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Sample records for density dependent approach

  1. 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.

  2. Intermolecular forces and nonbonded interactions: Superoperator nonlinear time-dependent density-functional-theory response approach

    SciTech Connect

    Harbola, Upendra; Mukamel, Shaul

    2004-11-01

    Electrostatic and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge-density response functions of the isolated molecules, which in turn are expanded using the collective electronic oscillator (CEO) eigenmodes of linearized time-dependent density-functional theory. Closed expressions for the intermolecular energy are derived to sixth order in charge fluctuation amplitudes.

  3. A consumer-resource approach to the density-dependent population dynamics of mutualism

    USGS Publications Warehouse

    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.

  4. Mixed quantum-classical dynamics with time-dependent external fields: A time-dependent density-functional-theory approach

    SciTech Connect

    Tavernelli, Ivano; Curchod, Basile F. E.; Rothlisberger, Ursula

    2010-05-15

    A mixed quantum-classical method aimed at the study of nonadiabatic dynamics in the presence of external electromagnetic fields is developed within the framework of time-dependent density functional theory. To this end, we use a trajectory-based description of the quantum nature of the nuclear degrees of freedom according to Tully's fewest switches trajectories surface hopping, where both the nonadiabatic coupling elements between the different potential energy surfaces, and the coupling with the external field are given as functionals of the ground-state electron density or, equivalently, of the corresponding Kohn-Sham orbitals. The method is applied to the study of the photodissociation dynamics of some simple molecules in gas phase.

  5. Hot-electron-assisted femtochemistry at surfaces: A time-dependent density functional theory approach

    NASA Astrophysics Data System (ADS)

    Gavnholt, Jeppe; Rubio, Angel; Olsen, Thomas; Thygesen, Kristian S.; Schiøtz, Jakob

    2009-05-01

    Using time-evolution time-dependent density functional theory (TDDFT) within the adiabatic local-density approximation, we study the interactions between single electrons and molecular resonances at surfaces. Our system is a nitrogen molecule adsorbed on a ruthenium surface. The surface is modeled at two levels of approximation, first as a simple external potential and later as a 20-atom cluster. We perform a number of calculations on an electron hitting the adsorbed molecule from inside the surface and establish a picture, where the resonance is being probed by the hot electron. This enables us to extract the position of the resonance energy through a fitting procedure. It is demonstrated that with the model we can extract several properties of the system, such as the presence of resonance peaks, the time electrons stay on the molecule before returning to the surface when hitting a molecular resonance and the lowering of the resonance energy due to an image charge effect. Finally we apply the TDDFT procedure to only consider the decay of molecular excitations and find that it agrees quite well with the width of the projected density of Kohn-Sham states.

  6. Linear optical response of current-carrying molecular junction: a nonequilibrium Green's function-time-dependent density functional theory approach.

    PubMed

    Galperin, Michael; Tretiak, Sergei

    2008-03-28

    We propose a scheme for calculation of linear optical response of current-carrying molecular junctions for the case when electronic tunneling through the junction is much faster than characteristic time of external laser field. We discuss relationships between nonequilibrium Green's function (NEGF) and time-dependent density functional theory (TDDFT) approaches and derive expressions for optical response and linear polarizability within NEGF-TDDFT scheme. Corresponding results for isolated molecule, derived within TDDFT approach previously, are reproduced when coupling to contacts is neglected. PMID:18376958

  7. Analytic derivative couplings in time-dependent density functional theory: Quadratic response theory versus pseudo-wavefunction approach

    SciTech Connect

    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.

  8. Analytical approach for the excited-state Hessian in time-dependent density functional theory: Formalism, implementation, and performance

    NASA Astrophysics Data System (ADS)

    Liu, Jie; Liang, WanZhen

    2011-11-01

    The paper presents the formalism, implementation, and performance of the analytical approach for the excited-state Hessian in the time-dependent density functional theory (TDDFT) that extends our previous work [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011)] on the analytical Hessian in TDDFT within Tamm-Dancoff approximation (TDA) to full TDDFT. In contrast to TDA-TDDFT, an appreciable advantage of full TDDFT is that it maintains the oscillator strength sum rule, and therefore yields more precise results for the oscillator strength and other related physical quantities. For the excited-state harmonic vibrational frequency calculation, however, full TDDFT does not seem to be advantageous since the numerical tests demonstrate that the accuracy of TDDFT with and without TDA are comparable to each other. As a common practice, the computed harmonic vibrational frequencies are scaled by a suitable scale factor to yield good agreement with the experimental fundamental frequencies. Here we apply both the optimized ground-state and excited-state scale factors to scale the calculated excited-state harmonic frequencies and find that the scaling decreases the root-mean-square errors. The optimized scale factors derived from the excited-state calculations are slightly smaller than those from the ground-state calculations.

  9. Investigation of intense femto-second laser ionization and dissociation of methane with time-dependent density-functional approach

    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.

  10. Kohn–Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space

    PubMed Central

    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 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

  11. Kohn-Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space.

    PubMed

    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

  12. Kohn-Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space.

    PubMed

    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.

  13. Tight-binding approximations to time-dependent density functional theory — A fast approach for the calculation of electronically excited states

    NASA Astrophysics Data System (ADS)

    Rüger, Robert; van Lenthe, Erik; Heine, Thomas; Visscher, Lucas

    2016-05-01

    We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.

  14. Evolution in population parameters: density-dependent selection or density-dependent fitness?

    PubMed

    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.

  15. First principles calculation of field emission from nanostructures using time-dependent density functional theory: A simplified approach

    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.

  16. Density-dependent covariant energy density functionals

    SciTech Connect

    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.

  17. Density dependence of nuclear symmetry energy

    NASA Astrophysics Data System (ADS)

    Behera, B.; Routray, T. R.; Tripathy, S. K.

    2016-10-01

    High density behavior of nuclear symmetry energy is studied on the basis of the stiffest density dependence of asymmetric contribution to energy per nucleon in charge neutral n + p + e + μ matter under beta equilibrium. The density dependence of nuclear symmetry energy obtained in this way is neither very stiff nor soft at high densities and is found to be in conformity with recent observations of neutron stars.

  18. Pseudospectral time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Ko, Chaehyuk; Malick, David K.; Braden, Dale A.; Friesner, Richard A.; Martínez, Todd J.

    2008-03-01

    Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.

  19. Density-dependent adjustment of inducible defenses

    PubMed Central

    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

  20. The cosmological dependence of cluster density profiles

    NASA Astrophysics Data System (ADS)

    Crone, Mary M.; Evrard, August E.; Richstone, Douglas O.

    1994-10-01

    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 kn. Einstein-de Sitter, open (Omega0 = 0.2 and 0.1) and flat, low density (Omega0 = 0.2 lambda0 = 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-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 Omega0. The Omega0 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 (106) accessible with our resolution. The low-density models show significant deviation from a power law above density contrasts approximately 105. We interpret this curvature as reflecting the non-scale-invariant nature of the background cosmology in these models. These

  1. 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

  2. Evolution of density-dependent cooperation.

    PubMed

    Seppänen, 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.

  3. Patterns of density dependence in measles dynamics.

    PubMed Central

    Finkenstädt, B; Keeling, M; Grenfell, B

    1998-01-01

    An important question in metapopulation dynamics is the influence of external perturbations on the population's long-term dynamic behaviour. In this paper we address the question of how spatiotemporal variations in demographic parameters affect the dynamics of measles populations in England and Wales. Specifically, we use nonparametric statistical methods to analyse how birth rate and population size modulate the negative density dependence between successive epidemics as well as their periodicity. For the observed spatiotemporal data from 60 cities, and for simulated model data, the demographic variables act as bifurcation parameters on the joint density of the trade-off between successive epidemics. For increasing population size, a transition occurs from an irregular unpredictable pattern in small communities towards a regular, predictable endemic pattern in large places. Variations in the birth rate parameter lead to a bifurcation from annual towards biennial cyclicity in both observed data and model data. PMID:9628034

  4. The computational foundations of time dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Whitfield, James

    2014-03-01

    The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. Since a quantum computer can efficiently produce such time-dependent densities, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds. Further, we find that systems do not immediately become non-representable but rather become ill-representable as one approaches this boundary. A representability parameter is defined in our work which quantifies the distance to the boundary of representability and the computational difficulty of finding the Kohn-Sham system.

  5. Sublinear scaling for time-dependent stochastic density functional theory

    SciTech Connect

    Gao, Yi; Neuhauser, Daniel; Baer, Roi; Rabani, Eran

    2015-01-21

    A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (≈16) of such orbitals is enough to obtain meaningful results for absorption spectrum and the RPA correlation energy per electron. We implement the approach for silicon nanocrystals using real-space grids and find that the overall scaling of the algorithm is sublinear with computational time and memory.

  6. An approach to fast fits of the unintegrated gluon density

    SciTech Connect

    Knutsson, Albert; Bacchetta, Alessandro; Kutak, Krzyzstof; Jung, Hannes

    2009-01-01

    An approach to fast fits of the unintegrated gluon density has been developed and used to determine the unintegrated gluon density by fits to deep inelastic scatting di-jet data from HERA. The fitting method is based on the determination of the parameter dependence by help of interpolating between grid points in the parameter-observable space before the actual fit is performed.

  7. Evolution of density- and patch-size-dependent dispersal rates.

    PubMed Central

    Poethke, Hans Joachim; Hovestadt, Thomas

    2002-01-01

    Based on a marginal value approach, we derive a nonlinear expression for evolutionarily stable (ES) dispersal rates in a metapopulation with global dispersal. For the general case of density-dependent population growth, our analysis shows that individual dispersal rates should decrease with patch capacity and-beyond a certain threshold-increase with population density. We performed a number of spatially explicit, individual-based simulation experiments to test these predictions and to explore further the relevance of variation in the rate of population increase, density dependence, environmental fluctuations and dispersal mortality on the evolution of dispersal rates. They confirm the predictions of our analytical approach. In addition, they show that dispersal rates in metapopulations mostly depend on dispersal mortality and inter-patch variation in population density. The latter is dominantly driven by environmental fluctuations and the rate of population increase. These conclusions are not altered by the introduction of neighbourhood dispersal. With patch capacities in the order of 100 individuals, kin competition seems to be of negligible importance for ES dispersal rates except when overall dispersal rates are low. PMID:11916481

  8. Stochasticity and determinism: how density-independent and density-dependent processes affect population variability.

    PubMed

    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

  9. Density dependence in Caenorhabditis larval starvation.

    PubMed

    Artyukhin, Alexander B; Schroeder, Frank C; Avery, Leon

    2013-09-27

    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.

  10. Statistical approach to nuclear level density

    SciTech Connect

    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.

  11. Nuclear level density: Shell-model approach

    NASA Astrophysics Data System (ADS)

    Sen'kov, Roman; Zelevinsky, Vladimir

    2016-06-01

    Knowledge of the nuclear level density is necessary for understanding various reactions, including those in the stellar environment. Usually the combinatorics of a Fermi gas plus pairing is used for finding the level density. Recently a practical algorithm avoiding diagonalization of huge matrices was developed for calculating the density of many-body nuclear energy levels with certain quantum numbers for a full shell-model Hamiltonian. The underlying physics is that of quantum chaos and intrinsic thermalization in a closed system of interacting particles. We briefly explain this algorithm and, when possible, demonstrate the agreement of the results with those derived from exact diagonalization. The resulting level density is much smoother than that coming from conventional mean-field combinatorics. We study the role of various components of residual interactions in the process of thermalization, stressing the influence of incoherent collision-like processes. The shell-model results for the traditionally used parameters are also compared with standard phenomenological approaches.

  12. THE DEPENDENCE OF STAR FORMATION EFFICIENCY ON GAS SURFACE DENSITY

    SciTech Connect

    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.

  13. Alternative Approaches to High Energy Density Fusion

    NASA Astrophysics Data System (ADS)

    Hammer, J.

    2016-10-01

    This paper explores selected approaches to High Energy Density (HED) fusion, beginning with discussion of ignition requirements at the National Ignition Facility (NIF). The needed improvements to achieve ignition are closely tied to the ability to concentrate energy in the implosion, manifested in the stagnation pressure, Pstag. The energy that must be assembled in the imploded state to ignite varies roughly as Pstag-2, so among other requirements, there is a premium on reaching higher Pstag to achieve ignition with the available laser energy. The U.S. inertial confinement fusion program (ICF) is pursuing higher Pstag on NIF through improvements to capsule stability and symmetry. One can argue that recent experiments place an approximate upper bound on the ultimate ignition energy requirement. Scaling the implosions consistently in spatial, temporal and energy scales shows that implosions of the demonstrated quality ignite robustly at 9-15 times the current energy of NIF. While lasers are unlikely to reach that bounding energy, it appears that pulsed-power sources could plausibly do so, giving a range of paths forward for ICF depending on success in improving energy concentration. In this paper, I show the scaling arguments then discuss topics from my own involvement in HED fusion. The recent Viewfactor experiments at NIF have shed light on both the observed capsule drive deficit and errors in the detailed modelling of hohlraums. The latter could be important factors in the inability to achieve the needed symmetry and energy concentration. The paper then recounts earlier work in Fast Ignition and the uses of pulsed-power for HED and fusion applications. It concludes with a description of a method for improving pulsed-power driven hohlraums that could potentially provide a factor of 10 in energy at NTF-like drive conditions and reach the energy bound for indirect drive ICF.

  14. Alternative Approaches to High Energy Density Fusion

    NASA Astrophysics Data System (ADS)

    Hammer, J.

    2016-03-01

    This paper explores selected approaches to High Energy Density (HED) fusion, beginning with discussion of ignition requirements at the National Ignition Facility (NIF). The needed improvements to achieve ignition are closely tied to the ability to concentrate energy in the implosion, manifested in the stagnation pressure, Pstag . The energy that must be assembled in the imploded state to ignite varies roughly as Pstag -2, so among other requirements, there is a premium on reaching higher Pstag to achieve ignition with the available laser energy. The U.S. inertial confinement fusion program (ICF) is pursuing higher Pstag on NIF through improvements to capsule stability and symmetry. One can argue that recent experiments place an approximate upper bound on the ultimate ignition energy requirement. Scaling the implosions consistently in spatial, temporal and energy scales shows that implosions of the demonstrated quality ignite robustly at 9-15 times the current energy of NIF. While lasers are unlikely to reach that bounding energy, it appears that pulsed-power sources could plausibly do so, giving a range of paths forward for ICF depending on success in improving energy concentration. In this paper, I show the scaling arguments then discuss topics from my own involvement in HED fusion. The recent Viewfactor experiments at NIF have shed light on both the observed capsule drive deficit and errors in the detailed modelling of hohlraums. The latter could be important factors in the inability to achieve the needed symmetry and energy concentration. The paper then recounts earlier work in Fast Ignition and the uses of pulsed- power for HED and fusion applications. It concludes with a description of a method for improving pulsed-power driven hohlraums that could potentially provide a factor of 10 in energy at NIF-like drive conditions and reach the energy bound for indirect drive ICF.

  15. Limitations of methods to test density-dependent fecundity hypothesis.

    PubMed

    Beja, Pedro; Palma, Luis

    2008-03-01

    1. Two main hypotheses are usually invoked to explain density dependence in fecundity: the habitat heterogeneity hypothesis (HHH) and the individual adjustment hypothesis (IAH). Although simple methods have been proposed to discriminate between the two hypotheses, their adequacy was tested for only a limited set of real and model populations. 2. In a computer simulation study based on a stochastic territory-based approach, Ferrer, Newton & Casado (2006, Journal of Animal Ecology, 75, 111-117) argued that a strong negative relationship between mean fecundity and its skewness in stable or increasing populations provides critical support for HHH, as this relationship should be lacking under IAH. A negative relationship between mean fecundity and its coefficient of variation (CV) was predicted under both hypotheses, although with a lower slope under IAH. 3. We used a comparable simulation approach, with model populations parameterized from an increasing Bonelli's eagle Hieraaetus fasciatus population (1992-2006), to show that both HHH and IAH can produce indistinguishable relationships between mean fecundity and both its CV and its skewness. 4. Strong negative correlations between the mean and both its CV and its skewness can emerge as statistical artifacts under biologically plausible assumptions, and so they may be largely inadequate to infer mechanisms underlying density dependence in demographic parameters. PMID:18254920

  16. Elevational variation in density dependence in a subtropical forest

    PubMed Central

    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

  17. Density-Dependent Growth in Invasive Lionfish (Pterois volitans)

    PubMed Central

    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

  18. Pathogens, density dependence and the coexistence of tropical trees

    PubMed Central

    Freckleton, Robert P; Lewis, Owen T

    2006-01-01

    There is increasing interest in the role played by density-dependent mortality from natural enemies, particularly plant pathogens, in promoting the coexistence and diversity of tropical trees. Here, we review four issues in the analysis of pathogen-induced density dependence that have been overlooked or inadequately addressed. First, the methodology for detecting density dependence must be robust to potential biases. Observational studies, in particular, require a careful analysis to avoid biases generated by measurement error, and existing studies could be criticized on these grounds. Experimental studies manipulating plant density and pathogen incidence will often be preferable, or should be run in parallel. Second, the form of density dependence is not well understood and, in particular, there are no data indicating whether pathogens cause compensating or overcompensating density responses. Owing to this, we argue that the potential for pathogen-induced density dependence to generate diversity-enhancing outcomes, such as the Janzen–Connell effect, remains uncertain, as coexistence is far more probable if density dependence is overcompensating. Third, there have been few studies examining the relative importance of intra- or interspecific density dependence resulting from pathogens (or, more widely, natural enemies). This is essentially equivalent to asking to what extent pathogens are host-specific. If pathogens are generalists, then mortality rates will respond to overall plant density, irrespective of plant species identity. This will weaken the intraspecific density dependence and reduce the diversity-promoting effects of pathogens. Finally, we highlight the need for studies that integrate observations and experiments on pathogens and density dependence into the whole life cycle of trees, because as yet it is not possible to be certain of the degree to which pathogens contribute to observed dynamics. PMID:17015362

  19. Information density and dependency length as complementary cognitive models.

    PubMed

    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.

  20. Density-dependent acoustic properties of PBX 9502

    SciTech Connect

    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.

  1. Density-potential mapping in time-dependent density-functional theory

    SciTech Connect

    Maitra, N. T.; Todorov, T. N.; Woodward, C.; Burke, K.

    2010-04-15

    The key questions of uniqueness and existence in time-dependent density-functional theory are usually formulated only for potentials and densities that are analytic in time. Simple examples, standard in quantum mechanics, lead, however, to nonanalyticities. We reformulate these questions in terms of a nonlinear Schroedinger equation with a potential that depends nonlocally on the wave function.

  2. Regulation of Aedes aegypti Population Dynamics in Field Systems: Quantifying Direct and Delayed Density Dependence

    PubMed Central

    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

  3. Dynamical instabilities in density-dependent hadronic relativistic models

    SciTech Connect

    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.

  4. Evolution of behavior by density-dependent natural selection.

    PubMed

    Guo, P Z; Mueller, L D; Ayala, F J

    1991-12-01

    Theories of density-dependent natural selection predict that evolution should favor those genotypes with the highest per capita rates of population growth under the current density conditions. These theories are silent about the mechanisms that may give rise to these increases in density-dependent growth rates. We have observed the evolution of six populations of Drosophila melanogaster recently placed in crowded environments after nearly 200 generations at low-population density in the laboratory. After 25 generations in these crowded cultures all six populations showed the predicted increase in population growth rates at high-population density with the concomitant decrease in their growth rates at low densities. These changes in rates of population growth are accompanied by changes in the feeding and pupation behavior of the larvae: those populations that have evolved at high-population densities have higher feeding rates and are less likely to pupate on or near the food surface than populations maintained at low densities. These changes in behavior serve to increase the competitive ability of larvae for limited food and reduce mortality under crowded conditions during the pupal stage of development. A detailed understanding of the mechanisms by which populations evolve under density-dependent natural selection will provide a framework for understanding the nature of trade-offs in life history evolution.

  5. Evolution of behavior by density-dependent natural selection

    SciTech Connect

    Pingzhong Guo; Mueller, L.D.; Ayala, F.J. )

    1991-12-01

    Theories of density-dependent natural selection predict that evolution should favor those genotypes with the highest per capita rates of population growth under the current density conditions. These theories are silent about the mechanisms that may give rise to these increases in density-dependent growth rates. The authors have observed the evolution of six populations of Drosophila melanogaster recently placed in crowded environments after nearly 200 generations at low-population density in the laboratory. After 25 generations in these crowded cultures all six populations showed the predicted increase in population growth rates at high-population density with the concomitant decrease in their growth rates at low densities. These changes in rates of population growth are accompanied by changes in the feeding and pupation behavior of the larvae: those populations that have evolve at high-population densities have higher feeding rates and are less likely to pupate on or near the food surface than populations maintained at low densities. A detailed understanding of the mechanisms by which populations evolve under density-dependent natural selection will provide a framework for understanding that nature of trade-offs in life history evolution.

  6. Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird.

    PubMed

    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

  7. Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird.

    PubMed

    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.

  8. Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird

    PubMed Central

    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

  9. An infrastructureless approach to estimate vehicular density in urban environments.

    PubMed

    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

  10. Female elk contacts are neither frequency nor density dependent

    USGS Publications Warehouse

    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 (∼2 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.

  11. Female elk contacts are neither frequency nor density dependent.

    PubMed

    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

  12. Transverse momentum dependent quark densities from Lattice QCD

    SciTech Connect

    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.

  13. Competition and the density dependence of metabolic rates.

    PubMed

    DeLong, John P; Hanley, Torrance C; Vasseur, David A

    2014-01-01

    Although mass and temperature are strong predictors of metabolic rates, there is considerable unexplained variation in metabolic rates both within and across species after body size and temperature are taken into account. Some of this variation may be due to changes in the rate of food intake with population density, as metabolism depends on the throughput of food to fuel biochemical reactions. Using data collected from the literature, we show that individual metabolic rates are negatively correlated with population density for a wide range of organisms including primary producers and consumers. Using new data for the zooplankter Daphnia ambigua, we also find genotypic variation in the relationship between metabolic rate and population density. The relationship between metabolic rate and population density generally follows a power law scaling, and within a population, density-correlated variation in metabolism can span two orders of magnitude. We suggest that density-dependent metabolic rates arise via competitive effects on foraging rates (both exploitation and interference competition), combined with an activity response to accommodate the resource constraint induced by competition. Standard ecological models predict the kind of density-dependent foraging patterns that could give rise to density-dependent metabolic rates, but this has generally not been investigated. Our results indicate that after body mass and temperature, population density represents an important third axis that may account for a large amount of unexplained variance in metabolic rates within and among species. The effect of population density on metabolism has implications for the scaling of metabolic rates from individuals to populations and the relative performance of species and genotypes and therefore also for community assembly and evolution.

  14. Transverse momentum dependent quark densities from Lattice QCD

    SciTech Connect

    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.

  15. Parity dependence of level densities in sup 49 V

    SciTech Connect

    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.

  16. Computational complexity of time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Whitfield, J. D.; Yung, M.-H.; Tempel, D. G.; Boixo, S.; Aspuru-Guzik, A.

    2014-08-01

    Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. We introduce a V-representability parameter which diverges at the boundary of the existence domain and serves to quantify the numerical difficulty of constructing the Kohn-Sham potential. For bounded values of V-representability, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds.

  17. Nonlinear Density Dependence of Singlet Fission Rate in Tetracene Films.

    PubMed

    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

  18. 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

  19. Sleep- and circadian-dependent modulation of REM density.

    PubMed

    Khalsa, Sat Bir S; Conroy, Deirdre A; Duffy, Jeanne F; Czeisler, Charles A; Dijk, Derk-Jan

    2002-03-01

    Rapid eye movement (REM) density, a measure of the frequency of rapid eye movements during REM sleep, is known to increase over the course of the sleep episode. However, the circadian modulation of REM density has not been thoroughly evaluated. Data from a forced desynchrony protocol, in which 20 consecutive sleep opportunities were systematically scheduled over the entire circadian cycle, were analysed. The REM density was evaluated from polysomnographically recorded REM sleep episodes, and analyzed as a function of time in the sleep opportunity and as a function of phase in the circadian cycle. The REM density showed a robust increase over the course of the sleep episode. This sleep-dependent increase was observed regardless of circadian phase, because data analyzed from different thirds of the circadian cycle exhibited a similar pattern. The REM density did not show a significant circadian-dependent modulation for data from the entire sleep opportunity. However, analysis of circadian modulation from separate thirds of the sleep opportunity revealed a significant circadian modulation in the last third of the sleep episode. Maximum REM densities were observed when the last third of the sleep episode coincided with the wake-maintenance zone, i.e.;8-10 h before the crest of the circadian rhythm of REM sleep propensity. These results confirm the dominant sleep-dependent modulation of REM density, and indicate that the density of REMs is greatest when sleep pressure is low, such as in the latter part of the sleep episode, at which time the circadian modulation of REM density is also appreciable.

  20. Consistent tangent matrices for density-dependent finite plasticity models

    NASA Astrophysics Data System (ADS)

    Pérez-Foguet, Agustí; Rodríguez-Ferran, Antonio; Huerta, Antonio

    2001-09-01

    The consistent tangent matrix for density-dependent plastic models within the theory of isotropic multiplicative hyperelastoplasticity is presented here. Plastic equations expressed as general functions of the Kirchhoff stresses and density are considered. They include the Cauchy-based plastic models as a particular case. The standard exponential return-mapping algorithm is applied, with the density playing the role of a fixed parameter during the nonlinear plastic corrector problem. The consistent tangent matrix has the same structure as in the usual density-independent plastic models. A simple additional term takes into account the influence of the density on the plastic corrector problem. Quadratic convergence results are shown for several representative examples involving geomaterial and powder constitutive models.

  1. Fitness and density-dependent population growth in Drosophila melanogaster

    SciTech Connect

    Mueller, L.D.; Ayala, F.J.

    1981-03-01

    The density-dependent rates of population growth were determined for 26 populations of Drosophila melanogaster maintained in the serial transfer system. Twenty-five populations were homozygous for an entire chromosome 2 sampled from nature; the other was a random heterozygous population. Rates of population growth around the carrying capacity cannot explain the large fitness depression of these lines. However, the homozygous lines show large differences in rates of population growth at low densities relative to the random heterozygous standard. The average relative fitness of the homozygous lines, as determined from the growth rates at the lowest density, is 0.51.

  2. 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.

  3. A Wigner Monte Carlo approach to density functional theory

    SciTech Connect

    Sellier, J.M. Dimov, I.

    2014-08-01

    In order to simulate quantum N-body systems, stationary and time-dependent density functional theories rely on the capacity of calculating the single-electron wave-functions of a system from which one obtains the total electron density (Kohn–Sham systems). In this paper, we introduce the use of the Wigner Monte Carlo method in ab-initio calculations. This approach allows time-dependent simulations of chemical systems in the presence of reflective and absorbing boundary conditions. It also enables an intuitive comprehension of chemical systems in terms of the Wigner formalism based on the concept of phase-space. Finally, being based on a Monte Carlo method, it scales very well on parallel machines paving the way towards the time-dependent simulation of very complex molecules. A validation is performed by studying the electron distribution of three different systems, a Lithium atom, a Boron atom and a hydrogenic molecule. For the sake of simplicity, we start from initial conditions not too far from equilibrium and show that the systems reach a stationary regime, as expected (despite no restriction is imposed in the choice of the initial conditions). We also show a good agreement with the standard density functional theory for the hydrogenic molecule. These results demonstrate that the combination of the Wigner Monte Carlo method and Kohn–Sham systems provides a reliable computational tool which could, eventually, be applied to more sophisticated problems.

  4. Density-dependent nest predation in waterfowl: the relative importance of nest density versus nest dispersion

    USGS Publications Warehouse

    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.

  5. The northern Yellowstone elk: density dependence and climatic conditions

    USGS Publications Warehouse

    Taper, Mark L.; Gogan, Peter J.P.

    2002-01-01

    We analyzed a time series of estimates of elk (Cervus elaphus) numbers on the northern Yellowstone winter range from 1964 to 1979 and 1986 to 1995 using a variety of discrete time stochastic population dynamic models. These models included adjustments for density, an increase in the area of winter range used by elk, lagged effects of the weather covariates of spring precipitation, snow depth and winter temperature, and the impacts of the 1988 drought and fires. An information-criteria-based model-selection process strongly supported evidence of density dependence. The best model, a Ricker model, distinguished between the 2 time periods. The bulk of the difference between the 2 periods is attributed to an increase in the amount of winter range used by elk. Inclusion of the covariates spring precipitation and spring precipitation squared greatly improved the model fit. We detected a short-lived increase in elk population growth rate following the 1988 drought and fires. Fertility and survivorship of adults appeared to have different density-dependent forms that together result in a biphasic relationships between population growth rate and density. This study confirms the presence of density-dependent regulation in the norther Yellowstone elk herd, and enhances our understanding of population dynamics of these ungulates.

  6. Cuticular antifungals in spiders: density- and condition dependence.

    PubMed

    González-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.

  7. Cuticular Antifungals in Spiders: Density- and Condition Dependence

    PubMed Central

    González-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

  8. The Gravitational Effect of the Ocean Density Contrast for a Depth-Dependent Seawater Density Model

    NASA Astrophysics Data System (ADS)

    Novak, P.; Tenzer, R.; Gladkikh, V.

    2010-12-01

    In geophysical studies investigating the lithosphere structure, the topographic and consolidated crust density contrast stripping corrections are computed and applied to observed gravity data. The gravitational field generated by the ocean density contrast represents a significant amount of the signal to be modelled and subsequently subtracted from the gravity field. The ocean density contrast is typically calculated as the difference between the mean density values of the Earth’s crust and seawater. The currently available global geopotential models and the global elevation and bathymetry (ocean bottom depth) data allow modelling the topography corrected and bathymetry stripped gravity field quantities to a very high spectral resolution (up to degree 2159 of spherical harmonics) using methods for a spherical harmonic analysis and synthesis of the gravity field. The approximation of the actual seawater density distribution by the mean value yields relative errors up to 2% in computed values of the bathymetric stripping corrections. To reduce these errors, we adopt a depth-dependent theoretical model of the seawater density distribution to account for increasing seawater density with pressure/depth. The smaller lateral seawater density variations due to salinity and temperature and other oceanographic factors are not taken into consideration. The approximation of the seawater density by the depth-dependent density model reduces the maximum errors to less than 0.6%. The corresponding depth-averaged errors are below 0.1%. The depth-dependent seawater density model is facilitated in the forward modelling of the bathymetric stripping corrections. The expressions for computing the gravitational field quantities generated by the depth-dependent ocean density contrast are formulated in the spectral representation by means of the spherical bathymetric functions. These newly derived expressions are used to compute globally the bathymetric stripping corrections. The

  9. Density of biogas digestate depending on temperature and composition.

    PubMed

    Gerber, Mandy; Schneider, Nico

    2015-09-01

    Density is one of the most important physical properties of biogas digestate to ensure an optimal dimensioning and a precise design of biogas plant components like stirring devices, pumps and heat exchangers. In this study the density of biogas digestates with different compositions was measured using pycnometers at ambient pressure in a temperature range from 293.15 to 313.15K. The biogas digestates were taken from semi-continuous experiments, in which the marine microalga Nannochloropsis salina, corn silage and a mixture of both were used as feedstocks. The results show an increase of density with increasing total solid content and a decrease with increasing temperature. Three equations to calculate the density of biogas digestate were set up depending on temperature as well as on the total solid content, organic composition and elemental composition, respectively. All correlations show a relative deviation below 1% compared to experimental data.

  10. Density of biogas digestate depending on temperature and composition.

    PubMed

    Gerber, Mandy; Schneider, Nico

    2015-09-01

    Density is one of the most important physical properties of biogas digestate to ensure an optimal dimensioning and a precise design of biogas plant components like stirring devices, pumps and heat exchangers. In this study the density of biogas digestates with different compositions was measured using pycnometers at ambient pressure in a temperature range from 293.15 to 313.15K. The biogas digestates were taken from semi-continuous experiments, in which the marine microalga Nannochloropsis salina, corn silage and a mixture of both were used as feedstocks. The results show an increase of density with increasing total solid content and a decrease with increasing temperature. Three equations to calculate the density of biogas digestate were set up depending on temperature as well as on the total solid content, organic composition and elemental composition, respectively. All correlations show a relative deviation below 1% compared to experimental data. PMID:26026294

  11. Density-dependent effects of prey defenses and predator offenses.

    PubMed

    Jeschke, Jonathan M

    2006-10-21

    Defenses protect prey, while offenses arm predators. Some defenses and offenses are constitutive (e.g. tortoise shells), while others are phenotypically plastic and not always expressed (e.g. neckteeth in water fleas). All of them are costly and only adaptive at certain prey densities. Here, I analyse such density-dependent effects, applying a functional response model to categorize defenses and offenses and qualitatively predict at which prey densities each category should evolve (if it is constitutive) or be expressed (if it is phenotypically plastic). The categories refer to the step of the predation cycle that a defense or offense affects: (1) search, (2) encounter, (3) detection, (4) attack, or (5) meal. For example, prey warning signals such as red coloration prevent predator attacks and are hence step 4 defenses, while sharp predator eyes enhance detection and are step 3 offenses. My theoretical analyses predict that step 1 defenses, which prevent predators from searching for their next meal (e.g. toxic substances), evolve or are expressed at intermediate prey densities. Other defenses, however, should be most beneficial at low prey densities. Regarding predators, step 1 offenses (e.g. immunity against prey toxins) are predicted to evolve or be expressed at high prey densities, other offenses at intermediate densities. I provide evidence from the literature that supports these predictions.

  12. Observation of number-density-dependent growth of plasmonic nanobubbles

    PubMed Central

    Nakajima, Takashi; Wang, Xiaolong; Chatterjee, Souvik; Sakka, Tetsuo

    2016-01-01

    Interaction dynamics of laser pulses and nanoparticles are of great interest in recent years. In many cases, laser-nanoparticle interactions result in the formation of plasmonic nanobubbles, and the dynamics of nanoparticles and nanobubbles are inseparable. So far, very little attention has been paid to the number density. Here we report the first observation of number-density-dependent growth of plasmonic nanobubbles. Our results show that the nanobubbles growth depends (does not depend) on the number density at high (low) laser fluence, although the inter-particle distance in the solution is as long as 14–30 μm. This cannot be explained by the existing physical picture, and we propose a new model which takes into account the pressure waves arising from nanoparticles. The numerical results based on this model agree well with the experimental results. Our findings imply that the number density can be a new doorknob to control laser-nanobubble as well as laser-nanoparticle interactions. PMID:27354184

  13. 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.

  14. Dependence of polar hole density on magnetic and solar conditions

    SciTech Connect

    Hoegy, W.R.; Grebowsky, J.M. )

    1991-04-01

    The dependence of electron density in the polar F region ionization hole on solar activity, universal time (UT), magnetic activity, season, and hemisphere is studied using data from the Langmuir probes on Atmosphere Explorer C and Dynamics Explorer 2. The AE-C data were obtained during solar minimum when the 3-month average 10.7-cm solar flux index varied from 70 to 140; the DE 2 data were obtained near solar maximum when 10.7-cm solar flux index varied from 120 to 220. The polar hole is a region on the nightside of the polar cap where reduced ionization exists because of the long transport time of ionization from the dayside across the polar cap. The behavior of this region as a function of 10.7-cm solar flux (F10.7), UT, and Kp is statistically modeled for equinox, summer, and winter conditions for each hemisphere separately. The strongest dependencies are observed in F10.7 and UT; the Kp dependence is weak because it poorly represents the complexities of convection across the polar cap. 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: there is a density minimum at about 20.3 hours UT in the south and at about 4.8 hours UT in the north; the minimum to maximum UT density variation is about a factor of 8.9 in the south and about a factor of 2.1 in the north. There is a seasonal variation in the dependence of ion density (N{sub i}) on solar flux (F10.7). Use of the relationship (N{sub i}{approximately}F10.7{sup D}) yields values of D of approximately unity (1.) in the summer polar hole and about 2.1 during equinox. There is an overall asymmetry in the density level between hemispheres; it was found that the winter hole density is about a factor of 10 greater in the north than in the south. The Utah State University time dependent ionosphere model gives similar UT behavior to that found in the AE-C and DE 2 data.

  15. Modelling interactions of toxicants and density dependence in wildlife populations

    USGS Publications Warehouse

    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 μg 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

  16. Advances in time-dependent current-density functional theory

    NASA Astrophysics Data System (ADS)

    Berger, Arjan

    In this work we solve the problem of the gauge dependence of molecular magnetic properties (magnetizabilities, circular dichroism) using time-dependent current-density functional theory [1]. We also present a new functional that accurately describes the optical absorption spectra of insulators, semiconductors and metals [2] N. Raimbault, P.L. de Boeij, P. Romaniello, and J.A. Berger Phys. Rev. Lett. 114, 066404 (2015) J.A. Berger, Phys. Rev. Lett. 115, 137402 (2015) This study has been partially supported through the Grant NEXT No. ANR-10-LABX-0037 in the framework of the Programme des Investissements d'Avenir.

  17. Autoionization in time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Kapoor, V.

    2016-06-01

    We compute the exact exchange-correlation potential of the time-dependent density-functional theory (TDDFT) for the correlated process of autoionization. The potential develops barriers which regulate the autoionization rate. TDDFT employing known and practicable exchange-correlation potentials does not capture any autoionization dynamics. Approximate exchange-correlation potentials capturing such dynamics would necessarily require memory effects and are unlikely to be developed, as will be illustrated.

  18. Numerical density-to-potential inversions in time-dependent density functional theory.

    PubMed

    Jensen, Daniel S; Wasserman, Adam

    2016-08-01

    We treat the density-to-potential inverse problem of time-dependent density functional theory as an optimization problem with a partial differential equation constraint. The unknown potential is recovered from a target density by applying a multilevel optimization method controlled by error estimates. We employ a classical optimization routine using gradients efficiently computed by the discrete adjoint method. The inverted potential has both a real and imaginary part to reduce reflections at the boundaries and other numerical artifacts. We demonstrate this method on model one-dimensional systems. The method can be straightforwardly extended to a variety of numerical solvers of the time-dependent Kohn-Sham equations and to systems in higher dimensions.

  19. 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 M⊙ pulsars can constrain the parameter of oscillator harmonic κ1≈0.53 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 M⊙ 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.

  20. Quantum Drude friction for time-dependent density functional theory.

    PubMed

    Neuhauser, Daniel; Lopata, Kenneth

    2008-10-01

    sophisticated description of the coupling, and to memory functionals. Our results open the way to very simple finite grid description of scattering and multistage conductance using time-dependent density functional theory away from the linear regime, just as absorbing potentials and self-energies are useful for noninteracting systems and leads. PMID:19045077

  1. Angular-momentum-dependent orbital-free density functional theory.

    PubMed

    Ke, Youqi; Libisch, Florian; Xia, Junchao; Wang, Lin-Wang; Carter, Emily A

    2013-08-01

    Orbital-free (OF) density functional theory (DFT) directly solves for the electron density rather than the wave function of many electron systems, greatly simplifying and enabling large scale first principles simulations. However, the required approximate noninteracting kinetic energy density functionals and local electron-ion pseudopotentials severely restrict the general applicability of conventional OFDFT. Here, we present a new generation of OFDFT called angular-momentum-dependent (AMD)-OFDFT to harness the accuracy of Kohn-Sham DFT and the simplicity of OFDFT. The angular momenta of electrons are explicitly introduced within atom-centered spheres so that the important ionic core region can be accurately described. In addition to conventional OF total energy functionals, we introduce a crucial nonlocal energy term with a set of AMD energies to correct errors due to the kinetic energy density functional and the local pseudopotential. We find that our AMD-OFDFT formalism offers substantial improvements over conventional OFDFT, as we show for various properties of the transition metal titanium.

  2. Implementation Strategies for Orbital-dependent Density Functionals

    NASA Astrophysics Data System (ADS)

    Bento, Marsal E.; Vieira, Daniel

    2016-10-01

    The development of density functional theory (DFT) has been focused primarily on two main pillars: (1) the pursuit of more accurate exchange-correlation (XC) density functionals; (2) the feasibility of computational implementation when dealing with many-body systems. In this context, this work is aimed on using one-dimensional quantum systems as theoretical laboratories to investigate the implementation of orbital functionals (OFs) of density. By definition, OFs are those which depend only implicitly on the density, via an explicit formulation in terms of Kohn-Sham orbitals. Typical examples are the XC functionals arising from the Perdew-Zunger self-interaction correction (PZSIC). Formally, via Kohn-Sham equations, the implementation of OFs must be performed by means of the optimized effective potential method (OEP), which is known by requiring an excessive computational effort even when dealing with few electrons systems. Here, we proceed a systematical investigation aiming to simplify or avoid the OEP procedure, taking as reference the implementation of the PZSIC correction applied to one-dimensional Hubbard chains.

  3. Semivariational approach to QCD at finite temperature and baryon density

    SciTech Connect

    Palumbo, Fabrizio

    2008-07-01

    Recently a new bosonization method has been used to derive, at zero fermion density, an effective action for relativistic field theories whose partition function is dominated by fermionic composites, chiral mesons in the case of QCD. This approach shares two important features with variational methods: the restriction to the subspace of the composites, and the determination of their structure functions by a variational calculation. But unlike standard variational methods it treats excited states on the same footing as the ground state. I show that this bosonization method is an approximation of an exact procedure in which composites are introduced in the presence of fermionic states with the quantum numbers of the constituents (quasiparticles). This procedure consists of an independent Bogoliubov transformation at each time slice. The time-dependent parameters of the transformation are then associated with composite fields. In this way states of nonvanishing fermion (baryon) number (neglected in the bosonization approach) are retained. By the exact procedure I derive an effective action for QCD at finite temperature and baryon density. I test the result on a four-fermion interaction model.

  4. Role of salt sources in density-dependent flow

    NASA Astrophysics Data System (ADS)

    Hidalgo, Juan J.; Carrera, Jesús; Medina, AgustíN.

    2009-05-01

    Flow equation expresses mass conservation for a fluid phase. In density-dependent problems, fluid consists of at least two components, termed salt and water here. Salt sources are usually properly accounted for when salt is dissolved in water (i.e., as a solute) but are neglected otherwise. An analysis of the effect of neglecting pure salt sources on flow regime and concentration distribution is performed. Two test cases are used to illustrate the issue. The first one is the saltwater bucket problem, which consists of adding salt to an otherwise isolated domain. The second one is the Elder problem. Discrepancies in concentrations are moderate for reasonably small salt mass fractions. However, currently available codes yield head drops in response to the addition of salt because fluid mass is kept constant while its density increases. Such results contradict basic physical principles and lead to an inversion in the flow direction.

  5. Density dependence of the saturated velocity in graphene

    NASA Astrophysics Data System (ADS)

    Ferry, D. K.

    2016-11-01

    The saturated velocity of a semiconductor is an important measure in bench-marking performance for either logic or microwave applications. Graphene has been of interest for such applications due to its apparently high value of the saturated velocity. Recent experiments have suggested that this value is very density dependent and can even exceed the band limiting Fermi velocity. Some of these measurements have also suggested that the scattering is dominated by the low energy surface polar mode of the SiO2 substrate. Here, we show that the saturated velocity of graphene on SiO2 is relatively independent of the density and that the scattering is dominated by the high energy surface polar mode of the substrate.

  6. Perspective: Fundamental aspects of time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Maitra, Neepa T.

    2016-06-01

    In the thirty-two years since the birth of the foundational theorems, time-dependent density functional theory has had a tremendous impact on calculations of electronic spectra and dynamics in chemistry, biology, solid-state physics, and materials science. Alongside the wide-ranging applications, there has been much progress in understanding fundamental aspects of the functionals and the theory itself. This Perspective looks back to some of these developments, reports on some recent progress and current challenges for functionals, and speculates on future directions to improve the accuracy of approximations used in this relatively young theory.

  7. Liquid cooled approaches for high density avionics

    NASA Astrophysics Data System (ADS)

    Levasseur, Robert

    Next-generation aircraft will require avionics that provide greater system performance in a smaller volume, a process that requires highly developed thermal management techniques. To meet this need, a liquid-cooled approach has been developed to replace the conventional air-cooled approach for high-power applications. Liquid-cooled chassis and flow-through modules have been developed to limit junction temperatures to acceptable levels. Liquid cooling also permits emergency operation after loss of coolant for longer time intervals, which is desirable for flight-critical airborne applications. Activity to date has emphasized the development of chassis and modules that support the US Department of Defense's (DoD) two-level maintenance initiative as governed by the Joint Integrated Avionics Working Group (JIAWG).

  8. Landauer Approach to Time-Dependent Transport

    NASA Astrophysics Data System (ADS)

    Chen, L. Y.; Nash, P. L.

    Based upon the nonequilibrium Green's function formalism, we present a time-dependent Landauer approach to transport through a mesoscopic system under an ac bias voltage. The system is modeled as an elastic scatterer coupled to large electron reservoirs through perfect conducting wires (leads). The chemical potentials of the reservoirs are driven apart by the bias and, consequently, current flows through the leads from one reservoir to another. We examine the nonequilibrium statistical processes of electrons in the leads. The electronic waves are quantized on the basis of orthonormal wave packets moving along the leads, scattered by the scatterer, and coupled to the reservoirs. The time for an electron to traverse the leads between the source and the drain reservoirs plus the phase delay time caused by the scatterer is found to be the relevant time scale in the time-dependent transport. The frequency dependence of the admittance is fully investigated.

  9. Current density partitioning in time-dependent current density functional theory

    SciTech Connect

    Mosquera, Martín A.; Wasserman, Adam

    2014-05-14

    We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.

  10. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J.; Lopata, Kenneth

    2016-09-01

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  11. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

    PubMed

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

    2016-09-01

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.

  12. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory.

    PubMed

    Sissay, Adonay; Abanador, Paul; Mauger, François; Gaarde, Mette; Schafer, Kenneth J; Lopata, Kenneth

    2016-09-01

    Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals. PMID:27608987

  13. Stochastic seasonality and nonlinear density-dependent factors regulate population size in an African rodent

    USGS Publications Warehouse

    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.

  14. 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.

  15. 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.

  16. Density Relaxation in Time-Dependent Density Functional Theory: Combining Relaxed Density Natural Orbitals and Multireference Perturbation Theories for an Improved Description of Excited States.

    PubMed

    Ronca, Enrico; Angeli, Celestino; Belpassi, Leonardo; De Angelis, Filippo; Tarantelli, Francesco; Pastore, Mariachiara

    2014-09-01

    Making use of the recently developed excited state charge displacement analysis [E. Ronca et al., J. Chem. Phys. 140, 054110 (2014)], suited to quantitatively characterize the charge fluxes coming along an electronic excitation, we investigate the role of the density relaxation effects in the overall description of electronically excited states of different nature, namely, valence, ionic, and charge transfer (CT), considering a large set of prototypical small and medium-sized molecular systems. By comparing the response densities provided by time-dependent density functional theory (TDDFT) and the corresponding relaxed densities obtained by applying the Z-vector postlinear-response approach [N. C. Handy and H. F. Schaefer, J. Chem. Phys. 81, 5031 (1984)] with those obtained by highly correlated state-of-the-art wave function calculations, we show that the inclusion of the relaxation effects is imperative to get an accurate description of the considered excited states. We also examine what happens at the quality of the response function when an increasing amount of Hartree-Fock (HF) exchange is included in the functional, showing that the usually improved excitation energies in the case of CT states are not always the consequence of an improved description of their overall properties. Remarkably, we find that the relaxation of the response densities is always able to reproduce, independently of the extent of HF exchange in the functional, the benchmark wave function densities. Finally, we propose a novel and computationally convenient strategy, based on the use of the natural orbitals derived from the relaxed TDDFT density to build zero-order wave function for multireference perturbation theory calculations. For a significant set of different excited states, the proposed approach provided accurate excitation energies, comparable to those obtained by computationally demanding ab initio calculations.

  17. Density Dependence Triggers Runaway Selection of Reduced Senescence

    PubMed Central

    Seymour, Robert M; Doncaster, C. Patrick

    2007-01-01

    In the presence of exogenous mortality risks, future reproduction by an individual is worth less than present reproduction to its fitness. Senescent aging thus results inevitably from transferring net fertility into younger ages. Some long-lived organisms appear to defy theory, however, presenting negligible senescence (e.g., hydra) and extended lifespans (e.g., Bristlecone Pine). Here, we investigate the possibility that the onset of vitality loss can be delayed indefinitely, even accepting the abundant evidence that reproduction is intrinsically costly to survival. For an environment with constant hazard, we establish that natural selection itself contributes to increasing density-dependent recruitment losses. We then develop a generalized model of accelerating vitality loss for analyzing fitness optima as a tradeoff between compression and spread in the age profile of net fertility. Across a realistic spectrum of senescent age profiles, density regulation of recruitment can trigger runaway selection for ever-reducing senescence. This novel prediction applies without requirement for special life-history characteristics such as indeterminate somatic growth or increasing fecundity with age. The evolution of nonsenescence from senescence is robust to the presence of exogenous adult mortality, which tends instead to increase the age-independent component of vitality loss. We simulate examples of runaway selection leading to negligible senescence and even intrinsic immortality. PMID:18166075

  18. The current density in quantum electrodynamics in time-dependent external potentials and the Schwinger effect

    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.

  19. Nuclear level density of even-even nuclei with temperature-dependent pairing energy

    NASA Astrophysics Data System (ADS)

    Dehghani, V.; Alavi, S. A.

    2016-10-01

    The influence of using a temperature-dependent pairing term on the back-shifted Fermi gas (BSFG) model of nuclear level density of some even-even nuclei has been investigated. We have chosen an approach to determine the adjustable parameters from theoretical calculations, directly. The exact Ginzburg-Landau (EGL) theory was used to determine the temperature-dependent pairing energy as back-shifted parameter of the BSFG model. The level density parameter of the BSFG model has been determined through the Thomas-Fermi approximation. The level densities of 96Mo, 106,112Cd, 106,108Pd, 164Dy, 232Th, 238U and heat capacities of 96Mo and 164Dy nuclei were calculated. Good agreement between theory and experiment was observed.

  20. The dependence of ZnO photoluminescence efficiency on excitation conditions and defect densities

    SciTech Connect

    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.

  1. A new approach for estimating the density of liquids

    NASA Astrophysics Data System (ADS)

    Sakagami, T.; Fuchizaki, K.; Ohara, K.

    2016-10-01

    We propose a novel approach with which to estimate the density of liquids. The approach is based on the assumption that the systems would be structurally similar when viewed at around the length scale (inverse wavenumber) of the first peak of the structure factor, unless their thermodynamic states differ significantly. The assumption was implemented via a similarity transformation to the radial distribution function to extract the density from the structure factor of a reference state with a known density. The method was first tested using two model liquids, and could predict the densities within an error of several percent unless the state in question differed significantly from the reference state. The method was then applied to related real liquids, and satisfactory results were obtained for predicted densities. The possibility of applying the method to amorphous materials is discussed.

  2. A new approach for estimating the density of liquids.

    PubMed

    Sakagami, T; Fuchizaki, K; Ohara, K

    2016-10-01

    We propose a novel approach with which to estimate the density of liquids. The approach is based on the assumption that the systems would be structurally similar when viewed at around the length scale (inverse wavenumber) of the first peak of the structure factor, unless their thermodynamic states differ significantly. The assumption was implemented via a similarity transformation to the radial distribution function to extract the density from the structure factor of a reference state with a known density. The method was first tested using two model liquids, and could predict the densities within an error of several percent unless the state in question differed significantly from the reference state. The method was then applied to related real liquids, and satisfactory results were obtained for predicted densities. The possibility of applying the method to amorphous materials is discussed. PMID:27494268

  3. Linear-response calculation in the time-dependent density functional theory

    SciTech Connect

    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.

  4. Differences in density-dependence drive dual offspring size strategies in fish.

    PubMed

    Olsson, Karin H; Gislason, Henrik; Andersen, Ken Haste

    2016-10-21

    Offspring size reflects the optimal balance between female fecundity and allocation of energy to each offspring. Most fish, in particular teleost species, produce many small eggs, while others, notably elasmobranch species, have low fecundity and large offspring. No general explanation has yet been put forwards to explain these different strategies between species which occupy similar habitats. We approach the problem by (1) examining the differences between life history parameters of teleost fish and elasmobranchs and (2) an evolutionary model. We show that life history parameters characterising growth, mortality and reproductive output are almost similar between teleosts and elasmobranchs. We find that a model which accounts for density-dependence predicts dual offspring size strategies: either invariant with adult size or proportional to adult size. The model predicts that the invariant strategy is associated with an absence of density-dependence in early life whereas proportional offspring are subject to density-dependence throughout life. Parameterising the model using life history data regenerates the observed dual offspring size pattern. We conjecture that the life stage where density-dependent competition occurs is an important factor behind the observed difference in offspring size strategies. PMID:27457096

  5. From patterns to processes: Phase and density dependencies in the Canadian lynx cycle

    PubMed Central

    Stenseth, Nils C.; Falck, Wilhelm; Chan, Kung-Sik; Bjørnstad, Ottar N.; O’Donoghue, Mark; Tong, Howell; Boonstra, Rudy; Boutin, Stan; Krebs, Charles J.; Yoccoz, Nigel G.

    1998-01-01

    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

  6. He 2++ molecular ion in a strong time-dependent magnetic field: a current-density functional study.

    PubMed

    Vikas

    2011-08-01

    The He 2++ molecular ion exposed to a strong ultrashort time-dependent (TD) magnetic field of the order of 10(9) G is investigated through a quantum fluid dynamics (QFD) and current-density functional theory (CDFT) based approach using vector exchange-correlation (XC) potential and energy density functional that depend not only on the electronic charge-density but also on the current density. The TD-QFD-CDFT computations are performed in a parallel internuclear-axis and magnetic field-axis configuration at the field-free equilibrium internuclear separation R = 1.3 au with the field-strength varying between 0 and 10(11) G. The TD behavior of the exchange- and correlation energy of the He 2++ is analyzed and compared with that obtained using a [B-TD-QFD-density functional theory (DFT)] approach based on the conventional TD-DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge-density alone. The CDFT based approach yields TD exchange- and correlation energy and TD electronic charge-density significantly different from that obtained using the conventional TD-DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT-based approach is traced to the TD current-density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He 2++ molecular ion is elucidated by treating electronic charge density as an electron-"fluid" in the terminology of QFD. PMID:21598275

  7. Density-dependent synthetic magnetism for ultracold atoms in optical lattices

    NASA Astrophysics Data System (ADS)

    Greschner, Sebastian; Huerga, Daniel; Sun, Gaoyong; Poletti, Dario; Santos, Luis

    2015-09-01

    Raman-assisted hopping can allow for the creation of density-dependent synthetic magnetism for cold neutral gases in optical lattices. We show that the density-dependent fields lead to a nontrivial interplay between density modulations and chirality. This interplay results in a rich physics for atoms in two-leg ladders, characterized by a density-driven Meissner-superfluid to vortex-superfluid transition, and a nontrivial dependence of the density imbalance between the legs. Density-dependent fields also lead to intriguing physics in square lattices. In particular, it leads to a density-driven transition between a nonchiral and a chiral superfluid, both characterized by nontrivial charge density-wave amplitude. We finally show how the physics due to the density-dependent fields may be easily probed in experiments by monitoring the expansion of doublons and holes in a Mott insulator, which presents a remarkable dependence on quantum fluctuations.

  8. Energy dependence of island nucleation density during ion beam deposition

    NASA Astrophysics Data System (ADS)

    Pomeroy, Joshua M.; Brock, Joel D.

    2002-03-01

    Thin copper films were grown on single crystal copper substrates using highly collimated copper ion beams with precisely controlled incidence energies. The energetic collisions between the copper ions and the surface can form adatom-vacancy pairs or sputter eject atoms into the vaccuum. Island nucleation densities are affected by these atomistic mechanisms, which increase surface adatom densities and surface defect densities. This paper reports STM measurements of the island nucleation density for films grown both thermally and at energies between 10-150 eV. The measured island nucleation density systematically deviates with increasing energy from the density predicted by mean field nucleation theory (J.A. Venables, et.al., Rep. Prog. Phys. 47 (1984) p. 399-459). This deviation can be understood using a phenomenological extension of mean field nucleation theory that includes the effects of adatom-vacancy pair production and sputter ejection on the effective flux.

  9. The density dependence of fluid properties and non-Newtonian flows: The Weissenberg effect

    SciTech Connect

    Rainwater, J.C.; Hanley, H.J.M.; Narayan, A. |

    1995-11-01

    Two approaches which describe the Weissenberg effect (height profile of a non-Newtonian fluid between rotating vertical concentric cylinders) are discussed. The first is based on an earlier calculation with rheological properties of a simple liquid obtained from nonequilibrium molecular dynamics (NEMD). The calculation is redone here using new results on the density dependence of the normal pressure differences. The NEMD calculations are restricted to Couette flow, but describe specifically, in a consistent manner, the effects of finite compressibility. The pressure, viscosity, and normal pressure differences are all found from NEMD to be sensitive functions of density, which requires that the equations of motion be solved iteratively and self-consistently, and a sample calculation is presented for the soft sphere fluid. The second approach is that of Joseph and Fosdick. Their assumptions and techniques are examined and compared with the NEMD calcula- tions.

  10. PMSE dependence on aerosol charge number density and aerosol size

    NASA Astrophysics Data System (ADS)

    Rapp, Markus; Lübken, Franz-Josef; Hoffmann, Peter; Latteck, Ralph; Baumgarten, Gerd; Blix, Tom A.

    2003-04-01

    It is commonly accepted that the existence of polar mesosphere summer echoes (PMSEs) depends on the presence of charged aerosols since these are comparatively heavy and reduce the diffusion of free electrons due to ambipolar forces. Simple microphysical modeling suggests that this diffusivity reduction is proportional to rA2 (rA = aerosol radius) but only if a significant amount of charges is bound on the aerosols such that NA∣ZA∣/ne > 1.2 (NA = number of aerosols, ZA = aerosol charge, ne = number of free electrons). The fact that the background electron profile frequently shows large depletions ("biteouts") at PMSE altitudes is taken as a support for this idea since within biteouts a major fraction of free electrons is missing, i.e., bound on aerosols. In this paper, we show from in situ measurements of electron densities and from radar and lidar observations that PMSEs can also exist in regions where only a minor fraction of free electrons is bound on aerosols, i.e., with no biteout and with NA∣ZA∣/ne ≪ 1. We show strong experimental evidence that it is instead the product NA∣ZA∣rA2 that is crucial for the existence of PMSEs. For example, small aerosol charge can be compensated by large aerosol radius. We show that this product replicates the main features of PMSEs, in particular the mean altitude distribution and the altitude of PMSEs in the presence of noctilucent clouds (NLCs). We therefore take this product as a "proxy" for PMSE. The agreement between this proxy and the main characteristics of PMSEs implies that simple microphysical models do not satisfactorily describe PMSE physics and need to be improved. The proxy can easily be used in models of the upper atmosphere to better understand seasonal and geographical variations of PMSEs, for example, the long debated difference between Northern and Southern hemisphere PMSEs.

  11. Ontogenetic and sex-specific differences in density-dependent habitat selection of a marine fish population.

    PubMed

    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.

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

    SciTech Connect

    Escartín, 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.

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

    PubMed

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

    2015-02-28

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

  14. 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 ∞ 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.

  15. A real-space stochastic density matrix approach for density functional electronic structure.

    PubMed

    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

  16. Time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities.

    PubMed

    Andrade, Xavier; Botti, Silvana; Marques, Miguel A L; Rubio, Angel

    2007-05-14

    The authors present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency-dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, they implemented it in a real-space (basis-set-free) code and applied it to benchmark molecules, namely, CO, H2O, and para-nitroaniline. Their results are in agreement with experimental and previous theoretical studies and fully validate their approach. PMID:17508791

  17. Diameter dependent failure current density of gold nanowires

    NASA Astrophysics Data System (ADS)

    Karim, S.; Maaz, K.; Ali, G.; Ensinger, W.

    2009-09-01

    Failure current density of single gold nanowires is investigated in this paper. Single wires with diameters ranging from 80 to 720 nm and length 30 µm were electrochemically deposited in ion track-etched single-pore polycarbonate membranes. The maximum current density was investigated while keeping the wires embedded in the polymer matrix and ramping up the current until failure occurred. The current density is found to increase with diminishing diameter and the wires with a diameter of 80 nm withstand 1.2 × 1012 A m-2 before undergoing failure. Possible reasons for these results are discussed in this paper.

  18. The multi-configurational time-dependent Hartree approach revisited

    SciTech Connect

    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.

  19. Mechanisms of density dependence in ducks: importance of space and per capita food.

    PubMed

    Nummi, Petri; Holopainen, Sari; Rintala, Jukka; Pöysä, Hannu

    2015-03-01

    The growth rate of populations usually varies over time, often in a density-dependent manner. Despite the large amount of literature on density dependence, relatively little is known of the mechanisms underlying the density-dependent processes affecting populations, especially per capita natality. We performed a 20-year study on the density dependence of brood production in two duck species differing in the stability of habitat use. Our study was conducted in a boreal watershed in southern Finland. We predicted that a diving duck common goldeneye Bucephala clangula, with more stable habitat use, would show stronger density dependence than a dabbling duck common teal Anas crecca. We investigated reproductive output in relation to the duck pair density per se as well as in relation to per capita food availability. As predicted, the reproductive output of the goldeneye showed a more density-dependent pattern than that of the teal. The number of goldeneye broods per pair decreased when the pair density increased. This was not the case with the teal. However, when the breeding success was measured by taking into account per capita food availability, both species showed density dependence. Our results imply that the occurrence of density dependent processes may vary even in sympatric ducks breeding in the same, relatively stable landscape. Our analysis also emphasizes that it is important to take into account per capita resource availability when studying the density dependence of breeding success. Both findings have important implications for the management and conservation of species. PMID:25398723

  20. Mechanisms of density dependence in ducks: importance of space and per capita food.

    PubMed

    Nummi, Petri; Holopainen, Sari; Rintala, Jukka; Pöysä, Hannu

    2015-03-01

    The growth rate of populations usually varies over time, often in a density-dependent manner. Despite the large amount of literature on density dependence, relatively little is known of the mechanisms underlying the density-dependent processes affecting populations, especially per capita natality. We performed a 20-year study on the density dependence of brood production in two duck species differing in the stability of habitat use. Our study was conducted in a boreal watershed in southern Finland. We predicted that a diving duck common goldeneye Bucephala clangula, with more stable habitat use, would show stronger density dependence than a dabbling duck common teal Anas crecca. We investigated reproductive output in relation to the duck pair density per se as well as in relation to per capita food availability. As predicted, the reproductive output of the goldeneye showed a more density-dependent pattern than that of the teal. The number of goldeneye broods per pair decreased when the pair density increased. This was not the case with the teal. However, when the breeding success was measured by taking into account per capita food availability, both species showed density dependence. Our results imply that the occurrence of density dependent processes may vary even in sympatric ducks breeding in the same, relatively stable landscape. Our analysis also emphasizes that it is important to take into account per capita resource availability when studying the density dependence of breeding success. Both findings have important implications for the management and conservation of species.

  1. Influence of boundary condition types on unstable density-dependent flow.

    PubMed

    Ataie-Ashtiani, Behzad; Simmons, Craig T; Werner, Adrian D

    2014-01-01

    Boundary conditions are required to close the mathematical formulation of unstable density-dependent flow systems. Proper implementation of boundary conditions, for both flow and transport equations, in numerical simulation are critical. In this paper, numerical simulations using the FEFLOW model are employed to study the influence of the different boundary conditions for unstable density-dependent flow systems. A similar set up to the Elder problem is studied. It is well known that the numerical simulation results of the standard Elder problem are strongly dependent on spatial discretization. This work shows that for the cases where a solute mass flux boundary condition is employed instead of a specified concentration boundary condition at the solute source, the numerical simulation results do not vary between different convective solution modes (i.e., plume configurations) due to the spatial discretization. Also, the influence of various boundary condition types for nonsource boundaries was studied. It is shown that in addition to other factors such as spatial and temporal discretization, the forms of the solute transport equation such as divergent and convective forms as well as the type of boundary condition employed in the nonsource boundary conditions influence the convective solution mode in coarser meshes. On basis of the numerical experiments performed here, higher sensitivities regarding the numerical solution stability are observed for the Adams-Bashford/Backward Trapezoidal time integration approach in comparison to the Euler-Backward/Euler-Forward time marching approach. The results of this study emphasize the significant consequences of boundary condition choice in the numerical modeling of unstable density-dependent flow. PMID:23659688

  2. Efficient time-dependent density functional theory approximations for hybrid density functionals: Analytical gradients and parallelization

    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

  3. Electrical conductivity of metals from real-time time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Andrade, Xavier; Correa, Alfredo

    In this presentation, I will discuss how to apply real-time electron dynamics to study electronic currents in crystalline systems and, in particular, how to use this method to predict electrical conductivities in different regimes. This approach presents many interesting theoretical challenges associated to the representation of bulk systems as infinitely periodic. For example, in order to induce electronic currents in the system, we use a gauge transformation that allows us to include finite electric fields in the simulation. We have implemented this approach using time-dependent density functional theory (TDDFT). This implementation allows us to induce, measure and visualize the current density as a function of time, in simulations with thousands of electrons (hundreds and even thousands of atoms). We have found that real-time TDDFT can describe how currents naturally decay in metals. From this dissipation process we can directly calculate the frequency-dependent conductivity, including the direct current (DC) conductivity that is not accessible from linear-response approaches like Kubo-Greenwood.

  4. Ion Upflow Dependence on Ionospheric Density and Solar Photoionization

    NASA Astrophysics Data System (ADS)

    Cohen, I. J.; Lessard, M.; Varney, R. H.; Oksavik, K.; Zettergren, M. D.; Lynch, K. A.

    2015-12-01

    Wahlund et al. [1992] first categorized the upflow of ionospheric ions into two types: that driven by ion frictional heating and that caused by auroral precipitation. 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 (MICA) 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, 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 (IPY) 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.

  5. Dependence of the N2 vibrational potential on density

    NASA Astrophysics Data System (ADS)

    Engelke, Ray

    1988-02-01

    Recently, part of the vibrational spectrum of the ground electronic (X 1∑+g) state of condensed phase N2, shocked to high density, has been measured by Schmidt, Moore, and Shaw. Densities (ρ) of nearly three times the ambient liquid value were obtained in the shock wave experiments. Due to the high temperatures achieved behind the shock waves, up to six vibrational levels of N2 were observed. These vibrational spectra show clear frequency shifts from their ambient condition values. Here, these experimental spectra are used to infer changes in the vibrational potential of N2 due to the high density environment. The vibrational portion of the Rydberg-Klein-Rees (RKR) method is used to do this. We find that, in the range of densities studied, the energies [E(n;ρ)] of the first five vibrational transitions of N2 can be accurately represented by E(n;ρ)=ωe(ρ)(n+ 1/2 )-ωexe(n+ 1/2 )2, where ωe(ρ)=ω0e+A[1-(ρ0/ρ)1/3] and ωexe is a constant which is independent of the thermodynamic state of the environment; here, ω0e and A are fitting constants and ρ0 and ρ are the ambient (liquid) and shocked densities of N2. Given E(n;ρ), one can obtain the classical turning point difference, r12, of the N2 potential as a function of n and ρ by using the RKR procedure. It is found that at the highest shock density observed (2.13 g/cm3), the relative change in r12 from the ambient condition values is about -1% for the first six vibrational levels.

  6. Density dependence, whitebark pine, and vital rates of grizzly bears

    USGS Publications Warehouse

    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 4.2–7.6% during 1983–2001 to 0.3–2.2% during 2002–2011. 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 (≥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 1983–2012, 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 10–15 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

  7. Angular momentum dependent orbital-free density functional theory: Formulation and implementation

    NASA Astrophysics Data System (ADS)

    Ke, Youqi; Libisch, Florian; Xia, Junchao; Carter, Emily A.

    2014-04-01

    Orbital-free density functional theory (OFDFT) directly solves for the ground-state electron density. It scales linearly with respect to system size, providing a promising tool for large-scale material simulations. Removal of the orbitals requires use of approximate noninteracting kinetic energy density functionals. If replacing ionic cores with pseudopotentials, removal of the orbitals also requires these pseudopotentials to be local. These are two severe challenges to the capabilities of conventional OFDFT. While main group elements are often well described within conventional OFDFT, transition metals remain intractable due to their localized d electrons. To advance the accuracy and general applicability of OFDFT, we have recently reported a general angular momentum dependent formulation as a next-generation OFDFT. In this formalism, we incorporate the angular momenta of electrons by devising a hybrid scheme based on a muffin tin geometry: inside spheres centered at the ionic cores, the electron density is expanded in a set of atom-centered basis functions combined with an onsite density matrix. The explicit treatment of the angular momenta of electrons provides an important basis for accurately describing the important ionic core region, which is not possible in conventional OFDFT. In addition to the conventional OFDFT total energy functional, we introduce a nonlocal energy term containing a set of angular momentum dependent energies to correct the errors due to the approximate kinetic energy density functional and local pseudopotentials. Our approach greatly increases the accuracy of OFDFT while largely preserving its numerical simplicity. Here, we provide details of the theoretical formulation and practical implementation, including the hybrid scheme, the derivation of the nonlocal energy term, the choice of basis functions, the direct minimization of the total energy, the procedure to determine the angular momentum dependent energies, the force formula with

  8. Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors

    EPA Science Inventory

    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...

  9. Reduced density matrix approach to calculation of electronic structure

    NASA Astrophysics Data System (ADS)

    Braams, Bastiaan J.; Jiang, Shidong; Nayakkankuppam, Madhu; Overton, Michael L.; Percus, Jerome K.

    1998-11-01

    The possibility of using the one-body and two-body reduced density matrices, rather than the many-body wavefunction, as the fundamental object of study for electronic structure calculations was actively explored in the 1960's and 1970's [1]-[3], but interest has waned since. In this approach the calculation of ground-state properties is reduced to a linear optimization problem subject to the representability conditions for the density matrices, which are a mixture of linear equalities and bounds on eigenvalues. We will review this approach, present a new family of representability conditions, and discuss our experience in using present-day methods for semi-definite programming for this application. [1] A. J. Coleman: Structure of fermion density matrices. Rev. Mod. Phys. 35 (1963) 668--689. [2] Claude Garrod and Jerome K. Percus: Reduction of the N-particle variational problem. J. Math. Phys. 5 (1964) 1756--1776. [3] M. Rosina and C. Garrod: The variational calculation of reduced density matrices. J. Comput. Phys. 18 (1975) 300--310.

  10. Relativistic Coulomb excitation within the time dependent superfluid local density approximation

    SciTech Connect

    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, 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 Γ↓≈0.4 MeV and the number of preequilibrium neutrons emitted has been quantified.

  11. Effects of density dependence in a temperate forest in northeastern China

    PubMed Central

    Yao, Jie; Zhang, Xinna; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2016-01-01

    Negative density dependence may cause reduced clustering among individuals of the same species, and evidence is accumulating that conspecific density-dependent self-thinning is an important mechanism regulating the spatial structure of plant populations. This study evaluates that specific density dependence in three very large observational studies representing three successional stages in a temperate forest in northeastern China. The methods include standard spatial point pattern analysis and a heterogeneous Poisson process as the null model to eliminate the effects of habitat heterogeneity. The results show that most of the species exhibit conspecific density-dependent self-thinning. In the early successional stage 11 of the 16 species, in the intermediate successional stage 18 of the 21 species and in the old growth stage all 21 species exhibited density dependence after removing the effects of habitat heterogeneity. The prevalence of density dependence thus varies among the three successional stages and exhibits an increase with increasing successional stage. The proportion of species showing density dependence varied depending on whether habitat heterogeneity was removed or not. Furthermore, the strength of density dependence is closely related with species abundance. Abundant species with high conspecific aggregation tend to exhibit greater density dependence than rare species. PMID:27604642

  12. Effects of density dependence in a temperate forest in northeastern China

    NASA Astrophysics Data System (ADS)

    Yao, Jie; Zhang, Xinna; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2016-09-01

    Negative density dependence may cause reduced clustering among individuals of the same species, and evidence is accumulating that conspecific density-dependent self-thinning is an important mechanism regulating the spatial structure of plant populations. This study evaluates that specific density dependence in three very large observational studies representing three successional stages in a temperate forest in northeastern China. The methods include standard spatial point pattern analysis and a heterogeneous Poisson process as the null model to eliminate the effects of habitat heterogeneity. The results show that most of the species exhibit conspecific density-dependent self-thinning. In the early successional stage 11 of the 16 species, in the intermediate successional stage 18 of the 21 species and in the old growth stage all 21 species exhibited density dependence after removing the effects of habitat heterogeneity. The prevalence of density dependence thus varies among the three successional stages and exhibits an increase with increasing successional stage. The proportion of species showing density dependence varied depending on whether habitat heterogeneity was removed or not. Furthermore, the strength of density dependence is closely related with species abundance. Abundant species with high conspecific aggregation tend to exhibit greater density dependence than rare species.

  13. Effects of density dependence in a temperate forest in northeastern China.

    PubMed

    Yao, Jie; Zhang, Xinna; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2016-09-08

    Negative density dependence may cause reduced clustering among individuals of the same species, and evidence is accumulating that conspecific density-dependent self-thinning is an important mechanism regulating the spatial structure of plant populations. This study evaluates that specific density dependence in three very large observational studies representing three successional stages in a temperate forest in northeastern China. The methods include standard spatial point pattern analysis and a heterogeneous Poisson process as the null model to eliminate the effects of habitat heterogeneity. The results show that most of the species exhibit conspecific density-dependent self-thinning. In the early successional stage 11 of the 16 species, in the intermediate successional stage 18 of the 21 species and in the old growth stage all 21 species exhibited density dependence after removing the effects of habitat heterogeneity. The prevalence of density dependence thus varies among the three successional stages and exhibits an increase with increasing successional stage. The proportion of species showing density dependence varied depending on whether habitat heterogeneity was removed or not. Furthermore, the strength of density dependence is closely related with species abundance. Abundant species with high conspecific aggregation tend to exhibit greater density dependence than rare species.

  14. Effects of density dependence in a temperate forest in northeastern China.

    PubMed

    Yao, Jie; Zhang, Xinna; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2016-01-01

    Negative density dependence may cause reduced clustering among individuals of the same species, and evidence is accumulating that conspecific density-dependent self-thinning is an important mechanism regulating the spatial structure of plant populations. This study evaluates that specific density dependence in three very large observational studies representing three successional stages in a temperate forest in northeastern China. The methods include standard spatial point pattern analysis and a heterogeneous Poisson process as the null model to eliminate the effects of habitat heterogeneity. The results show that most of the species exhibit conspecific density-dependent self-thinning. In the early successional stage 11 of the 16 species, in the intermediate successional stage 18 of the 21 species and in the old growth stage all 21 species exhibited density dependence after removing the effects of habitat heterogeneity. The prevalence of density dependence thus varies among the three successional stages and exhibits an increase with increasing successional stage. The proportion of species showing density dependence varied depending on whether habitat heterogeneity was removed or not. Furthermore, the strength of density dependence is closely related with species abundance. Abundant species with high conspecific aggregation tend to exhibit greater density dependence than rare species. PMID:27604642

  15. Adaptive landscapes and density-dependent selection in declining salmonid populations: going beyond numerical responses to human disturbance

    PubMed Central

    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

  16. Density functional and theoretical study of the temperature and pressure dependency of the plasmon energy of solids

    SciTech Connect

    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.

  17. 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.

  18. How important is self-consistency for the dDsC density dependent dispersion correction?

    SciTech Connect

    Brémond, Éric; Corminboeuf, Clémence; Golubev, Nikolay; 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.

  19. How important is self-consistency for the dDsC density dependent dispersion correction?

    PubMed

    Brémond, Éric; Golubev, Nikolay; Steinmann, Stephan N; Corminboeuf, Clémence

    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

  20. Using time-dependent density functional theory in real time for calculating electronic transport

    NASA Astrophysics Data System (ADS)

    Schaffhauser, Philipp; Kümmel, 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.

  1. Predation, habitat complexity, and variation in density-dependent mortality of temperate reef fishes.

    PubMed

    Johnson, Darren W

    2006-05-01

    Density dependence in demographic rates can strongly affect the dynamics of populations. However, the mechanisms generating density dependence (e.g., predation) are also dynamic processes and may be influenced by local conditions. Understanding the manner in which local habitat features affect the occurrence and/or strength of density dependence will increase our understanding of population dynamics in heterogeneous environments. In this study I conducted two separate field experiments to investigate how local predator density and habitat complexity affect the occurrence and form of density-dependent mortality of juvenile rockfishes (Sebastes spp.). I also used yearly censuses of rockfish populations on nearshore reefs throughout central California to evaluate mortality of juvenile rockfish at large spatial scales. Manipulations of predators (juvenile bocaccio, S. paucispinus) and prey (kelp, gopher, and black-and-yellow [KGB] rockfish, Sebastes spp.) demonstrated that increasing the density of predators altered their functional response and thus altered patterns of density dependence in mortality of their prey. At low densities of predators, the number of prey consumed per predator was a decelerating function, and mortality of prey was inversely density dependent. However, at high densities of predators, the number of prey killed per predator became an accelerating response, and prey mortality was directly density dependent. Results of field experiments and large-scale surveys both indicated that the strength of density-dependent mortality may also be affected by the structural complexity of the habitat. In small-scale field experiments, increased habitat complexity increased the strength of density-dependent mortality. However, at large scales, increasing complexity resulted in a decrease in the strength of density dependence. I suggest that these differences resulted from scale-dependent changes in the predatory response that generated mortality. Whether

  2. Frequency and Density-Dependent Selection on Life-History Strategies – A Field Experiment

    PubMed Central

    Mappes, Tapio; Koivula, Minna; Koskela, Esa; Oksanen, Tuula A.; Savolainen, Tiina; Sinervo, Barry

    2008-01-01

    Negative frequency-dependence, which favors rare genotypes, promotes the maintenance of genetic variability and is of interest as a potential explanation for genetic differentiation. Density-dependent selection may also promote cyclic changes in frequencies of genotypes. Here we show evidence for both density-dependent and negative frequency-dependent selection on opposite life-history tactics (low or high reproductive effort, RE) in the bank vole (Myodes glareolus). Density-dependent selection was evident among the females with low RE, which were especially favored in low densities. Instead, both negative frequency-dependent and density-dependent selection were shown in females with high RE, which were most successful when they were rare in high densities. Furthermore, selection at the individual level affected the frequencies of tactics at the population level, so that the frequency of the rare high RE tactic increased significantly at high densities. We hypothesize that these two selection mechanisms (density- and negative frequency-dependent selection) may promote genetic variability in cyclic mammal populations. Nevertheless, it remains to be determined whether the origin of genetic variance in life-history traits is causally related to density variation (e.g. population cycles). PMID:18301764

  3. Density-dependence of functional spiking networks in vitro

    SciTech Connect

    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.

  4. Demographic models reveal the shape of density dependence for a specialist insect herbivore on variable host plants.

    PubMed

    Miller, Tom E X

    2007-07-01

    1. It is widely accepted that density-dependent processes play an important role in most natural populations. However, persistent challenges in our understanding of density-dependent population dynamics include evaluating the shape of the relationship between density and demographic rates (linear, concave, convex), and identifying extrinsic factors that can mediate this relationship. 2. I studied the population dynamics of the cactus bug Narnia pallidicornis on host plants (Opuntia imbricata) that varied naturally in relative reproductive effort (RRE, the proportion of meristems allocated to reproduction), an important plant quality trait. I manipulated per-plant cactus bug densities, quantified subsequent dynamics, and fit stage-structured models to the experimental data to ask if and how density influences demographic parameters. 3. In the field experiment, I found that populations with variable starting densities quickly converged upon similar growth trajectories. In the model-fitting analyses, the data strongly supported a model that defined the juvenile cactus bug retention parameter (joint probability of surviving and not dispersing) as a nonlinear decreasing function of density. The estimated shape of this relationship shifted from concave to convex with increasing host-plant RRE. 4. The results demonstrate that host-plant traits are critical sources of variation in the strength and shape of density dependence in insects, and highlight the utility of integrated experimental-theoretical approaches for identifying processes underlying patterns of change in natural populations.

  5. High temperature intensifies negative density dependence of fitness in red flour beetles

    PubMed Central

    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

  6. Density-dependent effects on group size are sex-specific in a gregarious ungulate.

    PubMed

    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/km(2) 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/km(2) and we found evidence for a minimum group size at population density ≤0.70 elk/km(2). 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

  7. Density-Dependent Effects on Group Size Are Sex-Specific in a Gregarious Ungulate

    PubMed Central

    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

  8. Density matrix renormalization group approach to the massive Schwinger model

    NASA Astrophysics Data System (ADS)

    Byrnes, T. M.; Sriganesh, P.; Bursill, R. J.; Hamer, C. J.

    2002-07-01

    The massive Schwinger model is studied using a density matrix renormalization group approach to the staggered lattice Hamiltonian version of the model. Lattice sizes up to 256 sites are calculated, and the estimates in the continuum limit are almost two orders of magnitude more accurate than previous calculations. Coleman's picture of ``half-asymptotic'' particles at a background field θ=π is confirmed. The predicted phase transition at finite fermion mass (m/g) is accurately located and demonstrated to belong in the 2D Ising universality class.

  9. 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.

  10. 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.

  11. 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 Schrödinger 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 Harrison’s article.

  12. The density dependence of neutral hydrogen density and neutral hydrogen emission from PLT

    NASA Astrophysics Data System (ADS)

    Ruzic, D. N.; Heifetz, D. B.; Cohen, S. A.

    1987-02-01

    The efflux of atoms with energies greater than 10 eV from tokamaks results primarily from charge exchange. This flux is useful as a diagnostic of plasma properties such as particle transport, particle confinement, power balance, neutral density, and ion temperature. This flux also contributes to plasma contamination by sputtering of impurities from walls and limiters. We have measured the efflux of neutral hydrogen in the energy range from 10 to 2000 eV as a function of plasma parameters in the steady-state portion of ohmically heated discharges in PLT. Results have been obtained both near the main plasma limiter and far away from it. These data serve as a benchmark for comparing atomic emission during auxiliary heating and current drive. We find that the main parameter which affects the efflux is the plasma density. The total energy-integrated efflux, Γ, rises rapidly with overlinene to Γ = 4 × 10 15cm-2s-1 at overlinene = 1 × 10 13cm -3, and then falls a factor of 2-4. The total efflux is then relatively constant with overlinene up to overlinene ≈ 6 × 10 13cm -3. The average energy of the efflux rises from 180 eV at overlinene = 10 12 cm -3 to 500 eV at overlinene = 10 13 cm -3. It then decreases to approximately 150 eV at overlinene = 2 × 10 13cm -3, and drops slightly more to 100 eV at overlinene ≈ 6 × 10 13cm -3. Using the measured dΓ/dEdΩ spectra, electron temperature, and electron density as inputs and consistency checks, the ion temperature profiles and 3-dimensional neutral density profiles are calculated using the DEGAS code. From these calculations the particle confinement time, impurity generation by sputtering, and contribution of ions and charge-exchange neutrals to the power balance are evaluated as a function of electron density. The importance of the limiter to recycling at high densities is clearly demonstrated. The ratio of the ion flux onto the limiter versus the ion flux onto the wall goes from 4.8 at overlinene = 1.8 × 10 12cm -3

  13. 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.

  14. Experimental evidence for density-dependent regulation and selection on Trinidadian guppy life histories.

    PubMed

    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

  15. 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, φp, when the probe radius is much larger than the Debye length, λD. 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, Γ, for varying probe bias, Vb. The frequency range of the applied signal is restricted to avoid sheath resonant effects and ion contributions such that ωpi ≪ ω ≪ ωpe, where ωpi is the ion plasma frequency and ωpe is the electron plasma frequency. For a given frequency and applied bias, both Re(Zac) and Im(Zac) are available from Γ. When Re(Zac) is plotted versus Vb, a minimum predicted by theory occurs at φp [Walker et al., Phys. Plasmas 17, 113503 (2010)]. In addition, Im(Zac) appears at, or very near, a maximum at φp. 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, Γ 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).

  16. Charge density dependent two-channel conduction in organic electric double layer transistors (EDLTs).

    PubMed

    Xie, Wei; Liu, Feilong; Shi, Sha; Ruden, P Paul; Frisbie, C Daniel

    2014-04-23

    A transport model based on hole-density-dependent trapping is proposed to explain the two unusual conductivity peaks at surface hole densities above 10(13) cm(-2) in rubrene electric double layer transistors (EDLTs). Hole transport in rubrene is described to occur via multiple percolation pathways, where conduction is dominated by transport in the free-site channel at low hole density, and in the trap-site channel at larger hole density. PMID:24496822

  17. Reduced density matrix hybrid approach: application to electronic energy transfer.

    PubMed

    Berkelbach, Timothy C; Markland, Thomas E; Reichman, David R

    2012-02-28

    Electronic energy transfer in the condensed phase, such as that occurring in photosynthetic complexes, frequently occurs in regimes where the energy scales of the system and environment are similar. This situation provides a challenge to theoretical investigation since most approaches are accurate only when a certain energetic parameter is small compared to others in the problem. Here we show that in these difficult regimes, the Ehrenfest approach provides a good starting point for a dynamical description of the energy transfer process due to its ability to accurately treat coupling to slow environmental modes. To further improve on the accuracy of the Ehrenfest approach, we use our reduced density matrix hybrid framework to treat the faster environmental modes quantum mechanically, at the level of a perturbative master equation. This combined approach is shown to provide an efficient and quantitative description of electronic energy transfer in a model dimer and the Fenna-Matthews-Olson complex and is used to investigate the effect of environmental preparation on the resulting dynamics.

  18. Electron density dependence of impedance probe plasma potential measurements

    SciTech Connect

    Walker, D. N.; Blackwell, D. D.; Amatucci, W. E.

    2015-08-15

    In earlier works, we used spheres of various sizes as impedance probes in demonstrating a method of determining plasma potential, φ{sub p}, when the probe radius is much larger than the Debye length, λ{sub 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, Γ, for varying probe bias, V{sub b}. The frequency range of the applied signal is restricted to avoid sheath resonant effects and ion contributions such that ω{sub pi} ≪ ω ≪ ω{sub pe}, where ω{sub pi} is the ion plasma frequency and ω{sub pe} is the electron plasma frequency. For a given frequency and applied bias, both Re(Z{sub ac}) and Im(Z{sub ac}) are available from Γ. When Re(Z{sub ac}) is plotted versus V{sub b}, a minimum predicted by theory occurs at φ{sub p} [Walker et al., Phys. Plasmas 17, 113503 (2010)]. In addition, Im(Z{sub ac}) appears at, or very near, a maximum at φ{sub p}. As n{sub e} 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, Γ itself and Im(Z{sub ac}) and their derivatives are useful as accompanying indicators to Re(Z{sub ac}) 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(Z{sub ac})

  19. Cell density-dependent linoleic acid toxicity to Saccharomyces cerevisiae.

    PubMed

    Ferreira, Túlio César; de Moraes, Lídia Maria Pepe; Campos, Elida Geralda

    2011-08-01

    Since the discovery of the apoptotic pathway in Saccharomyces cerevisiae, several compounds have been shown to cause apoptosis in this organism. While the toxicity of polyunsaturated fatty acids (PUFA) peroxides towards S. cerevisiae has been known for a long time, studies on the effect of nonoxidized PUFA are scarce. The present study deals specifically with linoleic acid (LA) in its nonoxidized form and investigates its toxicity to yeast. Saccharomyces cerevisiae is unable to synthesize PUFA, but can take up and incorporate them into its membranes. Reports from the literature indicate that LA is not toxic to yeast cells. However, we demonstrated that yeast cell growth decreased in cultures treated with 0.1 mM LA for 4 h, and 3-(4,5 dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide reduction (a measure of respiratory activity) decreased by 47%. This toxicity was dependent on the number of cells used in the experiment. We show apoptosis induction by LA concomitant with increases in malondialdehyde, glutathione content, activities of catalase and cytochrome c peroxidase, and decreases in two metabolic enzyme activities. While the main purpose of this study was to show that LA causes cell death in yeast, our results indicate some of the molecular mechanisms of the cell toxicity of PUFA. PMID:21457450

  20. Time-dependent density functional theory of open quantum systems in the linear-response regime.

    PubMed

    Tempel, David G; Watson, Mark A; Olivares-Amaya, Roberto; Aspuru-Guzik, Alán

    2011-02-21

    Time-dependent density functional theory (TDDFT) has recently been extended to describe many-body open quantum systems evolving under nonunitary dynamics according to a quantum master equation. In the master equation approach, electronic excitation spectra are broadened and shifted due to relaxation and dephasing of the electronic degrees of freedom by the surrounding environment. In this paper, we develop a formulation of TDDFT linear-response theory (LR-TDDFT) for many-body electronic systems evolving under a master equation, yielding broadened excitation spectra. This is done by mapping an interacting open quantum system onto a noninteracting open Kohn-Sham system yielding the correct nonequilibrium density evolution. A pseudoeigenvalue equation analogous to the Casida equations of the usual LR-TDDFT is derived for the Redfield master equation, yielding complex energies and Lamb shifts. As a simple demonstration, we calculate the spectrum of a C(2 +) atom including natural linewidths, by treating the electromagnetic field vacuum as a photon bath. The performance of an adiabatic exchange-correlation kernel is analyzed and a first-order frequency-dependent correction to the bare Kohn-Sham linewidth based on the Görling-Levy perturbation theory is calculated.

  1. Incorporating density dependence into the oviposition preference-offspring performance hypothesis.

    PubMed

    Ellis, Alicia M

    2008-03-01

    1. Although theory predicts a positive relationship between oviposition preferences and the developmental performance of offspring, the strength of this relationship may depend not only on breeding site quality, but also on the complex interactions between environmental heterogeneity and density-dependent processes. Environmental heterogeneity may not only alter the strength of density dependence, but may also fundamentally alter density-dependent relationships and the preference-performance relationship. 2. Here I present results from a series of field experiments testing the effects of environmental heterogeneity and density-dependent feedback on offspring performance in tree-hole mosquitoes. Specifically, I asked: (i) how do oviposition activity, patterns of colonization and larval density differ among habitats and among oviposition sites with different resources; and (ii) how is performance influenced by the density of conspecifics, the type of resource in the oviposition site, and the type of habitat in which the oviposition site is located? 3. Performance did not differ among habitats at low offspring densities, but was higher in deciduous forest habitats than in evergreen forest habitats at high densities. Oviposition activity and larval densities were also higher in deciduous forests, suggesting a weak preference for these habitats. 4. The observed divergence of fitness among habitats with increasing density may select for consistent but weak preferences for deciduous habitats if regional abundances vary temporally. This would generate a negative preference-performance relationship when population densities are low, but a positive relationship when population densities are high. 5. This study demonstrates that failure to recognize that fitness differences among habitats may themselves be density-dependent may bias our assumptions about the ecological and evolutionary processes determining oviposition preferences in natural systems.

  2. Population-Level Density Dependence Influences the Origin and Maintenance of Parental Care.

    PubMed

    Reyes, Elijah; Thrasher, Patsy; Bonsall, Michael B; Klug, Hope

    2016-01-01

    Parental care is a defining feature of animal breeding systems. We now know that both basic life-history characteristics and ecological factors influence the evolution of care. However, relatively little is known about how these factors interact to influence the origin and maintenance of care. Here, we expand upon previous work and explore the relationship between basic life-history characteristics (stage-specific rates of mortality and maturation) and the fitness benefits associated with the origin and the maintenance of parental care for two broad ecological scenarios: the scenario in which egg survival is density dependent and the case in which adult survival is density dependent. Our findings suggest that high offspring need is likely critical in driving the origin, but not the maintenance, of parental care regardless of whether density dependence acts on egg or adult survival. In general, parental care is more likely to result in greater fitness benefits when baseline adult mortality is low if 1) egg survival is density dependent or 2) adult mortality is density dependent and mutant density is relatively high. When density dependence acts on egg mortality, low rates of egg maturation and high egg densities are less likely to lead to strong fitness benefits of care. However, when density dependence acts on adult mortality, high levels of egg maturation and increasing adult densities are less likely to maintain care. Juvenile survival has relatively little, if any, effect on the origin and maintenance of egg-only care. More generally, our results suggest that the evolution of parental care will be influenced by an organism's entire life history characteristics, the stage at which density dependence acts, and whether care is originating or being maintained.

  3. Population-Level Density Dependence Influences the Origin and Maintenance of Parental Care.

    PubMed

    Reyes, Elijah; Thrasher, Patsy; Bonsall, Michael B; Klug, Hope

    2016-01-01

    Parental care is a defining feature of animal breeding systems. We now know that both basic life-history characteristics and ecological factors influence the evolution of care. However, relatively little is known about how these factors interact to influence the origin and maintenance of care. Here, we expand upon previous work and explore the relationship between basic life-history characteristics (stage-specific rates of mortality and maturation) and the fitness benefits associated with the origin and the maintenance of parental care for two broad ecological scenarios: the scenario in which egg survival is density dependent and the case in which adult survival is density dependent. Our findings suggest that high offspring need is likely critical in driving the origin, but not the maintenance, of parental care regardless of whether density dependence acts on egg or adult survival. In general, parental care is more likely to result in greater fitness benefits when baseline adult mortality is low if 1) egg survival is density dependent or 2) adult mortality is density dependent and mutant density is relatively high. When density dependence acts on egg mortality, low rates of egg maturation and high egg densities are less likely to lead to strong fitness benefits of care. However, when density dependence acts on adult mortality, high levels of egg maturation and increasing adult densities are less likely to maintain care. Juvenile survival has relatively little, if any, effect on the origin and maintenance of egg-only care. More generally, our results suggest that the evolution of parental care will be influenced by an organism's entire life history characteristics, the stage at which density dependence acts, and whether care is originating or being maintained. PMID:27093056

  4. Population-Level Density Dependence Influences the Origin and Maintenance of Parental Care

    PubMed Central

    Reyes, Elijah; Thrasher, Patsy; Bonsall, Michael B.; Klug, Hope

    2016-01-01

    Parental care is a defining feature of animal breeding systems. We now know that both basic life-history characteristics and ecological factors influence the evolution of care. However, relatively little is known about how these factors interact to influence the origin and maintenance of care. Here, we expand upon previous work and explore the relationship between basic life-history characteristics (stage-specific rates of mortality and maturation) and the fitness benefits associated with the origin and the maintenance of parental care for two broad ecological scenarios: the scenario in which egg survival is density dependent and the case in which adult survival is density dependent. Our findings suggest that high offspring need is likely critical in driving the origin, but not the maintenance, of parental care regardless of whether density dependence acts on egg or adult survival. In general, parental care is more likely to result in greater fitness benefits when baseline adult mortality is low if 1) egg survival is density dependent or 2) adult mortality is density dependent and mutant density is relatively high. When density dependence acts on egg mortality, low rates of egg maturation and high egg densities are less likely to lead to strong fitness benefits of care. However, when density dependence acts on adult mortality, high levels of egg maturation and increasing adult densities are less likely to maintain care. Juvenile survival has relatively little, if any, effect on the origin and maintenance of egg-only care. More generally, our results suggest that the evolution of parental care will be influenced by an organism’s entire life history characteristics, the stage at which density dependence acts, and whether care is originating or being maintained. PMID:27093056

  5. Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

    PubMed

    Nishimoto, Yoshio

    2015-09-01

    We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well. PMID:26342360

  6. Time-dependent density-functional tight-binding method with the third-order expansion of electron density

    SciTech Connect

    Nishimoto, Yoshio

    2015-09-07

    We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

  7. Quantification of trap state densities in GaAs heterostructures grown at varying rates using intensity-dependent time resolved photoluminescence

    NASA Astrophysics Data System (ADS)

    Haughn, C. R.; Schmieder, K. J.; Zide, J. M. O.; Barnett, A.; Ebert, C.; Opila, R.; Doty, M. F.

    2013-05-01

    Time-resolved photoluminescence is an established technique for characterizing carrier lifetimes in semiconductors, but the dependence of lifetime on excitation fluence has been only qualitatively investigated. We develop a quantitative approach for fitting fluence-dependent PL decay data to a Shockely-Read-Hall model of carrier recombination in order to extract the trap state density. We demonstrate this approach by investigating growth rate-dependent trap densities in gallium arsenide-indium gallium phosphide double heterostructures. The techniques developed here can be applied for rapid, non-destructive quantification of trap state densities in a variety of materials.

  8. Intra- and interspecific density-dependent dispersal in an aquatic prey-predator system.

    PubMed

    Hauzy, Celine; Hulot, Florence D; Gins, Audrey; Loreau, Michel

    2007-05-01

    1. Dispersal intensity is a key process for the persistence of prey-predator metacommunities. Consequently, knowledge of the ecological mechanisms of dispersal is fundamental to understanding the dynamics of these communities. Dispersal is often considered to occur at a constant per capita rate; however, some experiments demonstrated that dispersal may be a function of local species density. 2. Here we use aquatic experimental microcosms under controlled conditions to explore intra- and interspecific density-dependent dispersal in two protists, a prey Tetrahymena pyriformis and its predator Dileptus sp. 3. We observed intraspecific density-dependent dispersal for the prey and interspecific density-dependent dispersal for both the prey and the predator. Decreased prey density lead to an increase in predator dispersal, while prey dispersal increased with predator density. 4. Additional experiments suggest that the prey is able to detect its predator through chemical cues and to modify its dispersal behaviour accordingly. 5. Density-dependent dispersal suggests that regional processes depend on local community dynamics. We discuss the potential consequences of density-dependent dispersal on metacommunity dynamics and stability.

  9. Estimation of density-dependent mortality of juvenile bivalves in the Wadden Sea.

    PubMed

    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.

  10. Estimation of density-dependent mortality of juvenile bivalves in the Wadden Sea.

    PubMed

    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

  11. Photonuclear reactions studied with the time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Nakatsukasa, Takashi

    2009-10-01

    Photonuclear reaction cross sections are known to be of fundamental importance in nuclear structure as well as a variety of applications, such as nucleosynthesis and nuclear power. Especially, it is highly desired to improve reliability of E1 strength distribution in unstable nuclei which are not experimentally reachable. We are performing systematic calculations of nuclear photoabsorption cross sections using the time-dependent density-functional theory. For this purpose, we have developed a new numerical approach to the linear response problems, ``Finite Amplitude Method'' (FAM). In this talk, we present recent results of our microscopic calculations with the FAM applied to the Skyrme functionals and discuss properties of nuclear E1 strength distribution in light- and medium-mass nuclei.

  12. Measuring the mobility of single crystalline wires and its dependence on temperature and carrier density.

    PubMed

    Amorim, Cleber A; Berengue, Olivia M; Kamimura, Hanay; Leite, Edson R; Chiquito, Adenilson J

    2011-05-25

    Kinetic transport parameters are fundamental for the development of electronic nanodevices. We present new results for the temperature dependence of mobility and carrier density in single crystalline In(2)O(3) samples and the method of extraction of these parameters which can be extended to similar systems. The data were obtained using a conventional Hall geometry and were quantitatively described by the semiconductor transport theory characterizing the electron transport as being controlled by the variable range hopping mechanism. A comprehensive analysis is provided showing the contribution of ionized impurities (low temperatures) and acoustic phonon (high temperatures) scattering mechanisms to the electron mobility. The approach presented here avoids common errors in kinetic parameter extraction from field effect data, serving as a versatile platform for direct investigation of any nanoscale electronic materials.

  13. Physical Origin of Density Dependent Force of the Skyrme Type within the Quark Meson Coupling Model

    SciTech Connect

    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.

  14. Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

    PubMed

    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, Alán; Rubio, Angel; Marques, Miguel A L

    2012-06-13

    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. PMID:22562950

  15. Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

    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, Alán; 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.

  16. Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

    PubMed

    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, Alán; Rubio, Angel; Marques, Miguel A L

    2012-06-13

    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.

  17. Sensitivity of the fusion cross section to the density dependence of the symmetry energy

    NASA Astrophysics Data System (ADS)

    Reinhard, P.-G.; Umar, A. S.; Stevenson, P. D.; Piekarewicz, J.; Oberacker, V. E.; Maruhn, J. A.

    2016-04-01

    Background: The study of the nuclear equation of state (EOS) and the behavior of nuclear matter under extreme conditions is crucial to our understanding of many nuclear and astrophysical phenomena. Nuclear reactions serve as one of the means for studying the EOS. Purpose: It is the aim of this paper to discuss the impact of nuclear fusion on the EOS. This is a timely subject given the expected availability of increasingly exotic beams at rare isotope facilities [A. B. Balantekin et al., Mod. Phys. Lett. A 29, 1430010 (2014), 10.1142/S0217732314300109]. In practice, we focus on 48Ca+48Ca fusion. Method: We employ three different approaches to calculate fusion cross sections for a set of energy density functionals with systematically varying nuclear matter properties. Fusion calculations are performed using frozen densities, using a dynamic microscopic method based on density-constrained time-dependent Hartree-Fock (DC-TDHF) approach, as well as direct TDHF study of above barrier cross sections. For these studies, we employ a family of Skyrme parametrizations with systematically varied nuclear matter properties. Results: The folding-potential model provides a reasonable first estimate of cross sections. DC-TDHF, which includes dynamical polarization, reduces the fusion barriers and delivers much better cross sections. Full TDHF near the barrier agrees nicely with DC-TDHF. Most of the Skyrme forces which we used deliver, on the average, fusion cross sections in good agreement with the data. Trying to read off a trend in the results, we find a slight preference for forces which deliver a slope of symmetry energy of L ≈50 MeV that corresponds to a neutron-skin thickness of 48Ca of Rskin=(0.180 -0.210 ) fm. Conclusions: Fusion reactions in the barrier and sub-barrier region can be a tool to study the EOS and the neutron skin of nuclei. The success of the approach will depend on reduced experimental uncertainties of fusion data as well as the development of fusion

  18. Density-dependent compensatory growth in brown trout (Salmo trutta) in nature.

    PubMed

    Sundström, L Fredrik; Kaspersson, Rasmus; Näslund, Joacim; Johnsson, Jörgen I

    2013-01-01

    Density-dependence is a major ecological mechanism that is known to limit individual growth. To examine if compensatory growth (unusually rapid growth following a period of imposed slow growth) in nature is density-dependent, one-year-old brown trout (Salmo trutta L.) were first starved in the laboratory, and then released back into their natural stream, either at natural or at experimentally increased population density. The experimental trout were captured three times over a one-year period. We found no differences in growth, within the first month after release (May-June), between the starved fish and the control group (i.e. no evidence of compensation). During the summer however (July-September), the starved fish grew more than the control group (i.e. compensation), and the starved fish released into the stream at a higher density, grew less than those released at a natural density, both in terms of weight and length (i.e. density-dependent compensation). Over the winter (October-April), there were no effects of either starvation or density on weight and length growth. After the winter, starved fish released at either density had caught up with control fish in body size, but recapture rates (proxy for survival) did not indicate any costs of compensation. Our results suggest that compensatory growth in nature can be density-dependent. Thus, this is the first study to demonstrate the presence of ecological restrictions on the compensatory growth response in free-ranging animals.

  19. Density-dependent movement and the consequences of the Allee effect in the model organism Tetrahymena.

    PubMed

    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.

  20. Influence of density dependence on predator–prey seabird interactions at large spatio-temporal scales

    PubMed Central

    Oro, Daniel; Martínez-Abraín, Alejandro; Paracuellos, Mariano; Nevado, Juan Carlos; Genovart, Meritxell

    2005-01-01

    Theoretical investigations of competitive dynamics have noted that numbers of predator and prey influence each other. However, few empirical studies have demonstrated how a life-history trait of the prey (such as fecundity) can be affected simultaneously by its own density and the density of predators. For instance, density dependence can reduce fecundity with increasing number of prey, while inverse density dependence or Allee effects may occur especially when the prey is a social organism. Here we analysed an intraguild predator–prey system of two seabird species at a large spatio-temporal scale. As expected, we found that fecundity of prey was negatively affected by predator density. Nevertheless, fecundity of prey also increased nonlinearly with its own density and strikingly with the prey–predator ratio. Small groups of prey were probably not able to defend their nests especially against large number of predators. At the highest prey densities (i.e. when anti-predator strategies should be most efficient), prey fecundity also lowered, suggesting the appearance of density dependence mediated by food competition. Allee effects and density dependence occurred across a broad range of population sizes of both the prey and the predator at several local populations facing different ecological environments. PMID:16543182

  1. Influence of density dependence on predator-prey seabird interactions at large spatio-temporal scales.

    PubMed

    Oro, Daniel; Martínez-Abraín, Alejandro; Paracuellos, Mariano; Nevado, Juan Carlos; Genovart, Meritxell

    2006-02-01

    Theoretical investigations of competitive dynamics have noted that numbers of predator and prey influence each other. However, few empirical studies have demonstrated how a life-history trait of the prey (such as fecundity) can be affected simultaneously by its own density and the density of predators. For instance, density dependence can reduce fecundity with increasing number of prey, while inverse density dependence or Allee effects may occur especially when the prey is a social organism. Here we analysed an intraguild predator-prey system of two seabird species at a large spatio-temporal scale. As expected, we found that fecundity of prey was negatively affected by predator density. Nevertheless, fecundity of prey also increased nonlinearly with its own density and strikingly with the prey-predator ratio. Small groups of prey were probably not able to defend their nests especially against large number of predators. At the highest prey densities (i.e. when anti-predator strategies should be most efficient), prey fecundity also lowered, suggesting the appearance of density dependence mediated by food competition. Allee effects and density dependence occurred across a broad range of population sizes of both the prey and the predator at several local populations facing different ecological environments. PMID:16543182

  2. Digging for answers: contributions of density- and frequency-dependent factors on ectoparasite burden in a social mammal.

    PubMed

    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.

  3. Magnetized strange quark matter in a mass-density-dependent model

    NASA Astrophysics Data System (ADS)

    Hou, Jia-Xun; Peng, Guang-Xiong; Xia, Cheng-Jun; Xu, Jian-Feng

    2015-01-01

    We investigate the properties of strange quark matter (SQM) in a strong magnetic field with quark confinement by the density dependence of quark masses considering the total baryon number conservation, charge neutrality and chemical equilibrium. It is found that an additional term should appear in the pressure expression to maintain thermodynamic consistency. At fixed density, the energy density of magnetized SQM varies with the magnetic field strength. By increasing the field strength an energy minimum exists located at about 6×1019 Gauss when the density is fixed at two times the normal nuclear saturation density.

  4. Strength of evidence for density dependence in abundance time series of 1198 species.

    PubMed

    Brook, Barry W; Bradshaw, Corey J A

    2006-06-01

    Population limitation is a fundamental tenet of ecology, but the relative roles of exogenous and endogenous mechanisms remain unquantified for most species. Here we used multi-model inference (MMI), a form of model averaging, based on information theory (Akaike's Information Criterion) to evaluate the relative strength of evidence for density-dependent and density-independent population dynamical models in long-term abundance time series of 1198 species. We also compared the MMI results to more classic methods for detecting density dependence: Neyman-Pearson hypothesis-testing and best-model selection using the Bayesian Information Criterion or cross-validation. Using MMI on our large database, we show that density dependence is a pervasive feature of population dynamics (median MMI support for density dependence = 74.7-92.2%), and that this holds across widely different taxa. The weight of evidence for density dependence varied among species but increased consistently, with the number of generations monitored. Best-model selection methods yielded similar results to MMI (a density-dependent model was favored in 66.2-93.9% of species time series), while the hypothesis-testing methods detected density dependence less frequently (32.6-49.8%). There were no obvious differences in the prevalence of density dependence across major taxonomic groups under any of the statistical methods used. These results underscore the value of using multiple modes of analysis to quantify the relative empirical support for a set of working hypotheses that encompass a range of realistic population dynamical behaviors.

  5. Simultaneous positive and negative density-dependent dispersal in a colonial bird species.

    PubMed

    Kim, Sin-Yeon; Torres, Roxana; Drummond, Hugh

    2009-01-01

    Contradictory patterns of density-dependent animal dispersal can potentially be reconciled by integrating the conspecific attraction hypothesis with the traditional competition hypothesis. We propose a hypothesis that predicts a U-shaped relationship between density and both natal and breeding dispersal distance. Using 10 years of observations on a breeding colony of the Blue-footed Booby (Sula nebouxii), the hypothesis was confirmed by documenting simultaneous positive and negative density-dependent dispersal distances in natal and breeding dispersal of males and breeding dispersal of females within the colony. Point-pattern analyses demonstrated that the breeding sites of Blue-footed Boobies were highly aggregated in all years within a large study area, and aggregation presumably resulted in heterogeneity in patch density throughout the colony. As predicted, at moderate to high densities, dispersal distances showed positive density dependence, with individuals moving to lower density patches. In contrast, at low to moderate densities, dispersal distances showed negative density dependence, with individuals moving to higher density patches. In both sexes of the 1994 cohort, the higher the mean density in patches used by an individual over the long term (up to age 11 years), the fewer fledglings it produced. A positive effect of density on long-term reproductive success was not detected, possibly because birds that failed during pair formation or incubation were not sampled. Density of conspecifics may be an important influence on habitat selection of breeders, and dispersal may tend to carry individuals to patches where pair formation opportunities are better and negative effects of competition on reproductive success are reduced.

  6. Simultaneous positive and negative density-dependent dispersal in a colonial bird species.

    PubMed

    Kim, Sin-Yeon; Torres, Roxana; Drummond, Hugh

    2009-01-01

    Contradictory patterns of density-dependent animal dispersal can potentially be reconciled by integrating the conspecific attraction hypothesis with the traditional competition hypothesis. We propose a hypothesis that predicts a U-shaped relationship between density and both natal and breeding dispersal distance. Using 10 years of observations on a breeding colony of the Blue-footed Booby (Sula nebouxii), the hypothesis was confirmed by documenting simultaneous positive and negative density-dependent dispersal distances in natal and breeding dispersal of males and breeding dispersal of females within the colony. Point-pattern analyses demonstrated that the breeding sites of Blue-footed Boobies were highly aggregated in all years within a large study area, and aggregation presumably resulted in heterogeneity in patch density throughout the colony. As predicted, at moderate to high densities, dispersal distances showed positive density dependence, with individuals moving to lower density patches. In contrast, at low to moderate densities, dispersal distances showed negative density dependence, with individuals moving to higher density patches. In both sexes of the 1994 cohort, the higher the mean density in patches used by an individual over the long term (up to age 11 years), the fewer fledglings it produced. A positive effect of density on long-term reproductive success was not detected, possibly because birds that failed during pair formation or incubation were not sampled. Density of conspecifics may be an important influence on habitat selection of breeders, and dispersal may tend to carry individuals to patches where pair formation opportunities are better and negative effects of competition on reproductive success are reduced. PMID:19294928

  7. Real time propagation of the exact two component time-dependent density functional theory.

    PubMed

    Goings, Joshua J; Kasper, Joseph M; Egidi, Franco; Sun, Shichao; Li, Xiaosong

    2016-09-14

    We report the development of a real time propagation method for solving the time-dependent relativistic exact two-component density functional theory equations (RT-X2C-TDDFT). The method is fundamentally non-perturbative and may be employed to study nonlinear responses for heavy elements which require a relativistic Hamiltonian. We apply the method to several group 12 atoms as well as heavy-element hydrides, comparing with the extensive theoretical and experimental studies on this system, which demonstrates the correctness of our approach. Because the exact two-component Hamiltonian contains spin-orbit operators, the method is able to describe the non-zero transition moment of otherwise spin-forbidden processes in non-relativistic theory. Furthermore, the two-component approach is more cost effective than the full four-component approach, with similar accuracy. The RT-X2C-TDDFT will be useful in future studies of systems containing heavy elements interacting with strong external fields. PMID:27634251

  8. Real time propagation of the exact two component time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Goings, Joshua J.; Kasper, Joseph M.; Egidi, Franco; Sun, Shichao; Li, Xiaosong

    2016-09-01

    We report the development of a real time propagation method for solving the time-dependent relativistic exact two-component density functional theory equations (RT-X2C-TDDFT). The method is fundamentally non-perturbative and may be employed to study nonlinear responses for heavy elements which require a relativistic Hamiltonian. We apply the method to several group 12 atoms as well as heavy-element hydrides, comparing with the extensive theoretical and experimental studies on this system, which demonstrates the correctness of our approach. Because the exact two-component Hamiltonian contains spin-orbit operators, the method is able to describe the non-zero transition moment of otherwise spin-forbidden processes in non-relativistic theory. Furthermore, the two-component approach is more cost effective than the full four-component approach, with similar accuracy. The RT-X2C-TDDFT will be useful in future studies of systems containing heavy elements interacting with strong external fields.

  9. Temperature extremes, density dependence, and southern pine beetle (Coleoptera: Curculionidae) population dynamics in east Texas.

    PubMed

    Friedenberg, Nicholas A; Sarkar, Sudipta; Kouchoukos, Nicholas; Billings, Ronald F; Ayres, Matthew P

    2008-06-01

    Previous studies of the southern pine beetle, Dendroctonus frontalis Zimm., established that its population in east Texas responds to a delayed density-dependent process, whereas no clear role of climate has been determined. We tested two biological hypotheses for the influence of extreme temperatures on annual southern pine beetle population growth in the context of four alternative hypotheses for density-dependent population regulation. The significance of climate variables and their interaction with population regulation depended on the model of density dependence. The best model included both direct and delayed density dependence of a cubic rather than linear form. Population growth declined with the number of days exceeding 32 degrees C, temperatures previously reported to reduce brood survival. Density dependence also changed with the number of hot days. Growth was highest in years with average minimum winter temperatures. Severely cold winters may reduce survival, whereas warm winters may reduce the efficiency of spring infestation formation. Whereas most previous studies have incorporated climate as an additive effect on growth, we found that the form of delayed density dependence changed with the number of days >32 degrees C. The interaction between temperature and regulation, a potentially common phenomenon in ecology, may explain why southern pine beetle outbreaks do not occur at perfectly regular intervals. Factors other than climate, such as forest management and direct suppression, may have contributed significantly to the timing, severity, and eventual cessation of outbreaks since the mid-1950s.

  10. Rapidity-dependent chemical potentials in a statistical approach

    NASA Astrophysics Data System (ADS)

    Broniowski, Wojciech; Biedroń, Bartłomiej

    2008-04-01

    We present a single-freeze-out model with thermal and geometric parameters dependent on the position within the fireball and use it to describe the rapidity distribution and transverse-momentum spectra of pions, kaons, protons and antiprotons measured at RHIC at \\sqrt{s_NN}=200\\,\\, GeV by BRAHMS. THERMINATOR is used to perform the necessary simulation, which includes all resonance decays. The result of the fit to the data is the expected growth of the baryon and strange chemical potentials with the spatial rapidity αpar. The value of the baryon chemical potential at αpar ~ 3 is about 200 MeV, i.e. it lies in the range of the highest SPS energies. The chosen geometry of the fireball has a decreasing transverse size as the magnitude of αpar is increased, which also corresponds to decreasing transverse flow. The strange chemical potential obtained from the fit to the K+/K- ratio is such that the local strangeness density in the fireball is compatible with zero. The resulting rapidity distribution of net protons are described qualitatively within the statistical approach. As a result of our study, the knowledge of the 'topography' of the fireball is acquired, allowing for other analyses and predictions. Research supported by the Polish Ministry of Education and Science, grants N202 034 32/0918 and 2 P03B 02828.

  11. Temporal changes in the strength of density-dependent mortality and growth in intertidal barnacles.

    PubMed

    Jenkins, Stuart R; Murua, Jefferson; Burrows, Michael T

    2008-05-01

    1. In demographically open marine systems, the extent to which density-dependent processes in the benthic adult phase are required for population persistence is unclear. At one extreme, represented by the recruitment limitation hypothesis, larval supply may be insufficient for the total population size to reach a carrying capacity and density-independent mortality predominates. At the opposite extreme, populations are saturated and density-dependent mortality is sufficiently strong to reshape patterns established at settlement. 2. We examined temporal variation in the way density-independent and density-dependent mortality interact in a typical sessile marine benthic invertebrate, the acorn barnacle Semibalanus balanoides (L.), over a 2-year period. 3. Recruitment was manipulated at two high recruitment sites in north Wales, UK to produce recruit densities covering the range naturally found in this species. Following manipulation, fixed quadrats were monitored using digital photography and temporal changes in mortality and growth rate were examined. 4. Over a 2-year period there was a clear, spatially consistent, over-compensatory relationship between the density of recruits and adult abundance indicating strong density-dependent mortality. The strength of density dependence intensified with increasing recruitment. 5. Density-dependent mortality did not operate consistently over the study period. It only operated in the early part of the benthic phase, but the pattern of adult abundance generated was maintained throughout the whole 2-year period. Thus, early life-history processes dictated adult population abundance and dynamics. 6. Examination of the natural recruitment regime in the area of study indicated that both positive and negative effects of recruitment will occur over scales varying from kilometres to metres.

  12. Time-dependent occupation numbers in reduced-density-matrix-functional theory: Application to an interacting Landau-Zener model

    SciTech Connect

    Requist, Ryan; Pankratov, Oleg

    2011-05-15

    We prove that if the two-body terms in the equation of motion for the one-body reduced density matrix are approximated by ground-state functionals, the eigenvalues of the one-body reduced density matrix (occupation numbers) remain constant in time. This deficiency is related to the inability of such an approximation to account for relative phases in the two-body reduced density matrix. We derive an exact differential equation giving the functional dependence of these phases in an interacting Landau-Zener model and study their behavior in short- and long-time regimes. The phases undergo resonances whenever the occupation numbers approach the boundaries of the interval [0,1]. In the long-time regime, the occupation numbers display correlation-induced oscillations and the memory dependence of the functionals assumes a simple form.

  13. The energy balance relation for weak solutions of the density-dependent Navier-Stokes equations

    NASA Astrophysics Data System (ADS)

    Leslie, T. M.; Shvydkoy, R.

    2016-09-01

    We consider the incompressible inhomogeneous Navier-Stokes equations with constant viscosity coefficient and density which is bounded and bounded away from zero. We show that the energy balance relation for this system holds for weak solutions if the velocity, density, and pressure belong to a range of Besov spaces of smoothness 1/3. A density-dependent version of the classical Kármán-Howarth-Monin relation is derived.

  14. 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.

  15. An evaluation of density-dependent and density-independent influences on population growth rates in Weddell seals

    USGS Publications Warehouse

    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

  16. Viking Doppler noise used to determine the radial dependence of electron density in the extended corona

    NASA Technical Reports Server (NTRS)

    Berman, A. L.; Wackley, J. A.; Rockwell, S. T.; Kwan, M.

    1977-01-01

    The common form for radial dependence of electron density in the extended corona is given. By assuming proportionality between Doppler noise and integrated signal path electron density, Viking Doppler noise can be used to solve for a numerical value of X.

  17. Relativistic Coulomb excitation within the time dependent superfluid local density approximation

    DOE PAGESBeta

    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, themore » 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 Γ↓≈0.4 MeV and the number of preequilibrium neutrons emitted has been quantified.« less

  18. Fusion of neutron-rich systems using time-dependent density-constrained DFT

    NASA Astrophysics Data System (ADS)

    Oberacker, Volker; Umar, A. S.

    2013-04-01

    In connection with experiments at Radioactive Ion Beam Facilities, we study fusion reactions with a new approach [1] which is based on a time-dependent density-constrained density functional theory (DFT). The only input is the Skyrme NN interaction, there are no adjustable parameters. We calculate heavy-ion interaction potentials V(R), mass parameters M(R), and total fusion cross sections. Some of the effects naturally included in these calculations are: neck formation, mass exchange, internal excitations, deformation effects, as well as nuclear alignment for deformed systems. Results will be presented for low-energy fusion reactions of ^12C+^16,24O and for ^16,24O+^16,24,28O which occur in the crust of neutron stars [2]. Finally, we will discuss fusion with neutron-rich halo nuclei, in particular ^11Li+^208Pb.[4pt] [1] Umar and Oberacker, PRC 74, 021601(R) (2006)[0pt] [2] Umar, Oberacker, and Horowitz, PRC 85, 055801 (2012)

  19. Practical methods in time-dependent density functional theory (TDDFT) at elevated temperatures

    NASA Astrophysics Data System (ADS)

    Magyar, Rudolph; Shulenburger, Luke; Baczewski, Andrew

    2014-03-01

    There is a great need to simulate dynamic material response properties under shock conditions where experimental data is often limited due to the extreme scales involved (MBars, 1000s of K, and manifold compressed solid densities). Knowing materials properties at this scale is vital element of simulations of planetary collisions, inertial confinement fusion experiments, and the surfaces of some stars. Considerable progress has been made using density functional molecular dynamics (DFT-MD) to model thermodynamic properties of material under these conditions; however, the approach is limited to cases in which the electrons are constrained to a thermodynamic distribution within the Mermin formulation. We will explore practical schemes to generalize this method to the time-dependent case. Several challenges come up such as the role of non-adiabatic electron-electron and electron-nuclear physics and the correct choice of initial state. One of the most straightforward choices of initial state is to project the Mermin state since the original Runge-Gross proof does not make explicit choice of occupations. We will present some numerical tests of finite systems to examine this formulation. We will also explore how simple models of non-adiabatic effects might be sufficiently accurate under extreme conditions. 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.

  20. Size selectivity of predation by brown bears depends on the density of their sockeye salmon prey.

    PubMed

    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

  1. Demographic variability and density-dependent dynamics of a free-ranging rhesus macaque population

    PubMed Central

    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

  2. Sexual segregation in North American elk: the role of density dependence

    PubMed Central

    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 1999–2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20 elk/km2, and a low-density population at 4 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 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

  3. An Empirical, Nonparametric Simulator for Multivariate Random Variables with Differing Marginal Densities and Nonlinear Dependence with Hydroclimatic Applications.

    PubMed

    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

  4. Density-dependent habitat selection by brown-headed cowbirds (Molothrus ater) in tallgrass prairie

    USGS Publications Warehouse

    Jensen, W.E.; Cully, J.F.

    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

  5. 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

  6. Spatial, temporal, and density-dependent components of habitat quality for a desert owl.

    PubMed

    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

  7. Spatial, Temporal, and Density-Dependent Components of Habitat Quality for a Desert Owl

    PubMed Central

    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

  8. 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.

  9. Time-dependent density functional methods for Raman spectra in open-shell systems.

    PubMed

    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

  10. 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; Lísal, 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.

  11. Excited State Absorption from Real-Time Time-Dependent Density Functional Theory.

    PubMed

    Fischer, Sean A; Cramer, Christopher J; Govind, Niranjan

    2015-09-01

    The optical response of excited states is a key property used to probe photophysical and photochemical dynamics. Additionally, materials with a large nonlinear absorption cross-section caused by two-photon (TPA) and excited state absorption (ESA) are desirable for optical limiting applications. The ability to predict the optical response of excited states would help in the interpretation of transient absorption experiments and aid in the search for and design of optical limiting materials. We have developed an approach to obtain excited state absorption spectra by combining real-time (RT) and linear-response (LR) time-dependent density functional theory (TDDFT). Being based on RT-TDDFT, our method is aimed at tackling larger molecular complexes and materials systems where excited state absorption is predominantly seen and many time-resolved experimental efforts are focused. To demonstrate our method, we have calculated the ground and excited state spectra of H₂⁺ and H₂ due to the simplicity in the interpretation of the spectra. We have validated our new approach by comparing our results for butadiene with previously published results based on quadratic response (QR). We also present results for oligofluorenes, where we compare our results with both QR-TDDFT and experimental measurements. Because our method directly measures the response of an excited state, stimulated emission features are also captured; although, these features are underestimated in energy which could be attributed to a change of the reference from the ground to the excited state.

  12. Filtered density function approach for reactive transport in groundwater

    NASA Astrophysics Data System (ADS)

    Suciu, Nicolae; Schüler, Lennart; Attinger, Sabine; Knabner, Peter

    2016-04-01

    Spatial filtering may be used in coarse-grained simulations (CGS) of reactive transport in groundwater, similar to the large eddy simulations (LES) in turbulence. The filtered density function (FDF), stochastically equivalent to a probability density function (PDF), provides a statistical description of the sub-grid, unresolved, variability of the concentration field. Besides closing the chemical source terms in the transport equation for the mean concentration, like in LES-FDF methods, the CGS-FDF approach aims at quantifying the uncertainty over the whole hierarchy of heterogeneity scales exhibited by natural porous media. Practically, that means estimating concentration PDFs on coarse grids, at affordable computational costs. To cope with the high dimensionality of the problem in case of multi-component reactive transport and to reduce the numerical diffusion, FDF equations are solved by particle methods. But, while trajectories of computational particles are modeled as stochastic processes indexed by time, the concentration's heterogeneity is modeled as a random field, with multi-dimensional, spatio-temporal sets of indices. To overcome this conceptual inconsistency, we consider FDFs/PDFs of random species concentrations weighted by conserved scalars and we show that their evolution equations can be formulated as Fokker-Planck equations describing stochastically equivalent processes in concentration-position spaces. Numerical solutions can then be approximated by the density in the concentration-position space of an ensemble of computational particles governed by the associated Itô equations. Instead of sequential particle methods we use a global random walk (GRW) algorithm, which is stable, free of numerical diffusion, and practically insensitive to the increase of the number of particles. We illustrate the general FDF approach and the GRW numerical solution for a reduced complexity problem consisting of the transport of a single scalar in groundwater

  13. Cascading effects of belowground predators on plant communities are density-dependent.

    PubMed

    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

  14. Density dependence in a recovering osprey population: demographic and behavioural processes.

    PubMed

    Bretagnolle, V; Mougeot, F; Thibault, J-C

    2008-09-01

    1. Understanding how density-dependent and independent processes influence demographic parameters, and hence regulate population size, is fundamental within population ecology. We investigated density dependence in growth rate and fecundity in a recovering population of a semicolonial raptor, the osprey Pandion haliaetus [Linnaeus, 1758], using 31 years of count and demographic data in Corsica. 2. The study population increased from three pairs in 1974 to an average of 22 pairs in the late 1990s, with two distinct phases during the recovery (increase followed by stability) and contrasted trends in breeding parameters in each phase. 3. We show density dependence in population growth rate in the second phase, indicating that the stabilized population was regulated. We also show density dependence in productivity (fledging success between years and hatching success within years). 4. Using long-term data on behavioural interactions at nest sites, and on diet and fish provisioning rate, we evaluated two possible mechanisms of density dependence in productivity, food depletion and behavioural interference. 5. As density increased, both provisioning rate and the size of prey increased, contrary to predictions of a food-depletion mechanism. In the time series, a reduction in fledging success coincided with an increase in the number of non-breeders. Hatching success decreased with increasing local density and frequency of interactions with conspecifics, suggesting that behavioural interference was influencing hatching success. 6. Our study shows that, taking into account the role of non-breeders, in particular in species or populations where there are many floaters and where competition for nest sites is intense, can improve our understanding of density-dependent processes and help conservation actions.

  15. Spatially heterogeneous populations with mixed negative and positive local density dependence.

    PubMed

    Knipl, Diána; Röst, Gergely

    2016-06-01

    Identifying the steady states of a population is a key issue in theoretical ecology, that includes the study of spatially heterogeneous populations. There are several examples of real ecosystems in patchy environments where the habitats are heterogeneous in their local density dependence. We investigate a multi-patch model of a single species with spatial dispersal, where the growth of the local population is logistic in some localities (negative density dependence) while other patches exhibit a strong Allee effect (positive density dependence). When the local dynamics is logistic in each patch and the habitats are interconnected by dispersal then the total population has only the extinction steady state and a componentwise positive equilibrium, corresponding to persistence in each patch. We show that animal populations in patchy environments can have a large number of steady states if local density dependence varies over the locations. It is demonstrated that, depending on the network topology of migration routes between the patches, the interaction of spatial dispersal and local density dependence can create a variety of coexisting stable positive equilibria. We give a detailed description of the multiple ways dispersal can rescue local populations from extinction. PMID:26801607

  16. Comparison of real-time and linear-response time-dependent density functional theories for molecular chromophores ranging from sparse to high densities of states

    SciTech Connect

    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.

  17. A physical-space approach for the probability hypothesis density and cardinalized probability hypothesis density filters

    NASA Astrophysics Data System (ADS)

    Erdinc, Ozgur; Willett, Peter; Bar-Shalom, Yaakov

    2006-05-01

    The probability hypothesis density (PHD) filter, an automatically track-managed multi-target tracker, is attracting increasing but cautious attention. Its derivation is elegant and mathematical, and thus of course many engineers fear it; perhaps that is currently limiting the number of researchers working on the subject. In this paper, we explore a physical-space approach - a bin model - which leads us to arrive the same filter equations as the PHD. Unlike the original derivation of the PHD filter, the concepts used are the familiar ones of conditional probability. The original PHD suffers from a "target-death" problem in which even a single missed detection can lead to the apparent disappearance of a target. To obviate this, PHD originator Mahler has recently developed a new "cardinalized" version of PHD (CPHD). We are able to extend our physical-space derivation to the CPHD case as well. We stress that the original derivations are mathematically correct, and need no embellishment from us; our contribution here is to offer an alternative derivation, one that we find appealing.

  18. Representing the thermal state in time-dependent density functional theory

    SciTech Connect

    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.

  19. Negative density dependence of seed dispersal and seedling recruitment in a neotropical palm.

    PubMed

    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

  20. 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.

  1. Negative density dependence of seed dispersal and seedling recruitment in a neotropical palm.

    PubMed

    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.

  2. Dependence of various SOL widths on plasma current and density in NSTX H-mode plasmas

    SciTech Connect

    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.

  3. Density-dependent intraspecific aggression regulates survival in northern Yellowstone wolves (Canis lupus).

    PubMed

    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

  4. Density-dependent intraspecific aggression regulates survival in northern Yellowstone wolves (Canis lupus).

    PubMed

    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

  5. 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

    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.

  6. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions.

    PubMed

    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.

  7. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

    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.

  8. Time-dependent density functional theory for open systems with a positivity-preserving decomposition scheme for environment spectral functions

    SciTech Connect

    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.

  9. Ionic strength-dependent changes in tentacular ion exchangers with variable ligand density. I. Structural properties.

    PubMed

    Bhambure, Rahul; Gillespie, Christopher M; Phillips, Michael; Graalfs, Heiner; Lenhoff, Abraham M

    2016-09-01

    The ligand density critically affects the performance of ion-exchange resins in such measures as the adsorption capacity and transport characteristics. However, for tentacular and other polymer-modified exchangers, the mechanistic basis of the effect of ligand density on performance is not yet fully understood. In this study we map the ionic strength-dependent structural changes in tentacular cation exchangers with variable ligand densities as the basis for subsequent investigation of effects on functional properties. Inverse size-exclusion chromatography (ISEC), scanning electron microscopy (SEM) and small-angle x-ray scattering (SAXS) were used to assess the effect of ionic strength on the pore size and intraparticle architecture of resin variants with different ligand densities. Comparison of ISEC and cryo-SEM results shows a considerable reduction in average pore size with increasing ligand density; these methods also confirm an increase of average pore size at higher ionic strengths. SAXS analysis of ionic strength-dependent conformational changes in the grafted polyelectrolyte layer shows a characteristic ionomer peak at values of the scattering vector q (0.1-0.2Å(-1)) that depend on the ligand density and the ionic strength of the solution. This peak attribution reflects nanoscale changes in the structure of the grafted polyelectrolyte chains that can in turn be responsible for observed pore-size changes in the resins. Finally, salt breakthrough experiments confirm a stronger Donnan exclusion effect on pore accessibility for small ions in the high ligand density variant. PMID:27544749

  10. Adaptive nest clustering and density-dependent nest survival in dabbling ducks

    USGS Publications Warehouse

    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 (˜50–400 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 – 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.

  11. Density-dependent habitat selection and partitioning between two sympatric ungulates.

    PubMed

    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.

  12. 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.

  13. An Approach to Calculate Mineralś Bulk Moduli KS from Chemical Composition and Density ρ

    NASA Astrophysics Data System (ADS)

    Breuer, S.; Schilling, F. R.; Mueller, B.; Drüppel, K.

    2015-12-01

    The elastic properties of minerals are fundamental parameters for technical and geotechnical applications and an important research topic towards a better understanding of the Earth's interior. Published elastic properties, chemical composition, and density data of 86 minerals (total of 258 data including properties of minerals at various p, T conditions) were collected into a database. It was used to test different hypotheses about relationships between these properties (e.g. water content in minerals and their Poisson's ratio). Furthermore, a scheme to model the average elastic properties, i.e. the bulk modulus KS, based on mineral density and composition was developed. Birch's law, a linearity between density ρ and wave velocity (e.g. vp.), is frequently used in seismic and seismology to derive density of the Earth's interior from seismic velocities. Applying the compiled mineral data contradicts the use of a simple velocity-density relation (e.g. Gardneŕs relation, 1974). The presented model-approach to estimate the mineralś bulk moduli Ks (as Voigt-Reuss-Hill average) is based on the idea of pressure-temperature (p-T) dependent ionś bulk moduli. Using a multi-exponential regression to ascertain the ionś bulk moduli and by applying an exponential scaling with density ρ, their bulk moduli could be modelled. As a result, > 88 % of the 258 bulk moduli data are predicted with an uncertainty of < 20 % compared to published values. Compared to other models (e.g. Anderson et al. 1970 and Anderson & Nafe 1965), the here presented approach to model the bulk moduli only requires the density ρ and chemical composition of the mineral and is not limited to a specific group of minerals, composition, or structure. In addition to this, by using the pressure and temperature dependent density ρ(p, T), it is possible to predict bulk moduli for varying p-T conditions. References:Gardner, G.H.F, Gardner, L.W. and Gregory, A.R. (1974). Geophysics, 39, No. 6, 770

  14. Quantum fluid dynamics based current-density functional study of a helium atom in a strong time-dependent magnetic field

    NASA Astrophysics Data System (ADS)

    Vikas, Hash(0x125f4490)

    2011-02-01

    Evolution of the helium atom in a strong time-dependent (TD) magnetic field ( B) of strength up to 1011 G is investigated through a quantum fluid dynamics (QFD) based current-density functional theory (CDFT). The TD-QFD-CDFT computations are performed through numerical solution of a single generalized nonlinear Schrödinger equation employing vector exchange-correlation potentials and scalar exchange-correlation density functionals that depend both on the electronic charge-density and the current-density. The results are compared with that obtained from a B-TD-QFD-DFT approach (based on conventional TD-DFT) under similar numerical constraints but employing only scalar exchange-correlation potential dependent on electronic charge-density only. The B-TD-QFD-DFT approach, at a particular TD magnetic field-strength, yields electronic charge- and current-densities as well as exchange-correlation potential resembling with that obtained from the time-independent studies involving static (time-independent) magnetic fields. However, TD-QFD-CDFT electronic charge- and current-densities along with the exchange-correlation potential and energy differ significantly from that obtained using B-TD-QFD-DFT approach, particularly at field-strengths >109 G, representing dynamical effects of a TD field. The work concludes that when a helium atom is subjected to a strong TD magnetic field of order >109 G, the conventional TD-DFT based approach differs "dynamically" from the CDFT based approach under similar computational constraints.

  15. Harnessing the meta-generalized gradient approximation for time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Bates, Jefferson E.; Furche, Filipp

    2012-10-01

    Density functionals within the meta-generalized gradient approximation (MGGA) are widely used for ground-state electronic structure calculations. However, the gauge variance of the kinetic energy density τ confounds applications of MGGAs to time-dependent systems, excited states, magnetic properties, and states with strong spin-orbit coupling. Becke and Tao used the paramagnetic current density to construct a gauge invariant generalized kinetic energy density hat{τ }. We show that τ _W ≤ hat{τ }, where τW is the von Weizsäcker kinetic energy density of a one-electron system. Thus, replacing τ by hat{τ } leads to current-dependent MGGAs (cMGGAs) that are not only gauge invariant but also restore the accuracy of MGGAs in iso-orbital regions for time-dependent and current-carrying states. The current dependence of cMGGAs produces a vector exchange-correlation (XC) potential in the time-dependent adiabatic Kohn-Sham (KS) equations. While MGGA response properties of current-free ground states become manifestly gauge-variant to second order, linear response properties are affected by a new XC kernel appearing in the cMGGA magnetic orbital rotation Hessian. This kernel reflects the first-order coupling of KS orbitals due to changes in the paramagnetic current density and has apparently been ignored in previous MGGA response implementations. Inclusion of the current dependence increases total computation times by less than 50%. Benchmark applications to 109 adiabatic excitation energies using the Tao-Perdew-Staroverov-Scuseria (TPSS) MGGA and its hybrid version TPSSh show that cMGGA excitation energies are slightly lower than the MGGA ones on average, but exhibit fewer outliers. Similarly, the optical rotations of 13 small organic molecules show a small but systematic improvement upon inclusion of the magnetic XC kernel. We conclude that cMGGAs should replace MGGAs in all applications involving time-dependent or current-carrying states.

  16. Harnessing the meta-generalized gradient approximation for time-dependent density functional theory.

    PubMed

    Bates, Jefferson E; Furche, Filipp

    2012-10-28

    Density functionals within the meta-generalized gradient approximation (MGGA) are widely used for ground-state electronic structure calculations. However, the gauge variance of the kinetic energy density τ confounds applications of MGGAs to time-dependent systems, excited states, magnetic properties, and states with strong spin-orbit coupling. Becke and Tao used the paramagnetic current density to construct a gauge invariant generalized kinetic energy density τ. We show that τ(W)≤τ, where τ(W) is the von Weizsäcker kinetic energy density of a one-electron system. Thus, replacing τ by τ leads to current-dependent MGGAs (cMGGAs) that are not only gauge invariant but also restore the accuracy of MGGAs in iso-orbital regions for time-dependent and current-carrying states. The current dependence of cMGGAs produces a vector exchange-correlation (XC) potential in the time-dependent adiabatic Kohn-Sham (KS) equations. While MGGA response properties of current-free ground states become manifestly gauge-variant to second order, linear response properties are affected by a new XC kernel appearing in the cMGGA magnetic orbital rotation Hessian. This kernel reflects the first-order coupling of KS orbitals due to changes in the paramagnetic current density and has apparently been ignored in previous MGGA response implementations. Inclusion of the current dependence increases total computation times by less than 50%. Benchmark applications to 109 adiabatic excitation energies using the Tao-Perdew-Staroverov-Scuseria (TPSS) MGGA and its hybrid version TPSSh show that cMGGA excitation energies are slightly lower than the MGGA ones on average, but exhibit fewer outliers. Similarly, the optical rotations of 13 small organic molecules show a small but systematic improvement upon inclusion of the magnetic XC kernel. We conclude that cMGGAs should replace MGGAs in all applications involving time-dependent or current-carrying states.

  17. Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach

    EPA Science Inventory

    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...

  18. On global motions of a compressible barotropic and selfgravitating gas with density-dependent viscosities

    NASA Astrophysics Data System (ADS)

    Ducomet, Bernard; Nečasová, 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 μ( ρ), and λ( ρ) satisfying the Bresch-Desjardins condition, when the pressure P( ρ) is not necessarily a monotone function of the density. We prove that this problem admits a global weak solution provided that the adiabatic exponent γ associated with P( ρ) satisfies {γ > 4/3}.

  19. Is predation on waterfowl nests density dependent? Tests at three spatial scales

    USGS Publications Warehouse

    Ackerman, Joshua T.; Blackmer, Alexis L.; Eadie, John M.

    2004-01-01

    We tested whether predation on duck nests (Anas spp.) was density dependent at three spatial scales using artificial and natural nests in the Suisun Marsh, California, USA. At the largest spatial scale, we used 5 years (1998–2002) of data to examine the natural variation in duck nest success and nest densities among 8–16 fields per year, each 5–33 ha in size (n=62 fields). At an intermediate spatial scale, we deployed artificial nests (2000, n=280) within 1-ha plots at three experimental densities (5, 10, and 20 nests ha−1) in a complete randomized block design and examined differences in nest predation. At the smallest spatial scale, we examined nest success in relation to nearest-neighbor fates and distances for artificial (2000, n=280) and natural nests (2000, n=507). We detected no relationship between nest success and the density of natural nests among fields in any year, nor when we pooled data for all years after controlling for year effects. The proportion of artificial nests that survived also did not depend on experimental nest densities within 1-ha plots. Overall, 15.0±12.4%, 15.0±11.0%, and 6.2±4.3% of artificial nests survived the 32-day exposure period in the low, intermediate, and high nest densities, respectively. Additionally, we detected no consistent effect of nearest-neighbor fate or distance on the success of artificial or natural nests. Thus, our results provide no evidence of density-dependent predation on duck nests at any scale of analysis, in contrast to a number of previous studies. Variation among geographical locations in the degree to which predation is density-dependent may reflect the composition of the predator community and the availability of alternate prey.

  20. Density, temperature, and bond-length dependence of dynamic friction on a molecular bond

    NASA Astrophysics Data System (ADS)

    Vergeles, Maxim; Szamel, Grzegorz

    1999-09-01

    We apply the theoretical formalism developed by us earlier [M. Vergeles and G. Szamel, J. Chem. Phys. 110, 6827 (1999)] to study density, temperature, and bond-length dependence of the dynamic friction on a molecular bond. We show that the theory reproduces all the trends seen in molecular dynamics (MD) simulations. The theoretical predictions agree reasonably well with the results of MD simulations except for very low densities or very short bond lengths.

  1. Density-mediated, context-dependent consumer-resource interactions between ants and extrafloral nectar plants.

    PubMed

    Chamberlain, Scott A; Holland, J Nathaniel

    2008-05-01

    Interspecific interactions are often mediated by the interplay between resource supply and consumer density. The supply of a resource and a consumer's density response to it may in turn yield context-dependent use of other resources. Such consumer-resource interactions occur not only for predator-prey and competitive interactions, but for mutualistic ones as well. For example, consumer-resource interactions between ants and extrafloral nectar (EFN) plants are often mutualistic, as EFN resources attract and reward ants which protect plants from herbivory. Yet, ants also commonly exploit floral resources, leading to antagonistic consumer-resource interactions by disrupting pollination and plant reproduction. EFN resources associated with mutualistic ant-plant interactions may also mediate antagonistic ant-flower interactions through the aggregative density response of ants on plants, which could either exacerbate ant-flower interactions or alternatively satiate and distract ants from floral resources. In this study, we examined how EFN resources mediate the density response of ants on senita cacti in the Sonoran Desert and their context-dependent use of floral resources. Removal of EFN resources reduced the aggregative density of ants on plants, both on hourly and daily time scales. Yet, the increased aggregative ant density on plants with EFN resources decreased rather than increased ant use of floral resources, including contacts with and time spent in flowers. Behavioral assays showed no confounding effect of floral deterrents on ant-flower interactions. Thus, ant use of floral resources depends on the supply of EFN resources, which mediates the potential for both mutualistic and antagonistic interactions by increasing the aggregative density of ants protecting plants, while concurrently distracting ants from floral resources. Nevertheless, only certain years and populations of study showed an increase in plant reproduction through herbivore protection or ant

  2. Density-dependent prey mortality is determined by the spatial scale of predator foraging.

    PubMed

    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.

  3. Exposing extinction risk analysis to pathogens: Is disease just another form of density dependence?

    USGS Publications Warehouse

    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

  4. Exact response functions within the time-dependent Gutzwiller approach

    NASA Astrophysics Data System (ADS)

    Bünemann, J.; Wasner, S.; Oelsen, E. v.; Seibold, G.

    2015-02-01

    We investigate the applicability of the two existing versions of a time-dependent Gutzwiller approach (TDGA) beyond the frequently used limit of infinite spatial dimensions. To this end, we study the two-particle response functions of a two-site Hubbard model where we can compare the exact results and those derived from the TDGA. It turns out that only the more recently introduced version of the TDGA can be combined with a diagrammatic approach which allows for the evaluation of Gutzwiller wave functions in finite dimensions. For this TDGA method, we derive the time-dependent Lagrangian for general single-band Hubbard models.

  5. Small-scale field experiments accurately scale up to predict density dependence in reef fish populations at large scales.

    PubMed

    Steele, Mark A; Forrester, Graham E

    2005-09-20

    Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats.

  6. Time-dependent first-principles approaches to PV materials

    SciTech Connect

    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.

  7. Bayesian Inference on the Effect of Density Dependence and Weather on a Guanaco Population from Chile

    PubMed Central

    Zubillaga, María; Skewes, Oscar; Soto, Nicolás; 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

  8. Lonely hearts or sex in the city? Density-dependent effects in mating systems

    PubMed Central

    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

  9. Bayesian inference on the effect of density dependence and weather on a guanaco population from Chile.

    PubMed

    Zubillaga, María; Skewes, Oscar; Soto, Nicolás; 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.

  10. Temperature and density dependence of XANES spectra in warm dense aluminum plasmas

    NASA Astrophysics Data System (ADS)

    Recoules, V.; Mazevet, S.

    2009-08-01

    Using ab initio molecular-dynamics simulations combined with linear-response theory, we calculate the density and temperature dependence of the x-ray absorption near-edge structure (XANES) of a dense aluminum plasma. At solid density and for temperatures increasing up to 6 eV, we see that the XANES spectrum loses its well-known room-temperature structure, first due to melting and second due to loss of correlation in the liquid. Similarly, as the density decreases and the system evolves from a liquid to a plasma, the XANES spectrum becomes less structured. As the density is further lowered and the system turns into an atomic fluid, a pre-edge forms as the 3p state becomes bound. We suggest that direct measurements of the XANES spectra in this density region is a unique opportunity to validate pressure ionization models routinely used in plasma physics modeling.

  11. Dynamics of observables and exactly solvable quantum problems: Using time-dependent density-functional theory to control quantum systems

    NASA Astrophysics Data System (ADS)

    Farzanehpour, M.; Tokatly, I. V.

    2016-05-01

    We use analytic (current) density-potential maps of time-dependent (current) density-functional theory [TD(C)DFT] to inverse engineer analytically solvable time-dependent quantum problems. In this approach the driving potential (the control signal) and the corresponding solution of the Schrödinger equation are parametrized analytically in terms of the basic TD(C)DFT observables. We describe the general reconstruction strategy and illustrate it with a number of explicit examples. First we consider the real space one-particle dynamics driven by a time-dependent electromagnetic field and recover, from the general TDDFT reconstruction formulas, the known exact solution for a driven oscillator with a time-dependent frequency. Then we use analytic maps of the lattice TD(C)DFT to control quantum dynamics in a discrete space. As a first example we construct a time-dependent potential which generates prescribed dynamics on a tight-binding chain. Then our method is applied to the dynamics of spin-1/2 driven by a time-dependent magnetic field. We design an analytic control pulse that transfers the system from the ground to excited state and vice versa. This pulse generates the spin flip thus operating as a quantum not gate.

  12. Fragmentation in isotopic and isobaric systems as probe of density dependence of nuclear symmetry energy

    NASA Astrophysics Data System (ADS)

    Kaur, Mandeep; Gautam, Sakshi; Puri, Rajeev K.

    2016-11-01

    We probe the density-dependent behavior of symmetry energy using the yield of various fragments in central collisions of various isotopic and isobaric colliding pairs. We calculate the yields of free nucleons, light charged particles and intermediate mass fragments in neutron-rich colliding systems as well as the ratio of relative yields of above fragments and free nucleons. Our findings reveal that the ratio of relative yield of light charged particles poses better candidate to probe the density dependence of nuclear symmetry energy.

  13. Quark Magnetar in Confined Isospin- and Density-dependent Mass Model

    NASA Astrophysics Data System (ADS)

    Chu, P. C.; Chen, L. W.; Wang, X.

    2015-11-01

    Within confined isospin- and density-dependent mass model, we study the equation of state(EOS) for the strange quark matter (SQM) and quark stars (QSs) under density-dependent magneticfields. The EOS of SQM is obtained self-consistently under a strong magnetic field, and thetransverse pressure which is perpendicular to the magnetic field is proved to be larger than thelongitudinal pressure that is parallel to the magnetic field. Our results indicate that the maximummass of quark magnetars can significantly increase (decrease) when the transverse (radial) magneticfield orientation is considered.

  14. Time-dependent renormalized Redfield theory II for off-diagonal transition in reduced density matrix

    NASA Astrophysics Data System (ADS)

    Kimura, Akihiro

    2016-09-01

    In our previous letter (Kimura, 2016), we constructed time-dependent renormalized Redfield theory (TRRT) only for diagonal transition in a reduced density matrix. In this letter, we formulate the general expression for off-diagonal transition in the reduced density matrix. We discuss the applicability of TRRT by numerically comparing the dependencies on the energy gap of the exciton relaxation rate by using the TRRT and the modified Redfield theory (MRT). In particular, we roughly show that TRRT improves MRT for the detailed balance about the excitation energy transfer reaction.

  15. Scale-dependent shifts in the species composition of flower visitors with changing floral density.

    PubMed

    Essenberg, Carla J

    2013-01-01

    Responses of flower-visiting animals to floral density can alter interactions between plants, influencing a variety of biological processes, including plant population dynamics and the evolution of flowering phenology. Many studies have found effects of floral or plant density on pollinator visitation rates at patch scales, but little is known about responses of flower visitors to floral densities at larger scales. Here, I present data from an observational field study in which I measured the effects of floral density on visitation to the annual composite Holocarpha virgata at both patch (4 m(2)) and site (12.6 ha) spatial scales. The species composition of flower visitors changed with floral density, and did so in different ways at the two scales. At the site scale, average floral density within patches of H. virgata or within patches of all summer-flowering species combined had a significant positive effect on per-flowerhead visitation by the long-horned bee Melissodes lupina and no significant effects on visitation by any other taxa. At the patch scale, per-flowerhead visitation by honeybees significantly increased whereas visitation by M. lupina often decreased with increasing floral density. For both species, responses to patch-scale floral density were strongest when site-scale floral density was high. The scale-dependence of flower visitor responses to floral density and the interactions between site- and patch-scale effects of floral density observed in this study underscore the importance of improving our understanding of pollinators' responses to floral density at population scales.

  16. Harnessing the Meta-Generalized Gradient Approximation for Time-Dependent Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Bates, Jefferson Earl

    Density functionals within the meta-generalized gradient approximation (MGGA) are widely used for ground-state electronic structure calculations. However, the gauge variance of the kinetic energy density tau confounds applications of MGGAs to time-dependent systems, excited states, magnetic properties, and states with strong spin-orbit coupling. Becke and Tao used the paramagnetic current density to construct a gauge invariant generalized kinetic energy density t̂ . We show that tauW ≤ t̂ , where tauW is the von Weizsacker kinetic energy density of a one-electron system. Thus, replacing tau by t̂ leads to current-dependent MGGAs (cMGGAs) that are not only gauge invariant, but also restore the accuracy of MGGAs in iso-orbital regions for time-dependent and current-carrying states. The current dependence of cMGGAs produces a vector exchange-correlation (XC) potential in the time-dependent adiabatic Kohn-Sham (KS) equations. While response properties of current-free ground states become manifestly gauge-variant to second order, linear response properties are affected by a new XC kernel appearing in the cMGGA magnetic orbital rotation Hessian. Inclusion of the current dependence increases total computation times by less than 50%. Benchmark applications to 109 adiabatic excitation energies using the Tao-Perdew-Staroverov-Scuseria (TPSS) MGGA and its hybrid version TPSSh show that cMGGA excitation energies are slightly lower than the MGGA ones on average, but exhibit fewer outliers. Similarly, the optical rotations of 13 small organic molecules show a small but systematic improvement upon inclusion of the magnetic XC kernel. We conclude that cMGGAs should replace MGGAs in all applications involving time-dependent or current-carrying states.

  17. Spatial and temporal features of density-dependent contaminant transport: Experimental investigation and numerical modeling

    NASA Astrophysics Data System (ADS)

    Zoia, Andrea; Latrille, Christelle; Beccantini, Alberto; Cartadale, Alain

    2009-10-01

    We investigate the spatial and temporal features of variable-density contaminant plumes migration in porous materials. Our analysis is supported by novel experimental results concerning concentration profiles inside a vertical column setup that has been conceived at CEA to this aim. The experimental method relies on X-ray spectrometry, which allows determining solute profiles as a function of time at several positions along the column. The salient outcomes of the measurements are elucidated, with focus on miscible fluids in homogeneous saturated media. The role of the injected solution molarity is evidenced. As molarity increases, the solutes plume transport progressively deviates from the usual Fickian behavior, and pollutants distribution becomes skewed in the direction dictated by gravity. By resorting to a finite elements approach, we numerically solve the nonlinear equations that rule the pollutants migration: a good agreement is found between the simulated profiles and the experimental data. At high molarity, a strong dependence on initial conditions is found. Finally, we qualitatively explore the (unstable) interfacial dynamics between the dense contaminant plume and the lighter resident fluid that saturates the column, and detail its evolution for finite-duration contaminant injections.

  18. Spatial and temporal features of density-dependent contaminant transport: experimental investigation and numerical modeling.

    PubMed

    Zoia, Andrea; Latrille, Christelle; Beccantini, Alberto; Cartadale, Alain

    2009-10-13

    We investigate the spatial and temporal features of variable-density contaminant plumes migration in porous materials. Our analysis is supported by novel experimental results concerning concentration profiles inside a vertical column setup that has been conceived at CEA to this aim. The experimental method relies on X-ray spectrometry, which allows determining solute profiles as a function of time at several positions along the column. The salient outcomes of the measurements are elucidated, with focus on miscible fluids in homogeneous saturated media. The role of the injected solution molarity is evidenced. As molarity increases, the solutes plume transport progressively deviates from the usual Fickian behavior, and pollutants distribution becomes skewed in the direction dictated by gravity. By resorting to a finite elements approach, we numerically solve the nonlinear equations that rule the pollutants migration: a good agreement is found between the simulated profiles and the experimental data. At high molarity, a strong dependence on initial conditions is found. Finally, we qualitatively explore the (unstable) interfacial dynamics between the dense contaminant plume and the lighter resident fluid that saturates the column, and detail its evolution for finite-duration contaminant injections.

  19. Nonadiabatic dynamics with intersystem crossings: A time-dependent density functional theory implementation

    SciTech Connect

    Franco de Carvalho, F.; Tavernelli, I.

    2015-12-14

    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 (SO{sub 2}) in gas and liquid phases.

  20. Nonadiabatic dynamics with intersystem crossings: A time-dependent density functional theory implementation

    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.

  1. Density-dependent light-assisted tunneling in fermionic optical lattices

    NASA Astrophysics Data System (ADS)

    Xu, Wenchao; Morong, William; Demarco, Brian

    2016-05-01

    Many recent theoretical proposals have discussed the possibility to realize density-dependent tunneling in optical lattices via external periodic driving. These methods enable the simulation of novel many-body quantum phases. Here we present experimental progress on realizing density-dependent tunneling for ultracold 40K atoms trapped in a cubic optical lattice via stimulated Raman transitions. After preparing a spin-polarized gas in the Mott insulator regime of the Hubbard model, a pair of Raman beams is applied to flip the spin of atoms. The Raman beams also introduce an effective density-dependent tunneling that can be tuned by the Raman frequency difference and Rabi rate. The Mott gap inferred from measurements of the fraction of atoms transferred between spin states as the Raman frequency difference is adjusted matches the prediction based on a tight-binding model. We also observe the interaction-dependent tunneling by measuring the fraction of doubly-occupied sites created by the Raman driving. This method allows the engineering of density-dependent tunneling and effective nearest-neighbor interactions in fermionic optical lattices. The authors acknowledge funding from the National Science Foundation (Grant No. PHY15-05468) and the Army Research Office (Grant No. W911NF-12-1-0462).

  2. Density dependence in group dynamics of a highly social mongoose, Suricata suricatta.

    PubMed

    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.

  3. Density dependence in group dynamics of a highly social mongoose, Suricata suricatta.

    PubMed

    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

  4. 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.

  5. Comparison of Methods for Predicting the Compositional Dependence of the Density and Refractive Index of Organic-Aqueous Aerosols.

    PubMed

    Cai, Chen; Miles, Rachael E H; Cotterell, Michael I; Marsh, Aleksandra; Rovelli, Grazia; Rickards, Andrew M J; Zhang, Yun-Hong; Reid, Jonathan P

    2016-08-25

    Representing the physicochemical properties of aerosol particles of complex composition is of crucial importance for understanding and predicting aerosol thermodynamic, kinetic, and optical properties and processes and for interpreting and comparing analysis methods. Here, we consider the representations of the density and refractive index of aqueous-organic aerosol with a particular focus on the dependence of these properties on relative humidity and water content, including an examination of the properties of solution aerosol droplets existing at supersaturated solute concentrations. Using bulk phase measurements of density and refractive index for typical organic aerosol components, we provide robust approaches for the estimation of these properties for aerosol at any intermediate composition between pure water and pure solute. Approximately 70 compounds are considered, including mono-, di- and tricarboxylic acids, alcohols, diols, nitriles, sulfoxides, amides, ethers, sugars, amino acids, aminium sulfates, and polyols. We conclude that the molar refraction mixing rule should be used to predict the refractive index of the solution using a density treatment that assumes ideal mixing or, preferably, a polynomial dependence on the square root of the mass fraction of solute, depending on the solubility limit of the organic component. Although the uncertainties in the density and refractive index predictions depend on the range of subsaturated compositional data available for each compound, typical errors for estimating the solution density and refractive index are less than ±0.1% and ±0.05%, respectively. Owing to the direct connection between molar refraction and the molecular polarizability, along with the availability of group contribution models for predicting molecular polarizability for organic species, our rigorous testing of the molar refraction mixing rule provides a route to predicting refractive indices for aqueous solutions containing organic molecules

  6. Comparison of Methods for Predicting the Compositional Dependence of the Density and Refractive Index of Organic-Aqueous Aerosols.

    PubMed

    Cai, Chen; Miles, Rachael E H; Cotterell, Michael I; Marsh, Aleksandra; Rovelli, Grazia; Rickards, Andrew M J; Zhang, Yun-Hong; Reid, Jonathan P

    2016-08-25

    Representing the physicochemical properties of aerosol particles of complex composition is of crucial importance for understanding and predicting aerosol thermodynamic, kinetic, and optical properties and processes and for interpreting and comparing analysis methods. Here, we consider the representations of the density and refractive index of aqueous-organic aerosol with a particular focus on the dependence of these properties on relative humidity and water content, including an examination of the properties of solution aerosol droplets existing at supersaturated solute concentrations. Using bulk phase measurements of density and refractive index for typical organic aerosol components, we provide robust approaches for the estimation of these properties for aerosol at any intermediate composition between pure water and pure solute. Approximately 70 compounds are considered, including mono-, di- and tricarboxylic acids, alcohols, diols, nitriles, sulfoxides, amides, ethers, sugars, amino acids, aminium sulfates, and polyols. We conclude that the molar refraction mixing rule should be used to predict the refractive index of the solution using a density treatment that assumes ideal mixing or, preferably, a polynomial dependence on the square root of the mass fraction of solute, depending on the solubility limit of the organic component. Although the uncertainties in the density and refractive index predictions depend on the range of subsaturated compositional data available for each compound, typical errors for estimating the solution density and refractive index are less than ±0.1% and ±0.05%, respectively. Owing to the direct connection between molar refraction and the molecular polarizability, along with the availability of group contribution models for predicting molecular polarizability for organic species, our rigorous testing of the molar refraction mixing rule provides a route to predicting refractive indices for aqueous solutions containing organic molecules

  7. Density-dependent natal dispersal patterns in a leopard population recovering from over-harvest.

    PubMed

    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 'mate competition', 'resource competition' and 'resident fitness' hypotheses predict density-dependent dispersal patterns, while the 'inbreeding avoidance' 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 ± 0.4 months. Age at commencement of dispersal was positively density-dependent. Although males (11.0 ± 2.5 km) generally dispersed further than females (2.7 ± 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

  8. Density-Dependent Natal Dispersal Patterns in a Leopard Population Recovering from Over-Harvest

    PubMed Central

    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 ‘mate competition’, ‘resource competition’ and ‘resident fitness’ hypotheses predict density-dependent dispersal patterns, while the ‘inbreeding avoidance’ 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 ± 0.4 months. Age at commencement of dispersal was positively density-dependent. Although males (11.0 ± 2.5 km) generally dispersed further than females (2.7 ± 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

  9. Density-dependent natal dispersal patterns in a leopard population recovering from over-harvest.

    PubMed

    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 'mate competition', 'resource competition' and 'resident fitness' hypotheses predict density-dependent dispersal patterns, while the 'inbreeding avoidance' 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 ± 0.4 months. Age at commencement of dispersal was positively density-dependent. Although males (11.0 ± 2.5 km) generally dispersed further than females (2.7 ± 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

  10. 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 the…

  11. Parental care masks a density-dependent shift from cooperation to competition among burying beetle larvae.

    PubMed

    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.

  12. Parental care masks a density-dependent shift from cooperation to competition among burying beetle larvae

    PubMed Central

    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

  13. Strong density-dependent competition and acquired immunity constrain parasite establishment: implications for parasite aggregation.

    PubMed

    Luong, Lien T; Vigliotti, Beth A; Hudson, Peter J

    2011-04-01

    The vast majority of parasites exhibit an aggregated frequency distribution within their host population, such that most hosts have few or no parasites while only a minority of hosts are heavily infected. One exception to this rule is the trophically transmitted parasite Pterygodermatites peromysci of the white-footed mouse (Peromyscus leucopus), which is randomly distributed within its host population. Here, we ask: what are the factors generating the random distribution of parasites in this system when the majority of macroparasites exhibit non-random patterns? We hypothesise that tight density-dependent processes constrain parasite establishment and survival, preventing the build-up of parasites within individual hosts, and preclude aggregation within the host population. We first conducted primary infections in a laboratory experiment using white-footed mice to test for density-dependent parasite establishment and survival of adult worms. Secondary or challenge infection experiments were then conducted to investigate underlying mechanisms, including intra-specific competition and host-mediated restrictions (i.e. acquired immunity). The results of our experimental infections show a dose-dependent constraint on within-host-parasite establishment, such that the proportion of mice infected rose initially with exposure, and then dropped off at the highest dose. Additional evidence of density-dependent competition comes from the decrease in worm length with increasing levels of exposure. In the challenge infection experiment, previous exposure to parasites resulted in a lower prevalence and intensity of infection compared with primary infection of naïve mice; the magnitude of this effect was also density-dependent. Host immune response (IgG levels) increased with the level of exposure, but decreased with the number of worms established. Our results suggest that strong intra-specific competition and acquired host immunity operate in a density-dependent manner to

  14. Disentangling the effects of climate, density dependence, and harvest on an iconic large herbivore's population dynamics.

    PubMed

    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 (β0 = 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 (β1 = -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

  15. Disentangling the effects of climate, density dependence, and harvest on an iconic large herbivore's population dynamics.

    PubMed

    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 (β0 = 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 (β1 = -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.

  16. Collective motion of self-propelled particles with density-dependent switching effect

    NASA Astrophysics Data System (ADS)

    Chen, Qiu-shi; Ma, Yu-qiang

    2016-05-01

    We study the effect of density-dependent angular response on large scale collective motion, that particles are more likely to switch their moving direction within lower local density region. We show that the presence of density-dependent angular response leads to three typical phases: polar liquid, micro-phase separation and disordered gas states. In our model, the transition between micro-phase separation and disordered gas is discontinuous. Giant number fluctuation is observed in polar liquid phase with statistically homogeneous order. In the micro-phase separation parameter space, high order and high density bands dominate the dynamics. We also compare our results with Vicsek model and show that the density-dependent directional switching response can stabilize the band state to very low noise condition. This band stripe could recruit almost all the particles in the system, which greatly enhances the coherence of the system. Our results could be helpful for understanding extremely coherent motion in nature and also would have practical implications for designing novel self-organization pattern.

  17. DENSITY-DEPENDENT FLOW IN ONE-DIMENSIONAL VARIABLY-SATURATED MEDIA

    EPA Science Inventory

    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...

  18. Density-dependent state-space model for population-abundance data with unequal time intervals.

    PubMed

    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.

  19. Spatial and temporal variability modify density dependence in populations of large herbivores.

    PubMed

    Wang, Guiming; Hobbs, N Thompson; Boone, Randall B; Illius, Andrew W; Gordon, Iain J; Gross, John E; Hamlin, Kenneth L

    2006-01-01

    A central challenge in ecology is to understand the interplay of internal and external controls on the growth of populations. We examined the effects of temporal variation in weather and spatial variation in vegetation on the strength of density dependence in populations of large herbivores. We fit three subsets of the model ln(Nt) = a + (1 + b) x ln(N(t-1)) + c x ln(N(t-2)) to five time series of estimates (Nt) of abundance of ungulates in the Rocky Mountains, USA. The strength of density dependence was estimated by the magnitude of the coefficient b. We regressed the estimates of b on indices of temporal heterogeneity in weather and spatial heterogeneity in resources. The 95% posterior intervals of the slopes of these regressions showed that temporal heterogeneity strengthened density-dependent feedbacks to population growth, whereas spatial heterogeneity weakened them. This finding offers the first empirical evidence that density dependence responds in different ways to spatial heterogeneity and temporal heterogeneity. PMID:16634300

  20. 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…

  1. Density-Dependent Demographic Variation Determines Extinction Rate of Experimental Populations

    PubMed Central

    2005-01-01

    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

  2. Density dependence of the symmetry energy from neutron skin thickness in finite nuclei

    SciTech Connect

    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.

  3. Density dependent state space model for population abundance data with unequal time intervals

    PubMed Central

    Dennis, Brian; Ponciano, José 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

  4. 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.

  5. Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout

    USGS Publications Warehouse

    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.

  6. Density-dependent home-range size revealed by spatially explicit capture–recapture

    USGS Publications Warehouse

    Efford, M.G.; Dawson, Deanna K.; Jhala, Y.V.; Qureshi, Q.

    2016-01-01

    The size of animal home ranges often varies inversely with population density among populations of a species. This fact has implications for population monitoring using spatially explicit capture–recapture (SECR) models, in which both the scale of home-range movements σ and population density D usually appear as parameters, and both may vary among populations. It will often be appropriate to model a structural relationship between population-specific values of these parameters, rather than to assume independence. We suggest re-parameterizing the SECR model using kp = σp √Dp, where kp relates to the degree of overlap between home ranges and the subscript p distinguishes populations. We observe that kp is often nearly constant for populations spanning a range of densities. This justifies fitting a model in which the separate kp are replaced by the single parameter k and σp is a density-dependent derived parameter. Continuous density-dependent spatial variation in σ may also be modelled, using a scaled non-Euclidean distance between detectors and the locations of animals. We illustrate these methods with data from automatic photography of tigers (Panthera tigris) across India, in which the variation is among populations, from mist-netting of ovenbirds (Seiurus aurocapilla) in Maryland, USA, in which the variation is within a single population over time, and from live-trapping of brushtail possums (Trichosurus vulpecula) in New Zealand, modelling spatial variation within one population. Possible applications and limitations of the methods are discussed. A model in which kp is constant, while density varies, provides a parsimonious null model for SECR. The parameter k of the null model is a concise summary of the empirical relationship between home-range size and density that is useful in comparative studies. We expect deviations from this model, particularly the dependence of kp on covariates, to be biologically interesting.

  7. Dependence of interstellar depletion on hydrogen column density - Possibilities and implications

    NASA Technical Reports Server (NTRS)

    Tarafdar, S. P.; Prasad, S. S.; Huntress, W. T., Jr.

    1983-01-01

    A reexamination of the observed column densities of various elements in diffuse clouds suggests that almost all elements including oxygen, nitrogen, sulfur, and argon may be depleted with respect to hydrogen in interstellar clouds with large hydrogen column density. The amount of depletion varies from element to element and increases with increasing column density of hydrogen nuclei. This result is in qualitative agreement with the depletion of oxygen and sulfur independently inferred from the gas phase chemistry of sulfur in dense clouds. The rate of increase of depletion with hydrogen column density implied by the present study is large. It is possible that observational selection effects may have amplified the real dependence on N(H). A broad spectrum of C/O ratios ranging from values greater than unity to values less than unity appears possible for interstellar clouds, which would have the effect of a large variation in chemical composition from cloud to cloud.

  8. Representing the thermal state in time-dependent density functional theory

    DOE PAGESBeta

    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 bymore » 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

  9. Representing the thermal state in time-dependent density functional theory

    SciTech Connect

    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

  10. Density-dependent productivity in a colonial vulture at two spatial scales.

    PubMed

    Fernández-Bellon, Darío; Cortés-Avizanda, Ainara; Arenas, Rafael; Donázar, José Antonio

    2016-02-01

    Understanding how density dependence modifies demographic parameters in long-lived vertebrates is a challenge for ecologists. Two alternative hypotheses have been used to explain the mechanisms behind density-dependent effects on breeding output: habitat heterogeneity and individual adjustment (also known as interference competition). A number of studies have highlighted the importance of habitat heterogeneity in density dependence in territorial species, but less information exists on demographic processes in colonial species. For these, we expect density-dependent mechanisms to operate at two spatial scales: colony and breeding unit. In this study, we used long-term data from a recovering population of Cinereous Vultures (Aegypius monachus) in southern Spain. We analyzed a long-term data set with information on 2162 breeding attempts at four colonies over a nine-year period (2002-2010) to evaluate environmental and population parameters influencing breeding output. Our results suggest that breeding productivity is subject to density-dependent processes at the colony and the nest site scale and is best explained by interference competition. Factors intrinsic to each colony, as well as environmental constraints linked to physiography and human presence, also play a role in regulatory processes. We detected the existence of a trade-off between the disadvantages of nesting too close to conspecifics and the benefits of coloniality. These could be mediated by the agonistic interactions between breeding pairs and the benefits derived from social sharing of information by breeding individuals. We propose that this trade-off may play a role in defining colony structure and may hold true for other colonial breeding bird species. Our findings also have important management implications for the conservation of this threatened species.

  11. Density-dependent productivity in a colonial vulture at two spatial scales.

    PubMed

    Fernández-Bellon, Darío; Cortés-Avizanda, Ainara; Arenas, Rafael; Donázar, José Antonio

    2016-02-01

    Understanding how density dependence modifies demographic parameters in long-lived vertebrates is a challenge for ecologists. Two alternative hypotheses have been used to explain the mechanisms behind density-dependent effects on breeding output: habitat heterogeneity and individual adjustment (also known as interference competition). A number of studies have highlighted the importance of habitat heterogeneity in density dependence in territorial species, but less information exists on demographic processes in colonial species. For these, we expect density-dependent mechanisms to operate at two spatial scales: colony and breeding unit. In this study, we used long-term data from a recovering population of Cinereous Vultures (Aegypius monachus) in southern Spain. We analyzed a long-term data set with information on 2162 breeding attempts at four colonies over a nine-year period (2002-2010) to evaluate environmental and population parameters influencing breeding output. Our results suggest that breeding productivity is subject to density-dependent processes at the colony and the nest site scale and is best explained by interference competition. Factors intrinsic to each colony, as well as environmental constraints linked to physiography and human presence, also play a role in regulatory processes. We detected the existence of a trade-off between the disadvantages of nesting too close to conspecifics and the benefits of coloniality. These could be mediated by the agonistic interactions between breeding pairs and the benefits derived from social sharing of information by breeding individuals. We propose that this trade-off may play a role in defining colony structure and may hold true for other colonial breeding bird species. Our findings also have important management implications for the conservation of this threatened species. PMID:27145615

  12. 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...

  13. 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).

  14. Nonadiabatic dynamics and simulation of time resolved photoelectron spectra within time-dependent density functional theory: Ultrafast photoswitching in benzylideneaniline

    SciTech Connect

    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.

  15. Peak-shifting in real-time time-dependent density functional theory.

    PubMed

    Provorse, Makenzie R; Habenicht, Bradley F; Isborn, Christine M

    2015-10-13

    In recent years, the development and application of real-time time-dependent density functional theory (RT-TDDFT) has gained momentum as a computationally efficient method for modeling electron dynamics and properties that require going beyond a linear response of the electron density. However, the RT-TDDFT method within the adiabatic approximation can unphysically shift absorption peaks throughout the electron dynamics. Here, we investigate the origin of these time-dependent resonances observed in RT-TDDFT spectra. Using both exact exchange and hybrid exchange-correlation approximate functionals, adiabatic RT-TDDFT gives time-dependent absorption spectra in which the peaks shift in energy as populations of the excited states fluctuate, while exact wave function methods yield peaks that are constant in energy but vary in intensity. The magnitude of the RT-TDDFT peak shift depends on the frequency and intensity of the applied field, in line with previous studies, but it oscillates as a function of time-dependent molecular orbital populations, consistent with a time-dependent superposition electron density. For the first time, we provide a rationale for the direction and magnitude of the time-dependent peak shifts based on the molecular electronic structure. For three small molecules, H2, HeH(+), and LiH, we give contrasting examples of peak-shifting to both higher and lower energies. The shifting is explained as coupled one-electron transitions to a higher and a lower lying state. Whether the peak shifts to higher or lower energies depends on the relative energetics of these one-electron transitions. PMID:26574268

  16. The impacts of marijuana dispensary density and neighborhood ecology on marijuana abuse and dependence

    PubMed Central

    Mair, Christina; Freisthler, Bridget; Ponicki, William R.; Gaidus, Andrew

    2015-01-01

    Background As an increasing number of states liberalize cannabis use and develop laws and local policies, it is essential to better understand the impacts of neighborhood ecology and marijuana dispensary density on marijuana use, abuse, and dependence. We investigated associations between marijuana abuse/dependence hospitalizations and community demographic and environmental conditions from 2001–2012 in California, as well as cross-sectional associations between local and adjacent marijuana dispensary densities and marijuana hospitalizations. Methods We analyzed panel population data relating hospitalizations coded for marijuana abuse or dependence and assigned to residential ZIP codes in California from 2001 through 2012 (20,219 space-time units) to ZIP code demographic and ecological characteristics. Bayesian space-time misalignment models were used to account for spatial variations in geographic unit definitions over time, while also accounting for spatial autocorrelation using conditional autoregressive priors. We also analyzed cross-sectional associations between marijuana abuse/dependence and the density of dispensaries in local and spatially adjacent ZIP codes in 2012. Results An additional one dispensary per square mile in a ZIP code was cross-sectionally associated with a 6.8% increase in the number of marijuana hospitalizations (95% credible interval 1.033, 1.105) with a marijuana abuse/dependence code. Other local characteristics, such as the median household income and age and racial/ethnic distributions, were associated with marijuana hospitalizations in cross-sectional and panel analyses. Conclusions Prevention and intervention programs for marijuana abuse and dependence may be particularly essential in areas of concentrated disadvantage. Policy makers may want to consider regulations that limit the density of dispensaries. PMID:26154479

  17. How does habitat filtering affect the detection of conspecific and phylogenetic density dependence?

    PubMed

    Wu, Junjie; Swenson, Nathan G; Brown, Calum; Zhang, Caicai; Yang, Jie; Ci, Xiuqin; Li, Jie; Sha, Liqing; Cao, Min; Lin, Luxiang

    2016-05-01

    Conspecific negative density dependence (CNDD) has been recognized as a key mechanism underlying species coexistence, especially in tropical forests. Recently, some studies have reported that seedling survival is also negatively correlated with the phylogenetic relatedness between neighbors and focal individuals, termed phylogenetic negative density dependence (PNDD). In contrast to CNDD or PNDD, shared habitat requirements between closely related individuals are thought to be a cause of observed positive effects of closely related neighbors, which may affect the strength and detectability of CNDD or PNDD. In order to investigate the relative importance of these mechanisms for tropical tree seedling survival, we used generalized linear mixed models to analyze how the survival of more than 10 000 seedlings of woody plant species related to neighborhood and habitat variables in a tropical rainforest in southwest China. By comparing models with and without habitat variables, we tested how habitat filtering affected the detection of CNDD and PNDD. The best-fitting model suggested that CNDD and habitat filtering played key roles in seedling survival; but that, contrary to our expectations, phylogenetic positive density dependence (PPDD) had a distinct and important effect. While habitat filtering affected the detection of CNDD by decreasing its apparent strength, it did not explain the positive effects of closely related neighbors. Our results demonstrate that a failure to control for habitat variables and phylogenetic relationships may obscure the importance of conspecific and heterospecific neighbor densities for seedling survival. PMID:27349095

  18. How does habitat filtering affect the detection of conspecific and phylogenetic density dependence?

    PubMed

    Wu, Junjie; Swenson, Nathan G; Brown, Calum; Zhang, Caicai; Yang, Jie; Ci, Xiuqin; Li, Jie; Sha, Liqing; Cao, Min; Lin, Luxiang

    2016-05-01

    Conspecific negative density dependence (CNDD) has been recognized as a key mechanism underlying species coexistence, especially in tropical forests. Recently, some studies have reported that seedling survival is also negatively correlated with the phylogenetic relatedness between neighbors and focal individuals, termed phylogenetic negative density dependence (PNDD). In contrast to CNDD or PNDD, shared habitat requirements between closely related individuals are thought to be a cause of observed positive effects of closely related neighbors, which may affect the strength and detectability of CNDD or PNDD. In order to investigate the relative importance of these mechanisms for tropical tree seedling survival, we used generalized linear mixed models to analyze how the survival of more than 10 000 seedlings of woody plant species related to neighborhood and habitat variables in a tropical rainforest in southwest China. By comparing models with and without habitat variables, we tested how habitat filtering affected the detection of CNDD and PNDD. The best-fitting model suggested that CNDD and habitat filtering played key roles in seedling survival; but that, contrary to our expectations, phylogenetic positive density dependence (PPDD) had a distinct and important effect. While habitat filtering affected the detection of CNDD by decreasing its apparent strength, it did not explain the positive effects of closely related neighbors. Our results demonstrate that a failure to control for habitat variables and phylogenetic relationships may obscure the importance of conspecific and heterospecific neighbor densities for seedling survival.

  19. 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 × 107 cm/s at a low sheet charge density of 7.8 × 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.

  20. Density-dependent electron transport and precise modeling of GaN high electron mobility transistors

    SciTech Connect

    Bajaj, Sanyam Shoron, Omor F.; Park, Pil Sung; Krishnamoorthy, Sriram; Akyol, Fatih; Hung, Ting-Hsiang; Reza, Shahed; Chumbes, Eduardo M.; Khurgin, Jacob; Rajan, Siddharth

    2015-10-12

    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 × 10{sup 7 }cm/s at a low sheet charge density of 7.8 × 10{sup 11 }cm{sup −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.

  1. Meta-GGA-based adiabatic time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Nazarov, Vladimir; Vignale, Giovanni

    2012-02-01

    The local-density approximation (LDA) to the ground-state density functional theory (DFT) is well known to allow for a generalization to the time-dependent case [1]. The assumption of the adiabaticity of the process greatly simplifies the theory. The further extension of the time-dependent DFT (TDDFT) to the generalized gradient approximation (GGA) is trivial. Here we address lifting the adiabatic TDDFT to the third rung of the ``Jacobs ladder'' [2] : We work out the kinetic energy density dependent (meta-GGA) TDDFT formalism. The new theory possesses remarkable properties not present in LDA and GGA: (i) It is non-local with respect to the particle density; (ii) In the case of bulk semiconductors, it supports the 1/q^2 singularity of the exchange-correlation kernel, where q is the wave-vector, the latter being important to reproduce the excitonic effect. We also present illustrative calculations of the optical absorption in semiconductors [3]. [4pt] [1] A. Zangwill and P. Soven, Phys. Rev. A, 21, 1561 (1980).[0pt] [2] J. Tao, J. P. Perdew, V. N. Staroverov, and G. E. Scuseria, Phys. Rev. Lett. 91, 146401 (2003).[0pt] [3] V. U. Nazarov and G. Vignale, Phys. Rev. Lett. 107, 216402(2011).

  2. A coarse-grain force field for RDX: Density dependent and energy conserving.

    PubMed

    Moore, Joshua D; Barnes, Brian C; Izvekov, Sergei; Lísal, 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

  3. Time-Dependent Density Wave Theory for Co-orbital Satellites

    NASA Astrophysics Data System (ADS)

    Stewart, Glen R.

    2009-05-01

    The standard theory of density waves in planetary rings assumes that the orbit of the perturbing satellite is on a fixed orbit. However, the co-orbital satellites, Janus and Epimetheus, trade orbits every four years. Cassini images of Saturn's rings record the time evolution of the density waves excited by these satellites. Ticareno et al. (Ap. J. 651: L65-L68, 2006) attempted to model the observations by assuming the steady-state density waves shift locations in the rings instantaneously when the co-orbital satellites trade orbits. They found that certain wave-like features are observed in the evanescent region of the wave that were not predicted by the steady state theory. We will present the results of a new time-dependent density wave theory that can model the perturbations by the co-orbital satellites during their orbital exchange. Similar to our previous result for temporally modulated density waves excited by the satellite, Pandora (Stewart and Sremcevic, DDA 2008), we find that the effective sound velocity in the wave plays an important role in propagating the time-dependent signal in the wave train. Comparisons with Cassini observations as well as predictions for the next co-orbital exchange event in January 2010 will be presented. This research was supported by NASA's Outer Planets Research Program.

  4. Time-Dependent Density Wave Theory for Co-orbital Satellites

    NASA Astrophysics Data System (ADS)

    Stewart, Glen R.

    2008-09-01

    The standard theory of density waves in planetary rings assumes that the orbit of the perturbing satellite is on a fixed orbit. However, the co-orbital satellites, Janus and Epimetheus, trade orbits every four years. Cassini images of Saturn's rings record the time evolution of the density waves excited by these satellites. Ticareno et al. (Ap. J. 651: L65-L68, 2006) attempted to model the observations by assuming the steady-state density waves shift locations in the rings instantaneously when the co-orbital satellites trade orbits. They found that certain wave-like features are observed in the evanescent region of the wave that are not predicted by the steady state theory. We will present the results of a new time-dependent density wave theory that can model the perturbations by the co-orbital satellites during their orbital exchange. Similar to our previous result for temporally modulated density waves excited by the satellite, Pandora (Stewart and Sremcevic, DDA 2008), we find that the effective sound velocity in the wave plays an important role in propagating the time-dependent signal in the wave train. Comparisons with Cassini observations as well as predictions for the next co-orbital exchange event in January 2010 will be presented.

  5. Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System

    PubMed Central

    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

  6. Anopheles mortality is both age- and Plasmodium-density dependent: implications for malaria transmission

    PubMed Central

    2009-01-01

    Background Daily mortality is an important determinant of a vector's ability to transmit pathogens. Original simplifying assumptions in malaria transmission models presume vector mortality is independent of age, infection status and parasite load. Previous studies illustrate conflicting evidence as to the importance of Plasmodium-induced vector mortality, but very few studies to date have considered the effect of infection density on mosquito survival. Methods A series of three experiments were conducted, each consisting of four cages of 400-1,000 Anopheles stephensi mosquitoes fed on blood infected with different Plasmodium berghei ookinete densities per microlitre of blood. Twice daily the numbers of dead mosquitoes in each group were recorded, and on alternate days a sample of live mosquitoes from each group were dissected to determine parasite density in both midgut and salivary glands. Results Survival analyses indicate that mosquito mortality is both age- and infection intensity-dependent. Mosquitoes experienced an initially high, partly feeding-associated, mortality rate, which declined to a minimum before increasing with mosquito age and parasite intake. As a result, the life expectancy of a mosquito is shown to be dependent on both insect age and the density of Plasmodium infection. Conclusion These results contribute to understanding in greater detail the processes that influence sporogony in the mosquito, indicate the impact that parasite density could have on malaria transmission dynamics, and have implications for the design, development, and evaluation of transmission-blocking strategies. PMID:19822012

  7. Evaluating systematic dependencies of type Ia supernovae : the influence of deflagration to detonation density.

    SciTech Connect

    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.

  8. EVALUATING SYSTEMATIC DEPENDENCIES OF TYPE Ia SUPERNOVAE: THE INFLUENCE OF DEFLAGRATION TO DETONATION DENSITY

    SciTech Connect

    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.

  9. Density-dependence across dispersal stages in a hermaphrodite land snail: insights from discrete choice models.

    PubMed

    Dahirel, Maxime; Vardakis, Michalis; Ansart, Armelle; Madec, Luc

    2016-08-01

    Dispersal movements, i.e. movements leading to gene flow, are key behaviours with important, but only partially understood, consequences for the dynamics and evolution of populations. In particular, density-dependent dispersal has been widely described, yet how it is determined by the interaction with individual traits, and whether density effects differ between the three steps of dispersal (departure, transience, and settlement), remains largely unknown. Using a semi-natural landscape, we studied dispersal choices of Cornu aspersum land snails, a species in which negative effects of crowding are well documented, and analysed them using dispersal discrete choice models, a new method allowing the analysis of dispersal decisions by explicitly considering the characteristics of all available alternatives and their interaction with individual traits. Subadults were more dispersive than adults, confirming existing results. In addition, departure and settlement were both density dependent: snails avoided crowded patches at both ends of the dispersal process, and subadults were more reluctant to settle into crowded patches than adults. Moreover, we found support for carry-over effects of release density on subsequent settlement decisions: snails from crowded contexts were more sensitive to density in their subsequent immigration choices. The fact that settlement decisions were informed indicates that costs of prospecting are not as important as previously thought in snails, and/or that snails use alternative ways to collect information, such as indirect social information (e.g. trail following). The observed density-dependent dispersal dynamics may play an important role in the ability of C. aspersum to successfully colonise frequently human-disturbed habitats around the world. PMID:27139427

  10. The nutrient density approach to healthy eating: challenges and opportunities.

    PubMed

    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.

  11. A time-dependent approach to electron-atom scattering

    NASA Astrophysics Data System (ADS)

    Buffington, Gavin Douglas

    1997-08-01

    This time-dependent approach utilizes a fully correlated two electron wave function developed by Bottcher, Schultz and Madison. A finite element spline basis is employed with the principle of collocation in order to express the wave function and Hamiltonian numerically. An initial state, composed of a wavepacket for the projectile and an isolated atomic wave function, is evolved in time according to the time-dependent Schrodinger equation. Probabilities for excitation and ionization are computed as a function of time by taking projections onto states and pseudostates of the target atom. The wavepacket approach obviates the need for consideration of three- body boundary conditions and the asymptotic form of the wave function. Cross sections for electron impact excitation and ionization are obtained and compared with results from other theoretical methods.

  12. Dependence of kinetic friction on velocity: master equation approach.

    PubMed

    Braun, O M; Peyrard, M

    2011-04-01

    We investigate the velocity dependence of kinetic friction with a model that makes minimal assumptions on the actual mechanism of friction so that it can be applied at many scales, provided the system involves multicontact friction. Using a recently developed master equation approach, we investigate the influence of two concurrent processes. First, at a nonzero temperature, thermal fluctuations allow an activated breaking of contacts that are still below the threshold. As a result, the friction force monotonically increases with velocity. Second, the aging of contacts leads to a decrease of the friction force with velocity. Aging effects include two aspects: the delay in contact formation and aging of a contact itself, i.e., the change of its characteristics with the duration of stationary contact. All these processes are considered simultaneously with the master equation approach, giving a complete dependence of the kinetic friction force on the driving velocity and system temperature, provided the interface parameters are known.

  13. Time-dependent HF approach to SHE dynamics

    NASA Astrophysics Data System (ADS)

    Umar, A. S.; Oberacker, V. E.

    2015-12-01

    We employ the time-dependent Hartree-Fock (TDHF) method to study various aspects of the reactions utilized in searches for superheavy elements. These include capture cross-sections, quasifission, prediction of PCN, and other interesting dynamical quantities. We show that the microscopic TDHF approach provides an important tool to shed some light on the nuclear dynamics leading to the formation of superheavy elements.

  14. Lengthscale-Dependent Solvation and Density Fluctuations in n-Octane.

    PubMed

    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.

  15. Hydrogen transfer in vibrationally relaxing benzoic acid dimers: Time-dependent density matrix dynamics and infrared spectra

    NASA Astrophysics Data System (ADS)

    Scheurer, Christoph; Saalfrank, Peter

    1996-02-01

    We employ time-dependent density matrix theory to characterize the concerted double-hydrogen transfer in benzoic acid dimers—the ``system''—embedded in their crystalline environment—the ``bath.'' The Liouville-von Neumann equation for the time evolution of the reduced nuclear density matrix is solved numerically, employing one- and two-dimensional models [R. Meyer and R. R. Ernst, J. Chem. Phys. 93, 5528 (1990)], the state representation for all operators and a matrix propagator based on Newton's polynomials [M. Berman, R. Kosloff, and H. Tal-Ezer, J. Phys. A 25, 1283 (1992)]. Dissipative processes such as environment-induced vibrational energy and phase relaxation, are accounted for within the Lindblad dynamical semigroup approach. The calculation of temperature-dependent relaxation matrix elements is based on a microscopic, perturbative theory proposed earlier [R. Meyer and R. R. Ernst, J. Chem. Phys. 93, 5528 (1990)]. For the evaluation of the dissipative system dynamics, we compute (i) time-dependent state populations, (ii) energy and entropy flow between system and bath, (iii) expectation values for the hydrogen transfer coordinate, (iv) characteristic dephasing times and (v) temperature-dependent infrared spectra, determined with a recently proposed method by Neugebauer et al. Various ``pure'' and ``thermal'' nonequilibrium initial states are considered, and their equilibration with the bath followed in time.

  16. 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 νee(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 νee(r,t) are derived and shown to depend on the frequency dependent correlation-current-density effect. Furthermore, via adiabatic coupling constant (λ) perturbation theory, we prove: (iv) the exchange potential νx(r,t) is the work done in a conservative field representative of Pauli correlations and lowest-order O(λ) correlation-kinetic and correlation-current-density effects; (v) the correlation potential νc(r,t) commences in O(λ2), 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 νee(r,t) to the electron-interaction and correlation-kinetic energy for arbitrary coupling constant strength λ, and show there are no explicit correlation-current-density

  17. Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine.

    PubMed

    Fischer, Sean A; Cramer, Christopher J; Govind, Niranjan

    2016-04-01

    Optical-limiting materials are capable of attenuating light to protect delicate equipment from high-intensity light sources. Phthalocyanines have attracted a lot of attention for optical-limiting applications due to their versatility and large nonlinear absorption. With excited-state absorption (ESA) being the primary mechanism for optical limiting behavior in phthalocyanines, the ability to tune the optical absorption of ground and excited states in phthalocyanines would allow for the development of advanced optical limiters. We recently developed a method for the calculation of ESA based on real-time time-dependent density functional theory propagation of an excited-state density. In this work, we apply the approach to zinc phthalocyanine, demonstrating the ability of our method to efficiently identify the optical limiting potential of a molecular complex.

  18. 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.

  19. Nuclear clustering in the energy density functional approach

    SciTech Connect

    Ebran, J.-P.; Khan, E.; Nikšić, T.; Vretenar, D.

    2015-10-15

    Nuclear Energy Density Functionals (EDFs) are a microscopic tool of choice extensively used over the whole chart to successfully describe the properties of atomic nuclei ensuing from their quantum liquid nature. In the last decade, they also have proved their ability to deal with the cluster phenomenon, shedding a new light on its fundamental understanding by treating on an equal footing both quantum liquid and cluster aspects of nuclei. Such a unified microscopic description based on nucleonic degrees of freedom enables to tackle the question pertaining to the origin of the cluster phenomenon and emphasizes intrinsic mechanisms leading to the emergence of clusters in nuclei.

  20. The local projection in the density functional theory plus U approach: A critical assessment

    NASA Astrophysics Data System (ADS)

    Wang, Yue-Chao; Chen, Ze-Hua; Jiang, Hong

    2016-04-01

    Density-functional theory plus the Hubbard U correction (DFT + U) method is widely used in first-principles studies of strongly correlated systems, as it can give qualitatively (and sometimes, semi-quantitatively) correct description of energetic and structural properties of many strongly correlated systems with similar computational cost as local density approximation or generalized gradient approximation. On the other hand, the DFT + U approach is limited both theoretically and practically in several important aspects. In particular, the results of DFT + U often depend on the choice of local orbitals (the local projection) defining the subspace in which the Hubbard U correction is applied. In this work we have systematically investigated the issue of the local projection by considering typical transition metal oxides, β-MnO2 and MnO, and comparing the results obtained from different implementations of DFT + U. We found that the choice of the local projection has significant effects on the DFT + U results, which are more significant for systems with stronger covalent bonding (e.g., MnO2) than those with more ionic bonding (e.g., MnO). These findings can help to clarify some confusion arising from the practical use of DFT + U and may also provide insights for the development of new first-principles approaches beyond DFT + U.

  1. The local projection in the density functional theory plus U approach: A critical assessment.

    PubMed

    Wang, Yue-Chao; Chen, Ze-Hua; Jiang, Hong

    2016-04-14

    Density-functional theory plus the Hubbard U correction (DFT + U) method is widely used in first-principles studies of strongly correlated systems, as it can give qualitatively (and sometimes, semi-quantitatively) correct description of energetic and structural properties of many strongly correlated systems with similar computational cost as local density approximation or generalized gradient approximation. On the other hand, the DFT + U approach is limited both theoretically and practically in several important aspects. In particular, the results of DFT + U often depend on the choice of local orbitals (the local projection) defining the subspace in which the Hubbard U correction is applied. In this work we have systematically investigated the issue of the local projection by considering typical transition metal oxides, β-MnO2 and MnO, and comparing the results obtained from different implementations of DFT + U. We found that the choice of the local projection has significant effects on the DFT + U results, which are more significant for systems with stronger covalent bonding (e.g., MnO2) than those with more ionic bonding (e.g., MnO). These findings can help to clarify some confusion arising from the practical use of DFT + U and may also provide insights for the development of new first-principles approaches beyond DFT + U. PMID:27083707

  2. Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus)

    PubMed Central

    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

  3. Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus).

    PubMed

    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.

  4. A new approach to mass spectrometer measurements of thermospheric density

    NASA Technical Reports Server (NTRS)

    Melfi, L. T., Jr.; Brock, F. J.; Brown, C. A., Jr.

    1974-01-01

    The gas sampling problem in satellite and high velocity probes was investigated by applying the theory of a drifting Maxwellian gas. A lens system using a free stream ion source was developed and experimentally evaluated over the pressure range of 0.00001 to 0.01 N/m sq (approx. 10 to the minus 7th power to 0.0001 torr). The source has high beam transparency, which minimizes gas-surface collisions within, or near, the ionization volume. It is shown that for high ion energy (60 eV), the extracted ion beam has an on-axis energy spread of less than 4 eV, and that 90 percent of the ions are within 2.5 deg of the beam axis. It is concluded that the molecular beam mass spectrometer concept, developed for gas density measurements in the upper atmosphere, substantially reduces gas-surface scattering and gas-surface reactions in the sample, and preserves the integrity of the gas sample during the analysis process. Studies show that both the Scout and Delta launch vehicles have adequate volume, control, velocity, and data acquisition capability necessary to obtain thermospheric number density in real time.

  5. Ignitor and the High Density Approach for Fusion*

    NASA Astrophysics Data System (ADS)

    Bombarda, F.; Coppi, B.

    2010-11-01

    The high plasma density regimes discovered by high magnetic field toroidal experiments have both outstanding confinement characteristics and degree of purity, and are at the basis of the Ignitor design. The main purpose of the Ignitor experiment is, in fact, that of establishing the reactor physics in regimes close to ignition, where the thermonuclear instability can set in with all its associated non linear effects. ``Extended limiter'' and double X-point configurations have been analyzed and relevant transport simulations show that similar burning plasma conditions can be attained with both, by Ohmic heating only or with modest amounts of ICRH auxiliary heating. The driving factor for the machine design (R01.32 m, a xb0.47x0.83 m^2, BT<=13 T, Ip<=11 MA) is the poloidal field pressure that can contain, under macroscopically stable conditions, the peak plasma pressures corresponding to ignition. Objectives other than ignition can be envisioned for the relatively near term, for example that of high flux neutron sources for material testing involving compact, high density fusion machines. This has been one of the incentives that have led the Ignitor Project to adopt magnesium diboride (MgB2) superconducting cables in the machine design, a first in fusion research. Accordingly, the largest coils (about 5 m diameter) of the machine will be made entirely of MgB2 cables. *Sponsored in part by ENEA of Italy and by the U.S. D.O.E.

  6. Optoelectronic Properties of Carbon Nanorings: Excitonic Effects from Time-Dependent Density Functional Theory

    PubMed Central

    2009-01-01

    The electronic structure and size-scaling of optoelectronic properties in cycloparaphenylene carbon nanorings are investigated using time-dependent density functional theory (TDDFT). The TDDFT calculations on these molecular nanostructures indicate that the lowest excitation energy surprisingly becomes larger as the carbon nanoring size is increased, in contradiction with typical quantum confinement effects. In order to understand their unusual electronic properties, I performed an extensive investigation of excitonic effects by analyzing electron-hole transition density matrices and exciton binding energies as a function of size in these nanoring systems. The transition density matrices allow a global view of electronic coherence during an electronic excitation, and the exciton binding energies give a quantitative measure of electron-hole interaction energies in the nanorings. Based on overall trends in exciton binding energies and their spatial delocalization, I find that excitonic effects play a vital role in understanding the unique photoinduced dynamics in these carbon nanoring systems. PMID:22481999

  7. Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation

    NASA Astrophysics Data System (ADS)

    Kühn, Michael; Weigend, Florian

    2015-01-01

    We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy)3 (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its "spin-forbidden" triplet-singlet transition.

  8. Laboratory calibration of density-dependent lines in the extreme ultraviolet spectral region

    SciTech Connect

    Lepson, J. K.; Beiersdorfer, P.; Gu, M. F.; Desai, P.; Bitter, M.; Roquemore, L.; Reinke, M. L.

    2012-05-25

    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 ({lambda}/{Delta}{lambda} >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.

  9. Negative frequency-dependent selection is intensified at higher population densities in protist populations

    PubMed Central

    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

  10. Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation

    SciTech Connect

    Kühn, 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. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy){sub 3} (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its “spin-forbidden” triplet-singlet transition.

  11. Temperature and density dependence of the shear viscosity of liquid sodium

    NASA Astrophysics Data System (ADS)

    Meyer, N.; Xu, H.; Wax, J.-F.

    2016-06-01

    The density and temperature dependence of the shear viscosity of liquid sodium is studied. The stress autocorrelation function is calculated by equilibrium molecular dynamics simulations, which allow us to obtain the value of shear viscosity using the Green-Kubo formula. The Fiolhais potential is used to calculate the interionic interactions, which are validated by comparison between simulation and experimental data along the liquid-gas coexistence curve. The behavior of viscosity over a wide range of the liquid phase of the phase diagram is studied. Along isochoric lines, it presents a minimum, while it monotonically increases along isotherms. An expression is proposed for the viscosity as a function of temperature and density which reproduces our data for liquid sodium at any density in the range [1000-2000 kg m-3 ] and any temperature in the range [700-7000 K]. The validity of the Stokes-Einstein relation over the investigated state points is discussed.

  12. Negative frequency-dependent selection is intensified at higher population densities in protist populations.

    PubMed

    Minter, Ewan J A; Watts, Phillip C; Lowe, Chris D; Brockhurst, Michael A

    2015-06-01

    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.

  13. Cell-density dependent effects of low-dose ionizing radiation on E. coli cells.

    PubMed

    Alipov, E D; Shcheglov, V S; Sarimov, R M; Belyaev, I Ya

    2003-01-01

    The changes in genome conformational state (GCS) induced by low-dose ionizing radiation in E. coli cells were measured by the method of anomalous viscosity time dependence (AVTD) in cellular lysates. Effects of X-rays at doses 0.1 cGy--1 Gy depended on post-irradiation time. Significant relaxation of DNA loops followed by a decrease in AVTD. The time of maximum relaxation was between 5-80 min depending on the dose of irradiation. U-shaped dose response was observed with increase of AVTD in the range of 0.1-4 Gy and decrease in AVTD at higher doses. No such increase in AVTD was seen upon irradiation of cells at the beginning of cell lysis while the AVTD decrease was the same. Significant differences in the effects of X-rays and gamma-rays at the same doses were observed suggesting a strong dependence of low-dose effects on LET. Effects of 0.01 cGy gamma-rays were studied at different cell densities during irradiation. We show that the radiation-induced changes in GCS lasted longer at higher cell density as compared to lower cell density. Only small amount of cells were hit at this dose and the data suggest cell-to-cell communication in response to low-dose ionizing radiation. This prolonged effect was also observed when cells were irradiated at high cell density and diluted to low cell density immediately after irradiation. These data suggest that cell-to-cell communication occur during irradiation or within 3 min post-irradiation. The cell-density dependent response to low-dose ionizing radiation was compared with previously reported data on exposure of E. coli cells to electromagnetic fields of extremely low frequency and extremely high frequency (millimeter waves). The body of our data show that cells can communicate in response to electromagnetic fields and ionizing radiation, presumably by reemission of secondary photons in infrared-submillimeter frequency range.

  14. Postcatastrophe population dynamics and density dependence of an endemic island duck

    USGS Publications Warehouse

    Seavy, N.E.; Reynolds, M.H.; Link, W.A.; Hatfield, J.S.

    2009-01-01

    Laysan ducks (Anas laysanensis) are restricted to approximately 9 km2 in the Northwestern Hawaiian Islands, USA. To evaluate the importance of density dependence for Laysan ducks, we conducted a Bayesian analysis to estimate the parameters of a Gompertz model and the magnitude of process variation and observation error based on the fluctuations in Laysan duck abundance on Laysan Island from 1994 to 2007. This model described a stationary distribution for the population at carrying capacity that fluctuates around a long-term mean of 456 ducks and is between 316 to 636 ducks 95% of the time. This range of expected variability can be used to identify changes in population size that warn of catastrophic events. Density-dependent population dynamics may explain the recovery of Laysan duck from catastrophic declines and allow managers to identify population monitoring thresholds.

  15. Energy density dependence of hydrogen combustion efficiency in atmospheric pressure microwave plasma

    SciTech Connect

    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)

  16. Krylov-space algorithms for time-dependent Hartree-Fock and density functional computations

    SciTech Connect

    Chernyak, Vladimir; Schulz, Michael F.; Mukamel, Shaul; Tretiak, Sergei; Tsiper, Eugene V.

    2000-07-01

    A fast, low memory cost, Krylov-space-based algorithm is proposed for the diagonalization of large Hamiltonian matrices required in time-dependent Hartree-Fock (TDHF) and adiabatic time-dependent density-functional theory (TDDFT) computations of electronic excitations. A deflection procedure based on the symplectic structure of the TDHF equations is introduced and its capability to find higher eigenmodes of the linearized TDHF operator for a given numerical accuracy is demonstrated. The algorithm may be immediately applied to the formally-identical adiabatic TDDFT equations. (c) 2000 American Institute of Physics.

  17. Temperature-dependence of Threshold Current Density-Length Product in Metallization Lines: A Revisit

    NASA Astrophysics Data System (ADS)

    Saptono Duryat, Rahmat; Kim, Choong-Un

    2016-04-01

    One of the important phenomena in Electromigration (EM) is Blech Effect. The existence of Threshold Current Density-Length Product or EM Threshold has such fundamental and technological consequences in the design, manufacture, and testing of electronics. Temperature-dependence of Blech Product had been thermodynamically established and the real behavior of such interconnect materials have been extensively studied. The present paper reviewed the temperature-dependence of EM threshold in metallization lines of different materials and structure as found in relevant published articles. It is expected that the reader can see a big picture from the compiled data, which might be overlooked when it was examined in pieces.

  18. Time-dependent Density Functional Results for the Dynamic Hyperpolarizability of C{sub 60}

    SciTech Connect

    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}

  19. Density dependence of electron mobility in the accumulation mode for fully depleted SOI films

    SciTech Connect

    Naumova, O. V. Zaitseva, E. G.; Fomin, B. I.; Ilnitsky, M. A.; Popov, V. P.

    2015-10-15

    The electron mobility µ{sub eff} in the accumulation mode is investigated for undepleted and fully depleted double-gate n{sup +}–n–n{sup +} silicon-on-insulator (SOI) metal–oxide–semiconductor field-effect transistors (MOSFET). To determine the range of possible values of the mobility and the dominant scattering mechanisms in thin-film structures, it is proposed that the field dependence of the mobility µ{sub eff} be replaced with the dependence on the density N{sub e} of induced charge carriers. It is shown that the dependences µ{sub eff}(N{sub e}) can be approximated by the power functions µ{sub eff}(N{sub e}) ∝ N{sub e}{sup -n}, where the exponent n is determined by the chargecarrier scattering mechanism as in the mobility field dependence. The values of the exponent n in the dependences µ{sub eff}(N{sub e}) are determined when the SOI-film mode near one of its surfaces varies from inversion to accumulation. The obtained results are explained from the viewpoint of the electron-density redistribution over the SOI-film thickness and changes in the scattering mechanisms.

  20. Effects of density dependence, zooplankton and temperature on blue whiting Micromesistius poutassou growth.

    PubMed

    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.

  1. A new time dependent density functional algorithm for large systems and plasmons in metal clusters

    SciTech Connect

    Baseggio, Oscar; Fronzoni, Giovanna; Stener, Mauro

    2015-07-14

    A new algorithm to solve the Time Dependent Density Functional Theory (TDDFT) equations in the space of the density fitting auxiliary basis set has been developed and implemented. The method extracts the spectrum from the imaginary part of the polarizability at any given photon energy, avoiding the bottleneck of Davidson diagonalization. The original idea which made the present scheme very efficient consists in the simplification of the double sum over occupied-virtual pairs in the definition of the dielectric susceptibility, allowing an easy calculation of such matrix as a linear combination of constant matrices with photon energy dependent coefficients. The method has been applied to very different systems in nature and size (from H{sub 2} to [Au{sub 147}]{sup −}). In all cases, the maximum deviations found for the excitation energies with respect to the Amsterdam density functional code are below 0.2 eV. The new algorithm has the merit not only to calculate the spectrum at whichever photon energy but also to allow a deep analysis of the results, in terms of transition contribution maps, Jacob plasmon scaling factor, and induced density analysis, which have been all implemented.

  2. Density-dependent prey mortality is determined by the spatial scale of predator foraging.

    PubMed

    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

  3. Travelling Waves for a Density Dependent Diffusion Nagumo Equation over the Real Line

    NASA Astrophysics Data System (ADS)

    Robert, A. Van Gorder

    2012-07-01

    We consider the density dependent diffusion Nagumo equation, where the diffusion coefficient is a simple power function. This equation is used in modelling electrical pulse propagation in nerve axons and in population genetics (amongst other areas). In the present paper, the δ-expansion method is applied to a travelling wave reduction of the problem, so that we may obtain globally valid perturbation solutions (in the sense that the perturbation solutions are valid over the entire infinite domain, not just locally; hence the results are a generalization of the local solutions considered recently in the literature). The resulting boundary value problem is solved on the real line subject to conditions at z → ±∞. Whenever a perturbative method is applied, it is important to discuss the accuracy and convergence properties of the resulting perturbation expansions. We compare our results with those of two different numerical methods (designed for initial and boundary value problems, respectively) and deduce that the perturbation expansions agree with the numerical results after a reasonable number of iterations. Finally, we are able to discuss the influence of the wave speed c and the asymptotic concentration value α on the obtained solutions. Upon recasting the density dependent diffusion Nagumo equation as a two-dimensional dynamical system, we are also able to discuss the influence of the nonlinear density dependence (which is governed by a power-law parameter m) on oscillations of the travelling wave solutions.

  4. 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.

  5. A Density Functional Approach to Polarizable Models: A Kim-Gordon-Response Density Interaction Potential for Molecular Simulations

    SciTech Connect

    Tabacchi, G; Hutter, J; Mundy, C

    2005-04-07

    A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density functional calculations.

  6. Density evolution in systems with slow approach to equilibrium

    NASA Astrophysics Data System (ADS)

    Nelson, Kevin Taylor

    This dissertation investigates the evolution of probability densities under the Frobenius-Perron operator U in chaotic iterated-map systems that are slow to reach equilibrium. It first concentrates on one-dimensional maps that are slow to reach equilibrium because they feature intermittent chaos due to the presence of a marginal fixed point. Using the method of shift states and coherent states under U, certain results are obtained concerning the spectrum of U in various functional spaces, using as the main example the cusp map f( x) = 1 - ∣1-2x . Those results are applied to obtain corrections to the well-known leading 1/t form of the x-x autocorrelation function C(t). The symbolic dynamics of one-dimensional maps are then investigated, with particular emphasis on the implications of the existence of intermittent chaos and with applications to topological conjugation. Next, the statistics of extreme values in one-dimensional maps are investigated. Fn(x) is defined as the probability that a point chosen from an initial probability distribution and its first n - 1 iterates under a particular map are all less than x; the properties of F n(x) are derived analytically for a wide variety of one-dimensional maps, and the conclusions are confirmed numerically. Finally, higher-dimensional area-preserving maps are investigated. The technique of local spectral decomposition for U, in which approximate right and left eigenstates for U are constructed localized on unstable periodic points, is used to study density evolution and correlation of observables over time.

  7. Nanowire-density-dependent field emission of n-type 3C-SiC nanoarrays

    SciTech Connect

    Wang, Lin; Gao, Fengmei; Chen, Shanliang; Yang, Weiyou; Li, Chengming

    2015-09-21

    The density of the nanowires is one of the key issues for their field emission (FE) properties of the nanoarrays, since it plays an important role on the electron emission sites and field screening effect. Here, we reported the nanowire-density-dependent FE properties of the n-type 3C-SiC nanoarrays. The highly oriented and large-scale SiC nanoarrays were grown on the 6H-SiC wafer via pyrolysis of polyureasilazane by adjusting the thicknesses of Au films used as the catalysts. The densities of the nanoarrays were tunable to be ∼2.9 × 10{sup 7}, ∼4.0 × 10{sup 7}, and ∼5.7 × 10{sup 7} nanowires/cm{sup 2} by controlling the Au film thicknesses of 50, 70, and 90 nm, respectively. The measured FE characteristics disclosed that the turn-on fields of the samples could be tailored to be of ∼1.79, 1.57, and 1.95 V/μm with the increase of the densities, suggesting that a suitable nanowire density could favor the enhanced electron emission from the SiC nanoarrays with improved emission sites and limited field screening effects.

  8. Chain Length and Grafting Density Dependent Enhancement in the Hydrolysis of Ester-Linked Polymer Brushes.

    PubMed

    Melzak, Kathryn A; Yu, Kai; Bo, Deng; Kizhakkedathu, Jayachandran N; Toca-Herrera, José 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

  9. Tri-trophic interactions affect density dependence of seed fate in a tropical forest palm.

    PubMed

    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.

  10. Time Dependent Solution for the He I Line Ratio Electron Temperature and Density Diagnostic in TEXTOR and DIII-D

    NASA Astrophysics Data System (ADS)

    Munoz Burgos, J. M.; Schmitz, O.; Unterberg, E. A.; Loch, S. D.; Balance, C. P.

    2010-11-01

    We developed a time dependent solution for the He I line ratio diagnostic. Stationary solution is applied for L-mode at TEXTOR. The radial range is typically limited to a region near the separatrix due to metastable effects, and the atomic data used. We overcome this problem by applying a time dependent solution and thus avoid unphysical results. We use a new R-Matrix with Pseudostates and Convergence Cross-Coupling electron impact excitation and ionization atomic data set into the Collisional Radiative Model (CRM). We include contributions from higher Rydberg states into the CRM by means of the projection matrix. By applying this solution (to the region near the wall) and the stationary solution (near the separatrix), we triple the radial range of the current diagnostic. We explore the possibility of extending this approach to H-mode plasmas in DIII-D by estimating line emission profiles from electron temperature and density Thomson scattering data.

  11. Dynamical quantum-electrodynamics embedding: combining time-dependent density functional theory and the near-field method.

    PubMed

    Gao, Yi; Neuhauser, Daniel

    2012-08-21

    We develop an approach for dynamical (ω > 0) embedding of mixed quantum mechanical (QM)/classical (or more precisely QM/electrodynamics) systems with a quantum sub-region, described by time-dependent density functional theory (TDDFT), within a classical sub-region, modeled here by the recently proposed near-field (NF) method. Both sub-systems are propagated simultaneously and are coupled through a common Coulomb potential. As a first step we implement the method to study the plasmonic response of a metal film which is half jellium-like QM and half classical. The resulting response is in good agreement with both full-scale TDDFT and the purely classical NF method. The embedding method is able to describe the optical response of the whole system while capturing quantum mechanical effects, so it is a promising approach for studying electrodynamics in hybrid molecules-metals nanostructures.

  12. Sampling-variance effects on detecting density dependence from temporal trends in natural populations

    USGS Publications Warehouse

    Shenk, T.M.; White, Gary C.; Burnham, K.P.

    1998-01-01

    Monte Carlo simulations were conducted to evaluate robustness of four tests to detect density dependence, from series of population abundances, to the addition of sampling variance. Population abundances were generated from random walk, stochastic exponential growth, and density-dependent population models. Population abundance estimates were generated with sampling variances distributed as lognormal and constant coefficients of variation (cv) from 0.00 to 1.00. In general, when data were generated under a random walk, Type I error rates increased rapidly for Bulmer's R, Pollard et al.'s, and Dennis and Taper's tests with increasing magnitude of sampling variance for n > 5 yr and all values of process variation. Bulmer's R* test maintained a constant 5% Type I error rate for n > 5 yr and all magnitudes of sampling variance in the population abundance estimates. When abundances were generated from two stochastic exponential growth models (R = 0.05 and R = 0.10), Type I errors again increased with increasing sampling variance; magnitude of Type I error rates were higher for the slower growing population. Therefore, sampling error inflated Type I error rates, invalidating the tests, for all except Bulmer's R* test. Comparable simulations for abundance estimates generated from a density-dependent growth rate model were conducted to estimate power of the tests. Type II error rates were influenced by the relationship of initial population size to carrying capacity (K), length of time series, as well as sampling error. Given the inflated Type I error rates for all but Bulmer, s R*, power was overestimated for the remaining tests, resulting in density: dependence being detected more often than it existed. Population abundances of natural populations are almost exclusively estimated rather than censused, assuring sampling error. Therefore, because these tests have been shown to be either invalid when only sampling variance occurs in the population abundances (Bulmer's R

  13. Experimental Examination of Intraspecific Density-Dependent Competition during the Breeding Period in Monarch Butterflies (Danaus plexippus)

    PubMed Central

    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

  14. Density-dependent life histories in female bank voles from fluctuating populations.

    PubMed

    Tkadlec, E; Zejda, J

    1998-11-01

    Using long-term data sets from two lowland floodplain forest bank vole populations in central Europe, we tested two predictions that with increasing densities: (i) proportions of nonparous females in winter populations would increase; and (ii) age of both nonparous and parous females would increase. These two predictions follow from the assumption that changes in age structure are driven by density-dependent shifts in age at first reproduction. Both populations were sampled by snap trapping between 1956 and 1976. For each year, we examined samples of animals collected between November and April for proportions of females with and without breeding experience and analysed their variation in age relative to the population density. The presence or absence of placental scars was used to discriminate between the parous and nonparous animals. Age was determined by measuring the length of the first mandibular molar (M1 ) roots. Both populations exhibited multi-annual fluctuations in numbers closely resembling those in northern Fennoscandia. The proportion of nonparous females in our total sample was 0.73, suggesting that it is uncommon for parous female bank voles to breed in two successive years and that their life histories are largely designed for breeding in one season only as a major reproductive strategy. Using a logistic-binomial regression model, we found that the probability of females being nonparous or parous at capture varied significantly with time, space and population density. The final model producing the best fit to data predicted that the proportion of nonparous females would be slightly larger over winter and substantially larger after high-density breeding seasons, which is consistent with the tested prediction. With increasing densities during the breeding seasons, both the nonparous and parous females became older at the onset of winter. Again, the field evidence was consistent with the predicted pattern. The age of parous females in the autumn at

  15. A Dynamic Approach to Modeling Dependence Between Human Failure Events

    SciTech Connect

    Boring, Ronald Laurids

    2015-09-01

    In practice, most HRA methods use direct dependence from THERP—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.

  16. A new weight-dependent direct statistical approach model

    SciTech Connect

    Burn, K.W.

    1997-02-01

    A weight-dependent capability is inserted into the direct statistical approach (DSA) to optimize splitting and Russian roulette (RR) parameters in Monte Carlo particle transport calculations. In the new model, splitting or RR is carried out on a progenitor arriving at a surface in such a way that the weight of the progeny is fixed (for the particular surface). Thus, the model is named the DSA weight line model. In the presence of weight-dependent games, all components of the second moment, and the time, are not separable. In the absence of weight-dependent games, the component of the second moment describing the weight-dependent splitting or RR is still not separable. Two approximations are examined to render this component separable under these circumstances. One of these approximations, named the noninteger approximation, looks promising. The new DSA model with the noninteger approximation is tested on four sample problems. Comparisons with the previous weight-independent DSA model and with the MCNP (version 4a) weight window generator are made.

  17. Resampling method for applying density-dependent habitat selection theory to wildlife surveys.

    PubMed

    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

  18. Resampling method for applying density-dependent habitat selection theory to wildlife surveys.

    PubMed

    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

  19. Predictions of Taylor's power law, density dependence and pink noise from a neutrally modeled time series.

    PubMed

    Keil, Petr; Herben, Tomás; Rosindell, James; Storch, David

    2010-07-01

    There has recently been increasing interest in neutral models of biodiversity and their ability to reproduce the patterns observed in nature, such as species abundance distributions. Here we investigate the ability of a neutral model to predict phenomena observed in single-population time series, a study complementary to most existing work that concentrates on snapshots in time of the whole community. We consider tests for density dependence, the dominant frequencies of population fluctuation (spectral density) and a relationship between the mean and variance of a fluctuating population (Taylor's power law). We simulated an archipelago model of a set of interconnected local communities with variable mortality rate, migration rate, speciation rate, size of local community and number of local communities. Our spectral analysis showed 'pink noise': a departure from a standard random walk dynamics in favor of the higher frequency fluctuations which is partly consistent with empirical data. We detected density dependence in local community time series but not in metacommunity time series. The slope of the Taylor's power law in the model was similar to the slopes observed in natural populations, but the fit to the power law was worse. Our observations of pink noise and density dependence can be attributed to the presence of an upper limit to community sizes and to the effect of migration which distorts temporal autocorrelation in local time series. We conclude that some of the phenomena observed in natural time series can emerge from neutral processes, as a result of random zero-sum birth, death and migration. This suggests the neutral model would be a parsimonious null model for future studies of time series data.

  20. Resampling Method for Applying Density-Dependent Habitat Selection Theory to Wildlife Surveys

    PubMed Central

    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

  1. Survival kinetics of starving bacteria is biphasic and density-dependent.

    PubMed

    Phaiboun, Andy; Zhang, Yiming; Park, Boryung; Kim, Minsu

    2015-04-01

    In the lifecycle of microorganisms, prolonged starvation is prevalent and sustaining life during starvation periods is a vital task. In the literature, it is commonly assumed that survival kinetics of starving microbes follows exponential decay. This assumption, however, has not been rigorously tested. Currently, it is not clear under what circumstances this assumption is true. Also, it is not known when such survival kinetics deviates from exponential decay and if it deviates, what underlying mechanisms for the deviation are. Here, to address these issues, we quantitatively characterized dynamics of survival and death of starving E. coli cells. The results show that the assumption--starving cells die exponentially--is true only at high cell density. At low density, starving cells persevere for extended periods of time, before dying rapidly exponentially. Detailed analyses show intriguing quantitative characteristics of the density-dependent and biphasic survival kinetics, including that the period of the perseverance is inversely proportional to cell density. These characteristics further lead us to identification of key underlying processes relevant for the perseverance of starving cells. Then, using mathematical modeling, we show how these processes contribute to the density-dependent and biphasic survival kinetics observed. Importantly, our model reveals a thrifty strategy employed by bacteria, by which upon sensing impending depletion of a substrate, the limiting substrate is conserved and utilized later during starvation to delay cell death. These findings advance quantitative understanding of survival of microbes in oligotrophic environments and facilitate quantitative analysis and prediction of microbial dynamics in nature. Furthermore, they prompt revision of previous models used to analyze and predict population dynamics of microbes. PMID:25838110

  2. The community reinforcement approach with homeless alcohol-dependent individuals.

    PubMed

    Smith, J E; Meyers, R J; Delaney, H D

    1998-06-01

    Homeless alcohol-dependent individuals were randomly assigned to receive either a behavioral intervention (i.e., the Community Reinforcement Approach [CRA]) or the standard treatment (STD) at a large day shelter. Ninety-one men and 15 women participated. The majority of participants were White (64%), but both Hispanic (19%) and Native American (13%) individuals were represented as well. Overall, the decline in drinking levels from intake through follow-ups was significant. As predicted, CRA participants significantly outperformed STD group members on drinking measures across the 5 follow-ups, which ranged from 2 months to 1 year after intake. Both conditions showed marked improvement in employment and housing stability.

  3. Time-dependent Kohn-Sham approach to quantum electrodynamics

    SciTech Connect

    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.

  4. Predicting critical temperatures of iron(II) spin crossover materials: density functional theory plus U approach.

    PubMed

    Zhang, Yachao

    2014-12-01

    A first-principles study of critical temperatures (T(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(c) of a pair of iron(II) SCO molecular crystals (α and β phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ΔE(HL) and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract T(c) by exploiting the ΔH/T - T and ΔS - T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the α 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(c) of the two phases. This study shows the applicability of the DFT+U approach for predicting T(c) of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior.

  5. Predicting critical temperatures of iron(II) spin crossover materials: Density functional theory plus U approach

    SciTech Connect

    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 (α and β phase), where identical constituent molecules are packed in different ways. We first calculate the adiabatic high spin-low spin energy splitting ΔE{sub HL} and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract T{sub c} by exploiting the ΔH/T − T and ΔS − T relationships. The results are in agreement with experiment. Analysis of geometries and electronic structures shows that the local ligand field in the α 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.

  6. Dependency of the Cusp Density Anomaly on the Variability of Forcing Inside and Outside the Cusp

    NASA Astrophysics Data System (ADS)

    Brinkman, D. G.; Walterscheid, R. L.; Clemmons, J. H.

    2014-12-01

    The Earth's magnetospheric cusp provides direct access of energetic particles to the thermosphere. These particles produce ionization and kinetic (particle) heating of the atmosphere. The increased ionization coupled with enhanced electric fields in the cusp produces increased Joule heating and ion drag forcing. These energy inputs largely determine the neutral density structure in the cusp region. Measurements by the CHAMP satellite (460-390- km altitude) have shown a region of strong enhanced density attributed to the combination of cusp particle and Joule heating. The Streak mission (325-123 km), on the other hand, observed a relative depletion in density in the cusp. While particle precipitation in the cusp is comparatively well constrained, the characteristics of the steady and fluctuating components of the electric field in the cusp are poorly constrained. Also, the significance of harder particle precipitation in areas adjacent to the cusp in particular at lower altitudes has not been addressed as it relates to the cusp density anomaly. We address the response of the cusp region to a range electrodynamical forcing with our high resolution two-dimensional time-dependent nonhydrostatic nonlinear dynamical model. We take advantage of our model's high resolution and focus on a more typical cusp width of 2 degrees in latitude. Earlier simulations have also shown a significant contribution from soft particle precipitation. We simulate the atmospheric response to a range of realizable magnitudes of the fluctuating and steady components of the electric field to examine the dependence of the magnitude of the cusp density anomaly on a large range of observed characteristics of the electrodynamical forcing and examine, in particular, the importance of particle heating relative to Joule heating. In addition we investigate the role of harder particle precipitation in areas adjacent to the cusp in determining the lower altitude cusp density and wind structure. We compare

  7. A kinetic approach to modeling the manufacture of high density strucutral foam: Foaming and polymerization

    SciTech Connect

    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

  8. Emergent fungal entomopathogen does not alter density dependence in a viral competitor.

    PubMed

    Liebhold, Andrew M; Plymale, Ruth; Elkinton, Joseph S; Hajek, Ann E

    2013-06-01

    Population cycles in forest Lepidoptera often result from recurring density-dependent epizootics of entomopathogens. While these systems are typically dominated by a single pathogen species, insects are often infected by multiple pathogens, yet little is known how pathogens interact to affect host dynamics. The apparent invasion of northeastern North America by the fungal entomopathogen Entomophaga maimaiga some time prior to 1989 provides a unique opportunity to evaluate such interactions. Prior to the arrival of E. maimaga, the oscillatory dynamics of host gypsy moth, Lymantria dispar, populations were apparently driven by epizootics of a nucleopolyhedrovirus. Subsequent to its emergence, E. maimaiga has caused extensive mortality in host populations, but little is known about how it has altered multigenerational dynamics of the gypsy moth and its virus. Here we compared demographic data collected in gypsy moth populations prior to vs. after E. maimaiga's invasion. We found that the recently invading fungal pathogen virtually always causes greater levels of mortality in hosts than does the virus, but fungal mortality is largely density independent. Moreover, the presence of the fungus has apparently not altered the gypsy moth-virus density-dependent interactions that were shown to drive periodic oscillations in hosts before the arrival of the fungus. PMID:23923480

  9. Synthesizing mechanisms of density dependence in reef fishes: behavior, habitat configuration, and observational scale.

    PubMed

    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

  10. Quantum electrodynamical time-dependent density functional theory for many-electron systems on a lattice

    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).

  11. Dependence of light attenuation and backscattering on collagen concentration and chondrocyte density in agarose scaffolds

    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 (ρ = 0.853, p < 0.001) and between µt and collagen concentration (ρ = 0.694, p < 0.001). µb correlated significantly with chondrocyte density (ρ = 0.504, p < 0.001) but not with collagen concentration (ρ = 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.

  12. Dependence of light attenuation and backscattering on collagen concentration and chondrocyte density in agarose scaffolds.

    PubMed

    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 (ρ = 0.853, p < 0.001) and between µt and collagen concentration (ρ = 0.694, p < 0.001). µb correlated significantly with chondrocyte density (ρ = 0.504, p < 0.001) but not with collagen concentration (ρ = 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. PMID:25310088

  13. Density-dependent resistance of the gypsy moth Lymantria dispar to its nucleopolyhedrovirus, and the consequences for population dynamics.

    PubMed

    Reilly, James R; Hajek, Ann E

    2008-01-01

    The processes controlling disease resistance can strongly influence the population dynamics of insect outbreaks. Evidence that disease resistance is density-dependent is accumulating, but the exact form of this relationship is highly variable from species to species. It has been hypothesized that insects experiencing high population densities might allocate more energy to disease resistance than those at lower densities, because they are more likely to encounter density-dependent pathogens. In contrast, the increased stress of high-density conditions might leave insects more vulnerable to disease. Both scenarios have been reported for various outbreak Lepidoptera in the literature. We tested the relationship between larval density and disease resistance with the gypsy moth (Lymantria dispar) and one of its most important density-dependent mortality factors, the nucleopolyhedrovirus (NPV) LdMNPV, in a series of bioassays. Larvae were reared in groups at different densities, fed the virus individually, and then reared individually to evaluate response to infection. In this system, resistance to the virus decreased with increasing larval density. Similarly, time to death was faster at high densities than at lower densities. Implications of density-resistance relationships for insect-pathogen population dynamics were explored in a mathematical model. In general, an inverse relationship between rearing density and disease resistance has a stabilizing effect on population dynamics.

  14. Evolution of competitive ability in Drosophila by density-dependent natural selection.

    PubMed

    Mueller, L D

    1988-06-01

    The theory of density-dependent natural selection predicts that populations kept at extreme densities should evolve different competitive abilities for limited resources. These predictions have been tested with laboratory populations of Drosophila melanogaster. Six independent populations were maintained in two environments, called r and K, for 128 generations. In the r environment, population sizes were small and resources for larvae and adults were abundant. In contrast the populations in the K environment were large and crowded, and resources, such as food and space, were in short supply. The relative competitive ability for food has been estimated for each population. Populations from the K environment consume food at a rate that is 58% greater than the average rate for the r population. The differentiation of competitive abilities in these populations is due to natural selection and is consistent with predictions from the theory of evolutionary ecology.

  15. Density-dependent recruitment of the bloater (Coregonus hoyi) in Lake Michigan

    USGS Publications Warehouse

    Brown, Edward H.; 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.

  16. Density dependent hadronic models and the relation between neutron stars and neutron skin thickness

    SciTech Connect

    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.

  17. Density-dependent cooperation as a mechanism for persistence and coexistence.

    PubMed

    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

  18. Effective electron displacements: A tool for time-dependent density functional theory computational spectroscopy

    SciTech Connect

    Guido, Ciro A. Cortona, Pietro; Adamo, Carlo

    2014-03-14

    We extend our previous definition of the metric Δr 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 Γ, permits applications in those situations where the Δr-index is not helpful: transitions in centrosymmetric systems and Rydberg excitations. The Γ-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 Γ values give insight about the functional performances in reproducing different type of transitions, and allow one to define a “confidence radius” for GGA and hybrid functionals.

  19. Verdict: Time-Dependent Density Functional Theory "Not Guilty" of Large Errors for Cyanines.

    PubMed

    Jacquemin, Denis; Zhao, Yan; Valero, Rosendo; Adamo, Carlo; Ciofini, Ilaria; Truhlar, Donald G

    2012-04-10

    We assess the accuracy of eight Minnesota density functionals (M05 through M08-SO) and two others (PBE and PBE0) for the prediction of electronic excitation energies of a family of four cyanine dyes. We find that time-dependent density functional theory (TDDFT) with the five most recent of these functionals (from M06-HF through M08-SO) is able to predict excitation energies for cyanine dyes within 0.10-0.36 eV accuracy with respect to the most accurate available Quantum Monte Carlo calculations, providing a comparable accuracy to the latest generation of CASPT2 calculations, which have errors of 0.16-0.34 eV. Therefore previous conclusions that TDDFT cannot treat cyanine dyes reasonably accurately must be revised.

  20. Size-dependent error of the density functional theory ionization potential in vacuum and solution

    SciTech Connect

    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.

  1. Size-dependent error of the density functional theory ionization potential in vacuum and solution

    SciTech Connect

    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.

  2. Size-dependent error of the density functional theory ionization potential in vacuum and solution

    DOE PAGESBeta

    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 potentialmore » 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.« less

  3. Turbo charging time-dependent density-functional theory with Lanczos chains.

    PubMed

    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.

  4. 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.

  5. Studies of spuriously shifting resonances in time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Luo, Kai; Fuks, Johanna I.; Maitra, Neepa T.

    2016-07-01

    Adiabatic approximations in time-dependent density functional theory (TDDFT) will in general yield unphysical time-dependent shifts in the resonance positions of a system driven far from its ground-state. This spurious time-dependence is explained in Fuks et al. [Phys. Rev. Lett. 114, 183002 (2015)] in terms of the violation of an exact condition by the non-equilibrium exchange-correlation kernel of TDDFT. Here we give details on the derivation and discuss reformulations of the exact condition that apply in special cases. In its most general form, the condition states that when a system is left in an arbitrary state, the TDDFT resonance position for a given transition in the absence of time-dependent external fields and ionic motion is independent of the state. Special cases include the invariance of TDDFT resonances computed with respect to any reference interacting stationary state of a fixed potential, and with respect to any choice of appropriate stationary Kohn-Sham reference state. We then present several case studies, including one that utilizes the adiabatically exact approximation, that illustrate the conditions and the impact of their violation on the accuracy of the ensuing dynamics. In particular, charge-transfer across a long-range molecule is hampered, and we show how adjusting the frequency of a driving field to match the time-dependent shift in the charge-transfer resonance frequency results in a larger charge transfer over time.

  6. Studies of spuriously shifting resonances in time-dependent density functional theory.

    PubMed

    Luo, Kai; Fuks, Johanna I; Maitra, Neepa T

    2016-07-28

    Adiabatic approximations in time-dependent density functional theory (TDDFT) will in general yield unphysical time-dependent shifts in the resonance positions of a system driven far from its ground-state. This spurious time-dependence is explained in Fuks et al. [Phys. Rev. Lett. 114, 183002 (2015)] in terms of the violation of an exact condition by the non-equilibrium exchange-correlation kernel of TDDFT. Here we give details on the derivation and discuss reformulations of the exact condition that apply in special cases. In its most general form, the condition states that when a system is left in an arbitrary state, the TDDFT resonance position for a given transition in the absence of time-dependent external fields and ionic motion is independent of the state. Special cases include the invariance of TDDFT resonances computed with respect to any reference interacting stationary state of a fixed potential, and with respect to any choice of appropriate stationary Kohn-Sham reference state. We then present several case studies, including one that utilizes the adiabatically exact approximation, that illustrate the conditions and the impact of their violation on the accuracy of the ensuing dynamics. In particular, charge-transfer across a long-range molecule is hampered, and we show how adjusting the frequency of a driving field to match the time-dependent shift in the charge-transfer resonance frequency results in a larger charge transfer over time. PMID:27475342

  7. Density dependence and risk of extinction in a small population of sea otters

    USGS Publications Warehouse

    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).

  8. 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 11×11×11 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 “normalized radius”, 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.

  9. A practical approach to lake water density from electrical conductivity and temperature

    NASA Astrophysics Data System (ADS)

    Moreira, Santiago; Schultze, Martin; Rahn, Karsten; Boehrer, Bertram

    2016-07-01

    Density calculations are essential to study stratification, circulation patterns, internal wave formation and other aspects of hydrodynamics in lakes and reservoirs. Currently, the most common procedure is the use of CTD (conductivity, temperature and depth) profilers and the conversion of measurements of temperature and electrical conductivity into density. In limnic waters, such approaches are of limited accuracy if they do not consider lake-specific composition of solutes, as we show. A new approach is presented to correlate density and electrical conductivity, using only two specific coefficients based on the composition of solutes. First, it is necessary to evaluate the lake-specific coefficients connecting electrical conductivity with density. Once these coefficients have been obtained, density can easily be calculated based on CTD data. The new method has been tested against measured values and the most common equations used in the calculation of density in limnic and ocean conditions. The results show that our new approach can reproduce the density contribution of solutes with a relative error of less than 10 % in lake waters from very low to very high concentrations as well as in lakes of very particular water chemistry, which is better than all commonly implemented density calculations in lakes. Finally, a web link is provided for downloading the corresponding density calculator.

  10. Turing space in reaction-diffusion systems with density-dependent cross diffusion

    NASA Astrophysics Data System (ADS)

    Zemskov, E. P.; Kassner, K.; Hauser, M. J. B.; Horsthemke, W.

    2013-03-01

    Reaction-diffusion systems with cross-diffusion terms that depend linearly on density are studied via linear stability analysis and weakly nonlinear analysis. We obtain and analyze the conditions for the Turing instability and derive a universal form of these conditions. We discuss the features of the pattern-forming regions in parameter space for a cross activator-inhibitor system, the Brusselator model, and for a pure activator-inhibitor system, the two-variable Oregonator model. The supercritical or subcritical character of the Turing bifurcation for the Brusselator is determined by deriving an amplitude equation for patterns near the instability threshold.

  11. Density-dependent changes in the feeding behaviour of Macrodon atricauda of southern Brazil.

    PubMed

    Cardoso, L G; Haimovici, M

    2016-07-01

    Long-term density-dependent changes in the population dynamics of the king weakfish Macrodon atricauda of southern Brazil between 1976 and 2013 may be related to a change in diet and an increase in feeding intensity. The importance of the small crustacean, Artemesia longinaris, increased in the diet of adults, whereas the importance of teleosts decreased and the frequency of full stomachs increased. Macrodon atricauda currently benefits from a high availability of A. longinaris, which results in a higher energy intake per individual, which, in turn, induces faster body growth and an earlier onset of sexual maturation.

  12. Excitons in solids with time-dependent density-functional theory: the bootstrap kernel and beyond

    NASA Astrophysics Data System (ADS)

    Byun, Young-Moo; Yang, Zeng-Hui; Ullrich, Carsten

    Time-dependent density-functional theory (TDDFT) is an efficient method to describe the optical properties of solids. Lately, a series of bootstrap-type exchange-correlation (xc) kernels have been reported to produce accurate excitons in solids, but different bootstrap-type kernels exist in the literature, with mixed results. In this presentation, we reveal the origin of the confusion and show a new empirical TDDFT xc kernel to compute excitonic properties of semiconductors and insulators efficiently and accurately. Our method can be used for high-throughput screening calculations and large unit cell calculations. Work supported by NSF Grant DMR-1408904.

  13. Measuring Depth-dependent Dislocation Densities and Elastic Strains in an Indented Ni-based Superalloy

    SciTech Connect

    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.

  14. Charge transfer in time-dependent density-functional theory via spin-symmetry breaking

    SciTech Connect

    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.

  15. Descriptions of Carbon Isotopes Within Density-Dependent Relativistic Hartree-Fock Theory

    NASA Astrophysics Data System (ADS)

    Lu, Xiao-Li; Long, Wen-Hui

    2013-11-01

    Within the density-dependent relativistic Hartree-Fock-Bogoliubov (DDRHFB) theory, the structure properties of Carbon isotopes are systematically studied, by taking the finite-range Gogny D1S with prefix factor 1.1 as the pairing force. The self-consistent DDRHFB calculations indicate the single neutron halo structures in both 17C and 19C. It is also found that close to the neutron drip line there exists distinct odd-even staggering on neutron radii, which is tightly related with the block effect.

  16. Electronic excitation spectra from time-dependent density functional response theory using plane-wave methods

    NASA Astrophysics Data System (ADS)

    Doltsinis, Nikos L.; Sprik, Michiel

    2000-11-01

    The time-dependent density functional response theory method for the computation of electronic excitation spectra has been implemented in a plane-wave basis set/pseudo-potential formalism. We compare our test results for N2 and H2CO to literature atomic basis set calculations and find good agreement. We also discuss some of the technical complications specific to the use of plane-wave basis sets. As an application, the thermally broadened photoabsorption spectrum of formamide at room temperature is computed by averaging over a number of vibrational configurations sampled from an ab initio molecular dynamics run and compared to experiment.

  17. Pressure Dependence of the Charge-Density-Wave Gap in Rare-Earth Tri-Tellurides

    SciTech Connect

    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}.

  18. Density determination of nano-layers depending to the thickness by non-destructive method

    SciTech Connect

    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,…) 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, ρ=f(h/λ{sub T}), for all the investigated layer/substrate combination. Such expression could be of great importance in the density prediction of even layers thicknesses.

  19. Electric Double Layer electrostatics of spherical polyelectrolyte brushes with pH-dependent charge density

    NASA Astrophysics Data System (ADS)

    Li, Hao; Chen, Guang; Sinha, Shayandev; Das, Siddhartha; Soft Matter, Interfaces,; Energy Laboratory (Smiel) Team

    Understanding the electric double layer (EDL) electrostatics of spherical polyelectrolyte (PE) brushes, which are spherical particles grafted with PE layers, is essential for appropriate use of PE-grfated micro-nanoparticles for targeted drug delivery, oil recovery, water harvesting, emulsion stabilization, emulsion breaking, etc. Here we elucidate the EDL electrostatics of spherical PE brushes for the case where the PE exhibits pH-dependent charge density. This pH-dependence necessitates the consideration of explicit hydrogen ion concentration, which in turn dictates the distribution of monomers along the length of the grafted PE. This monomer distribution is shown to be a function of the nature of the sphere (metallic or a charged or uncharged dielectric or a liquid-filled sphere). All the calculations are performed for the case where the PE electrostatics can be decoupled from the PE elastic and excluded volume effects. Initial predictions are also provided for the case where such decoupling is not possible.

  20. Generalized information (entanglement) entropies depending on the probability (density matrix), (modified gravity)

    NASA Astrophysics Data System (ADS)

    Obregón, Octavio; Cabo Bizet, Nana Geraldine

    2016-03-01

    Generalized information (entanglement) entropy(ies) that depend only on the probability (the density matrix) will be exhibited. It will be shown that these generalized information entropy(ies) are obtained by means of the superstatistics proposal and they correspond to generalized entanglement entropy(ies) that are at the same time a consequence of generalizing the Replica trick. Following the entropic force formulation, these generalized entropy(ies) provide a modified Newtońs law of gravitation. We discuss the difficulties to get an associated theory of gravity. Moreover, our results show corrections to the von Neumann entropy S0 that are larger than the usual UV ones and also than the corrections to the length dependent AdS3 entropy which result comparable to the UV ones. The correction terms due to the new entropy would modify the Ryu-Takayanagi identification between the CFT and the gravitational AdS3 entropies.

  1. Time-dependent density-functional theory method in the electron nuclear dynamics framework

    NASA Astrophysics Data System (ADS)

    Ajith Perera, S.; McLaurin, Patrick M.; Grimes, Thomas V.; Morales, Jorge A.

    2010-08-01

    A time-dependent density-functional theory (DFT) dynamics method in the electron nuclear dynamics (END) framework is presented. This time-dependent variational method treats simultaneously the nuclei and electrons of a system without utilizing predetermined potential energy surfaces. Like the simplest-level END, this method adopts a classical-mechanics description for the nuclei and a Thouless single-determinantal representation for the electrons. However, the electronic description is now expressed in a Kohn-Sham DFT form that provides electron correlation effects absent in the simplest-level END. Current implementation of this method employs the adiabatic approximation in the exchange-correlation action and potential. Simulations of molecular vibrations and proton-molecule reactions attest to the accuracy of the present method.

  2. Demographic, mechanistic and density-dependent determinants of population growth rate: a case study in an avian predator.

    PubMed Central

    Hone, Jim; Sibly, Richard M

    2002-01-01

    Identifying the determinants of population growth rate is a central topic in population ecology. Three approaches (demographic, mechanistic and density-dependent) used historically to describe the determinants of population growth rate are here compared and combined for an avian predator, the barn owl (Tyto alba). The owl population remained approximately stable (r approximately 0) throughout the period from 1979 to 1991. There was no evidence of density dependence as assessed by goodness of fit to logistic population growth. The finite (lambda) and instantaneous (r) population growth rates were significantly positively related to food (field vole) availability. The demographic rates, annual adult mortality, juvenile mortality and annual fecundity were reported to be correlated with vole abundance. The best fit (R(2) = 0.82) numerical response of the owl population described a positive effect of food (field voles) and a negative additive effect of owl abundance on r. The numerical response of the barn owl population to food availability was estimated from both census and demographic data, with very similar results. Our analysis shows how the demographic and mechanistic determinants of population growth rate are linked; food availability determines demographic rates, and demographic rates determine population growth rate. The effects of food availability on population growth rate are modified by predator abundance. PMID:12396509

  3. Demographic, mechanistic and density-dependent determinants of population growth rate: a case study in an avian predator.

    PubMed

    Hone, Jim; Sibly, Richard M

    2002-09-29

    Identifying the determinants of population growth rate is a central topic in population ecology. Three approaches (demographic, mechanistic and density-dependent) used historically to describe the determinants of population growth rate are here compared and combined for an avian predator, the barn owl (Tyto alba). The owl population remained approximately stable (r approximately 0) throughout the period from 1979 to 1991. There was no evidence of density dependence as assessed by goodness of fit to logistic population growth. The finite (lambda) and instantaneous (r) population growth rates were significantly positively related to food (field vole) availability. The demographic rates, annual adult mortality, juvenile mortality and annual fecundity were reported to be correlated with vole abundance. The best fit (R(2) = 0.82) numerical response of the owl population described a positive effect of food (field voles) and a negative additive effect of owl abundance on r. The numerical response of the barn owl population to food availability was estimated from both census and demographic data, with very similar results. Our analysis shows how the demographic and mechanistic determinants of population growth rate are linked; food availability determines demographic rates, and demographic rates determine population growth rate. The effects of food availability on population growth rate are modified by predator abundance. PMID:12396509

  4. Understanding spatial distributions: negative density-dependence in prey causes predators to trade-off prey quantity with quality.

    PubMed

    Bijleveld, Allert I; MacCurdy, Robert B; Chan, Ying-Chi; Penning, Emma; Gabrielson, Rich M; Cluderay, John; Spaulding, Eric L; Dekinga, Anne; Holthuijsen, Sander; ten Horn, Job; Brugge, Maarten; van Gils, Jan A; Winkler, David W; Piersma, Theunis

    2016-04-13

    Negative density-dependence is generally studied within a single trophic level, thereby neglecting its effect on higher trophic levels. The 'functional response' couples a predator's intake rate to prey density. Most widespread is a type II functional response, where intake rate increases asymptotically with prey density; this predicts the highest predator densities at the highest prey densities. In one of the most stringent tests of this generality to date, we measured density and quality of bivalve prey (edible cockles Cerastoderma edule) across 50 km² of mudflat, and simultaneously, with a novel time-of-arrival methodology, tracked their avian predators (red knots Calidris canutus). Because of negative density-dependence in the individual quality of cockles, the predicted energy intake rates of red knots declined at high prey densities (a type IV, rather than a type II functional response). Resource-selection modelling revealed that red knots indeed selected areas of intermediate cockle densities where energy intake rates were maximized given their phenotype-specific digestive constraints (as indicated by gizzard mass). Because negative density-dependence is common, we question the current consensus and suggest that predators commonly maximize their energy intake rates at intermediate prey densities. Prey density alone may thus poorly predict intake rates, carrying capacity and spatial distributions of predators. PMID:27053747

  5. Understanding spatial distributions: negative density-dependence in prey causes predators to trade-off prey quantity with quality.

    PubMed

    Bijleveld, Allert I; MacCurdy, Robert B; Chan, Ying-Chi; Penning, Emma; Gabrielson, Rich M; Cluderay, John; Spaulding, Eric L; Dekinga, Anne; Holthuijsen, Sander; ten Horn, Job; Brugge, Maarten; van Gils, Jan A; Winkler, David W; Piersma, Theunis

    2016-04-13

    Negative density-dependence is generally studied within a single trophic level, thereby neglecting its effect on higher trophic levels. The 'functional response' couples a predator's intake rate to prey density. Most widespread is a type II functional response, where intake rate increases asymptotically with prey density; this predicts the highest predator densities at the highest prey densities. In one of the most stringent tests of this generality to date, we measured density and quality of bivalve prey (edible cockles Cerastoderma edule) across 50 km² of mudflat, and simultaneously, with a novel time-of-arrival methodology, tracked their avian predators (red knots Calidris canutus). Because of negative density-dependence in the individual quality of cockles, the predicted energy intake rates of red knots declined at high prey densities (a type IV, rather than a type II functional response). Resource-selection modelling revealed that red knots indeed selected areas of intermediate cockle densities where energy intake rates were maximized given their phenotype-specific digestive constraints (as indicated by gizzard mass). Because negative density-dependence is common, we question the current consensus and suggest that predators commonly maximize their energy intake rates at intermediate prey densities. Prey density alone may thus poorly predict intake rates, carrying capacity and spatial distributions of predators.

  6. Molecular studies of pH-dependent ligand interactions with the low-density lipoprotein receptor.

    PubMed

    Yamamoto, Taichi; Chen, Hsuan-Chih; Guigard, Emmanuel; Kay, Cyril M; Ryan, Robert O

    2008-11-01

    The release of ligand from the low-density lipoprotein receptor (LDLR) has been postulated to involve a "histidine switch"-induced intramolecular rearrangement that discharges bound ligand. A recombinant soluble low-density lipoprotein receptor (sLDLR) was employed in ligand binding experiments with a fluorescently tagged variant apolipoprotein E N-terminal domain (apoE-NT). Binding was monitored as a function of fluorescence resonance energy transfer (FRET) from excited Trp residues in sLDLR to an extrinsic fluorophore covalently attached to Trp-null apoE3-NT. In binding experiments with wild-type (WT) sLDLR, FRET-dependent AEDANS fluorescence decreased as the pH was lowered. To investigate the role of His190, His562, and His586 in sLDLR in pH-dependent ligand binding and discharge, site-directed mutagenesis studies were performed. Compared to WT sLDLR, triple His --> Ala mutant sLDLR displayed attenuated pH-dependent ligand binding and a decreased level of ligand release as a function of low pH. When these His residues were substituted for Lys, the positively charged side chain of which does not ionize over this pH range, ligand binding was nearly abolished at all pH values. When sequential His to Lys mutants were examined, the evidence suggested that His562 and His586 function cooperatively. Whereas the sedimentation coefficient for WT sLDLR increased when the pH was reduced from 7 to 5, no such change occurred in the case of the triple Lys mutant receptor or a His562Lys/His586Lys double mutant receptor. The data support the existence of a cryptic, histidine side chain ionization-dependent alternative ligand that modulates ligand discharge via conformational reorganization.

  7. Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancer.

    PubMed

    Mori, Masaki; Triboulet, Robinson; Mohseni, Morvarid; Schlegelmilch, Karin; Shrestha, Kriti; Camargo, Fernando D; Gregory, Richard I

    2014-02-27

    Global downregulation of microRNAs (miRNAs) is commonly observed in human cancers and can have a causative role in tumorigenesis. The mechanisms responsible for this phenomenon remain poorly understood. Here, we show that YAP, the downstream target of the tumor-suppressive Hippo-signaling pathway regulates miRNA biogenesis in a cell-density-dependent manner. At low cell density, nuclear YAP binds and sequesters p72 (DDX17), a regulatory component of the miRNA-processing machinery. At high cell density, Hippo-mediated cytoplasmic retention of YAP facilitates p72 association with Microprocessor and binding to a specific sequence motif in pri-miRNAs. Inactivation of the Hippo pathway or expression of constitutively active YAP causes widespread miRNA suppression in cells and tumors and a corresponding posttranscriptional induction of MYC expression. Thus, the Hippo pathway links contact-inhibition regulation to miRNA biogenesis and may be responsible for the widespread miRNA repression observed in cancer.

  8. Density-dependent habitat selection of spawning Chinook salmon: broad-scale evidence and implications.

    PubMed

    Falcy, Matthew R

    2015-03-01

    An extensive body of theory suggests that density-dependent habitat selection drives many fundamental ecological processes. The ideal free distribution and the ideal despotic distribution make contrasting predictions about the effect of total population size on relative abundances among habitats. Empirical assessment of these habitat selection models is uncommon because data must be collected over large temporal and spatial scales. I ask whether fluctuation in Chinook salmon (Oncorhynchus tshawytscha) spawner population size through time leads to different relative densities over space. Twenty-six years of monitoring data on spawning Chinook salmon across the entire coast of Oregon, USA, were used to evaluate models that make contrasting statements about the interactions of a latent population abundance parameter with physical habitat characteristics. There is strong information-theoretic support for models that include terms that allow the spatial variation in density to change as population size changes through time. Analysis of the best model reveals nonlinear isodars, which suggests a 'despotic' or 'preemptive' distribution of individuals across habitats, indicating that dominant or early-arriving individuals exclude others from breeding sites. This finding has implications for genetic dynamics, population dynamics and conservation metrics of these highly valued fish. The novel application of modelling techniques used here to assess mechanisms of habitat selection from observational data can be used in the emerging field of eco-evolutionary dynamics. PMID:25283166

  9. A DENSITY DEPENDENCE FOR PROTOSTELLAR LUMINOSITY IN CLASS I SOURCES: COLLABORATIVE ACCRETION

    SciTech Connect

    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 μm 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.

  10. Fruit removal rate depends on neighborhood fruit density, frugivore abundance, and spatial context.

    PubMed

    Smith, Adam D; McWilliams, Scott R

    2014-03-01

    Fleshy-fruited plants depend fundamentally on interactions with frugivores for effective seed dispersal. Recent models of frugivory within spatially explicit networks make two general predictions regarding these interactions: rate of fruit removal increases (i.e., is facilitated) as densities of conspecific neighborhood fruits increase, and fruit removal rate varies positively with frugivore abundance. We conducted a field experiment that constitutes the first empirical and simultaneous test of these two primary predictions. We manipulated neighborhood abundances of arrowwood (Viburnum recognitum and Viburnum dentatum) fruits in southern New England's maritime shrub community and monitored removal rates by autumn-migrating birds. Focal arrowwood plants in neighborhoods with high conspecific fruit density sustained moderately decreased fruit removal rates (i.e., competition) relative to those in low-density neighborhoods, a result that agrees with most field research to date but contrasts with theoretical expectation. We suggest the spatial contexts that favor competition (i.e., high-abundance neighborhoods and highly aggregated landscapes) are considerably more common than the relatively uniform, low-aggregation fruiting landscapes that promote facilitation. Patterns of arrowwood removal by avian frugivores generally varied positively with, and apparently in response to, seasonal changes in migratory frugivore abundance. However, we suggest that dense stands of arrowwood concentrated frugivore activity at the neighborhood scale, thus counteracting geographic patterns of frugivore abundance. Our results underscore the importance of considering spatial context (e.g., fruit distribution and aggregation, frugivory hubs) in plant-avian frugivore interactions.

  11. Thermodynamics predicts density-dependent energy use in organisms and ecological communities.

    PubMed

    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.

  12. Cosmological Constraints from the Redshift Dependence of the Alcock-Paczynski Test: Galaxy Density Gradient Field

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Dong; Park, Changbom; Forero-Romero, J. E.; Kim, Juhan

    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 Ω 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 DAH , the product of the angular diameter distance and the Hubble parameter.

  13. Cosmological constraints from the redshift dependence of the Alcock-Paczynski test: galaxy density gradient field

    SciTech Connect

    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 Ω {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.

  14. Photoabsorption spectra of small cationic xenon clusters from time-dependent density functional theory

    SciTech Connect

    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.

  15. Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

    SciTech Connect

    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.

  16. Nalmefene: a new approach to the treatment of alcohol dependence.

    PubMed

    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

  17. Nalmefene: a new approach to the treatment of alcohol dependence

    PubMed Central

    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

  18. Nalmefene: a new approach to the treatment of alcohol dependence.

    PubMed

    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.

  19. A comprehensive approach to age-dependent dosimetric modeling

    SciTech Connect

    Leggett, R.W.; Cristy, M.; Eckerman, K.F.

    1986-01-01

    In the absence of age-specific biokinetic models, current retention models of the International Commission on Radiological Protection (ICRP) frequently are used as a point of departure for evaluation of exposures to the general population. These models were designed and intended for estimation of long-term integrated doses to the adult worker. Their format and empirical basis preclude incorporation of much valuable physiological information and physiologically reasonable assumptions that could be used in characterizing the age-specific behavior of radioelements in humans. In this paper we discuss a comprehensive approach to age-dependent dosimetric modeling in which consideration is given not only to changes with age in masses and relative geometries of body organs and tissues but also to best available physiological and radiobiological information relating to the age-specific biobehavior of radionuclides. This approach is useful in obtaining more accurate estimates of long-term dose commitments as a function of age at intake, but it may be particularly valuable in establishing more accurate estimates of dose rate as a function of age. Age-specific dose rates are needed for a proper analysis of the potential effects on estimates or risk of elevated dose rates per unit intake in certain stages of life, elevated response per unit dose received during some stages of life, and age-specific non-radiogenic competing risks.

  20. Time-dependent density functional theory with twist-averaged boundary conditions

    NASA Astrophysics Data System (ADS)

    Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.

    2016-05-01

    Background: Time-dependent density functional theory is widely used to describe excitations of many-fermion systems. In its many applications, three-dimensional (3D) coordinate-space representation is used, and infinite-domain calculations are limited to a finite volume represented by a spatial box. For finite quantum systems (atoms, molecules, nuclei, hadrons), the commonly used periodic or reflecting boundary conditions introduce spurious quantization of the continuum states and artificial reflections from boundary; hence, an incorrect treatment of evaporated particles. Purpose: The finite-volume artifacts for finite systems can be practically cured by invoking an absorbing potential in a certain boundary region sufficiently far from the described system. However, such absorption cannot be applied in the calculations of infinite matter (crystal electrons, quantum fluids, neutron star crust), which suffer from unphysical effects stemming from a finite computational box used. Here, twist-averaged boundary conditions (TABC) have been used successfully to diminish the finite-volume effects. In this work, we extend TABC to time-dependent modes. Method: We use the 3D time-dependent density functional framework with the Skyrme energy density functional. The practical calculations are carried out for small- and large-amplitude electric dipole and quadrupole oscillations of 16O. We apply and compare three kinds of boundary conditions: periodic, absorbing, and twist-averaged. Results: Calculations employing absorbing boundary conditions (ABC) and TABC are superior to those based on periodic boundary conditions. For low-energy excitations, TABC and ABC variants yield very similar results. With only four twist phases per spatial direction in TABC, one obtains an excellent reduction of spurious fluctuations. In the nonlinear regime, one has to deal with evaporated particles. In TABC, the floating nucleon gas remains in the box; the amount of nucleons in the gas is found to be

  1. The Impairment of Osteogenesis in Bone Sialoprotein (BSP) Knockout Calvaria Cell Cultures Is Cell Density Dependent

    PubMed Central

    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

  2. The Local Plasma Frequency Approach in Description of the Impact-Parameter Dependence of Energy Loss

    NASA Astrophysics Data System (ADS)

    Khodyrev, V. A.

    The LPF approach of Lindhard and Scharff is generalized to describe on the same basis the impact parameter dependence of energy loss in ion-atom collision. To make this feasible the energy loss is represented as an integral of the local energy deposition over the atomic shell volume. The local energy loss is determined by the induced electron current and the intensity of the projectile field at a given point. The LPF approach consists in an approximate description of the induced current using the corresponding expression for a uniform electron gas. With an appropriate description of the electron gas response, the atomic shell polarization and the state of electron motion are considered. The developed approach provides a possibility to test the accuracy of the customary approximation where the energy loss is expressed through the electron density on the ion trajectory, the local density approximation. A comparison with the available experimental results displays the adequateness of the developed approach if, additionally, the higher-order corrections over the projectile charge are taken into account.

  3. Time-Dependent Ginzburg-Landau Equation and Boltzmann Transport Equation for Charge-Density-Wave Conductors

    NASA Astrophysics Data System (ADS)

    Takane, Yositake; Hayashi, Masahiko; Ebisawa, Hiromichi

    2016-08-01

    The time-dependent Ginzburg-Landau equation and the Boltzmann transport equation for charge-density-wave (CDW) conductors are derived from a microscopic one-dimensional model by applying the Keldysh Green's function approach under a quasiclassical approximation. The effects of an external electric field and impurity pinning of the CDW are fully taken into account without relying on a phenomenological argument. These equations simultaneously describe the spatiotemporal dynamics of both the CDW and quasiparticles; thus, they serve as a starting point to develop a general framework to analyze various nonequilibrium phenomena, such as current conversion between the CDW condensate and quasiparticles, in realistic CDW conductors. It is shown that, in typical situations, the equations correctly describe the nonlinear behavior of electric conductivity in a simpler manner.

  4. Density-dependent processes in the life history of fishes: evidence from laboratory populations of zebrafish Danio rerio.

    PubMed

    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 'bottom-up' 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

  5. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD).

    PubMed

    Yokogawa, D

    2016-09-01

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced. PMID:27608983

  6. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD)

    NASA Astrophysics Data System (ADS)

    Yokogawa, D.

    2016-09-01

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced.

  7. Dependence of the critical temperature in overdoped copper oxides on superfluid density

    NASA Astrophysics Data System (ADS)

    Božović, I.; He, X.; Wu, J.; Bollinger, A. T.

    2016-08-01

    The physics of underdoped copper oxide superconductors, including the pseudogap, spin and charge ordering and their relation to superconductivity, is intensely debated. The overdoped copper oxides are perceived as simpler, with strongly correlated fermion physics evolving smoothly into the conventional Bardeen–Cooper–Schrieffer behaviour. Pioneering studies on a few overdoped samples indicated that the superfluid density was much lower than expected, but this was attributed to pair-breaking, disorder and phase separation. Here we report the way in which the magnetic penetration depth and the phase stiffness depend on temperature and doping by investigating the entire overdoped side of the La2‑xSrxCuO4 phase diagram. We measured the absolute values of the magnetic penetration depth and the phase stiffness to an accuracy of one per cent in thousands of samples; the large statistics reveal clear trends and intrinsic properties. The films are homogeneous; variations in the critical superconducting temperature within a film are very small (less than one kelvin). At every level of doping the phase stiffness decreases linearly with temperature. The dependence of the zero-temperature phase stiffness on the critical superconducting temperature is generally linear, but with an offset; however, close to the origin this dependence becomes parabolic. This scaling law is incompatible with the standard Bardeen–Cooper–Schrieffer description.

  8. Dependence of the critical temperature in overdoped copper oxides on superfluid density.

    PubMed

    Božović, I; He, X; Wu, J; Bollinger, A T

    2016-08-18

    The physics of underdoped copper oxide superconductors, including the pseudogap, spin and charge ordering and their relation to superconductivity, is intensely debated. The overdoped copper oxides are perceived as simpler, with strongly correlated fermion physics evolving smoothly into the conventional Bardeen-Cooper-Schrieffer behaviour. Pioneering studies on a few overdoped samples indicated that the superfluid density was much lower than expected, but this was attributed to pair-breaking, disorder and phase separation. Here we report the way in which the magnetic penetration depth and the phase stiffness depend on temperature and doping by investigating the entire overdoped side of the La2-xSrxCuO4 phase diagram. We measured the absolute values of the magnetic penetration depth and the phase stiffness to an accuracy of one per cent in thousands of samples; the large statistics reveal clear trends and intrinsic properties. The films are homogeneous; variations in the critical superconducting temperature within a film are very small (less than one kelvin). At every level of doping the phase stiffness decreases linearly with temperature. The dependence of the zero-temperature phase stiffness on the critical superconducting temperature is generally linear, but with an offset; however, close to the origin this dependence becomes parabolic. This scaling law is incompatible with the standard Bardeen-Cooper-Schrieffer description. PMID:27535534

  9. Dependence of the critical temperature in overdoped copper oxides on superfluid density

    NASA Astrophysics Data System (ADS)

    Božović, I.; He, X.; Wu, J.; Bollinger, A. T.

    2016-08-01

    The physics of underdoped copper oxide superconductors, including the pseudogap, spin and charge ordering and their relation to superconductivity, is intensely debated. The overdoped copper oxides are perceived as simpler, with strongly correlated fermion physics evolving smoothly into the conventional Bardeen-Cooper-Schrieffer behaviour. Pioneering studies on a few overdoped samples indicated that the superfluid density was much lower than expected, but this was attributed to pair-breaking, disorder and phase separation. Here we report the way in which the magnetic penetration depth and the phase stiffness depend on temperature and doping by investigating the entire overdoped side of the La2-xSrxCuO4 phase diagram. We measured the absolute values of the magnetic penetration depth and the phase stiffness to an accuracy of one per cent in thousands of samples; the large statistics reveal clear trends and intrinsic properties. The films are homogeneous; variations in the critical superconducting temperature within a film are very small (less than one kelvin). At every level of doping the phase stiffness decreases linearly with temperature. The dependence of the zero-temperature phase stiffness on the critical superconducting temperature is generally linear, but with an offset; however, close to the origin this dependence becomes parabolic. This scaling law is incompatible with the standard Bardeen-Cooper-Schrieffer description.

  10. Density-dependent life-history compensation of an iteroparous salmonid.

    PubMed

    Johnston, Fiona D; Post, John R

    2009-03-01

    Over the course of a decade, the bull trout (Salvelinus confluentus) population in Lower Kananaskis Lake, Alberta, Canada, recovered from a heavily overexploited state, experiencing a 28-fold increase in adult abundance after the implementation of zero-harvest regulations. This system provided a unique opportunity to monitor the changes in life-history characteristics in a natural population throughout the recovery process. The purpose of this study was to examine the degree to which life-history traits were able to compensate for harvest-induced changes and the implications of this for management. Density-dependent changes in growth, survival, and reproductive life-history characteristics were observed. As density increased, maturation was delayed, and the frequency of skipped reproductive events, primarily by individuals of poor condition, increased. However, size at maturation and the proportion of fish skipping reproduction differed between the sexes, suggesting that life-history trade-offs differ between the sexes. The rapid response of these life-history traits to changes in density suggests that these changes were primarily due to phenotypic plasticity, although the importance of natural and artificial selection should not be discounted. The magnitude of the variation in the traits represents the degree to which the population was able to compensate for overharvest, although the overexploited state of the population at the beginning of the study demonstrates it was not able to fully compensate for this mortality. However, no evidence of depensatory processes was found. This, in combination with the plasticity of the life-history traits, has important implications for the resilience of the population to overharvest. Furthermore, density-dependent growth may have the unintended result of making size-based regulations less conservative at low levels of population abundance, as younger fish, perhaps even immature fish, become vulnerable to harvest. Finally, the

  11. The dependence of the IMF on the density- temperature relation of pre-stellar gas

    NASA Astrophysics Data System (ADS)

    Kitsionas, S.; Whitworth, A. P.; Klessen, R. S.; Jappsen, A.-K.

    It has been recently shown by several authors that fragmentation of pre-stellar gas (i.e. at densities from 10^4 to 10^10 particles cm^-3 and temperatures of order 10-30K) depends on the gas thermodynamics much more than it was anticipated in earlier studies, in which only an isothermal behaviour has been assumed for the gas. We shall review the results of a number of numerical hydrodynamic simulations (e.g. Li et al. 2003, Jappsen et al. 2005, Bonnell et al. 2006) in which departure from isothermality has been attempted by employing a polytropic equation of state (eos) with exponent different from unity. In particular, in these studies it has been shown that the dominant fragmentation scale of pre-stellar gas, and hence the peak of the initial mass function (IMF), depends on a polytropic exponent that changes value at a critical density. Furthermore, this critical density depends on the gas metallicity and fundamental constants rather than on initial conditions, thus allowing for the first time to infer theoretically the notion of a universal IMF (at least for its low-mass end). We shall subsequently present two test cases in which such an equation of state has been used in the context of smoothed particle hydrodynamic (SPH) numerical simulations. In the first case star formation is triggered by means of low-mass clump collisions. These calculations have shown that clump collisions can be a relatively efficient mechanism for the formation of solar mass protostars and their lower mass companions (efficiency greater or of order 20%; Kitsionas & Whitworth 2006). In the second case, the use of a polytropic eos with an exponent varying according to the metallicity of starburst regions (Spaans & Silk 2000, 2005) is shown to be sufficient to obtain a top heavy IMF similar to that observed e.g. in the Galactic centre (Klessen, Spaans & Jappsen 2006). These are preliminary results in the direction of revisiting earlier calculations that were resolving the opacity limit for

  12. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality.

    PubMed

    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

  13. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality.

    PubMed

    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

  14. Impact of density-dependent migration flows on epidemic outbreaks in heterogeneous metapopulations.

    PubMed

    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.

  15. Optimized Effective Potential for Quantum Electrodynamical Time-Dependent Density Functional Theory.

    PubMed

    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

  16. Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales

    PubMed Central

    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

  17. Turing bifurcation in a reaction-diffusion system with density-dependent dispersal

    NASA Astrophysics Data System (ADS)

    Kumar, Niraj; Horsthemke, Werner

    2010-05-01

    Motivated by the recent finding [N. Kumar, G.M. Viswanathan, V.M. Kenkre, Physica A 388 (2009) 3687] that the dynamics of particles undergoing density-dependent nonlinear diffusion shows sub-diffusive behaviour, we study the Turing bifurcation in a two-variable system with this kind of dispersal. We perform a linear stability analysis of the uniform steady state to find the conditions for the Turing bifurcation and compare it with the standard Turing condition in a reaction-diffusion system, where dispersal is described by simple Fickian diffusion. While activator-inhibitor kinetics are a necessary condition for the Turing instability as in standard two-variable systems, the instability can occur even if the diffusion constant of the inhibitor is equal to or smaller than that of the activator. We apply these results to two model systems, the Brusselator and the Gierer-Meinhardt model.

  18. Isospin effects and the density dependence of the nuclear symmetry energy

    SciTech Connect

    Souza, S. R.; Tsang, M. B.; Lynch, W. G.; Steiner, A. W.; Carlson, B. V.; Donangelo, R.

    2009-10-15

    The density dependence of the nuclear symmetry energy is inspected using the statistical multifragmentation model with Skyrme effective interactions. The model consistently considers the expansion of the fragments' volumes at finite temperature at the freeze-out stage. By selecting parametrizations of the Skyrme force that lead to very different equations of state for the symmetry energy, we investigate the sensitivity of the isoscaling parameter and the isotopic distributions to differences in the symmetry energy. Our results suggest that, in spite of being sensitive to the thermal dilation of the fragments' volumes, it is difficult to distinguish among the Skyrme forces from the isoscaling analysis. On the other hand, the isotopic distribution of the emitted fragments turns out to be very sensitive to the force employed in the calculation.

  19. Density dependence of the nuclear symmetry energy from measurements of neutron radii in nuclei

    SciTech Connect

    Viñas, 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 ≤ L ≤ 70 MeV, in a reasonable agreement with other estimates that use different observables and methods to extract L.

  20. Inelastic collisions and density-dependent excitation suppression in a {sup 87}Sr optical lattice clock

    SciTech Connect

    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.

  1. Time-dependent local density approximation study of attosecond time delays in the photoionization of xenon

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, Maia; Madjet, Mohamed; Chakraborty, Himadri

    2016-05-01

    We investigate Wigner-Smith (WS) time delays of the photoionization from various subshells of xenon using the time-dependent local density approximation (TDLDA) with the Leeuwen and Baerends exchange-correlation functional. At the 4d giant dipole resonance region as well as near all the Cooper minimum anti-resonances in 5p, 5s and 4d photoemissions, effects of electron correlations uniquely determine the shapes of the emission quantum phase. The Wigner-Smith time delay derived from this phase indicates significant variations as a function of energy. The results qualitatively support our TDLDA predictions at the fullerene plasmon region and at 3p Cooper minimum in argon, and should encourage attosecond measurements of Xe photoemission via two-photon interferometric techniques, such as RABITT. The work is supported by the NSF, USA.

  2. {alpha}-cluster structure above doubly closed shells in a generalized density-dependent cluster model

    SciTech Connect

    Ni Dongdong; Ren Zhongzhou

    2011-01-15

    An extension of the generalized density-dependent cluster model (GDDCM) is presented to study {alpha}-cluster structure above doubly closed shells. In all cases, the microscopic {alpha}-core potential is numerically constructed in the double-folding model with CDM3Y6 nucleon-nucleon interactions plus proton-proton Coulomb interactions. The properties of intraband E2 transitions and {alpha} decays are calculated by the exact solution of the Schroedinger equation with appropriate boundary conditions. It is found that the enhanced B(E2) transition strengths are well reproduced without any effective charge and the calculations of {alpha}-decay properties show good agreement with the available experimental data. This indicates that the GDDCM has universal applicability and equal validity regardless of whether the {alpha}-cluster states are in light or heavy nuclei.

  3. Density-dependent competition and selection on immune function in genetic lizard morphs

    PubMed Central

    Svensson, Erik; Sinervo, Barry; Comendant, Tosha

    2001-01-01

    Density-dependent territorial interactions have been suggested to cause immunosuppression and thereby decrease fitness, but empirical support from natural populations is lacking. Data from a natural lizard population (Uta stansburiana) showed that breeding females surrounded by many territorial neighbors had suppressed immune function. Furthermore, variation in immunological condition had different effects on the fitness of the two heritable female throat-color morphs in this population. These interactive fitness effects caused correlational selection between female throat color and immune responsiveness. Population genetic theory predicts that this should have lead to the buildup and preservation of a genetic correlation between female morphotype and immunological condition. Accordingly, the throat color of a female was genetically correlated (rA = −1.36; SE = 0.55) with her daughter's immune responsiveness. PMID:11592973

  4. Density dependence of the nuclear symmetry energy from measurements of neutron radii in nuclei

    NASA Astrophysics Data System (ADS)

    Viñas, X.; Centelles, M.; Roca-Maza, X.; Warda, M.

    2014-07-01

    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 208Pb, and from the electric dipole polarizability obtained via polarized proton inelastic scattering at forward angles in 208Pb. 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 ≤ L ≤ 70 MeV, in a reasonable agreement with other estimates that use different observables and methods to extract L.

  5. Extrinsic spin-orbit coupling and density dependent weak antilocalization in three-dimensional topological insulators

    NASA Astrophysics Data System (ADS)

    Liu, Weizhe; Adroguer, Pierre; Bi, Xintao; Hankiewicz, Ewelina; Culcer, Dimitrie

    2015-03-01

    Topological insulators (TIs) have revolutionized our understanding of insulating behaviour. Three-dimensional TIs are insulators in the bulk but conducting along their surfaces. Much of recent researches on 3D TIs focus on overcoming the transport bottleneck, namely the fact that surface transport is overwhelmed by bulk transport stemming from unintentional doping. The key to overcoming this bottleneck is identifying unambiguous signatures of surface state transport. We will discuss one such signature: weak antilocalization, meaning that coherent backscattering increases the electrical conductivity. The features of this effect, however, are rather subtle, because in TI the impurities have also strong spin-orbit coupling. I will show that spin-orbit coupled impurities introduce an additional time scale, which is expected to be shorter than the dephasing time, and the resulting conductivity has a distinguished part with linear dependent on the carrier number density. The result we predict is directly observable experimentally.

  6. Integration of Density Dependence and Concentration Response Models Provides an Ecologically Relevant Assessment of Populations Exposed to Toxicants

    EPA Science Inventory

    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 ...

  7. Parents benefit from eating offspring: density-dependent egg survivorship compensates for filial cannibalism.

    PubMed

    Klug, Hope; Lindström, Kai; St Mary, Colette M

    2006-10-01

    Why should animals knowingly consume their own young? It is difficult to imagine many circumstances in which eating one's own young (i.e., filial cannibalism) actually increases an individual's fitness; however, filial cannibalism commonly co-occurs with parental care in fishes. The evolutionary significance of filial cannibalism remains unclear. The most commonly accepted explanation is that filial cannibalism is a mechanism by which caring males gain energy or nutrients that they reinvest into future reproduction, thereby increasing net reproductive success. There is mixed support for this hypothesis and, at best, it can only explain filial cannibalism in some species. A recent alternative hypothesis suggests that filial cannibalism improves the survivorship of remaining eggs by increasing oxygen availability, and thus increases current reproductive success. This theory has received little attention as of yet. We evaluated the hypothesis of oxygen-mediated filial cannibalism in the sand goby by examining the effect of oxygen and egg density on the occurrence of filial cannibalism, evaluating the effects of partial clutch cannibalism on the survivorship of remaining eggs, and comparing potential costs and benefits of filial cannibalism related to the net number of eggs surviving. Indeed, we found that oxygen level and egg density affected the occurrence of cannibalism and that simulated partial clutch cannibalism improved survivorship of the remaining eggs. Additionally, because increased egg survivorship, stemming from partial egg removal, compensated for the cost of cannibalism (i.e., number of eggs removed) at a range of cannibalism levels, filial cannibalism potentially results in no net losses in reproductive success. However, oxygen did not affect egg survivorship. Thus, we suggest a more general hypothesis of filial cannibalism mediated by density-dependent egg survivorship.

  8. A relativistic time-dependent density functional study of the excited states of the mercury dimer.

    PubMed

    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.

  9. Density-Dependent Relations among Properties of Hadronic Matter and Applications to Hadron-Quark Stars

    SciTech Connect

    Uechi, Hiroshi; Uechi, Schun T.

    2011-05-06

    Density-dependent relations among the saturation properties of symmetric nuclear matter and hyperonic matter, and properties of hadron-(strange) quark stars are shown by applying the conserving nonlinear {sigma}-{omega}-{rho} hadronic mean-field theory. Nonlinear interactions are renormalized self-consistently as effective coupling constants, effective masses, and sources of equations of motion by maintaining thermodynamic consistency to the mean-field approximation. Effective masses and coupling constants at the saturation point of symmetric nuclear matter simultaneously determine the binding energy and saturation properties of hyperonic matter. The coupling constants expected from the hadronic mean-field model and SU(6) quark model for the vector coupling constants are compared by calculating masses of hadron-quark neutron stars. The nonlinear {sigma}-{omega}-{rho} mean-field approximation with vacuum fluctuation corrections and strange quark matter defined by the MIT-bag model were employed to examine properties of hadron-(strange) quark stars. We found that hadron-(strange) quark stars become more stable at high densities compared to pure hadronic and strange quark stars.

  10. Performance of Tamm-Dancoff approximation on nonadiabatic couplings by time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Hu, Chunping; Sugino, Osamu; Watanabe, Kazuyuki

    2014-02-01

    The Tamm-Dancoff approximation (TDA), widely used in physics to decouple excitations and de-excitations, is well known to be good for the calculation of excitation energies but not for oscillator strengths. In particular, the sum rule is violated in the latter case. The same concern arises within the TDA in the calculation of nonadiabatic couplings (NACs) by time-dependent density functional theory (TDDFT), due to the similarities in the TDDFT formulations of NACs and oscillator strengths [C. Hu, H. Hirai, and O. Sugino, J. Chem. Phys. 127, 064103 (2007)]. In this study, we present a systematic evaluation of the performance of TDDFT/TDA for the calculation of NACs. In the cases we considered, including a variety of systems possessing Jahn-Teller and Renner-Teller intersections, as well as an example with accidental conical intersections, it is found that the TDDFT/TDA performs better than the full TDDFT, contrary to the conjecture that the TDA might cause the NAC results to deteriorate and violate the sum rule. The surprisingly good performance of the TDA for NACs is probably because the TDA can partially compensate for the local-density-approximation error and give better excitation energies in the vicinity of intersections of potential energy surfaces. Our study also shows that it is important to use the TDA based on the rigorous full-TDDFT formulation of NACs, instead of using it based on an alternative approximate formulation.

  11. Heliocentric distance and temporal dependence of the interplanetary density-magnetic field magnitude correlation

    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.

  12. Open Quantum Transport and Non-Hermitian Real-Time Time-Dependent Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin; Zhao, Yanxiang; Chen, Hanning

    Sub-nanometer electronic devices are notoriously difficult to simulate, with the most widely adopted transport schemes predicting currents that diverge from experiment by several orders of magnitude. This deviation arises from numerous factors, including the inability of these methods to accommodate dynamic processes such as charge reorganization. A promising alternative entails the direct propagation of an electronic structure calculation, as exemplified by real-time time-dependent density functional theory (RT-TDDFT). Unfortunately this framework is inherently that of a closed system, and modifications must be made to handle incoming and outgoing particle fluxes. To this end, we establish a formal correspondence between the quantum master equation for an open, many-particle system and its description in terms of RT-TDDFT and non-Hermitian boundary potentials. By dynamically constraining the particle density within the boundary regions corresponding to the device leads, a simulation may be selectively converged to the non-equilibrium steady state associated with a given electrostatic bias. Our numerical tests demonstrate that this algorithm is both highly stable and readily integrated into existing electronic structure frameworks

  13. The phenology of space: Spatial aspects of bison density dependence in Yellowstone National Park

    USGS Publications Warehouse

    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.

  14. Plasmon excitations in sodium atomic planes: a time-dependent density functional theory study.

    PubMed

    Wang, Bao-Ji; Xu, Yuehua; Ke, San-Huang

    2012-08-01

    The collective electronic excitation in planar sodium clusters is studied by time-dependent density functional theory calculations. The formation and development of the resonances in photoabsorption spectra are investigated in terms of the shape and size of the two-dimensional (2D) systems. The nature of these resonances is revealed by the frequency-resolved induced charge densities present on a real-space grid. For long double chains, the excitation is similar to that in long single atomic chains, showing longitudinal modes, end and central transverse modes. However, for 2D planes consisting of (n × n) atoms with n being up to 16, new 2D characteristic modes emerge regardless of the symmetries considered. For in-plane excitations, besides the equivalent end mode, mixed modes with contrary polarity occur. The relation between the frequency of the primary modes and the system size is similar to the case of a 2D electron gas but with a correction due to the realistic atomic structure. For excitations perpendicular to the plane there are corner, side center, bulk center, and circuit modes. Our calculation reveals the importance of dimensionality for plasmon excitation and how it evolves from 1D to 2D.

  15. Reversal of density dependence of juvenile Littorina littorea (Gastropoda) growth in response to periphyton nutrient status

    NASA Astrophysics Data System (ADS)

    Sommer, Ulrich

    2001-05-01

    Experimental periphyton communities were grown in aquaria receiving media of differently enriched seawater (fully enriched, without Si enrichment, without N and P enrichment) and supplied differently with medium (batch and weekly replacement). Periphyton was subject to grazing by 1-6 individuals of juvenile Littorina littorea. Periphyton biomass was higher in the replacement aquaria than in the batch aquaria and higher in the full and the -Si medium than in the -NP medium. The N:C ratio of the periphyton increased with Littorina number in the batch aquaria and was unaffected by Littorina number in the replacement aquaria. Diatoms were most dominant in the -NP treatments and rarest in the -Si treatments. Chlorophytes were dominant in the -Si and the fully enriched treatments, but also Cyanobacteria contributed significantly to periphyton biomass in those treatments under nutrient replacement. Somatic growth of Littorina was negatively correlated to Littorina density in the replacement aquaria and positively density dependent in the batch aquaria. The latter is explained by improved food quality under stronger grazing pressure.

  16. A relativistic time-dependent density functional study of the excited states of the mercury dimer

    NASA Astrophysics Data System (ADS)

    Kullie, Ossama

    2014-01-01

    In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s2 + 6s6p), (6s2 + 6s7s), and (6s2 + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2.

  17. Transgenerational effects modulate density-dependent prophylactic resistance to viral infection in a lepidopteran pest

    PubMed Central

    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 host–pathogen interactions. PMID:25808002

  18. Density-dependent reproductive and vegetative allocation in the aquatic plant Pistia stratiotes (Araceae).

    PubMed

    Coelho, Flávia Freitas; Deboni, Liene; Lopes, Frederico Santos

    2005-01-01

    Pistia stratiotes is an aquatic macrophyte that grows in temporary-ponds in the southern Pantanal, Brazil. It reproduces both sexually and asexually and is usually observed forming dense mats on the water surface, a condition favored by the plant's vegetative reproduction coupled with an ability for rapid growth. In this study we examined the effect of densely crowded conditions on the production of reproductive and vegetative structures. In addition, we verified whether there is a trade-off between clonal growth and investment in sexual reproductive structures, and whether there is an allocation pattern with plant size. Individual plant biomass and the number of the rosettes producing sexual reproductive structures and vegetative growth structures both increased with density. Increase in plant size resulted in increased proportional allocation to sexual reproductive structures and vegetative growth structures. Allocation of biomass to reproduction did not occur at the expense of clonal growth. Thus, the density response appears as a increase of rosettes producing sexual reproductive structures and vegetative growth structures. Therefore, long leaves and stolons may be adaptive under densely crowded conditions where competition for light is intense. An important aspect in the study of trade-offs is the size-dependency of the allocation patterns .Usually, larger plants produce more biomass. Therefore, larger plants can allocate more biomass to both vegetative and sexual reproduction than smaller plants and thus show a positive correlation between both traits rather than the expected negative one. PMID:17354448

  19. Density-dependent prophylaxis in crowded beet webworm, Loxostege sticticalis (Lepidoptera: Pyralidae) larvae to a parasitoid and a fungal pathogen

    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...

  20. Assessment of the ΔSCF density functional theory approach for electronic excitations in organic dyes

    SciTech Connect

    Kowalczyk, T.; Yost, S. R.; Van Voorhis, T.

    2010-01-01

    This paper assesses the accuracy of the ΔSCF method for computing low-lying HOMO→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 ΔSCF density functional theory. In light of this performance, we reconsider the ad hoc ΔSCF 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 ΔSCF for simulating individual excited states are discussed.

  1. Density-dependent habitat selection and performance by a large mobile reef fish.

    PubMed

    Lindberg, William J; Frazer, Thomas K; Portier, Kenneth M; Vose, Frederic; Loftin, James; Murie, Debra J; Mason, Doran M; Nagy, Brian; Hart, Mary K

    2006-04-01

    condition. Density-dependent habitat selection for shelter and individual growth dynamics were therefore interdependent ecological processes that help to explain how patchy reef habitat sustains gag production. Moreover, gag selected shelter at the expense of maximizing their growth. Thus, mobile reef fishes could experience density-dependent effects on growth, survival, and/or reproduction (i.e., demographic parameters) despite reduced stock sizes as a consequence of fishing.

  2. Ionization and fragmentation of complex molecules studied with a density functional theory based approach

    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.

  3. Modeling solvation effects in real-space and real-time within density functional approaches

    SciTech Connect

    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.

  4. 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.

  5. Modeling solvation effects in real-space and real-time within density functional approaches.

    PubMed

    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

  6. A unifying probabilistic Bayesian approach to derive electron density from MRI for radiation therapy treatment planning

    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

  7. A unifying probabilistic Bayesian approach to derive electron density from MRI for radiation therapy treatment planning.

    PubMed

    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

  8. High current density PQQ-dependent alcohol and aldehyde dehydrogenase bioanodes.

    PubMed

    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 ± 2.1 µA 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 ± 59 µA cm(-2) and 925 ± 68 µA 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.

  9. Dependence of the critical temperature in overdoped copper oxides on superfluid density

    DOE PAGESBeta

    Božović, I.; He, X.; Wu, J.; Bollinger, A. T.

    2016-08-17

    The physics of underdoped copper-oxide superconductors, including the pseudogap, spin and charge ordering, and their relation to superconductivity1-3, is intensely debated. The overdoped side is perceived as simpler, with strongly-correlated fermion physics evolving smoothly into the conventional Bardeen-Cooper-Schrieffer (BCS) behavior. Pioneering studies on a few overdoped samples4-11 indicated that the superfluid density was much smaller than expected, but this was attributed to pair-breaking, disorder, and phase separation. Here, we test this conjecture by studying how the magnetic penetration depth λ and the phase stiffness ρs depend on temperature and doping, scanning densely the entire overdoped side of the La2-xSrxCuO4 (LSCO)more » phase diagram. We have measured the absolute values of λ and ρs to the accuracy of ±1% in thousands of cuprate samples; the large statistics reveals clear trends and intrinsic properties. The films are quite homogeneous; variations in the critical temperature (Tc) within a film are very small (< 1 K). At every doping, ρs(T) decreases linearly with temperature. The Tc(ρ s0) dependence is linear but with an offset, (Tc - T0) ∝ ρs0 where T0 ≈ 7 K, except very close to the origin where Tc ∝ √ρ s0. This scaling law defies the standard BCS description, posing a challenge to theory.« less

  10. Oxidized low-density lipoproteins upregulate proline oxidase to initiate ROS-dependent autophagy.

    PubMed

    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.

  11. Cell-density-dependent expression of Borrelia burgdorferi lipoproteins in vitro.

    PubMed Central

    Indest, K J; Ramamoorthy, R; Solé, M; Gilmore, R D; Johnson, B J; Philipp, M T

    1997-01-01

    Previously, we had identified non-OspA-OspB surface proteins of Borrelia burgdorferi that are targeted by the antibody-dependent complement-mediated killing mechanism. Here we demonstrate by Western blotting that one of these proteins, P35, is upregulated at the onset of stationary phase in vitro. Northern analysis revealed that the upregulation of P35 is at the level of transcription. In addition, the expression of an open reading frame (ORF) located downstream of the p35 gene was found to be regulated in the same fashion as that of P35. This ORF encodes a 7.5-kDa lipoprotein. The transcriptional start sites for both of these genes were determined, to aid in the identification of the putative promoter regions. Additional sequencing of the 5' flanking region of the p35 gene revealed a region of dyad symmetry 52 bp upstream of the transcription start site. Southern analysis demonstrated that the expression of these genes was not due to a cell-density-dependent rearrangement in the genome of B. burgdorferi. These findings provide an in vitro model for studying mechanisms of gene regulation in B. burgdorferi. PMID:9119447

  12. 2007 Time_Dependent Density-Functional Therory (July 15-20, 2007 Colby College, Maine)

    SciTech Connect

    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.

  13. 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.

  14. Approach for computing 1D fracture density: application to fracture corridor characterization

    NASA Astrophysics Data System (ADS)

    Viseur, Sophie; Chatelée, Sebastien; Akriche, Clement; Lamarche, Juliette

    2016-04-01

    Fracture density is an important parameter for characterizing fractured reservoirs. Many stochastic simulation algorithms that generate fracture networks indeed rely on the determination of a fracture density on volumes (P30) to populate the reservoir zones with individual fracture surfaces. However, only 1D fracture density (P10) are available from subsurface data and it is then important to be able to accurately estimate this entity. In this paper, a novel approach is proposed to estimate fracture density from scan-line or well data. This method relies on regression, hypothesis testing and clustering techniques. The objective of the proposed approach is to highlight zones where fracture density are statistically very different or similar. This technique has been applied on both synthetic and real case studies. These studies concern fracture corridors, which are particular tectonic features that are generally difficult to characterize from subsurface data. These tectonic features are still not well known and studies must be conducted to better understand their internal spatial organization and variability. The presented synthetic cases aim at showing the ability of the approach to extract known features. The real case study illustrates how this approach allows the internal spatial organization of fracture corridors to be characterized.

  15. Evaluating the B-cell density with various activation functions using White Noise Path Integral Approach

    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.

  16. Modeling the potential energy field caused by mass density distribution with Eton approach

    NASA Astrophysics Data System (ADS)

    Alkahtani, Badr Saad T.; Atangana, Abdon

    2016-04-01

    A new approach for modeling real world problems called the "Eton Approach" was presented in this paper. The "Eton approach" combines both the concept of the variable order derivative together with Atangana derivative with memory derivative. The Atangana derivative with memory is used to account for the memory and fractional derivative for its filter effect. The approach was used to describe the potential energy field that is caused by a given charge or mass density distribution.We solve the modified model numerically and present supporting numerical simulations.

  17. Momentum-dependent band spin splitting in semiconducting MnO2: a density functional calculation.

    PubMed

    Noda, Yusuke; Ohno, Kaoru; Nakamura, Shinichiro

    2016-05-11

    Recently, manganese-oxide compounds have attracted considerable attention, in particular, as candidate materials for photochemical water-splitting reactions. Here, we investigate electronic states of pristine manganese dioxides (MnO2) in different crystal phases using spin-polarized density functional theory (DFT) with Hubbard U correction. Geometrical structures and band dispersions of α-, β-, δ-, and λ-MnO2 crystals with collinear magnetic [ferromagnetic (FM) and antiferromagnetic (AFM)] orders are discussed in detail. We reveal that penalty energies that arise by violating the Goodenough-Kanamori rule are important and the origin of the magnetic interactions of the MnO2 crystals is governed by the superexchange interactions of Mn-O-Mn groups. In addition, it is found that momentum-dependent band spin splitting occurs in the AFM α-, β-, and δ-MnO2 crystals while no spin splitting occurs in the AFM λ-MnO2 crystal. Our results show that spin-split band dispersions stem from the different orientations of Mn-centred oxygen octahedra. Such interesting electronic states of the MnO2 crystals are unraveled by our discussion on the relationship between the effective (spin-dependent) single-electron potentials and the space-group symmetry operations that map up-spin Mn atoms onto down-spin Mn atoms. This work provides a basis to understand the relationship between the spin-dependent electronic states and the crystallography of manganese oxides. Another relationship to the recent experimental observations of the photochemical oxygen evolution of MnO2 crystals is also discussed.

  18. Normal mode analysis of single bunch, charge density dependent behavior in electron/positron beams

    NASA Astrophysics Data System (ADS)

    Ehrlichman, Michael

    Accelerator science in coming years will be increasingly dependent upon high single-bunch charges and/or small emittances. Under these conditions, single-particle dynamics are not a sufficient description of beam behavior and interactions between the beam particles must be taken into account. One such interaction is when collisions between the particles that compose a bunch perturb the motion of the colliding particles significantly and frequently enough to impact the beam dynamics. Multiple, small-angle, collisions blow up the emittance of the bunch and are referred to as intrabeam scattering (IBS). Here are documented the theoretical and experimental studies of IBS in storage rings undertaken as part of the CesrTA program. Under the conditions where IBS becomes dominant, other multi-particle effects can also appear. The additional effects we investigate include potential well distortion, coherent current-dependent tune shift, and direct space charge. CesrTA design and analysis is conducted in a normal mode coordinates environment which allows for natural handling of coupling. To that end, we develop a 6D normal modes decomposition of the linear beam optics. Multi-particle effects are also important for Energy Recovery Linear Accelerators (ERLs). Because the beam circulates for only a short period of time in an ERL, the beam lifetime imposed by Touschek scattering is not significant. However, the particles scattered out of the bunch can generate a radiation hazard where they collide with the beam pipe. We re-derive Piwinski's original Touschek scattering equation to check its validity when applied to ERL beams, then repurpose the formula to generate a profile of where scattered particles are generated and where they are lost. The results presented here advance our understanding of charge-dependent behavior in the sorts of high charge-density accelerators that will be implemented in coming years.

  19. Momentum-dependent band spin splitting in semiconducting MnO2: a density functional calculation.

    PubMed

    Noda, Yusuke; Ohno, Kaoru; Nakamura, Shinichiro

    2016-05-11

    Recently, manganese-oxide compounds have attracted considerable attention, in particular, as candidate materials for photochemical water-splitting reactions. Here, we investigate electronic states of pristine manganese dioxides (MnO2) in different crystal phases using spin-polarized density functional theory (DFT) with Hubbard U correction. Geometrical structures and band dispersions of α-, β-, δ-, and λ-MnO2 crystals with collinear magnetic [ferromagnetic (FM) and antiferromagnetic (AFM)] orders are discussed in detail. We reveal that penalty energies that arise by violating the Goodenough-Kanamori rule are important and the origin of the magnetic interactions of the MnO2 crystals is governed by the superexchange interactions of Mn-O-Mn groups. In addition, it is found that momentum-dependent band spin splitting occurs in the AFM α-, β-, and δ-MnO2 crystals while no spin splitting occurs in the AFM λ-MnO2 crystal. Our results show that spin-split band dispersions stem from the different orientations of Mn-centred oxygen octahedra. Such interesting electronic states of the MnO2 crystals are unraveled by our discussion on the relationship between the effective (spin-dependent) single-electron potentials and the space-group symmetry operations that map up-spin Mn atoms onto down-spin Mn atoms. This work provides a basis to understand the relationship between the spin-dependent electronic states and the crystallography of manganese oxides. Another relationship to the recent experimental observations of the photochemical oxygen evolution of MnO2 crystals is also discussed. PMID:27119122

  20. 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

  1. Enhancing and controlling single-atom high-harmonic generation spectra: a time-dependent density-functional scheme

    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.

  2. Dependence of the Perpendicular Residual Leakage Magnetic Flux Density on Fatigue Damage in an Austenitic Stainless Steel

    NASA Astrophysics Data System (ADS)

    Oka, M.; Yakushiji, T.; Tsuchida, Y.; Enokizono, M.

    2003-03-01

    In order to estimate the amount of plane bending fatigue damage in an austenitic stainless steel (SUS304), we were investigating the relationship between plane bending fatigue damage and the perpendicular residual leakage magnetic flux density caused by martensitic structure induced by plane bending fatigue. A specimen such as SUS304 had been excited in a constant external magnetic field perpendicularly to measure dependence of the perpendicular residual leakage magnetic flux density on plane bending fatigue damage accurately. The Z component of the magnetic flux density at 1 mm above a specimen is measured by using a thin-film flux-gate (FG) magnetic sensor. Residual magnetization is caused by partial martensitic structure in an austenitic stainless steel induced by cyclic bending stress. From our experiments, we can evaluate dependence of the perpendicular residual leakage magnetic flux density on plane bending fatigue damage and know the relationship between growth of a crack and the perpendicular residual leakage magnetic flux density.

  3. Modeling fast electron dynamics with real-time time-dependent density functional theory: application to small molecules and chromophores

    SciTech Connect

    Lopata, Kenneth A.; Govind, Niranjan

    2011-05-10

    The response of matter to external fields forms the basis for a vast wealth of fundamental physical processes ranging from light harvesting to nanoscale electron transport. Accurately modeling ultrafast electron dynamics in excited systems thus o_ers unparalleled insight, but requires an inherently non-linear time-resolved approach. To this end, an e_cient and massively parallel real-time real-space time-dependent density functional theory (RT-TDDFT) implementation in NWChem is presented. The implementation is first validated against linearresponse TDDFT and experimental results for a series of molecules subjected to small electric field perturbations. Second, non-linear excitation of green fluorescent protein is studied, which shows a blue-shift in the spectrum with increasing perturbation, as well as a saturation in absorption. Next, the charge dynamics of optically excited zinc porphyrin is presented in real-time and real-space, with relevance to charge injection in photovoltaic devices. Finally, intermolecular excitation in an adenine-thymine base pair is studied using the BNL range separated functional [Baer, R.; Neuhauser, D. Phys. Rev. Lett. 2005, 94, 043002], demonstrating the utility of a real-time approach in capturing charge transfer processes.

  4. The Effects of Text Density Levels and the Cognitive Style of Field Dependence on Learning from a CBI Tutorial

    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 randomly…

  5. 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

  6. Angular Dependence of Transport AC Losses in Superconducting Wire with Position-Dependent Critical Current Density in a DC Magnetic Field

    NASA Astrophysics Data System (ADS)

    Su, Xing-liang; Xiong, Li-ting; Gao, Yuan-wen; Zhou, You-he

    2013-07-01

    Transport AC losses play a very important role in high temperature superconductors (HTSs), which usually carry AC transport current under applied magnetic field in typical application-like conditions. In this paper, we propose the analytical formula for transport AC losses in HTS wire by considering critical current density of both inhomogeneous and anisotropic field dependent. The angular dependence of critical current density is described by effective mass theory, and the HTS wire has inhomogeneous distribution cross-section of critical current density. We calculate the angular dependence of normalized AC losses under different DC applied magnetic fields. The numerical results of this formula agree well with the experiment data and are better than the results of Norris formula. This analytical formula can explain the deviation of experimental transport current losses from the Norris formula and apply to calculate transport AC losses in realistic practical condition.

  7. A Multiple Motives Approach to Tobacco Dependence: The Wisconsin Inventory of Smoking Dependence Motives (WISDM-68)

    ERIC Educational Resources Information Center

    Piper, Megan E.; Piasecki, Thomas M.; Federman, E. Belle; Bolt, Daniel M.; Smith, Stevens S.; Fiore, Michael C.; Baker, Timothy C.

    2004-01-01

    The dependence construct fills an important explanatory role in motivational accounts of smoking and relapse. Frequently used measures of dependence are either atheoretical or grounded in a unidimensional model of physical dependence. This research creates a multidimensional measure of dependence that is based on theoretically grounded motives for…

  8. A relativistic time-dependent density functional study of the excited states of the mercury dimer

    SciTech Connect

    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}.