distance between participantsâ€™ residence and the nearest retailer (proximity) and the number of retailers within 500-meter and 1-kilometer service areas (density). Results. More than half of the sample lived within 250 meters of a tobacco retailer. A median of 3 retailers were within 500 meters of participantsâ€™ residences, and a median of 12 were within 1 kilometer. Among smokers with SMI, tobacco retailer densities were 2-fold greater than for the general population and were associated with poorer mental health, greater nicotine dependence, and lower self-efficacy for quitting. Conclusions. Our findings provide further evidence of the tobacco retail environment as a potential vector contributing to tobacco-related disparities among individuals with SMI and suggest that this group may benefit from progressive environmental protections that restrict tobacco retail licenses and reduce aggressive point-of-sale marketing. PMID:24922145
Density-dependent predation influences the evolution and behavior of masquerading prey
Skelhorn, John; Rowland, Hannah M.; Delf, Jon; Speed, Michael P.; Ruxton, Graeme D.
2011-01-01
Predation is a fundamental process in the interaction between species, and exerts strong selection pressure. Hence, anti-predatory traits have been intensively studied. Although it has long been speculated that individuals of some species gain protection from predators by sometimes almost-uncanny resemblances to uninteresting objects in the local environment (such as twigs or stones), demonstration of antipredatory benefits to such â€œmasqueradeâ€ have only very recently been demonstrated, and the fundamental workings of this defensive strategy remain unclear. Here we use laboratory experiments with avian predators and twig-mimicking caterpillars as masqueraders to investigate (i) the evolutionary dynamics of masquerade; and (ii) the behavioral adaptations associated with masquerade. We show that the benefit of masquerade declines as the local density of masqueraders relative to their models (twigs, in our system) increases. This occurs through two separate mechanisms: increasing model density both decreased predatorsâ€™ motivation to search for masqueraders, and made masqueraders more difficult to detect. We further demonstrated that masquerading organisms have evolved complex microhabitat selection strategies that allow them to best exploit the density-dependent properties of masquerade. Our results strongly suggest the existence of opportunity costs associated with masquerade. Careful evaluation of such costs will be vital to the development of a fuller understanding of both the distribution of masquerade across taxa and ecosystems, and the evolution of the life history strategies of masquerading prey. PMID:21464318
NASA Astrophysics Data System (ADS)
Emmert, J. T.
2015-04-01
We examine 1967-2005 thermospheric mass density trends (as well as 1967-2013 trends) derived from satellite orbit data, as a function of altitude, solar flux, and geomagnetic activity. At 400 km altitude, the estimated 1967-2005 trend is -2.0 ± 0.5% per decade. The estimated trends become increasingly negative with increasing height between 250 and 575 km, suggesting an exospheric temperature trend of -1 to -2 K per decade, which is much smaller than temperature trends that have been inferred from ground-based incoherent scatter radar measurements. The orbit-derived trend height profiles are in good agreement with model simulations of the enhanced cooling that results from increasing concentration of CO2 in the mesosphere and lower thermosphere. In contrast to earlier results, the solar flux dependence of the estimated trends is weak, relative to the trend uncertainty. There is some indication that the trends may be stronger during very low geomagnetic activity conditions. Estimation of the solar flux and geomagnetic activity dependence of the trends is complicated by monotonic decreases in these drivers over the past four solar minima together with the CO2 increase, all of which drive interminima decreases in density.
Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities
Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz
2005-03-01
Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP.
Oliveira, Micael J. T.; Nogueira, Fernando; Marques, Miguel A. L.; Rubio, Angel
2009-12-07
Upon ionization, rare-gas (like Ar and Xe) clusters shift their absorption spectrum from the ultraviolet to the visible. This happens as bonding becomes much stronger due to the removal of an electron from a strongly antibonding orbital. In this article, we study the absorption spectrum of small cationic xenon clusters (Xe{sub n}{sup +}, with n=3,...,35) by means of time-dependent density functional theory. These calculations include relativistic effects through the use of relativistic j-dependent pseudopotentials in a two-spinor formulation of the Kohn-Sham equations. The peak positions in our calculated spectra are in fairly good agreement with experiment and confirm that absorption is mainly due to a charged linear core composed of 3, 4, or 5 Xe atoms where the positive charge is localized. However, we find large deviations concerning the oscillator strengths, which can be partially explained by the unsatisfactory treatment of exchange in common density functionals. Furthermore, we find that adequate ground-state geometries are necessary for the correct prediction of the qualitative features of the spectra.
Thermodynamics predicts density-dependent energy use in organisms and ecological communities
NASA Astrophysics Data System (ADS)
Yen, Jian D. L.; Paganin, David M.; Thomson, James R.; Mac Nally, Ralph
2015-04-01
Linking our knowledge of organisms to our knowledge of ecological communities and ecosystems is a key challenge for ecology. Individual size distributions (ISDs) link the size of individual organisms to the structure of ecological communities, so that studying ISDs might provide insight into how organism functioning affects ecosystems. Similarly shaped ISDs among ecosystems, coupled with allometric links between organism size and resource use, suggest the possibility of emergent resource-use patterns in ecological communities. We drew on thermodynamics to develop a maximization principle that predicted both organism and community energy use. These predictions highlighted the importance of density-dependent metabolic rates and were able to explain nonlinear relationships between community energy use and community biomass. We analyzed data on fish community energy use and biomass and found evidence of nonlinear scaling, which was predicted by the thermodynamic principle developed here and is not explained by other theories of ISDs. Detailed measurements of organism energy use will clarify the role of density dependence in driving metabolic rates and will further test our derived thermodynamic principle. Importantly, our study highlights the potential for fundamental links between ecology and thermodynamics.
Grøtan, Vidar; Saether, Bernt-Erik; Lillegård, Magnar; Solberg, Erling J; Engen, Steinar
2009-10-01
The effects of variation in climate on population dynamics are likely to differ within the distributional range of a species, yet the consequences of such regional variation on demography and population dynamics are rarely considered. Here we examine how density dependence and different climate variables affect spatio-temporal variation in recruitment rates of Norwegian moose using data collected over a large geographical area during the hunting season. After accounting for observation error by a Bayesian Markov chain Monte Carlo technique, temporal variation in recruitment rates was relatively independent of fluctuations in local population size. In fact, a positive relationship was as common as a density-dependent decrease in fecundity rates. In general, high recruitment rates were found during autumn 1 year after years with a warm February, and after a warm May or cold June in year t - 1 or in year t. Large regional variation was also found in the effects of some of the weather variables, especially during spring. These patterns demonstrate both direct and delayed effects of weather on the recruitment of moose that possibly operate through an effect of body mass on the proportion of the females that sexually mature as 1.5 or 2.5 years old. PMID:19657678
Li, Xiao-Dong; Park, Changbom; Forero-Romero, J. E.; Kim, Juhan E-mail: cbp@kias.re.kr E-mail: kjhan@kias.re.kr
2014-12-01
We propose a method based on the redshift dependence of the Alcock-Paczynski (AP) test to measure the expansion history of the universe. It uses the isotropy of the galaxy density gradient field to constrain cosmological parameters. If the density parameter Î© {sub m} or the dark energy equation of state w are incorrectly chosen, the gradient field appears to be anisotropic with the degree of anisotropy varying with redshift. We use this effect to constrain the cosmological parameters governing the expansion history of the universe. Although redshift-space distortions (RSD) induced by galaxy peculiar velocities also produce anisotropies in the gradient field, these effects are close to uniform in magnitude over a large range of redshift. This makes the redshift variation of the gradient field anisotropy relatively insensitive to the RSD. By testing the method on mock surveys drawn from the Horizon Run 3 cosmological N-body simulations, we demonstrate that the cosmological parameters can be estimated without bias. Our method is complementary to the baryon acoustic oscillation or topology methods as it depends on D{sub AH} , the product of the angular diameter distance and the Hubble parameter.
Warming and nitrogen affect size structuring and density dependence in a host–parasitoid food web
de Sassi, Claudio; Staniczenko, Phillip P. A.; Tylianakis, Jason M.
2012-01-01
Body size is a major factor constraining the trophic structure and functioning of ecological communities. Food webs are known to respond to changes in basal resource abundance, and climate change can initiate compounding bottom-up effects on food-web structure through altered resource availability and quality. However, the effects of climate and co-occurring global changes, such as nitrogen deposition, on the density and size relationships between resources and consumers are unknown, particularly in host–parasitoid food webs, where size structuring is less apparent. We use a Bayesian modelling approach to explore the role of consumer and resource density and body size on host–parasitoid food webs assembled from a field experiment with factorial warming and nitrogen treatments. We show that the treatments increased resource (host) availability and quality (size), leading to measureable changes in parasitoid feeding behaviour. Parasitoids interacted less evenly within their host range and increasingly focused on abundant and high-quality (i.e. larger) hosts. In summary, we present evidence that climate-mediated bottom-up effects can significantly alter food-web structure through both density- and trait-mediated effects. PMID:23007092
Warming and nitrogen affect size structuring and density dependence in a host-parasitoid food web.
de Sassi, Claudio; Staniczenko, Phillip P A; Tylianakis, Jason M
2012-11-01
Body size is a major factor constraining the trophic structure and functioning of ecological communities. Food webs are known to respond to changes in basal resource abundance, and climate change can initiate compounding bottom-up effects on food-web structure through altered resource availability and quality. However, the effects of climate and co-occurring global changes, such as nitrogen deposition, on the density and size relationships between resources and consumers are unknown, particularly in host-parasitoid food webs, where size structuring is less apparent. We use a Bayesian modelling approach to explore the role of consumer and resource density and body size on host-parasitoid food webs assembled from a field experiment with factorial warming and nitrogen treatments. We show that the treatments increased resource (host) availability and quality (size), leading to measureable changes in parasitoid feeding behaviour. Parasitoids interacted less evenly within their host range and increasingly focused on abundant and high-quality (i.e. larger) hosts. In summary, we present evidence that climate-mediated bottom-up effects can significantly alter food-web structure through both density- and trait-mediated effects. PMID:23007092
Herbivore-Specific, Density-Dependent Induction of Plant Volatiles: Honest or “Cry Wolf” Signals?
Shiojiri, Kaori; Ozawa, Rika; Kugimiya, Soichi; Uefune, Masayoshi; van Wijk, Michiel; Sabelis, Maurice W.; Takabayashi, Junji
2010-01-01
Plants release volatile chemicals upon attack by herbivorous arthropods. They do so commonly in a dose-dependent manner: the more herbivores, the more volatiles released. The volatiles attract predatory arthropods and the amount determines the probability of predator response. We show that seedlings of a cabbage variety (Brassica oleracea var. capitata, cv Shikidori) also show such a response to the density of cabbage white (Pieris rapae) larvae and attract more (naive) parasitoids (Cotesia glomerata) when there are more herbivores on the plant. However, when attacked by diamondback moth (Plutella xylostella) larvae, seedlings of the same variety (cv Shikidori) release volatiles, the total amount of which is high and constant and thus independent of caterpillar density, and naive parasitoids (Cotesia vestalis) of diamondback moth larvae fail to discriminate herbivore-rich from herbivore-poor plants. In contrast, seedlings of another cabbage variety of B. oleracea (var. acephala: kale) respond in a dose-dependent manner to the density of diamondback moth larvae and attract more parasitoids when there are more herbivores. Assuming these responses of the cabbage cultivars reflect behaviour of at least some genotypes of wild plants, we provide arguments why the behaviour of kale (B. oleracea var acephala) is best interpreted as an honest signaling strategy and that of cabbage cv Shikidori (B. oleracea var capitata) as a “cry wolf” signaling strategy, implying a conflict of interest between the plant and the enemies of its herbivores: the plant profits from being visited by the herbivore's enemies, but the latter would be better off by visiting other plants with more herbivores. If so, evolutionary theory on alarm signaling predicts consequences of major interest to students of plant protection, tritrophic systems and communication alike. PMID:20808961
Time-dependent density functional theory of magneto-optical response of periodic insulators
NASA Astrophysics Data System (ADS)
Rubio, Angel; Tokatly, Ilya V.; Lebedeva, Irina V.
2014-03-01
Though the linear response theory has been successfully used for molecular systems for a long time, the extension of this theory to solids is not straightforward since the position operator is ill defined in extended periodic systems. The theoretical description of homogeneous static magnetic field in periodic systems is particularly challenging as the corresponding vector potential breaks the translational invariance of the Hamiltonian. We present a unified approach to calculation of all-order response to arbitrary electromagnetic fields both for periodic and molecular systems within the formalism of non-equilibrium Green functions. The approach is applied to derive the expression for the magneto-optical response of insulating solids in the approximation of non-interacting electrons. The formula obtained is completely identical to the expression for molecular systems if the proper position and orbital magnetization operators are chosen. The terms corresponding to changes in the optical response due to the orbital magnetization of Bloch states and due to the modified density of Bloch states in the magnetic field are identified. A computational scheme based on the density matrix-perturbation theory is developed for practical calculations of the magneto-optical response. The financial support from the Marie Curie Fellowship PIIF-GA-2012-326435 (RespSpatDisp) is gratefully acknowledged.
Dixon, David A.); Matsuzawa, Nobuyuki N.; Ishitani, Ahihiko; Uda, Tsuyoshi
2001-05-30
Time-dependent density functional theory (TD-DFT) calculations of the photoabsorption of molecules in the vacuum region have been performed in order to aid in the design of transparent materials for use as photoresists for F2 lithography (157 nm). The method including an empirical equation for correcting the calculated transition energy is described. We have used the TD-DFT approach to predict the photoabsorption of substituted benzenes, and cycloalkane including norbornane. The calculations show that norbornane is the best cycloalkane on which to start substitution studies. We report results on the mono-, di-, and tera-fluorinated derivatives. The results show that tetrafluoro-norbornanes have the lowest absorption in the 157 nm range for the molecules that we studied.
Bouet, Guenaelle; Bouleftour, Wafa; Juignet, Laura; Linossier, Marie-Thérèse; Thomas, Mireille; Vanden-Bossche, Arnaud; Aubin, Jane E; Vico, Laurence; Marchat, David; Malaval, Luc
2015-01-01
Bone sialoprotein (BSP) belongs to the "small integrin-binding ligand N-linked glycoprotein" (SIBLING) family, whose members interact with bone cells and bone mineral. BSP is strongly expressed in bone and we previously showed that BSP knockout (BSP-/-) mice have a higher bone mass than wild type (BSP+/+) littermates, with lower bone remodelling. Because baseline bone formation activity is constitutively lower in BSP-/- mice, we studied the impact of the absence of BSP on in vitro osteogenesis in mouse calvaria cell (MCC) cultures. MCC BSP-/- cultures exhibit fewer fibroblast (CFU-F), preosteoblast (CFU-ALP) and osteoblast colonies (bone nodules) than wild type, indicative of a lower number of osteoprogenitors. No mineralized colonies were observed in BSP-/- cultures, along with little/no expression of either osteogenic markers or SIBLING proteins MEPE or DMP1. Osteopontin (OPN) is the only SIBLING expressed in standard density BSP-/- culture, at higher levels than in wild type in early culture times. At higher plating density, the effects of the absence of BSP were partly rescued, with resumed expression of osteoblast markers and cognate SIBLING proteins, and mineralization of the mutant cultures. OPN expression and amount are further increased in high density BSP-/- cultures, while PHEX and CatB expression are differentiatlly regulated in a manner that may favor mineralization. Altogether, we found that BSP regulates mouse calvaria osteoblast cell clonogenicity, differentiation and activity in vitro in a cell density dependent manner, consistent with the effective skeletogenesis but the low levels of bone formation observed in vivo. The BSP knockout bone microenvironment may alter the proliferation/cell fate of early osteoprogenitors. PMID:25710686
Blocking of human immunodeficiency virus infection depends on cell density and viral stock age.
Layne, S P; Merges, M J; Spouge, J L; Dembo, M; Nara, P L
1991-01-01
Quantitative infectivity assays were used to study how the blocking activity of soluble CD4 (sCD4) is affected by sCD4 concentration, target cell density, and viral stock age. During incubation with 20 nM sCD4, human immunodeficiency virus type 1 (HIV-1) stocks underwent irreversible inactivation. In contrast, inactivation with 2 nM sCD4 was almost entirely reversible. At lower sCD4 concentrations (less than or equal to 2 nM) and target cell densities of 6.25 x 10(4) ml-1, sCD4 blocking activity for HIV-1 gave a gp120-sCD4 association constant (Kassoc) of 1.7 x 10(9) M-1, which agrees with chemical measurements. At the higher density of 1.6 x 10(7) cells ml-1, however, the blocking activity was 20-fold less. During incubation of HIV-1 stock optimized for infectivity by rapid harvest, sCD4 blocking activity increased 20-fold during a 3-h window. These results show that competitive blocking activity depends strongly on target cell density and virion age. Thus, unappreciated variations in HIV stocks and assay conditions may hinder comparisons of blockers from laboratory to laboratory, and the age of HIV challenge stocks may influence studies of drug and vaccine efficacy. The results also suggest that blocking of viral particles in lymphoid compartments will require very high competitive blocker concentrations, which may explain the refractory outcomes from sCD4-based drug trials in humans. PMID:1674549
Bouet, Guenaelle; Bouleftour, Wafa; Juignet, Laura; Linossier, Marie-Thérèse; Thomas, Mireille; Vanden-Bossche, Arnaud; Aubin, Jane E.; Vico, Laurence; Marchat, David; Malaval, Luc
2015-01-01
Bone sialoprotein (BSP) belongs to the "small integrin-binding ligand N-linked glycoprotein" (SIBLING) family, whose members interact with bone cells and bone mineral. BSP is strongly expressed in bone and we previously showed that BSP knockout (BSP-/-) mice have a higher bone mass than wild type (BSP+/+) littermates, with lower bone remodelling. Because baseline bone formation activity is constitutively lower in BSP-/- mice, we studied the impact of the absence of BSP on in vitro osteogenesis in mouse calvaria cell (MCC) cultures. MCC BSP-/- cultures exhibit fewer fibroblast (CFU-F), preosteoblast (CFU-ALP) and osteoblast colonies (bone nodules) than wild type, indicative of a lower number of osteoprogenitors. No mineralized colonies were observed in BSP-/- cultures, along with little/no expression of either osteogenic markers or SIBLING proteins MEPE or DMP1. Osteopontin (OPN) is the only SIBLING expressed in standard density BSP-/- culture, at higher levels than in wild type in early culture times. At higher plating density, the effects of the absence of BSP were partly rescued, with resumed expression of osteoblast markers and cognate SIBLING proteins, and mineralization of the mutant cultures. OPN expression and amount are further increased in high density BSP-/- cultures, while PHEX and CatB expression are differentiatlly regulated in a manner that may favor mineralization. Altogether, we found that BSP regulates mouse calvaria osteoblast cell clonogenicity, differentiation and activity in vitro in a cell density dependent manner, consistent with the effective skeletogenesis but the low levels of bone formation observed in vivo. The BSP knockout bone microenvironment may alter the proliferation/cell fate of early osteoprogenitors. PMID:25710686
Hazlerigg, Charles R. E.; Lorenzen, Kai; Thorbek, Pernille; Wheeler, James R.; Tyler, Charles R.
2012-01-01
Population regulation is fundamental to the long-term persistence of populations and their responses to harvesting, habitat modification, and exposure to toxic chemicals. In fish and other organisms with complex life histories, regulation may involve density dependence in different life-stages and vital rates. We studied density dependence in body growth and mortality through the life-cycle of laboratory populations of zebrafish Danio rerio. When feed input was held constant at population-level (leading to resource limitation), body growth was strongly density-dependent in the late juvenile and adult phases of the life-cycle. Density dependence in mortality was strong during the early juvenile phase but declined thereafter and virtually ceased prior to maturation. Provision of feed in proportion to individual requirements (easing resource limitation) removed density dependence in growth and substantially reduced density dependence in mortality, thus indicating that â€˜bottom-upâ€™ effects act on growth as well as mortality, but most strongly on growth. Both growth and mortality played an important role in population regulation, with density-dependent growth having the greater impact on population biomass while mortality had the greatest impact on numbers. We demonstrate a clear ontogenic pattern of change in density-dependent processes within populations of a very small (maximum length 5 mm) fish, maintained in constant homogeneous laboratory conditions. The patterns are consistent with those distilled from studies on wild fish populations, indicating the presence of broad ontogenic patterns in density-dependent processes that are invariant to maximum body size and hold in homogeneous laboratory, as well as complex natural environments. PMID:22655056
Cui, Shenghui; Meng, Jianghong; Bhagwat, Arvind A.
2001-01-01
The cell density-dependent acid sensitivity phenotypes of Escherichia coli strains K-12 and O157:H7 were examined with reference to three possible mechanisms of acid resistance. There was no evidence of any diffusible substance released from dead cells which could influence the cell density-dependent acid survival phenotype. Instead, cell density-dependent acid survival phenotype was associated with induction of glutamate- and arginine-decarboxylase acid survival pathways and concomitant availability of glutamate and arginine during acid challenge. PMID:11571202
Li Qingfeng; Li Zhuxia; Zhao Euguang; Gupta, Raj K.
2005-05-01
Based on the UrQMD (ultrarelativistic quantum molecular dynamics) model, we have investigated the influence of the symmetry potential on the negatively and positively charged {pi} and {sigma} hyperon production ratios in heavy ion collisions at the SIS (SchwerIonen Synchrotron) energies. We find that, in addition to {pi}{sup -}/{pi}{sup +} ratio, the {sigma}{sup -}/{sigma}{sup +} ratio can be taken as a sensitive probe for investigating the density dependence of the symmetry potential of nuclear matter at high densities (1-4 times normal baryon density). This sensitivity of the symmetry potential to both the {pi}{sup -}/{pi}{sup +} and {sigma}{sup -}/{sigma}{sup +} ratios is found to depend strongly on the incident beam energy. Furthermore, the {sigma}{sup -}/{sigma}{sup +} ratio is shown to carry the information about the isospin-dependent part of the {sigma} hyperon single-particle potential.
Constraining depth-dependent anisotropy: A new approach
NASA Astrophysics Data System (ADS)
Ishii, M.; Okeler, A.
2014-12-01
Splitting of shear waves is commonly used to infer anisotropy of the Earth's interior. However, most data, such as SKS splitting, provide depth-integrated measure of anisotropy along the ray path, and it is difficult to separate contributions from different layers within the Earth. There have been efforts to focus on specific depth range by analyzing differences in splitting between two ray paths, but these studies only report observed differences or rely upon forward modeling with limited parameter-space search. We have developed a new approach to examine the P-to-S converted phases that allows one to construct depth-dependent multi-layer anisotropy models through combination of inversion and grid search. In addition to the conventional fast splitting direction and delay time, the technique allows one to investigate the tilt of the symmetry axis and dip of the discontinuity associated with the P-to-S conversion. Furthermore, the formulation is such that it naturally extends to include and examine multiple layers with different anisotropic properties. With these flexibilities, we can address anisotropic contributions from different layers in two separate procedures. The first scheme takes advantage of data with similar ray paths (e.g., SKS and SKKS waves recorded at the same station). The rays sample different structure when their ray paths differ (e.g., near the core-mantle boundary), but they sample the same structure when the paths are similar (e.g., in the upper part of the mantle and crust). Using our new approach, we can set up the problem as a two-layer anisotropy model where the layer with ray paths sampling different regions (e.g., lowermost mantle) is allowed to vary laterally. The second type of problem that can be addressed by the new approach is layer-by-layer investigation of anisotropy from top to bottom. This procedure combines the new method with receiver function analysis to obtain anisotropic properties of each layer using P-to-S converted waves from different discontinuities such as the Moho, 410-km and 660-km discontinuities. The application of the methods to real data shows significant lateral variations in anisotropy, both in deep Earth and near the surface.
NASA Astrophysics Data System (ADS)
Inakura, Tsunenori
2014-09-01
Equation of state (EOS) is again shot into the limelight by discovery of the two-solar-mass neutron star. That heavy neutron star eliminates inadequate EOSs which can not support two-solar-mass neutron stars. Now there are several attempts to constrain the neutron matter EOS. In nuclear physics, it is expected to clarify density-dependence of the nuclear symmetry energy, L. We focus our attentions to dipole polarizability of unstable nuclei which has neutron skin. Since the neutron skin is approximately neutron matter, we believe that dynamics of unstable nuclei is affected by the neutron skin and we can extract the properties of neutron matter from it. Although some theoretical calculations using the random-phase approximation demonstrate a strong correlation between L and the dipole polarizability, almost all calculations are performed only for 3 nuclei, 68Ni, 132Sn, and 208Pb with a single interaction. There remains uncertainties on interaction and nuclide dependence. We performed a systematic calculation of the E 1 modes with several interactions. We show that the correlation between L and the dipole polarizability has somewhat depends on interactions and nuclide and that 54Ca, 140Sn are more suitable for extracting constraint on L from the experiments.
Mixed convection and density-dependent seawater circulation in coastal aquifers
NASA Astrophysics Data System (ADS)
Smith, Anthony J.
2004-08-01
Density-dependent circulation of seawater in coastal aquifers results in submarine groundwater discharge (SGD) across the seabed that is a mixture of terrestrial groundwater and former marine water. In this study, the controls of the relative amount of seawater to freshwater in SGD were investigated numerically using the FEFLOW and SUTRA codes. It was found that the key controls could be expressed in the form of a single nondimensional recirculation number that incorporates the combined effects of free convection, forced convection, and hydrodynamic dispersion on convective overturn within the coastal salt wedge. Anisotropy effects were incorporated into the recirculation number with limited success based on the principle of equivalent isotropic hydraulic conductivity. The type of boundary condition employed along the seabed was shown to be important. Convective overturn was substantially increased if backward dispersion of salt into the aquifer from along the outflowing portion of the seabed boundary was prevented. Overall, the results demonstrated a strong dependence of convective overturn on the aquifer dispersivities, suggesting that results from numerical simulations are problematic to apply to real aquifer systems that typically exhibit uncertain, scale-dependent dispersion properties.
[A broad educational approach to insulin-dependent diabetics].
de Poret, D; Pouliquen, A; Dejours, C; Assan, R
1985-02-01
Self monitoring of diabetes requires technical knowledge and suitable diabetes oriented behaviour; the latter arises from the patient's psycho-affective functioning, maturity and self sufficiency. A group of 9 insulin dependent ambulatory, adult, diabetics met 15 times over 5 months. The somatic and psycho-affective aspects of the disease were approached by an original methodology. Group animation was focussed on the participants themselves. Dynamic mobilisation of the persons was sought by listening to their explicit and implicit requests, by acting out (case studies and role-playing), by restatement and questioning. Diabetes oriented and psycho-affective behaviours were assessed on the basis of questionnaires and statements. At the end of the study, the psycho-affective attitude of the participants towards their illness was modified. The aggressiveness, mockery and rejection of diabetes and diabetics, initially noted, were progressively replaced by self-awareness and acceptance. As a result, better adjustment of technical behaviour responses was noted. Without precluding any psychodynamic explanation (reunification of the person), this study suggests that the participant's reactions towards their own image can be improved with consequential educational benefit. PMID:3979647
Bruggeman, Jason E; Swem, Ted; Andersen, David E; Kennedy, Patricia L; Nigro, Debora
2015-10-01
Intrinsic and extrinsic factors affect vital rates and population-level processes, and understanding these factors is paramount to devising successful management plans for wildlife species. For example, birds time migration in response, in part, to local and broadscale climate fluctuations to initiate breeding upon arrival to nesting territories, and prolonged inclement weather early in the breeding season can inhibit egg-laying and reduce productivity. Also, density-dependent regulation occurs in raptor populations, as territory size is related to resource availability. Arctic Peregrine Falcons (Falco peregrinus tundrius; hereafter Arctic peregrine) have a limited and northern breeding distribution, including the Colville River Special Area (CRSA) in the National Petroleum Reserve-Alaska, USA. We quantified influences of climate, topography, nest productivity, prey habitat, density dependence, and interspecific competition affecting Arctic peregrines in the CRSA by applying the Dail-Madsen model to estimate abundance and vital rates of adults on nesting cliffs from 1981 through 2002. Arctic peregrine abundance increased throughout the 1980s, which spanned the population's recovery from DDT-induced reproductive failure, until exhibiting a stationary trend in the 1990s. Apparent survival rate (i.e., emigration; death) was negatively correlated with the number of adult Arctic peregrines on the cliff the previous year, suggesting effects of density-dependent population regulation. Apparent survival and arrival rates (i.e., immigration; recruitment) were higher during years with earlier snowmelt and milder winters, and apparent survival was positively correlated with nesting season maximum daily temperature. Arrival rate was positively correlated with average Arctic peregrine productivity along a cliff segment from the previous year and initial abundance was positively correlated with cliff height. Higher cliffs with documented higher productivity (presumably indicative of higher-quality habitat), are a priority for continued protection from potential nearby development and disturbance to minimize population-level impacts. Climate change. may affect Arctic peregrines in multiple ways, including through access to more snow-free nest sites and a lengthened breeding season that may increase likelihood of nest success. Our work provides insight into factors affecting a population during and after recovery, and demonstrates how the Dail-Madsen model can be used for any unmarked population with multiple years of abundance data collected through repeated surveys. PMID:26591458
Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K
2014-01-01
Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong. PMID:25077023
Impact of density-dependent migration flows on epidemic outbreaks in heterogeneous metapopulations
NASA Astrophysics Data System (ADS)
Ripoll, J.; Avinyó, A.; Pellicer, M.; Saldaña, J.
2015-08-01
We investigate the role of migration patterns on the spread of epidemics in complex networks. We enhance the SIS-diffusion model on metapopulations to a nonlinear diffusion. Specifically, individuals move randomly over the network but at a rate depending on the population of the departure patch. In the absence of epidemics, the migration-driven equilibrium is described by quantifying the total number of individuals living in heavily or lightly populated areas. Our analytical approach reveals that strengthening the migration from populous areas contains the infection at the early stage of the epidemic. Moreover, depending on the exponent of the nonlinear diffusion rate, epidemic outbreaks do not always occur in the most populated areas as one might expect.
Impact of density-dependent migration flows on epidemic outbreaks in heterogeneous metapopulations.
Ripoll, J; Avinyó, A; Pellicer, M; Saldaña, J
2015-08-01
We investigate the role of migration patterns on the spread of epidemics in complex networks. We enhance the SIS-diffusion model on metapopulations to a nonlinear diffusion. Specifically, individuals move randomly over the network but at a rate depending on the population of the departure patch. In the absence of epidemics, the migration-driven equilibrium is described by quantifying the total number of individuals living in heavily or lightly populated areas. Our analytical approach reveals that strengthening the migration from populous areas contains the infection at the early stage of the epidemic. Moreover, depending on the exponent of the nonlinear diffusion rate, epidemic outbreaks do not always occur in the most populated areas as one might expect. PMID:26382456
Debris spatial density dependence on control volume resolution in the geosynchronous environment
NASA Astrophysics Data System (ADS)
Lewis, H. G.; Swinerd, G. G.; Martin, C. E.; Smith, D. A. J.
The debris environment of the Earth can be characterised using spatial density within the cells, or bins, of a spherical control volume, which has dimensions of geocentric radius (altitude), declination and right ascension. The characterisation of the debris environment in this way allows model predictions and measurement data from the USSTRATCOM catalogue, radar and returned surfaces to be compared. In addition, the volume-centred approach enables semi-deterministic models to compute debris fluxes relative to given target spacecraft orbits, provided the volume cells are of sufficiently high resolution. In this way semi-deterministic models employ the spatial density representation of the debris environment to predict future collision events and the future environment. The determination of debris spatial density for discrete sectors of near-Earth space is an integral part of the semi-deterministic models, IDES (Integrated Debris Evolution Suite), LEGEND (LEO-to-GEO Environment Debris model) and DAMAGE (Debris Analysis and Monitoring Architecture for the Geosynchronous Environment). Comparative model studies for the Inter-Agency Space Debris Coordination Committee (IADC) utilise an agreed baseline incorporating the sizes of control volume cells but the sensitivity to the choice of these sizes has not been previously explored due to the computational expense involved. The results of two such sensitivity studies performed using DAMAGE are presented in this paper. DAMAGE characterized the current debris environment by simulating the debris source (launch and fragmentations only) and sink processes for objects larger than 10 cm from the beginning of the space age to May 2001. The simulated environment in the altitude range 35,000 km to 36,800 km was found to be generally consistent with the equivalent historical evolution performed using IDES and the two-line element (TLE) catalogue. Results from the sensitivity studies suggest that computed spatial densities are stable for altitude bin sizes of 25 km or less and for declination bin sizes of 2.5 degrees or less but only outside the declination range [+1, -1] degrees (i.e. close to the Geostationary ring). Within this declination range, spatial density estimates varied by a factor of ten.
The shell model Monte Carlo approach to level densities: Recent developments and perspectives
NASA Astrophysics Data System (ADS)
Alhassid, Y.
2015-12-01
We review recent advances in the shell model Monte Carlo approach for the microscopic calculation of statistical and collective properties of nuclei. We discuss applications to the calculation of i) level densities in nickel isotopes, implementing a recent method to circumvent the odd-particle sign problem; ii) state densities in heavy nuclei; iii) spin distributions of nuclear levels; and iv) finite-temperature quadrupole distributions.
Density dependence of the nuclear symmetry energy from measurements of neutron radii in nuclei
ViÃ±as, X.; Centelles, M.; Roca-Maza, X.; Warda, M.
2014-07-23
We study the density dependence of the nuclear symmetry energy, characterized by its slope parameter L, by means of the information provided by the neutron radius and the neutron skin thickness in finite nuclei. These quantities are extracted from the analysis of data obtained in antiprotonic atoms, from the parity-violating asymmetry at low-momentum transfer in polarized electron scattering in {sup 208}Pb, and from the electric dipole polarizability obtained via polarized proton inelastic scattering at forward angles in {sup 208}Pb. All these experiments provide different constraints on the slope L of the symmetry energy but the corresponding values have a considerable overlap in a range around 50 MeV â‰¤ L â‰¤ 70 MeV, in a reasonable agreement with other estimates that use different observables and methods to extract L.
Thickness dependence of the charge-density-wave transition temperature in VSe{sub 2}
Yang, Jiyong; Liu, Yan; Du, Haifeng; Ning, Wei; Zheng, Guolin; Jin, Chiming; Han, Yuyan; Wang, Ning; Tian, Mingliang Zhang, Yuheng; Wang, Weike; Yang, Zhaorong
2014-08-11
A set of three-dimensional charge-density-wave (3D CDW) VSe{sub 2} nano-flakes with different thicknesses were obtained by the scotch tape-based micro-mechanical exfoliation method. Resistivity measurements showed that the 3D CDW transition temperature T{sub p} decreases systematically from 105?K in bulk to 81.8?K in the 11.6?nm thick flake. The Hall resistivity ?{sub xy} of all the flakes showed a linear dependent behavior against the magnetic field with a residual electron concentration of the order of ?10{sup 21}?cm{sup ?3} at 5?K. The electron concentration n increases slightly as the thickness d decreases, possibly due to the CDW gap is reduced with the decrease of the thickness.
NASA Astrophysics Data System (ADS)
Kvasil, J.; Kleinig, W.; Nesterenko, V. O.; Reinhard, P.-G.; Vesely, P.
2008-04-01
The isovector giant dipole resonance (GDR) in deformed nuclei 154Sm and 238U is described within the self-consistent separable RPA (random-phase-approximation) with Skyrme forces SkT6, SkM*, SLy6 and SkI3. We examine dependence of the description on the Skyrme force and gross-structure effects, as well as influence of the Coulomb interaction, multipole mixing, and time-odd densities. The results are analyzed in terms of isovector characteristics of the nuclear matter. It is shown that GDR in deformed nuclei can serve as a robust test for Skyrme forces with different effective masses. The best description of the resonance is obtained for the SLy6 force.
NASA Astrophysics Data System (ADS)
Tsubonoya, Keisuke; Hu, Chunping; Watanabe, Kazuyuki
2014-07-01
Low-energy electron scattering with nanoflakes is investigated using a time-dependent density functional theory (TDDFT) simulation in real time and real space. By representing the incident electron as a finite-sized wave packet, we obtain diffraction patterns that show not only the regular features of conventional low-energy electron diffraction (LEED) for periodic structures but also special features resulting from the local atomic inhomogeneity. We have also found a signature of ? plasmon excitation upon electron impact on a graphene flake. The present study shows the remarkable potential of TDDFT for simulating the electron scattering process, which is important for clarifying the local and periodic atomic geometries as well as the electronic excitations in nanostructures.
Optimized Effective Potential for Quantum Electrodynamical Time-Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Pellegrini, Camilla; Flick, Johannes; Tokatly, Ilya V.; Appel, Heiko; Rubio, Angel
2015-08-01
We propose an orbital exchange-correlation functional for applying time-dependent density functional theory to many-electron systems coupled to cavity photons. The time nonlocal equation for the electron-photon optimized effective potential (OEP) is derived. In the static limit our OEP energy functional reduces to the Lamb shift of the ground state energy. We test the new approximation in the Rabi model. It is shown that the OEP (i) reproduces quantitatively the exact ground-state energy from the weak to the deep strong coupling regime and (ii) accurately captures the dynamics entering the ultrastrong coupling regime. The present formalism opens the path to a first-principles description of correlated electron-photon systems, bridging the gap between electronic structure methods and quantum optics for real material applications.
Density-dependent analysis of nonequilibrium paths improves free energy estimates
Minh, David D. L.
2009-01-01
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities such as free energy differences. Here, we consider analyzing paths generated with one protocol using another one. It is posited that analysis protocols which minimize the lag, the difference between the nonequilibrium and the instantaneous equilibrium densities, will reduce the dissipation of reprocessed trajectories and lead to better free energy estimates. Indeed, when minimal lag analysis protocols based on exactly soluble propagators or relative entropies are applied to several test cases, substantial gains in the accuracy and precision of estimated free energy differences are observed. PMID:19485432
Global stability of a delayed SIR epidemic model with density dependent birth and death rates
NASA Astrophysics Data System (ADS)
Yoshida, Naoki; Hara, Tadayuki
2007-04-01
An SIR epidemic model with density dependent birth and death rates is formulated. In our model it is assumed that the total number of the population is governed by logistic equation. The transmission of infection is assumed to be of the standard form, namely proportional to I(t-h)/N(t-h) where N(t) is the total (variable) population size, I(t) is the size of the infective population and a time delay h is a fixed time during which the infectious agents develop in the vector. We consider transmission dynamics for the model. Stability of an endemic equilibrium is investigated. The stability result is stated in terms of a threshold parameter, that is, a basic reproduction number R0.
NASA Astrophysics Data System (ADS)
Cheng, Xue-mei; Huang, Yao; Ma, Jian-yi; Li, Xiang-yuan
2007-06-01
The absorption spectral properties of para-aminobenzophenone (p-ABP) were investigated in gas phase and in solution by time-dependent density functional theory. Calculations suggest that the singlet states vary greatly with the solvent polarities. In various polar solvents, including acetonitrile, methanol, ethanol, dimethyl sulfoxide, and dimethyl formamide, the excited S1 states with charge transfer character result from ? ? ?* transitions. However, in nonpolar solvents, cyclohexane, and benzene, the S1 states are the result of n ? ?* transitions related to local excitation in the carbonyl group. The excited T1 states were calculated to have ??* character in various solvents. From the variation of the calculated excited states, the band due to ? ? ?* transition undergoes a redshift with an increase in solvent polarity, while the band due to n ? ?* transition undergoes a blueshift with an increase in solvent polarity. In addition, the triplet yields and the photoreactivities of p-ABP in various solvents are discussed.
Asymmetric density dependence shapes species abundances in a tropical tree community.
Comita, Liza S; Muller-Landau, Helene C; Aguilar, Salomón; Hubbell, Stephen P
2010-07-16
The factors determining species commonness and rarity are poorly understood, particularly in highly diverse communities. Theory predicts that interactions with neighbors of the same (conspecific) and other (heterospecific) species can influence a species' relative abundance, but empirical tests are lacking. By using a hierarchical model of survival for more than 30,000 seedlings of 180 tropical tree species on Barro Colorado Island, Panama, we tested whether species' sensitivity to neighboring individuals relates to their relative abundance in the community. We found wide variation among species in the effect of conspecific, but not heterospecific, neighbors on survival, and we found a significant relationship between the strength of conspecific neighbor effects and species abundance. Specifically, rare species suffered more from the presence of conspecific neighbors than common species did, suggesting that conspecific density dependence shapes species abundances in diverse communities. PMID:20576853
Optimized Effective Potential for Quantum Electrodynamical Time-Dependent Density Functional Theory.
Pellegrini, Camilla; Flick, Johannes; Tokatly, Ilya V; Appel, Heiko; Rubio, Angel
2015-08-28
We propose an orbital exchange-correlation functional for applying time-dependent density functional theory to many-electron systems coupled to cavity photons. The time nonlocal equation for the electron-photon optimized effective potential (OEP) is derived. In the static limit our OEP energy functional reduces to the Lamb shift of the ground state energy. We test the new approximation in the Rabi model. It is shown that the OEP (i) reproduces quantitatively the exact ground-state energy from the weak to the deep strong coupling regime and (ii) accurately captures the dynamics entering the ultrastrong coupling regime. The present formalism opens the path to a first-principles description of correlated electron-photon systems, bridging the gap between electronic structure methods and quantum optics for real material applications. PMID:26371646
Correlation in time-dependent density-functional-theory studies of antiproton-helium collisions
NASA Astrophysics Data System (ADS)
Baxter, Matthew; Kirchner, Tom
2013-06-01
Correlation effects are examined in the context of time-dependent density-functional-theory calculations of antiproton-helium collisions. An approximation for the correlation potential as well as two models for the correlation integral are explored. The first of these makes use of frozen correlation, while the second is appropriated from the world of laser-induced ionization. Total cross sections for both single and double ionization in the impact energy range 5-2000 keV are presented. While the results of the first model provide little improvement over an independent electron model description the second model agrees quite well with experimental results for both single and double ionization. Our results also lend credence to the belief that an appropriate approximation of the correlation integral is more important in reproducing correlation effects than the correlation potential.
Correlation in time-dependent density functional theory studies of antiproton-helium collisions
NASA Astrophysics Data System (ADS)
Baxter, Matthew
Correlation effects are examined in the context of time-dependent density functional theory (TDDFT) calculations of antiproton helium collisions. An approximation for the correlation potential as well as two models for the correlation integral (Ic) are explored. While one of these models (frozen correlation (FCM)) is entirely new the other is appropriated from the world of laser-induced ionization (Wilken and Bauer (WB)). Total cross sections for both single and double ionization in the range 1-2000 keV are presented. These calculations make use of the basis generator method (BGM) and incorporate microscopic response. While the FCM results provide little improvement over an independent electron model description the WB model agrees quite well with experimental results for both single and double ionization. Our results also lend credence to the belief that an appropriate approximation of Ic is more important in reproducing correlation effects than the correlation potential.
Correlation in time-dependent density functional theory studies of antiproton-helium collisions
NASA Astrophysics Data System (ADS)
Baxter, Matthew; Kirchner, Tom
2013-05-01
Correlation effects are examined in the context of time-dependent density functional theory calculations of antiproton helium collisions. An approximation for the correlation potential as well as two models for the correlation integral (Ic) are explored. While one of these models (frozen correlation (FCM)) is entirely new the other is appropriated from the world of laser-induced ionization (Wilken and Bauer (WB)). Total cross sections for both single and double ionization in the range 1-2000 keV are presented. These calculations make use of the basis generator method and incorporate microscopic response. While the FCM results provide little improvement over an independent electron model description the WB model agrees quite well with experimental results for both single and double ionization. Our results also lend credence to the belief that an appropriate approximation of Ic is more important in reproducing correlation effects than the correlation potential. This work has been supported by NSERC Canada.
Time-dependent density functional study on the photoisomerization mechanism of azobenzene
NASA Astrophysics Data System (ADS)
Oyama, Norihisa; Tateyama, Yoshitaka; Miyamoto, Yoshiyuki; Ohno, Takahisa
2004-03-01
Photochemical reactions in organic molecules have attracted considerable attention in semiconductor physics and also in bioscience. Azobenzene is a simple molecule which shows the reversible photoisomerization at high quantum yields, and can be used as a light-driven molecular switch and so on. However, the photoisomerization process of azobenzene is still an open question because of its femtosecond ultra-fast reaction. In this talk, we present time-dependent density functional calculations for the azobenzene molecule, and discuss the mechanism of photoisomerization induced by S1 and S2 excitations. This research is partially supported by ACT-JST, and also by FSIS and Special Coordination Funds of MEXT of Japanese Government. The calculations were carried out partly using the Numerical Materials Simulator in National Institute for Materials Science, and partly using the NEC-SX5 at Cybermedia Center of Osaka University.
Bishof, M.; Martin, M. J.; Swallows, M. D.; Benko, C.; Lin, Y.; Quemener, G.; Rey, A. M.; Ye, J.
2011-11-15
We observe two-body loss of {sup 3} P{sub 0} {sup 87}Sr atoms trapped in a one-dimensional optical lattice. We measure loss rate coefficients for atomic samples between 1 and 6 {mu}K that are prepared either in a single nuclear-spin sublevel or with equal populations in two sublevels. The measured temperature and nuclear-spin preparation dependence of rate coefficients agree well with calculations and reveal that rate coefficients for distinguishable atoms are only slightly enhanced over those of indistinguishable atoms. We further observe a suppression of excitation and losses during interrogation of the {sup 1} S{sub 0}-{sup 3} P{sub 0} transition as density increases and Rabi frequency decreases, which suggests the presence of strong interactions in our dynamically driven many-body system.
Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales
Martínez-García, Ricardo; Murgui, Clara; Hernández-García, Emilio; López, Cristóbal
2015-01-01
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological organisms (like mussels) that tend to cluster at short ranges as a defensive strategy, and strongly disperse if there is a high population pressure at large ranges for optimizing foraging. We perform stochastic simulations of a particle-level model of the system, and derive and analyze a continuous density description (a nonlinear diffusion equation). In both cases we show that this interplay of scale-dependent-behaviors gives rise to a rich formation of spatial patterns ranging from labyrinths to periodic cluster arrangements. In most cases these clusters have the very peculiar appearance of ring-like structures, i.e., organisms arranging in the perimeter of the clusters, which we discuss in detail. PMID:26147351
Kowalczyk, T.; Yost, S. R.; Van Voorhis, T.
2010-01-01
This paper assesses the accuracy of the Î”SCF method for computing low-lying HOMOâ†’LUMO transitions in organic dye molecules. For a test set of vertical excitation energies of 16 chromophores, surprisingly similar accuracy is observed for time-dependent density functional theory and for Î”SCF density functional theory. In light of this performance, we reconsider the ad hoc Î”SCF prescription and demonstrate that it formally obtains the exact stationary density within the adiabatic approximation, partially justifying its use. The relative merits and future prospects of Î”SCF for simulating individual excited states are discussed.
Exploring Non-Equilibrium Dynamics in Time Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Luo, Kai
Time-dependent density functional theory(TDDFT) is a method of choice for calculations of excitation spectra and response properties in materials science and quantum chemistry. The many-body problem is mapped into a set of one-body Schrodinger equations, called the Kohn-Sham(KS) equations. In principle, the one-body potential can be chosen such that the density of the interacting system is exactly reproduced by the KS system. However, one component of the one-body potential has to be approximated and is typically "diabatic". Though in linear response regime adiabatic approximations give quite good spectra, it is important to explore their performances in non-equilibrium dynamics. In this thesis, I will present the results of the explorations on non-equilibrium dynamics in TDDFT. For the first study, a decomposition of exact exchange-correlation potential into kinetic and interaction components is derived. We compare the components with that of "adiabatic" counterparts in non-perturbative dynamics and find that the interaction component is less poorly approximated adiabatically than the kinetic component. A salient feature is that step structures generically appear, of relevance in the second study. We prove that the step structures only appear in the non-linear response regime. We find an exact condition which is typically violated by the approximations in use today. Spuriously time-dependent spectra in TDDFT can be explained and we find that the more the condition is violated the worse the dynamics is. In last, we envision that orbital functionals are able to incorporate the memory effects and compensate the deficiencies of the "adiabatic" approximations.
Modeling solvation effects in real-space and real-time within density functional approaches.
Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea
2015-10-14
The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water. PMID:26472367
Modeling solvation effects in real-space and real-time within density functional approaches
NASA Astrophysics Data System (ADS)
Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea
2015-10-01
The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water.
NASA Astrophysics Data System (ADS)
Kirchner, Tom
2013-05-01
Ion-impact induced ionization and fragmentation of complex molecules have important applications in many branches of science. If the molecule is H2O an obvious topic to address is the radiobiological relevance of these processes, e.g. in the context of hadron therapy, to name just one example. From a more fundamental physics viewpoint ion-molecule collision systems constitute interesting many-body systems, whose analysis poses challenges to both experimentalists and theorists. This talk will describe a theoretical approach to ion-molecule collisions, which is based on density functional theory to describe the nonperturbative electron dynamics. The basis generator method applied in the past successfully to ion-atom collisions is adapted to deal with the multi-center problem one faces when one considers molecular targets. Cross sections for single- and multiple-electron processes (capture and transfer to the continuum) are obtained directly from solving time-dependent Kohn-Sham-type orbital equations and using a Slater determinant based analysis. Fragmentation yields are predicted on the basis of a semi-phenomenological model which uses the calculated cross sections as input. Results will be presented for various ions impacting on water molecules in the energy range of 10-5000 keV/amu and compared with experimental data and previous theoretical calculations where available. First applications of the model to collisions involving CH4 molecules will also be discussed. This work has been supported by SHARCNET and NSERC Canada.
Quantum confined stark effect in wide parabolic quantum wells: real density matrix approach
NASA Astrophysics Data System (ADS)
ZieliÅ„ska-RaczyÅ„ska, Sylwia; Czajkowski, Gerard; Ziemkiewicz, David
2015-12-01
We show how to compute the optical functions of wide parabolic quantum wells (WPQWs) exposed to uniform electric F applied in the growth direction, in the excitonic energy region. The effect of the coherence between the electron-hole pair and the electromagnetic field of the propagating wave including the electron-hole screened Coulomb potential is adopted, and the valence band structure is taken into account in the cylindrical approximation. The role of the interaction potential and of the applied electric field, which mix the energy states according to different quantum numbers and create symmetry forbidden transitions, is stressed. We use the real density matrix approach (RDMA) and an effective e-h potential, which enable to derive analytical expressions for the WPQWs electrooptical functions. Choosing the susceptibility, we performed numerical calculations appropriate to a GaAs/GaAlAs WPQWs. We have obtained a red shift of the absorption maxima (quantum confined Stark effect), asymmetric upon the change of the direction of the applied field ( F â†’ - F), parabolic for the ground state and strongly dependent on the confinement parameters (the QWs sizes), changes in the oscillator strengths, and new peaks related to the states with different parity for electron and hole.
NASA Technical Reports Server (NTRS)
Roberts, D. A.
1990-01-01
The Helios, IMP 8, ISEE 3, ad Voyager 2 spacecraft are used to examine the solar cycle and heliocentric distance dependence of the correlation between density n and magnetic field magnitude B in the solar wind. Previous work had suggested that this correlation becomes progressively more negative with heliocentric distance out to 9.5 AU. Here it is shown that this evolution is not a solar cycle effect, and that the correlations become even more strongly negative at heliocentric distance larger than 9.5 AU. There is considerable variability in the distributions of the correlations at a given heliocentric distance, but this is not simply related to the solar cycle. Examination of the evolution of correlations between density and speed suggest that most of the structures responsible for evolution in the anticorrelation between n and B are not slow-mode waves, but rather pressure balance structures. The latter consist of both coherent structures such as tangential discontinuities and the more generally pervasive 'pseudosound' which may include the coherent structures as a subset.
The phenology of space: Spatial aspects of bison density dependence in Yellowstone National Park
Taper, M.L.; Meagher, M.; Jerde, C.L.
2000-01-01
The Yellowstone bison represent the only bison population in the United States that survived in the wild the near-extermination of the late 1800's. This paper capitalizes on a unique opportunity provided by the record of the bison population of Yellowstone National Park (YNP). This population has been intensely monitored for almost four decades. The analysis of long-term spatio-temporal data from 1970-1997 supports the following conclusions. 1) Even though the Yellowstone bison herd exhibits an extended period of what appears to be linear growth, this pattern can be explained with classical density dependent dynamics if one realizes that perhaps the primary response of the herd to increased density is range expansion. 2) Several spatial aspects of social behavior in the YNP bison may be behavioral adaptations by the bison to environmental changes. These behavioral strategies may buffer, temporarily at least, bison population dynamics from the immediate repercussions of possible environmental stress and habitat deterioration. 3) Bison ecological carrying capacity for YNP is on the order of 2800 to 3200 animals. 4) There do appear to be indications of changes in the bison dynamics that are associated with increasing use of sections of the interior road system in winter. 5) The possibility of habitat degradation is indicated.
Time-dependent density functional theory calculation of van der Waals coefficient of sodium clusters
NASA Astrophysics Data System (ADS)
Banerjee, Arup; Chakrabarti, Aparna; Ghanty, Tapan K.
2007-10-01
In this paper we employ all-electron ab initio time-dependent density functional theory based method to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) C6 of sodium atom clusters containing even number of atoms ranging from 2 to 20 atoms. The dispersion coefficients are obtained via Casimir-Polder relation [Phys. Rev. 3, 360 (1948)]. The calculations are carried out with two different exchange-correlation potentials: (i) the asymptotically correct statistical average of orbital potential (SAOP) and (ii) Vosko-Wilk-Nusair representation [Can. J. Phys. 58, 1200 (1980)] of exchange-correlation potential within local density approximation. A comparison with the other theoretical results has been performed. We also present the results for the static polarizabilities of sodium clusters and also compare them with other theoretical and experimental results. These comparisons reveal that the SAOP results for C6 and static polarizability are quite accurate and very close to the experimental results. We examine the relationship between volume of the cluster and van der Waals coefficient, and find that to a very high degree of correlation C6 scales as the square of the volume. We also present the results for van der Waals coefficient corresponding to cluster-Ar atom and cluster-N2 molecule interactions.
Banerjee, Arup; Chakrabarti, Aparna; Ghanty, Tapan K
2007-10-01
In this paper we employ all-electron ab initio time-dependent density functional theory based method to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) C(6) of sodium atom clusters containing even number of atoms ranging from 2 to 20 atoms. The dispersion coefficients are obtained via Casimir-Polder relation [Phys. Rev. 3, 360 (1948)]. The calculations are carried out with two different exchange-correlation potentials: (i) the asymptotically correct statistical average of orbital potential (SAOP) and (ii) Vosko-Wilk-Nusair representation [Can. J. Phys. 58, 1200 (1980)] of exchange-correlation potential within local density approximation. A comparison with the other theoretical results has been performed. We also present the results for the static polarizabilities of sodium clusters and also compare them with other theoretical and experimental results. These comparisons reveal that the SAOP results for C(6) and static polarizability are quite accurate and very close to the experimental results. We examine the relationship between volume of the cluster and van der Waals coefficient, and find that to a very high degree of correlation C(6) scales as the square of the volume. We also present the results for van der Waals coefficient corresponding to cluster-Ar atom and cluster-N(2) molecule interactions. PMID:17919007
Wilson, Kenneth; Graham, Robert I
2015-03-01
There is an increasing appreciation of the importance of transgenerational effects on offspring fitness, including in relation to immune function and disease resistance. Here, we assess the impact of parental rearing density on offspring resistance to viral challenge in an insect species expressing density-dependent prophylaxis (DDP); i.e. the adaptive increase in resistance or tolerance to pathogen infection in response to crowding. We quantified survival rates in larvae of the cotton leafworm (Spodoptera littoralis) from either gregarious- or solitary-reared parents following challenge with the baculovirus S. littoralis nucleopolyhedrovirus. Larvae from both the parental and offspring generations exhibited DDP, with gregarious-reared larvae having higher survival rates post-challenge than solitary-reared larvae. Within each of these categories, however, survival following infection was lower in those larvae from gregarious-reared parents than those from solitary-reared, consistent with a transgenerational cost of DDP immune upregulation. This observation demonstrates that crowding influences lepidopteran disease resistance over multiple generations, with potential implications for the dynamics of host-pathogen interactions. PMID:25808002
Wilson, Kenneth; Graham, Robert I.
2015-01-01
There is an increasing appreciation of the importance of transgenerational effects on offspring fitness, including in relation to immune function and disease resistance. Here, we assess the impact of parental rearing density on offspring resistance to viral challenge in an insect species expressing density-dependent prophylaxis (DDP); i.e. the adaptive increase in resistance or tolerance to pathogen infection in response to crowding. We quantified survival rates in larvae of the cotton leafworm (Spodoptera littoralis) from either gregarious- or solitary-reared parents following challenge with the baculovirus S. littoralis nucleopolyhedrovirus. Larvae from both the parental and offspring generations exhibited DDP, with gregarious-reared larvae having higher survival rates post-challenge than solitary-reared larvae. Within each of these categories, however, survival following infection was lower in those larvae from gregarious-reared parents than those from solitary-reared, consistent with a transgenerational cost of DDP immune upregulation. This observation demonstrates that crowding influences lepidopteran disease resistance over multiple generations, with potential implications for the dynamics of hostâ€“pathogen interactions. PMID:25808002
A relativistic time-dependent density functional study of the excited states of the mercury dimer.
Kullie, Ossama
2014-01-14
In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s(2) + 6s6p), (6s(2) + 6s7s), and (6s(2) + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2. PMID:24437874
Steady-state conduction in high density polyethylene with field-dependent mobility
NASA Astrophysics Data System (ADS)
Kumar, A.; Perlman, M. M.
1992-01-01
A theory of steady-state conduction of injected space-charge-limited carriers (SCLCs) into high density polyethylene (HDPE) is presented. Injected carriers are deeply trapped at crystalline-amorphous boundaries before the steady state is reached. At elevated temperatures, they are thermally excited to the conduction band in the crystalline regions, and then hop with field-dependent mobility through defect states of the amorphous regions. A hopping site separation of 2.2 nm, corresponding to 9.4×1019/cm3, yields good agreement with experimental current-field characteristics for fields up to 0.5 MV/cm, in the temperature range 61-85.5 °C. The final current I versus field F and temperature T equation shows that the activation energy of the detrapping and transport processes are additive on a semilog plot of I/T vs 1/T. The total activation energy is 1.15 eV at 0.2 MV/cm, in agreement with others. The steady-state field distributions in the sample are calculated, and are independent of temperature in the above temperature and field ranges. The conditions under which our theory reduces to that of simple SCLC, field-independent mobility theory, and differences in conduction between linear low density polyethylene and HDPE are discussed.
The assessment of toxic exposure on wildlife populations involves the integration of organism level effects measured in toxicity tests (e.g., chronic life cycle) and population models. These modeling exercises typically ignore density dependence, primarily because information on ...
Gudur, Madhu Sudhan Reddy; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang
2014-11-01
MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm's accuracy of electron density mapping and its ability to detect bone in the head for eight patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as receiver operating characteristics for bone detection (HU > 200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p = 2? × ?10(-4)), 283 for the intensity approach (p = 2? × ?10(-6)) and 282 without density correction (p = 5? × ?10(-6)). For 90% sensitivity in bone detection, the proposed method achieved a specificity of 86%, compared with 80, 11 and 10% using deformable registration, intensity and without density correction, respectively. Notably, the Bayesian approach was more robust against anatomical differences between patients, with a specificity of 62% in the worst case (patient), compared to 30% specificity in registration-based approach. In conclusion, the proposed unifying Bayesian method provides accurate electron density estimation and bone detection from MRI of the head with highly heterogeneous anatomy. PMID:25321341
NASA Astrophysics Data System (ADS)
Sudhan Reddy Gudur, Madhu; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang
2014-11-01
MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm’s accuracy of electron density mapping and its ability to detect bone in the head for eight patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as receiver operating characteristics for bone detection (HU > 200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p = 2? × ?10-4), 283 for the intensity approach (p = 2? × ?10-6) and 282 without density correction (p = 5? × ?10-6). For 90% sensitivity in bone detection, the proposed method achieved a specificity of 86%, compared with 80, 11 and 10% using deformable registration, intensity and without density correction, respectively. Notably, the Bayesian approach was more robust against anatomical differences between patients, with a specificity of 62% in the worst case (patient), compared to 30% specificity in registration-based approach. In conclusion, the proposed unifying Bayesian method provides accurate electron density estimation and bone detection from MRI of the head with highly heterogeneous anatomy.
Evaluating Systematic Dependence of Type Ia Supernovae: The Influence of Progenitor Central Density
NASA Astrophysics Data System (ADS)
Krueger, Brendan K.; Jackson, A. P.; Calder, A. C.; Townsley, D. M.; Brown, E. F.; Timmes, F. X.
2011-01-01
We present a study of type Ia supernovae in the single-degenerate scenario, in which a white dwarf accretes mass from a companion star until it approaches the Chandrasekhar limiting mass and an explosion ensues. We investigate progenitor models with a range of central densities to study the influence of this parameter on explosion outcome. We present a suite of simulations from a well-controlled statistical study that allows us to quantify the effects of a variety of initial conditions. We present details of the models, including the mass and distribution of 56Ni, the radioactive decay of which powers the light curve. Our results indicate that progenitors with a higher central density produce less 56Ni and hence a dimmer event. We combine our results with those from previous studies by our collaboration to explore trends in explosion brightness that follow from properties related to the morphology and color of the host galaxy. This work was supported by NASA under grant No. NNX09AD19G and utilized resources at the New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory, which is supported by the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 and by the State of New York.
Direct microscopic calculation of nuclear level densities in the shell model Monte Carlo approach
NASA Astrophysics Data System (ADS)
Alhassid, Y.; Bonett-Matiz, M.; Liu, S.; Nakada, H.
2015-08-01
Nuclear level densities are required for estimating statistical nuclear reaction rates. The shell model Monte Carlo method is a powerful approach for microscopic calculation of state densities in very large model spaces. However, these state densities include the spin degeneracy of each energy level, whereas experiments often measure level densities, in which each level is counted only once. To enable the direct comparison of theory with experiments, we introduce a method to calculate directly the level density in the shell model Monte Carlo approach. The method employs a projection on the minimal absolute value of the magnetic quantum number. We apply the method to nuclei in the iron region and to the strongly deformed rare-earth nucleus 162Dy . We find very good agreement with experimental data obtained by various methods, including level counting at low energies, charged particle spectra and Oslo method data at intermediate energies, neutron and proton resonance data, and Ericson's fluctuation analysis at higher excitation energies. We also extract a thermal moment of inertia from the ratio between the state density and the level density, and observe that in even-even nuclei it exhibits a signature of a phase transition to a superconducting phase below a certain excitation energy.
NASA Astrophysics Data System (ADS)
Aban, C. J. G.; Bacolod, R. O.; Confesor, M. N. P.
2015-06-01
A The White Noise Path Integral Approach is used in evaluating the B-cell density or the number of B-cell per unit volume for a basic type of immune system response based on the modeling done by Perelson and Wiegel. From the scaling principles of Perelson [1], the B- cell density is obtained where antigens and antibodies mutates and activation function f(|S-SA|) is defined describing the interaction between a specific antigen and a B-cell. If the activation function f(|S-SA|) is held constant, the major form of the B-cell density evaluated using white noise analysis is similar to the form of the B-cell density obtained by Perelson and Wiegel using a differential approach.A piecewise linear functionis also used to describe the activation f(|S-SA|). If f(|S-SA|) is zero, the density decreases exponentially. If f(|S-SA|) = S-SA-SB, the B- cell density increases exponentially until it reaches a certain maximum value. For f(|S-SA|) = 2SA-SB-S, the behavior of B-cell density is oscillating and remains to be in small values.
Rüger, Robert; van Lenthe, Erik; Lu, You; Frenzel, Johannes; Heine, Thomas; Visscher, Lucas
2015-01-13
During the last two decades density functional based linear response approaches have become the de facto standard for the calculation of optical properties of small- and medium-sized molecules. At the heart of these methods is the solution of an eigenvalue equation in the space of single-orbital transitions, whose quickly increasing number makes such calculations costly if not infeasible for larger molecules. This is especially true for time-dependent density functional tight binding (TD-DFTB), where the evaluation of the matrix elements is inexpensive. For the relatively large systems that can be studied the solution of the eigenvalue equation therefore determines the cost of the calculation. We propose to do an oscillator strength based truncation of the single-orbital transition space to reduce the computational effort of TD-DFTB based absorption spectra calculations. We show that even a sizable truncation does not destroy the principal features of the absorption spectrum, while naturally avoiding the unnecessary calculation of excitations with small oscillator strengths. We argue that the reduced computational cost of intensity-selected TD-DFTB together with its ease of use compared to other methods lowers the barrier of performing optical property calculations of large molecules and can serve to make such calculations possible in a wider array of applications. PMID:26574214
NASA Astrophysics Data System (ADS)
Nassar, Mohamed K.; Ginn, Timothy R.
2014-08-01
We investigate the effect of computational error on the inversion of a density-dependent flow and transport model, using SEAWAT and UCODE-2005 in an inverse identification of hydraulic conductivity and dispersivity using head and concentration data from a 2-D laboratory experiment. We investigated inversions using three different solution schemes including variation of number of particles and time step length, in terms of the three aspects: the shape and smoothness of the objective function surface, the consequent impacts to the optimization, and the resulting Pareto analyses. This study demonstrates that the inversion is very sensitive to the choice of the forward model solution scheme. In particular, standard finite difference methods provide the smoothest objective function surface; however, this is obtained at the cost of numerical artifacts that can lead to erroneous warping of the objective function surface. Total variation diminishing (TVD) schemes limit these impacts at the cost of more computation time, while the hybrid method of characteristics (HMOC) approach with increased particle numbers and/or reduced time step gives both smoothed and accurate objective function surface. Use of the most accurate methods (TVD and HMOC) did lead to successful inversion of the two parameters; however, with distinct results for Pareto analyses. These results illuminate the sensitivity of the inversion to a number of aspects of the forward solution of the density-driven flow problem and reveal that parameter values may result that are erroneous but that counteract numerical errors in the solution.
Technology Transfer Automated Retrieval System (TEKTRAN)
Transmission of parasites and pathogens is generally positively density-dependent. Thus, as an insect population's density increases, the risk of an individual becoming attacked or infected increases. In some insect species, individuals experiencing crowded conditions are more resistant to natural e...
NASA Astrophysics Data System (ADS)
Normani, S. D.; Sykes, J. F.; Jensen, M. R.
2009-04-01
A high resolution sub-regional scale (84 km2) density-dependent, fracture zone network groundwater flow model with hydromechanical coupling and pseudo-permafrost, was developed from a larger 5734 km2 regional scale groundwater flow model of a Canadian Shield setting in fractured crystalline rock. The objective of the work is to illustrate aspects of regional and sub-regional groundwater flow that are relevant to the long-term performance of a hypothetical nuclear fuel repository. The discrete fracture dual continuum numerical model FRAC3DVS-OPG was used for all simulations. A discrete fracture zone network model delineated from surface features was superimposed onto an 789887 element flow domain mesh. Orthogonal fracture faces (between adjacent finite element grid blocks) were used to best represent the irregular discrete fracture zone network. The crystalline rock between these structural discontinuities was assigned properties characteristic of those reported for the Canadian Shield at the Underground Research Laboratory at Pinawa, Manitoba. Interconnectivity of permeable fracture features is an important pathway for the possibly relatively rapid migration of average water particles and subsequent reduction in residence times. The multiple 121000 year North American continental scale paleoclimate simulations are provided by W.R. Peltier using the University of Toronto Glacial Systems Model (UofT GSM). Values of ice sheet normal stress, and proglacial lake depth from the UofT GSM are applied to the sub-regional model as surface boundary conditions, using a freshwater head equivalent to the normal stress imposed by the ice sheet at its base. Permafrost depth is applied as a permeability reduction to both three-dimensional grid blocks and fractures that lie within the time varying permafrost zone. Two different paleoclimate simulations are applied to the sub-regional model to investigate the effect on the depth of glacial meltwater migration into the subsurface. In addition, different conceptualizations of fracture permeability with depth, and various hydromechanical loading efficiencies are used to investigate glacial meltwater penetration. The importance of density dependent flow, due to pore waters deep in the Canadian Shield with densities of up to 1200 kg/m3 and total dissolved solids concentrations in excess of 300 g/L, is also illustrated. Performance measures used in the assessment include depth of glacial meltwater penetration using a tracer, and mean life expectancy. Consistent with the findings from isotope and geochemical assessments, the analyses support the conclusion that for the discrete fracture zone and matrix properties simulated in this study, glacial meltwaters would not likely impact a deep geologic repository in a crystalline rock setting.
NASA Astrophysics Data System (ADS)
Zelovich, Tamar; Kronik, Leeor; Hod, Oded
2014-03-01
A new method for simulating electron dynamics in open quantum systems out of equilibrium, motivated by the intuitive and practical nature of the damped Liouville von-Neumann equation approach of SÃ¡nchez et al. [J. Chem Phys, 124, 214708 (2006)], is presented. The new approach is based on a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to define the bias voltage across the system uniquely while maintaining a proper thermal distribution within the lead models. Furthermore, it allows us to investigate time-dependent effects in non-linear and multi-lead configurations. We investigate the degree of conservation of exact conditions such as the N-representability of the density matrix and suggest ways to remedy the violation of Pauli's exclusion principle. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic models of molecular electronics junctions.
Reconstructive approaches to one- and two-electron density matrix theory
NASA Astrophysics Data System (ADS)
Herbert, John Michael
Novel computational methods for electronic structure theory are explored, in which the fundamental variable is either the one- or the two-electron reduced density matrix (1- or 2-RDM), rather than the electronic wavefunction. A unifying theme among these methods is density matrix reconstruction, that is, decoupling approximations that express higher-order density matrices as functionals of lower-order ones. On the 2-RDM side, a connected (extensive) version of the Contracted Schrodinger Equation (CSE) is developed, in which the basic unknowns are the RDM cumulants through order four. Reconstruction functionals that neglect the 3- and 4-RDM cumulants are examined and revealed to be significantly less accurate than suggested by previous minimal-basis results. Exact 3-RDM cumulants for some four-electron systems are calculated and found to be comparable in importance to unconnected products of lower-order cumulants. Decoupling approximations for the 3- and 4-RDM cumulants are developed based upon a renormalized, diagrammatic perturbation theory for the three- and four-particle Green's functions, in which the effective, pairwise interaction is extracted from the two-particle cumulant. Diagram rules suitable for both the time-dependent and time-independent versions of this perturbation theory are derived. Reconstructive approaches to natural orbital (1-RDM) functional theory are also examined, wherein the 2-RDM is parametrized in terms of the natural orbitals and their (generally fractional) occupancies. It is demonstrated, at the theorem level, that proposed "corrected Hartree" and "corrected Hartree-Fock" natural orbital functionals necessarily violate positivity of the 2-RDM, which is closely related to their failure to respect antisymmetry. Calculations demonstrate that negative eigenvalues of the 2-RDM are associated with a large, stabilizing (but ultimately spurious) contribution to the energy. Nevertheless, a partially self-interaction-corrected version of the corrected Hartree functional is shown to yield high-quality potential energy curves---comparable to multireference configuration interaction---for the strongly-correlated diatomic molecules HF and C2. A new class of functionals that preserve both anti-symmetry and positivity are proposed and subjected to some preliminary tests.
Habershon, Scott
2013-09-14
We introduce a new approach for calculating quantum time-correlation functions and time-dependent expectation values in many-body thermal systems; both electronically adiabatic and non-adiabatic cases can be treated. Our approach uses a path integral simulation to sample an initial thermal density matrix; subsequent evolution of this density matrix is equivalent to solution of the time-dependent Schrödinger equation, which we perform using a linear expansion of Gaussian wavepacket basis functions which evolve according to simple classical-like trajectories. Overall, this methodology represents a formally exact approach for calculating time-dependent quantum properties; by introducing approximations into both the imaginary-time and real-time propagations, this approach can be adapted for complex many-particle systems interacting through arbitrary potentials. We demonstrate this method for the spin Boson model, where we find good agreement with numerically exact calculations. We also discuss future directions of improvement for our approach with a view to improving accuracy and efficiency.
High current density PQQ-dependent alcohol and aldehyde dehydrogenase bioanodes.
Aquino Neto, Sidney; Hickey, David P; Milton, Ross D; De Andrade, Adalgisa R; Minteer, Shelley D
2015-10-15
In this paper, we explore the bioelectrooxidation of ethanol using pyrroloquinoline quinone (PQQ)-dependent alcohol and aldehyde dehydrogenase (ADH and AldDH) enzymes for biofuel cell applications. The bioanode architectures were designed with both direct electron transfer (DET) and mediated electron transfer (MET) mechanisms employing high surface area materials such as multi-walled carbon nanotubes (MWCNTs) and MWCNT-decorated gold nanoparticles, along with different immobilization techniques. Three different polymeric matrices were tested (tetrabutyl ammonium bromide (TBAB)-modified Nafion; octyl-modified linear polyethyleneimine (C8-LPEI); and cellulose) in the DET studies. The modified Nafion membrane provided the best electrical communication between enzymes and the electrode surface, with catalytic currents as high as 16.8 Â± 2.1 ÂµA cm(-2). Then, a series of ferrocene redox polymers were evaluated for MET. The redox polymer 1,1'-dimethylferrocene-modified linear polyethyleneimine (FcMe2-C3-LPEI) provided the best electrochemical response. Using this polymer, the electrochemical assays conducted in the presence of MWCNTs and MWCNTs-Au indicated a Jmax of 781 Â± 59 ÂµA cm(-2) and 925 Â± 68 ÂµA cm(-2), respectively. Overall, from the results obtained here, DET using the PQQ-dependent ADH and AldDH still lacks high current density, while the bioanodes that operate via MET employing ferrocene-modified LPEI redox polymers show efficient energy conversion capability in ethanol/air biofuel cells. PMID:25988787
Dependence of rate of physical erosion on orientation and density in mineralised tissues.
Boyde, A
1984-01-01
Bone, dentine and enamel samples were treated with a gas-propelled jet of an abrasive, NaHCO3, which is physically much softer than any of these tissues in their fully mineralised condition. It was nevertheless found that they are all eroded by this treatment, which can therefore be used as a new kind of qualitative test of physical properties relating to wear resistance. General correlations were found between both degree of mineralisation and between structure orientation and erosion rate, surface-parallel-feature zones being worn more rapidly. Bone domains with surface-parallel collagen were eroded faster than those with perpendicular lamellae even if they were more densely mineralised. Rates of dentine wear depended on both density and tubule orientation, with peritubular zones and better mineralised incremental layers being more resistant. Enamel tufts wear more rapidly than the surrounding well mineralised regions. Enamel diazones wear less than parazones (areas with surface parallel prisms). At the prism scale, enamel is removed more rapidly near prism boundary discontinuities and in tubular enamel, at tubule walls. As regards the common orientation dependent effects seen in these three tissues, a cohesive explanation would be that structure discontinuities can be better exploited in a wear process if they allow cleavage from the surface; which tendency will increase with parallelism to the surface. PMID:6476409
Electroosmotic transport in polyelectrolyte-grafted nanochannels with pH-dependent charge density
NASA Astrophysics Data System (ADS)
Chen, Guang; Das, Siddhartha
2015-05-01
"Smart" polyelectrolyte-grafted or "soft" nanochannels with pH-responsiveness have shown great promise for applications like manipulation of ion transport, ion sensing and selection, current rectification, and many more. In this paper, we develop a theory to study the electroosmotic transport in a polyelectrolyte-grafted (or soft) nanochannel with pH-dependent charge density. In one of our recent studies, we have identified that explicit consideration of hydrogen ion concentration is mandatory for appropriately describing the electrostatics of such systems and the resulting monomer concentration must obey a non-unique, cubic distribution. Here, we use this electrostatic calculation to study the corresponding electroosmotic transport. We establish that the effect of pH in the electroosmotic transport in polyelectrolyte-grafted nanochannels introduces two separate issues: first is the consideration of the hydrogen and hydroxyl ion concentrations in describing the electroosmotic body force, and second is the consideration of the appropriate drag force that bears the signature of this cubic monomeric distribution. Our results indicate that the strength of the electroosmotic velocity for the pH-dependent case is always smaller than that for the pH-independent case, with the extent of this difference being a function of the system parameters. Such nature of the electroosmotic transport will be extremely significant in suppressing the electroosmotic flow strength with implications in large number applications such as capillary electrophoresis induced separation, electric field mediated DNA elongation, electrophoretic DNA nanopore sequencing, and many more.
A minimal model for excitons within time-dependent density-functional theory.
Yang, Zeng-hui; Li, Yonghui; Ullrich, Carsten A
2012-07-01
The accurate description of the optical spectra of insulators and semiconductors remains an important challenge for time-dependent density-functional theory (TDDFT). Evidence has been given in the literature that TDDFT can produce bound as well as continuum excitons for specific systems, but there are still many unresolved basic questions concerning the role of dynamical exchange and correlation (xc). In particular, the roles of the long spatial range and the frequency dependence of the xc kernel f(xc) for excitonic binding are still not very well explored. We present a minimal model for excitons in TDDFT, consisting of two bands from a one-dimensional (1D) Kronig-Penney model and simple approximate xc kernels, providing an easily accessible model system for studying excitonic effects in TDDFT. For the 1D model system, it is found that adiabatic xc kernels can produce at most two bound excitons, confirming that the long spatial range of f(xc) is not a necessary condition. It is shown how the Wannier model, featuring an effective electron-hole interaction, emerges from TDDFT. The collective, many-body nature of excitons is explicitly demonstrated. PMID:22779671
Spillmann, Frank; Trimpert, Christiane; Peng, Jun; Eckerle, Lars G; Staudt, Alexander; Warstat, Katrin; Felix, Stephan B; Pieske, Burkert; Tschöpe, Carsten; Van Linthout, Sophie
2015-10-16
Palmitate has been implicated in the induction of cardiomyocyte apoptosis via reducing the activity of 5' AMP-activated protein kinase (AMPK). We sought to evaluate whether high-density lipoproteins (HDLs), known for their cardioprotective features and their potential to increase AMPK activity, can reduce palmitate-induced cardiomyocyte apoptosis and whether this effect is AMPK-dependent. Therefore, cardiomyocytes were isolated from adult Wistar rat hearts via perfusion on a Langendorff-apparatus and cultured in free fatty acid-free BSA control medium or 0.5 mM palmitate medium in the presence or absence of HDL (5 ?g protein/ml) with or without 0.1 ?M of the AMPK-inhibitor compound S for the analysis of Annexin V/propidium, genes involved in apoptosis and fatty acid oxidation, and cardiomyocyte contractility. We found that HDLs decreased palmitate-induced cardiomyocyte apoptosis as indicated by a reduction in Annexin V-positive cardiomyocytes and an increase in Bcl-2 versus Bax ratio. Concomitantly, HDLs increased the palmitate-impaired expression of genes involved in fatty acid oxidation. Furthermore, HDLs improved the palmitate-impaired cardiomyocyte contractility. All effects were mediated in an AMPK-dependent manner, concluding that HDLs reduce palmitate-induced cardiomyocyte apoptosis, resulting in improved cardiomyocyte contractility through a mechanism involving AMPK. PMID:26362182
Oxidized low-density lipoproteins upregulate proline oxidase to initiate ROS-dependent autophagy.
Zabirnyk, Olga; Liu, Wei; Khalil, Shadi; Sharma, Anit; Phang, James M
2010-03-01
Epidemiological studies showed that high levels of oxidized low-density lipoproteins (oxLDLs) are associated with increased cancer risk. We examined the direct effect of physiologic concentrations oxLDL on cancer cells. OxLDLs were cytotoxic and activate both apoptosis and autophagy. OxLDLs have ligands for peroxisome proliferator-activated receptor gamma and upregulated proline oxidase (POX) through this nuclear receptor. We identified 7-ketocholesterol (7KC) as a main component responsible for the latter. To elucidate the role of POX in oxLDL-mediated cytotoxicity, we knocked down POX via small interfering RNA and found that this (i) further reduced viability of cancer cells treated with oxLDL; (ii) decreased oxLDL-associated reactive oxygen species generation; (iii) decreased autophagy measured via beclin-1 protein level and light-chain 3 protein (LC3)-I into LC3-II conversion. Using POX-expressing cell model, we established that single POX overexpression was sufficient to activate autophagy. Thus, it led to autophagosomes accumulation and increased conversion of LC3-I into LC3-II. Moreover, beclin-1 gene expression was directly dependent on POX catalytic activity, namely the generation of POX-dependent superoxide. We conclude that POX is critical in the cellular response to the noxious effects of oxLDL by activating protective autophagy. PMID:19942609
Density-dependent lineage instability of MDA-MB-435 breast cancer cells.
Nerlich, Andreas G; Bachmeier, Beatrice E
2013-04-01
The use of cell lines in cancer research is strongly dependent on the avoidance of contaminations, the correct attribution of a cell line to the initial primary tumor and stability. Previous studies have identified expression of melanocytic molecular markers in the widely used breast cancer cell line, MDA-MB-435. In the present study the three breast cancer cell lines, MCF-7, MDA-MB-231 and MDA-MB-435, were systematically analyzed for mRNA and protein expression of major epithelial (cytokeratin isoforms), mammary (mammaglobin) and melanocytic (melan A and S100-protein) markers. Protein expression was identified by immunocytochemistry and quantitative RT-PCR was used to determine mRNA levels. While MCF-7 and MDA-MB-231 cells unambiguously revealed an epithelial/mammary phenotype, MDA-MB-435 cells were found to exhibit epithelial/mammary and melanocytic features dependent on cell density. Subconfluent cells demonstrated epithelial characteristics only, however, densely growing, confluent cells also expressed melanocytic markers. Consistent with gain of melanocytic features, the expression levels of mammaglobin mRNA decreased in these cells. These results indicate that the three cell lines are primarily of epithelial phenotype, however, MDA-MB-435 cells revealed lineage infidelity in dense cultures with a gain in melanocytic phenotype. These characteristics must be taken into consideration when analyzing cancer-relevant genes and their expression profiles in vitro. PMID:23599796
2007 Time_Dependent Density-Functional Therory (July 15-20, 2007 Colby College, Maine)
Ullrich Carsten Nancy Ryan Gray
2008-09-19
Time-dependent density-functional theory (TDDFT) provides an efficient, elegant, and formally exact way of describing the dynamics of interacting many-body quantum systems, circumventing the need for solving the full time-dependent Schroedinger equation. In the 20 years since it was first rigorously established in 1984, the field of TDDFT has made rapid and significant advances both formally as well as in terms of successful applications in chemistry, physics and materials science. Today, TDDFT has become the method of choice for calculating excitation energies of complex molecules, and is becoming increasingly popular for describing optical and spectroscopic properties of a variety of materials such as bulk solids, clusters and nanostructures. Other growing areas of applications of TDDFT are nonlinear dynamics of strongly excited electronic systems and molecular electronics. The purpose and scope of this Gordon Research Conference is to provide a platform for discussing the current state of the art of the rapidly progressing, highly interdisciplinary field of TDDFT, to identify and debate open questions, and to point out new promising research directions. The conference will bring together experts with a diverse background in chemistry, physics, and materials science.
NASA Astrophysics Data System (ADS)
Castro, Alberto; Rubio, Angel; Gross, Eberhard K. U.
2015-08-01
High harmonic generation (HHG) provides a flexible framework for the development of coherent light sources in the extreme-ultraviolet and soft X-ray regimes. However it suffers from low conversion efficiencies as the control of the HHG spectral and temporal characteristics requires manipulating electron trajectories on attosecond time scale. The phase matching mechanism has been employed to selectively enhance specific quantum paths leading to HHG. A few important fundamental questions remain open, among those how much of the enhancement can be achieved by the single-emitter and what is the role of correlations (or the electronic structure) in the selectivity and control of HHG generation. Here we address those questions by examining computationally the possibility of optimizing the HHG spectrum of isolated hydrogen and helium atoms by shaping the slowly varying envelope of a 800 nm, 200-cycles long laser pulse. The spectra are computed with a fully quantum mechanical description, by explicitly computing the time-dependent dipole moment of the systems using a time-dependent density-functional approach (or the single-electron Schrödinger equation for the case of H), on top of a one-dimensional model. The sought optimization corresponds to the selective enhancement of single harmonics, which we find to be significant. This selectivity is entirely due to the single atom response, and not to any propagation or phase-matching effect. Moreover, we see that the electronic correlation plays a role in the determining the degree of optimization that can be obtained.
Hu, Zhongwei; Autschbach, Jochen; Jensen, Lasse
2016-03-01
A general implementation for damped cubic response properties is presented using time-dependent density functional theory (TDDFT) and Slater-type orbital basis sets. To directly calculate two-photon absorption (TPA) cross sections, we also present an implementation of a reduced damped cubic response approach. Validation of the implementations includes a detailed comparison between response theory and the sum-over-states approach for calculating the nonlinear optical properties of LiH, as well as a comparison between the simulated and experimental TPA and third-harmonic generation (THG) spectra for the dimethylamino-nitrostilbene (DANS) molecule. The study of LiH demonstrates the incorrect pole structure obtained in response theory due to the adiabatic approximation typically employed for the exchange-correlation kernel. For DANS, we find reasonable agreement between simulated and experimental TPA and THG spectra. Overall, this work shows that care must be taken when calculating higher-order response functions in the vicinity of one-photon poles due to the approximate kernels typically used in the simulations. PMID:26841327
Shape evolution and collective dynamics of quasifission in the time-dependent Hartree-Fock approach
NASA Astrophysics Data System (ADS)
Umar, A. S.; Oberacker, V. E.; Simenel, C.
2015-08-01
Background: At energies near the Coulomb barrier, capture reactions in heavy-ion collisions result either in fusion or in quasifission. The former produces a compound nucleus in statistical equilibrium, while the second leads to a reseparation of the fragments after partial mass equilibration without formation of a compound nucleus. Extracting the compound nucleus formation probability is crucial to predict superheavy-element formation cross sections. It requires a good knowledge of the fragment angular distribution which itself depends on quantities such as moments of inertia and excitation energies which have so far been somewhat arbitrary for the quasifission contribution. Purpose: Our main goal is to utilize the time-dependent Hartee-Fock (TDHF) approach to extract ingredients of the formula used in the analysis of experimental angular distributions. These include the moment-of-inertia and temperature. Methods: We investigate the evolution of the nuclear density in TDHF calculations leading to quasifission. We study the dependence of the relevant quantities on various initial conditions of the reaction process. Results: The evolution of the moment of inertia is clearly nontrivial and depends strongly on the characteristics of the collision. The temperature rises quickly when the kinetic energy is transformed into internal excitation. Then, it rises slowly during mass transfer. Conclusions: Fully microscopic theories are useful to predict the complex evolution of quantities required in macroscopic models of quasifission.
Factors Influencing Density-Dependent Groundwater Flow in the Michigan Basin
NASA Astrophysics Data System (ADS)
Sykes, J. F.; Normani, S. D.; Yin, Y.
2010-12-01
Regional-scale density-dependent groundwater flow is analyzed in an approximately 18000 sq km domain of the Michigan basin centered on a site at Tiverton Ontario near the shore of Lake Huron for a proposed deep geologic repository (DGR) for low and intermediate level nuclear waste. Flow was also analyzed in an approximately 600 km west-to-east cross-section through the center of the basin. Both domains extend from the Precambrian basement to the surface and include minimal upscaling of the complex stratigraphy in the basin. The model FRAC3DVS-OPG was used for all analyses. The hydraulic gradients across the basin are small as both Lake Huron and Lake Michigan have the same water surface elevation. As a result, groundwater flow in the basin is expected to be stagnant. Hydrogeologic parameters for the models were developed from borehole and petrophysics data from the DGR site for units from the Cambrian sandstone to the Devonian. Literature data were used for the shallower units in Michigan. Excluding the surficial drift, the hydraulic conductivity in the basin ranges from 3x10e-6 m/s in the Cambrian to less than 10e-14 m/s in the Ordovician sediments. Groundwater flow is sensitive to the distribution of total dissolved solids concentration with concentrations ranging up to 384 g/L in the Guelph formation in the Silurian. Both TDS data from porewater and groundwater at the DGR site and literature data for TDS versus depth were assigned to the sedimentary rock. The TDS distribution with depth for the Precambrian rock was assigned using both data for the Canadian Shield and a literature based model. Data at the DGR site indicates that the Cambrian is overpressured with respect to the surface while the Ordovician sediments are underpressured. It is hypothesized that the underpressures are the result of the presence of a gas phase in the units. The steps in determining a converged solution for saturated density-dependent flow were as follows: (1) solve steady state density-independent flow, (2) assign a TDS concentration distribution and allow the initial equivalent freshwater heads to equilibrate to the fixed TDS distribution, (3) allow the resulting heads to equilibrate to the TDS concentration with solute transport enabled. Convergence of a solution for the regional-scale model was not achieved without the middle step. For the Michigan Basin cross-section, the 3rd step would not yield a converged solution using FRAC3DVS-OPG. Flow in both analyses is sensitive to surface topography and the TDS distribution. The overpressure in the Cambrian could be described by density differences across the basin and surface topography differences. The underpressures can be described with a gas water analysis using TOUGH2-MP. Paleoclimate analyses that included mechanical loading could not describe the underpressures. Flow in the intracratonic Michigan Basin is complex and dynamic as a result of glaciation. Converged solutions are difficult to achieve. Flow in the low permeability units such as those of the Ordovician and Silurian is negligible with solute transport being diffusion dominant. The analyses provide a bench mark for evaluating the upscaling of stratigraphic units required in continental-scale simulations.
ERIC Educational Resources Information Center
Ipek, Ismail
2011-01-01
The purpose of this study was to investigate the effects of variations in text density levels and the cognitive style of field dependence on learning from a CBI tutorial, based on the dependent measures of achievement, reading comprehension, and reading rate, and of lesson completion time. Eighty college undergraduate students were randomlyâ€¦
A relativistic time-dependent density functional study of the excited states of the mercury dimer
Kullie, Ossama E-mail: ossama.kullie@unistra.fr
2014-01-14
In previous works on Zn{sub 2} and Cd{sub 2} dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s{sup 2} + 6s6p), (6s{sup 2} + 6s7s), and (6s{sup 2} + 6s7p) atomic asymptotes for the mercury dimer Hg{sub 2}. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg{sub 2} including a comparative analysis with the lighter dimers of the group 12, Cd{sub 2}, and Zn{sub 2}, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg{sub 2}.
Thermodynamic evidence for a valley-dependent density of states in bulk bismuth
NASA Astrophysics Data System (ADS)
Steinke, Lucia
2015-03-01
A moderate magnetic field confines both hole-like and electron-like carriers of semi-metallic bismuth to their lowest Landau levels. In contrast to holes, which are ordinary quasi-particles, electrons in bismuth are described by the Dirac Hamiltonian with a band mass becoming a thousandth of the bare electron mass along one crystalline axis. These Dirac electrons can occupy each of the three rotationally equivalent elongated ellipsoids of the Fermi surface. The valley degeneracy offers electrons an additional degree of freedom, a subject of recent attention. Here, we employ magnetostriction to map the angle-resolved Landau spectrum and quantify the number of electrons in each valley for a magnetic field slightly tilted off the trigonal axis. Unlike transport measurements, magnetostriction provides a thermodynamic probe that directly couples to the density of states: resonances in the magnetostriction coefficient can be linked to the evacuation of Landau levels with increasing field, and electron and hole spectra are distinguished by tracing the angle dependence of the magnetostriction peaks. We find that while the electron valleys remain identical in their spectrum, they substantially differ in their density of states at the Fermi level, with an ~ 20% difference in the peak height for two different electron valleys. This experimental observation establishes that, even in the absence of internal strain, the electron fluid does not keep the rotational symmetry of the lattice, at low temperature and high magnetic field. The valley imbalance is found to be restricted to electrons in the immediate vicinity of the Fermi level. This effect, reminiscent of Coulomb pseudo-gap in localized electronic state, emerges as the most striking departure from the non-interacting picture of electrons in bulk bismuth in the vicinity of the quantum limit.
NASA Astrophysics Data System (ADS)
Bast, Radovan; Jensen, Hans Jørgen Aa; Saue, Trond
We report an implementation of adiabatic time-dependent density functional theory based on the 4-component relativistic Dirac-Coulomb Hamiltonian and a closed-shell reference. The implementation includes noncollinear spin magnetization and full derivatives of functionals, including hybrid generalized gradient approximation (GGA) functionals. We avoid reducing the generalized eigenvalue problem to half the dimension involving the square of excitation energies since this may introduce spurious roots and also squares the matrix condition number. Rather we impose structure in terms of hermiticity and time reversal symmetry on trial vectors to obtain even better reductions in terms of memory and run time, and without invoking approximations. Further reductions are obtained by exploiting point group symmetries for D2h and subgroups in a symmetry scheme where symmetry reductions translate into reduction of algebra from quaternion to complex or real. For hybrid GGAs with noncollinear spin magnetization we derive a new computationally advantageous equation for the full second variational derivatives of such exchange-correlation functionals. We apply our implementation to calculations on the ns2 ? ns1np1 excitation energies in the Zn, Cd, and Hg atoms (n = 4-6) and (vertical) excitation energies of UO 22+; and we test the performance of various functionals by comparison with experimental data (group 12 atoms) or higher-level computational results (UO 22+). The results indicate that the adiabatic local density approximation (ALDA) is a good approximation for some GGA functionals, but not all. Furthermore, the results also indicate that ALDA is an extremely bad approximation for hybrid functionals, unless one only employs ALDA for the pure DFT contribution to the exchange-correlation kernel and retains the fraction of exact exchange; we denote this approximation ALDAh.
The Dependency Structure of Coordinate Phrases: A Corpus Approach
ERIC Educational Resources Information Center
Temperley, David
2005-01-01
Hudson (1990) proposes that each conjunct in a coordinate phrase forms dependency relations with heads or dependents outside the coordinate phrase (the "multi-head" view). This proposal is tested through corpus analysis of Wall Street Journal text. For right-branching constituents (such as direct-object NPs), a short-long preference for conjunct…
Accuracy of estimated geometric parameters of trees depending on the LIDAR data density
NASA Astrophysics Data System (ADS)
Hadas, Edyta; Estornell, Javier
2015-04-01
The estimation of dendrometric variables has become important for spatial planning and agriculture projects. Because classical field measurements are time consuming and inefficient, airborne LiDAR (Light Detection and Ranging) measurements are successfully used in this area. Point clouds acquired for relatively large areas allows to determine the structure of forestry and agriculture areas and geometrical parameters of individual trees. In this study two LiDAR datasets with different densities were used: sparse with average density of 0.5pt/m2 and the dense with