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Sample records for density dependent approach

  1. Why Density Dependent Propulsion?

    NASA Technical Reports Server (NTRS)

    Robertson, Glen A.

    2011-01-01

    In 2004 Khoury and Weltman produced a density dependent cosmology theory they call the Chameleon, as at its nature, it is hidden within known physics. The Chameleon theory has implications to dark matter/energy with universe acceleration properties, which implies a new force mechanism with ties to the far and local density environment. In this paper, the Chameleon Density Model is discussed in terms of propulsion toward new propellant-less engineering methods.

  2. 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.

  3. Density dependent neurodynamics.

    PubMed

    Halnes, Geir; Liljenström, Hans; Arhem, Peter

    2007-01-01

    The dynamics of a neural network depends on density parameters at (at least) two different levels: the subcellular density of ion channels in single neurons, and the density of cells and synapses at a network level. For the Frankenhaeuser-Huxley (FH) neural model, the density of sodium (Na) and potassium (K) channels determines the behaviour of a single neuron when exposed to an external stimulus. The features of the onset of single neuron oscillations vary qualitatively among different regions in the channel density plane. At a network level, the density of neurons is reflected in the global connectivity. We study the relation between the two density levels in a network of oscillatory FH neurons, by qualitatively distinguishing between three regions, where the mean network activity is (1) spiking, (2) oscillating with enveloped frequencies, and (3) bursting, respectively. We demonstrate that the global activity can be shifted between regions by changing either the density of ion channels at the subcellular level, or the connectivity at the network level, suggesting that different underlying mechanisms can explain similar global phenomena. Finally, we model a possible effect of anaesthesia by blocking specific inhibitory ion channels.

  4. Determining the functional form of density dependence: deductive approaches for consumer-resource systems having a single resource.

    PubMed

    Abrams, Peter A

    2009-09-01

    Consumer-resource models are used to deduce the functional form of density dependence in the consumer population. A general approach to determining the form of consumer density dependence is proposed; this involves determining the equilibrium (or average) population size for a series of different harvest rates. The relationship between a consumer's mortality and its equilibrium population size is explored for several one-consumer/one-resource models. The shape of density dependence in the resource and the shape of the numerical and functional responses all tend to be "inherited" by the consumer's density dependence. Consumer-resource models suggest that density dependence will very often have both concave and convex segments, something that is impossible under the commonly used theta-logistic model. A range of consumer-resource models predicts that consumer population size often declines at a decelerating rate with mortality at low mortality rates, is insensitive to or increases with mortality over a wide range of intermediate mortalities, and declines at a rapidly accelerating rate with increased mortality when mortality is high. This has important implications for management and conservation of natural populations.

  5. Macroscopic dielectric function within time-dependent density functional theory—Real time evolution versus the Casida approach

    NASA Astrophysics Data System (ADS)

    Sander, Tobias; Kresse, Georg

    2017-02-01

    Linear optical properties can be calculated by solving the time-dependent density functional theory equations. Linearization of the equation of motion around the ground state orbitals results in the so-called Casida equation, which is formally very similar to the Bethe-Salpeter equation. Alternatively one can determine the spectral functions by applying an infinitely short electric field in time and then following the evolution of the electron orbitals and the evolution of the dipole moments. The long wavelength response function is then given by the Fourier transformation of the evolution of the dipole moments in time. In this work, we compare the results and performance of these two approaches for the projector augmented wave method. To allow for large time steps and still rely on a simple difference scheme to solve the differential equation, we correct for the errors in the frequency domain, using a simple analytic equation. In general, we find that both approaches yield virtually indistinguishable results. For standard density functionals, the time evolution approach is, with respect to the computational performance, clearly superior compared to the solution of the Casida equation. However, for functionals including nonlocal exchange, the direct solution of the Casida equation is usually much more efficient, even though it scales less beneficial with the system size. We relate this to the large computational prefactors in evaluating the nonlocal exchange, which renders the time evolution algorithm fairly inefficient.

  6. Spatially explicit analyses unveil density dependence.

    PubMed Central

    Veldtman, Ruan; McGeoch, Melodie A.

    2004-01-01

    Density-dependent processes are fundamental in the understanding of species population dynamics. Whereas the benefits of considering the spatial dimension in population biology are widely acknowledged, the implications of doing so for the statistical detection of spatial density dependence have not been examined. The outcome of traditional tests may therefore differ from those that include ecologically relevant locational information on both the prey species and natural enemy. Here, we explicitly incorporate spatial information on individual counts when testing for density dependence between an insect herbivore and its parasitoids. The spatially explicit approach used identified significant density dependence more frequently and in different instances than traditional methods. The form of density dependence detected also differed between methods. These results demonstrate that the explicit consideration of patch location in density-dependence analyses is likely to significantly alter current understanding of the prevalence and form of spatial density dependence in natural populations. PMID:15590593

  7. Sampling variability and estimates of density dependence: a composite-likelihood approach.

    PubMed

    Lele, Subhash R

    2006-01-01

    It is well known that sampling variability, if not properly taken into account, affects various ecologically important analyses. Statistical inference for stochastic population dynamics models is difficult when, in addition to the process error, there is also sampling error. The standard maximum-likelihood approach suffers from large computational burden. In this paper, I discuss an application of the composite-likelihood method for estimation of the parameters of the Gompertz model in the presence of sampling variability. The main advantage of the method of composite likelihood is that it reduces the computational burden substantially with little loss of statistical efficiency. Missing observations are a common problem with many ecological time series. The method of composite likelihood can accommodate missing observations in a straightforward fashion. Environmental conditions also affect the parameters of stochastic population dynamics models. This method is shown to handle such nonstationary population dynamics processes as well. Many ecological time series are short, and statistical inferences based on such short time series tend to be less precise. However, spatial replications of short time series provide an opportunity to increase the effective sample size. Application of likelihood-based methods for spatial time-series data for population dynamics models is computationally prohibitive. The method of composite likelihood is shown to have significantly less computational burden, making it possible to analyze large spatial time-series data. After discussing the methodology in general terms, I illustrate its use by analyzing a time series of counts of American Redstart (Setophaga ruticilla) from the Breeding Bird Survey data, San Joaquin kit fox (Vulpes macrotis mutica) population abundance data, and spatial time series of Bull trout (Salvelinus confluentus) redds count data.

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

    PubMed

    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.

  9. 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.

  10. 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.

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

    PubMed

    Liu, Jie; Liang, WanZhen

    2011-11-14

    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.

  12. Density: A Discovery Approach.

    ERIC Educational Resources Information Center

    Rieck, William

    1994-01-01

    Describes an activity that allows students to discover the concept of density and that density is a determining physical property of a pure substance. Makes suggestions to further enhance students' understanding of density. (ZWH)

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Density Gradient Dependent Helicon Modes

    NASA Astrophysics Data System (ADS)

    Panevsky, Martin; Bengtson, Roger

    2002-11-01

    Radially localized helicon modes have been proposed to provide a fuller description of helicon discharges over a wide span of operating conditions and gas types [1]. These plasma modes could be of vital importance to the VASIMR engine. They depend on a radial density gradient and appear to operate over a range of frequencies inaccessible to traditional helicon discharges. Our work focuses on confirming experimentally the existence and properties of these helicon modes in Argon, Helium, and Hydrogen. We investigate the density profile, power deposition, wavefields, and dispersion relation of the new helicon modes which differ substantially from the properties of the traditional helicon plasma. We are using a set of dual half-turn helical antennas driven at 13.56 MHz. Our diagnostics includes a system for monitoring the plasma impedance, a set of Langmuir probes, a set of magnetic probes, as well as sensors for monitoring the pressure and DC magnetic field. *Work supported in part by Advanced Space Propulsion Lab, Johnson Space Center, NASA [1] B. N. Breizman and A. V. Arefiev, Phys. Rev. 84, 3863 (2000)

  19. 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.

  20. Size-dependent density of zirconia nanoparticles

    PubMed Central

    Opalinska, Agnieszka; Dzwolak, Wojciech; Chudoba, Tadeusz; Presz, Adam; Lojkowski, Witold

    2015-01-01

    Summary The correlation between density and specific surface area of ZrO2 nanoparticles (NPs) was studied. The NPs were produced using a hydrothermal process involving microwave heating. The material was annealed at 1100 °C which resulted in an increase in the average grain size of the ZrO2 NPs from 11 to 78 nm and a decrease in the specific surface area from 97 to 15 m2/g. At the same time, the density increased from 5.22 g/m3 to 5.87 g/m3. This effect was interpreted to be the result of the presence of a hydroxide monolayer on the NP surface. A smaller ZrO2 grain size was correlated with a larger contribution of the low density surface layer to the average density. To prove the existence of such a layer, the material was synthesized using 50% heavy water. Fourier transform infrared spectroscopy (FTIR) permitted the identification of the –OD groups created during synthesis. It was found that the –OD groups persisted on the ZrO2 surface even after annealing at 1100 °C. This hydroxide layer is responsible for the decrease in the average density of the NPs as their size decreases. This study of the correlation between particle size and density may be used to assess the quality of the NPs. In most cases, the technological aim is to avoid an amorphous layer and to obtain fully crystalline nanoparticles with the highest density possible. However, due to the effect of the surface layers, there is a maximum density which can be achieved for a given average NP diameter. The effect of the surface layer on the NP density becomes particularly evident for NPs smaller than 50 nm, and thus, the density of nanoparticles is size dependent. PMID:25671149

  1. Density dependent expression of a diatom retrotransposon.

    PubMed

    Oliver, Matthew J; Schofield, Oscar; Bidle, Kay

    2010-01-01

    Retrotransposons are mobile genetic elements that encode for their own replication. Many studies have linked their expression to stress caused by environmental factors. Genome sequencing and EST libraries of the coastal diatom Phaeodactylum tricornutum indicate that this organism has an active copia-like retrotransposon (Blackbeard), which is variably expressed under different culture conditions. In this study, we induce physiologic stress in P. tricornutum and measure Blackbeard expression over time. However, we find the dominant pattern of Blackbeard expression is related to cell culture density, not short-term physiologic stress. Density dependent expression of a retrotransposon in a diatom provides significant insight into the biogeography of diatom genome mutation. We suggest the shallow coastal ocean, where diatom densities are high, may be the geographic locus for generating genomic diversity in diatom lineages.

  2. Density dependence: an ecological Tower of Babel.

    PubMed

    Herrando-Pérez, Salvador; Delean, Steven; Brook, Barry W; Bradshaw, Corey J A

    2012-11-01

    The concept of density dependence represents the effect of changing population size on demographic rates and captures the demographic role of social and trophic mechanisms (e.g. competition, cooperation, parasitism or predation). Ecologists have coined more than 60 terms to denote different statistical and semantic properties of this concept, resulting in a formidable lexicon of synonymies and polysemies. We have examined the vocabulary of density dependence used in the modern ecological literature from the foundational lexicon developed by Smith, Allee, Haldane, Neave and Varley. A few simple rules suffice to abate terminological inconsistency and to enhance the biological meaning of this important concept. Correct citation of original references by ecologists and research journals could ameliorate terminological standards in our discipline and avoid linguistic confusion of mathematically and theoretically complex patterns.

  3. Charge transfer optical absorption and fluorescence emission of 4-(9-acridyl)julolidine from long-range-corrected time dependent density functional theory in polarizable continuum approach

    NASA Astrophysics Data System (ADS)

    Kityk, A. V.

    2014-07-01

    A long-range-corrected time-dependent density functional theory (LC-TDDFT) in combination with polarizable continuum model (PCM) have been applied to study charge transfer (CT) optical absorption and fluorescence emission energies basing on parameterized LC-BLYP xc-potential. The molecule of 4-(9-acridyl)julolidine selected for this study represents typical CT donor-acceptor dye with strongly solvent dependent optical absorption and fluorescence emission spectra. The result of calculations are compared with experimental spectra reported in the literature to derive an optimal value of the model screening parameter ω. The first absorption band appears to be quite well predictable within DFT/TDDFT/PCM with the screening parameter ω to be solvent independent (ω≈0.245 Bohr-1) whereas the fluorescence emission exhibits a strong dependence on the range separation with ω-value varying on a rising solvent polarity from about 0.225 to 0.151 Bohr-1. Dipolar properties of the initial state participating in the electronic transition have crucial impact on the effective screening.

  4. Partitioned density functional approach for a Lennard-Jones fluid.

    PubMed

    Zhou, Shiqi

    2003-12-01

    The existing classical density functional approach for nonuniform Lennard-Jones fluid, which is based on dividing the Lennard-Jones interaction potential into a short-range, repulsive part, and a smoothly varying, long-range, attractive tail, was improved by dividing the bulk second-order direct correlation function into strongly density-depending short-range part and weakly density-depending long-range part. The latter is treated by functional perturbation expansion truncated at the lowest order whose accuracy depends on how weakly the long-range part depends on the bulk density. The former is treated by the truncated functional perturbation expansion which is rewritten in the form of the simple weighted density approximation and incorporates the omitted higher-order terms by applying Lagrangian theorem of differential calculus to the reformulated form. The two approximations are put into the density profile equation of the density functional theory formalism to predict the density distribution for Lennard-Jones fluid in contact with a hard wall or between two hard walls within the whole density range for reduced temperature T(*)=1.35 and a density point for reduced temperature T(*)=1. The present partitioned density functional theory performs much better than several previous density functional perturbation theory approaches and a recently proposed bridge density functional approximation.

  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. Shell Model Approach to Nuclear Level Density

    NASA Astrophysics Data System (ADS)

    Horoi, Mihai

    2000-04-01

    Nuclear level densities (NLD) are traditionally estimated using variations of Fermi Gas Formula (FGF) or combinatoric techniques. Recent investigations using Monte Carlo Shell Model (MCSM) techniques indicate that a shell model description of NLD may be an accurate and stable approach. Full shell model calculations of NLD are very difficult. We calculated the NLD for all nuclei in the sd shell and show that the results can be described by a single particle combinatoric model, which depends on two parameters similar to FGF. We further investigated other models and find that a sum of gaussians with means and variances given by French and Ratcliff averages (Phys. Rev. C 3, 94(1971)) is able to accurately describe shell model NLD, even when shell effects are present. The contribution of the spurious center-of-mass motion to the shell model NLD is also discussed.

  7. Selective fishing induces density-dependent growth.

    PubMed

    Svedäng, Henrik; Hornborg, Sara

    2014-06-12

    Over the last decades, views on fisheries management have oscillated between alarm and trust in management progress. The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort. Here we report a case study on how striving for higher yields from the Eastern Baltic cod stock by increasing selectivity has become exceedingly detrimental for its productivity. Although there is a successive increase in numbers of undersized fish, growth potential is severely reduced, and fishing mortality in fishable size has increased. Once density-dependent growth is introduced, the process is self-enforcing as long as the recruitment remains stable. Our findings suggest that policies focusing on maximum yield while targeting greater sizes are risky and should instead prioritize catch rates over yield. Disregarding the underlying population structure may jeopardize stock productivity, with dire consequences for the fishing industry and ecosystem structure and function.

  8. 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

  9. 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.

  10. Time-dependent density functional theory for quantum transport.

    PubMed

    Zheng, Xiao; Chen, GuanHua; Mo, Yan; Koo, SiuKong; Tian, Heng; Yam, ChiYung; Yan, YiJing

    2010-09-21

    Based on our earlier works [X. Zheng et al., Phys. Rev. B 75, 195127 (2007); J. S. Jin et al., J. Chem. Phys. 128, 234703 (2008)], we propose a rigorous and numerically convenient approach to simulate time-dependent quantum transport from first-principles. The proposed approach combines time-dependent density functional theory with quantum dissipation theory, and results in a useful tool for studying transient dynamics of electronic systems. Within the proposed exact theoretical framework, we construct a number of practical schemes for simulating realistic systems such as nanoscopic electronic devices. Computational cost of each scheme is analyzed, with the expected level of accuracy discussed. As a demonstration, a simulation based on the adiabatic wide-band limit approximation scheme is carried out to characterize the transient current response of a carbon nanotube based electronic device under time-dependent external voltages.

  11. Density-Dependent Metabolic Heterogeneity in Human Mesenchymal Stem Cells

    PubMed Central

    Liu, Yijun; Munoz, Nathalie; Bunnell, Bruce A.; Logan, Timothy M.; Ma, Teng

    2016-01-01

    Human mesenchymal stem cells (hMSCs) are intrinsically heterogeneous and comprise subpopulations that differ in their proliferation, multi-potency, and functional properties, which are commonly demonstrated by culturing hMSCs at different plating densities. The objective of this study was to investigate the metabolic profiles of different subpopulations of hMSC by testing the hypothesis that the clonogenic hMSC subpopulation, which is selectively enriched in clonal density (CD) and low density (LD) culture (10 and 100 cells per square centimeter, respectively), possesses a metabolic phenotype that differs from that of hMSC in medium- or high-density (MD: 1,000 and HD: 3,000 cells per square centimeter, respectively). Cells at CD and LD conditions exhibited elevated expression of CD146 and colony forming unit-fibroblast compared with cells at MD- or HD. Global metabolic profiles revealed by gas chromatography-mass spectrometry of cell extracts showed clear distinction between LD and HD cultures, and density-dependent differences in coupling of glycolysis to the TCA cycle. Metabolic inhibitors revealed density-dependent differences in glycolysis versus oxidative phosphorylation (OXPHOS) for ATP generation, in glutamine metabolism, in the dependence on the pentose phosphate pathway for maintaining cellular redox state, and sensitivity to exogenous reactive oxygen species. We also show that active OXPHOS is not required for proliferation in LD culture but that OXPHOS activity increases senescence in HD culture. Together, the results revealed heterogeneity in hMSC culture exists at the level of primary metabolism. The unique metabolic characteristics of the clonogenic subpopulation suggest a novel approach for optimizing in vitro expansion of hMSCs. PMID:26274841

  12. Density-dependence at sea for coho salmon (Oncorhynchus kisutch)

    USGS Publications Warehouse

    Emlen, J.M.; Reisenbichler, R.R.; McGie, A.M.; Nickelson, T.E.

    1990-01-01

    The success of expanded salmon hatchery programs will depend strongly on the degree of density-induced diminishing returns per smolt released. Several authors have addressed the question of density-dependent mortality at sea in coho salmon (Oncorhynchus kisutch), but have come to conflicting conclusions. We believe there are compelling reasons to reinvestigate the data, and have done so for public hatchery fish, using a variety of approaches. The results provide evidence that survival of these public hatchery fish is negatively affected, directly by the number of public hatchery smolts and indirectly by the number of private hatchery smolts. These results are weak, statistically, and should be considered primarily as a caution to those who, on the basis of other published work, believe that density-dependence does not exist. The results reported here also re-emphasize the often overlooked point that inferences drawn from data are strongly biased by investigators' views of how the systems of interest work and by the statistical assumptions they make preparatory to the analysis of those data.

  13. Analyzing chiral condensate dependence on temperature and density

    NASA Astrophysics Data System (ADS)

    Rockcliffe, Keighley

    2016-09-01

    Determining the thermodynamic properties of the chiral condensate, the order parameter for chiral symmetry restoration, gives insight into whether there are phase transitions in dense astrophysical objects, such as young neutron stars. The chiral condensate is the scalar density of quarks in the ground state, and its presence violates chiral symmetry. Chiral effective field theory is used to study the behavior of the scalar quark condensate with changing temperature and density of neutron matter. Two-body and three-body chiral nuclear forces were employed to find the free energy and its dependence on the pion mass at lower temperatures. With increasing temperature (up to 100 MeV), the chiral condensate is strongly reduced, indicating a fast approach to chiral symmetry restoration. Chiral restoration seems to be hindered, however, at higher densities (around 0.2 fm-3). The role of the different perturbative contributions and their change with temperature and density was extracted. Although the dominant contribution is the noninteracting term in the perturbation series expansion, nuclear interactions are important particularly at high densities where they delay chiral symmetry restoration.

  14. 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.

  15. Density dependence in Caenorhabditis larval starvation

    PubMed Central

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

    2013-01-01

    Availability of food is often a limiting factor in nature. Periods of food abundance are followed by times of famine, often in unpredictable patterns. Reliable information about the environment is a critical ingredient of successful survival strategy. One way to improve accuracy is to integrate information communicated by other organisms. To test whether such exchange of information may play a role in determining starvation survival strategies, we studied starvation of L1 larvae in C. elegans and other Caenorhabditis species. We found that some species in genus Caenorhabditis, including C. elegans, survive longer when starved at higher densities, while for others survival is independent of the density. The density effect is mediated by chemical signal(s) that worms release during starvation. This starvation survival signal is independent of ascarosides, a class of small molecules widely used in chemical communication of C. elegans and other nematodes. PMID:24071624

  16. 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.

  17. 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.

  18. Dependence of quartz wettability on fluid density

    NASA Astrophysics Data System (ADS)

    Al-Yaseri, Ahmed Zarzor; Roshan, Hamid; Lebedev, Maxim; Barifcani, Ahmed; Iglauer, Stefan

    2016-04-01

    Wettability is one of the most important parameters in multiphase flow through porous rocks. However, experimental measurements or theoretical predictions are difficult and open to large uncertainty. In this work we demonstrate that gas densities (which are much simpler to determine than wettability and typically well known) correlate remarkably well with wettability. This insight can significantly improve wettability predictions, thus derisking subsurface operations (e.g., CO2 geostorage or hydrocarbon recovery), and significantly enhance fundamental understanding of natural geological processes.

  19. Time-dependent density-functional description of nuclear dynamics

    NASA Astrophysics Data System (ADS)

    Nakatsukasa, Takashi; Matsuyanagi, Kenichi; Matsuo, Masayuki; Yabana, Kazuhiro

    2016-10-01

    The basic concepts and recent developments in the time-dependent density-functional theory (TDDFT) for describing nuclear dynamics at low energy are presented. The symmetry breaking is inherent in nuclear energy density functionals, which provides a practical description of important correlations at the ground state. Properties of elementary modes of excitation are strongly influenced by the symmetry breaking and can be studied with TDDFT. In particular, a number of recent developments in the linear response calculation have demonstrated their usefulness in the description of collective modes of excitation in nuclei. Unrestricted real-time calculations have also become available in recent years, with new developments for quantitative description of nuclear collision phenomena. There are, however, limitations in the real-time approach; for instance, it cannot describe the many-body quantum tunneling. Thus, the quantum fluctuations associated with slow collective motions are explicitly treated assuming that time evolution of densities is determined by a few collective coordinates and momenta. The concept of collective submanifold is introduced in the phase space associated with the TDDFT and used to quantize the collective dynamics. Selected applications are presented to demonstrate the usefulness and quality of the new approaches. Finally, conceptual differences between nuclear and electronic TDDFT are discussed, with some recent applications to studies of electron dynamics in the linear response and under a strong laser field.

  20. 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.

  1. Skyrmion Approach to Finite Density and Temperature

    NASA Astrophysics Data System (ADS)

    Park, Byung-Yoon; Riska, D. O.

    We review an approach, developed over the past few years, to describe hadronic matter at finite density and temperature, whose underlying theoretical framework is the Skyrme model, an effective low energy theory rooted in large Nc QCD. In this approach matter is described by various crystal structures of skyrmions, classical topological solitons carrying baryon number, from which conventional baryons appear by quantization. Chiral and scale symmetries play a crucial role in the dynamics as described by pion, dilaton and vector meson degrees of freedom. When compressed or heated skyrmion matter describes a rich phase diagram which has strong connections with the confinement/deconfinement phase transition.

  2. 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

  3. Density-dependent growth in invasive Lionfish (Pterois volitans).

    PubMed

    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.

  4. Viscosity and density dependence during maximal flow in man.

    PubMed

    Staats, B A; Wilson, T A; Lai-Fook, S J; Rodarte, J R; Hyatt, R E

    1980-02-01

    Maximal expiratory flow curves were obtained from ten healthy subjects white breathing air and three other gas mixtures with different densities and viscosities. From these data, the magnitudes of the dependence of maximal flow on gas density and viscosity were obtained. The scaling laws of fluid mechanics, together with a model for the flow-limiting mechanism, were used to obtain a prediction of the relationship between the density dependence and the viscosity dependence of maximal flow. Although the data for individual subjects were too variable to allow a precise comparison with this prediction, the relationship between the mean density dependence and the mean viscosity dependence of all usbjects agreed with the theoretic prediction. This agreement supports the assumption, which is frequently made, that flow resistance rather than tissue visoelasticity is the dominant contributor to peripheral resistance. Information on the relationships between the pressure drop to the flow-limiting segment and flow, gas density and viscosity, and lung volume were also obtained.

  5. 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.

  6. Density dependence of reactor performance with thermal confinement scalings

    SciTech Connect

    Stotler, D.P.

    1992-03-01

    Energy confinement scalings for the thermal component of the plasma published thus far have a different dependence on plasma density and input power than do scalings for the total plasma energy. With such thermal scalings, reactor performance (measured by Q, the ratio of the fusion power to the sum of the ohmic and auxiliary input powers) worsens with increasing density. This dependence is the opposite of that found using scalings based on the total plasma energy, indicating that reactor operation concepts may need to be altered if this density dependence is confirmed in future research.

  7. 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.

  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 Central

    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.

  12. Transverse momentum dependent quark densities from Lattice QCD

    SciTech Connect

    Musch, B. U.; Haegler, Ph.; Negele, J. W.; Schaefer, A.

    2011-10-24

    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. 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.

  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. 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

  17. Radial propagation in population dynamics with density-dependent diffusion

    NASA Astrophysics Data System (ADS)

    Ngamsaad, Waipot

    2014-01-01

    Population dynamics that evolve in a radial symmetric geometry are investigated. The nonlinear reaction-diffusion model, which depends on population density, is employed as the governing equation for this system. The approximate analytical solution to this equation is found. It shows that the population density evolves from the initial state and propagates in a traveling-wave-like manner for a long-time scale. If the distance is insufficiently long, the curvature has an ineluctable influence on the density profile and front speed. In comparison, the analytical solution is in agreement with the numerical solution.

  18. 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.

  19. Towards simple orbital-dependent density functionals for molecular dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Igor Ying; Richter, Patrick; Scheffler, Matthias

    2015-03-01

    Density functional theory (DFT) is one of the leading first-principles electronic-structure theories. However, molecular dissociation remains a challenge, because it requires a well-balanced description of the drastically different electronic structure at different bond lengths. One typical and well-documented case is the dissociation of both H2+ and H2, for which all popular DFT functionals fail. We start from the Bethe-Goldstone equation to propose a simple orbital-dependent correlation functional which generalizes the linear adiabatic connection approach. The resulting scheme is based on second-order perturbation theory (PT2), but includes the self-consistent coupling of electron-hole pairs, which ensures the correct H2 dissociation limit and gives a finite correlation energy for systems with a (near)-degenerate energy gap. This coupling PT2-like (CPT2) approximation delivers a significant improvement over all existing functionals for both H2 and H2+ dissociation. We will demonstrate the reason for this improvement analytically for H2 in a minimal basis.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Existence, uniqueness, and construction of the density-potential mapping in time-dependent density-functional theory.

    PubMed

    Ruggenthaler, Michael; Penz, Markus; van Leeuwen, Robert

    2015-05-27

    In this work we review the mapping from densities to potentials in quantum mechanics, which is the basic building block of time-dependent density-functional theory and the Kohn-Sham construction. We first present detailed conditions such that a mapping from potentials to densities is defined by solving the time-dependent Schrödinger equation. We specifically discuss intricacies connected with the unboundedness of the Hamiltonian and derive the local-force equation. This equation is then used to set up an iterative sequence that determines a potential that generates a specified density via time propagation of an initial state. This fixed-point procedure needs the invertibility of a certain Sturm-Liouville problem, which we discuss for different situations. Based on these considerations we then present a discussion of the famous Runge-Gross theorem which provides a density-potential mapping for time-analytic potentials. Further we give conditions such that the general fixed-point approach is well-defined and converges under certain assumptions. Then the application of such a fixed-point procedure to lattice Hamiltonians is discussed and the numerical realization of the density-potential mapping is shown. We conclude by presenting an extension of the density-potential mapping to include vector-potentials and photons.

  5. Approach of high density coal preparation method

    SciTech Connect

    Yang, Y.; Chen, Q.

    1996-12-31

    Density difference of aged anthracite coal of high density and discard is less than that of general coal and discard; conventional separation methods are difficult to be used. For the special coal, coal dry beneficiation technology with air-dense medium fluidized bed has obvious superiority over other separation methods.

  6. 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.

  7. Numerical Density-to-Potential Inversions in Time-dependent Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Jensen, Daniel; Inchaustegui, Jean Pierre; Wasserman, Adam

    2014-03-01

    Time-dependent Density Functional Theory (TDDFT) is a formally exact method for solving the quantum many-body problem. In Kohn-Sham TDDFT, a fictitious noninteracting system is defined that exactly reproduces the time-dependent density of the interacting system. The potential that determines this noninteracting system (the time-dependent Kohn-Sham potential) has been proven to exist under certain restrictions, but finding the exact Kohn-Sham potential for a given density remains challenging. We show that this ill-posed inverse problem requires some form of regularization to produce realistic Kohn-Sham potentials. We explore various forms of regularization and illustrate how they work on simple one-dimensional model systems. We also show how our method can be applied to problems with both particle-in-a-box and periodic boundary conditions subject to oscillating electric fields.

  8. 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

  9. Density dependence, spatial scale and patterning in sessile biota.

    PubMed

    Gascoigne, Joanna C; Beadman, Helen A; Saurel, Camille; Kaiser, Michel J

    2005-09-01

    Sessile biota can compete with or facilitate each other, and the interaction of facilitation and competition at different spatial scales is key to developing spatial patchiness and patterning. We examined density and scale dependence in a patterned, soft sediment mussel bed. We followed mussel growth and density at two spatial scales separated by four orders of magnitude. In summer, competition was important at both scales. In winter, there was net facilitation at the small scale with no evidence of density dependence at the large scale. The mechanism for facilitation is probably density dependent protection from wave dislodgement. Intraspecific interactions in soft sediment mussel beds thus vary both temporally and spatially. Our data support the idea that pattern formation in ecological systems arises from competition at large scales and facilitation at smaller scales, so far only shown in vegetation systems. The data, and a simple, heuristic model, also suggest that facilitative interactions in sessile biota are mediated by physical stress, and that interactions change in strength and sign along a spatial or temporal gradient of physical stress.

  10. 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

  11. 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.

  12. 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.

  13. Excitons in Time-Dependent Density-Functional Theory.

    PubMed

    Ullrich, Carsten A; Yang, Zeng-hui

    2016-01-01

    This chapter gives an overview of the description of the optical and dielectric properties of bulk insulators and semiconductors in time-dependent density-functional theory (TDDFT), with an emphasis on excitons. We review the linear-response formalism for periodic solids, discuss excitonic exchange-correlation kernels, calculate exciton binding energies for various materials, and compare the treatment of excitons with TDDFT and with the Bethe-Salpeter equation.

  14. Cycles, stochasticity and density dependence in pink salmon population dynamics

    PubMed Central

    Krkošek, Martin; Hilborn, Ray; Peterman, Randall M.; Quinn, Thomas P.

    2011-01-01

    Complex dynamics of animal populations often involve deterministic and stochastic components. A fascinating example is the variation in magnitude of 2-year cycles in abundances of pink salmon (Oncorhynchus gorbuscha) stocks along the North Pacific rim. Pink salmon have a 2-year anadromous and semelparous life cycle, resulting in odd- and even-year lineages that occupy the same habitats but are reproductively isolated in time. One lineage is often much more abundant than the other in a given river, and there are phase switches in dominance between odd- and even-year lines. In some regions, the weak line is absent and in others both lines are abundant. Our analysis of 33 stocks indicates that these patterns probably result from stochastic perturbations of damped oscillations owing to density-dependent mortality caused by interactions between lineages. Possible mechanisms are cannibalism, disease transmission, food depletion and habitat degradation by which one lineage affects the other, although no mechanism has been well-studied. Our results provide comprehensive empirical estimates of lagged density-dependent mortality in salmon populations and suggest that a combination of stochasticity and density dependence drives cyclical dynamics of pink salmon stocks. PMID:21147806

  15. Implementation Strategies for Orbital-dependent Density Functionals

    NASA Astrophysics Data System (ADS)

    Bento, Marsal E.; Vieira, Daniel

    2016-12-01

    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.

  16. Balancing selection shapes density-dependent foraging behaviour.

    PubMed

    Greene, Joshua S; Brown, Maximillian; Dobosiewicz, May; Ishida, Itzel G; Macosko, Evan Z; Zhang, Xinxing; Butcher, Rebecca A; Cline, Devin J; McGrath, Patrick T; Bargmann, Cornelia I

    2016-11-10

    The optimal foraging strategy in a given environment depends on the number of competing individuals and their behavioural strategies. Little is known about the genes and neural circuits that integrate social information into foraging decisions. Here we show that ascaroside pheromones, small glycolipids that signal population density, suppress exploratory foraging in Caenorhabditis elegans, and that heritable variation in this behaviour generates alternative foraging strategies. We find that natural C. elegans isolates differ in their sensitivity to the potent ascaroside icas#9 (IC-asc-C5). A quantitative trait locus (QTL) regulating icas#9 sensitivity includes srx-43, a G-protein-coupled icas#9 receptor that acts in the ASI class of sensory neurons to suppress exploration. Two ancient haplotypes associated with this QTL confer competitive growth advantages that depend on ascaroside secretion, its detection by srx-43 and the distribution of food. These results suggest that balancing selection at the srx-43 locus generates alternative density-dependent behaviours, fulfilling a prediction of foraging game theory.

  17. Exploration of a modified density dependence in the Skyrme functional

    SciTech Connect

    Erler, J.; Reinhard, P.-G.; Kluepfel, P.

    2010-10-15

    A variant of the basic Skyrme-Hartree-Fock functional is considered dealing with a new form of density dependence. It employs only integer powers and thus will allow a more sound basis for projection schemes (particle number, angular momentum). We optimize the new functional with exactly the same adjustment strategy as used in an earlier study with a standard Skyrme functional. This allows direct comparisons of the performance of the new functional relative to the standard one. We discuss various observables: bulk properties of finite nuclei, nuclear matter, giant resonances, superheavy elements, and energy systematics. The new functional performs at least as well as the standard one, but offers a wider range of applicability (e.g., for projection) and more flexibility in the regime of high densities.

  18. 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.

  19. Density dependence in an age-structured population of great tits: identifying the critical age classes.

    PubMed

    Gamelon, Marlène; Grøtan, Vidar; Engen, Steinar; Bjørkvoll, Eirin; Visser, Marcel E; Saether, Bernt-Erik

    2016-09-01

    Classical approaches for the analyses of density dependence assume that all the individuals in a population equally respond and equally contribute to density dependence. However, in age-structured populations, individuals of different ages may differ in their responses to changes in population size and how they contribute to density dependence affecting the growth rate of the whole population. Here we apply the concept of critical age classes, i.e., a specific scalar function that describes how one or a combination of several age classes affect the demographic rates negatively, in order to examine how total density dependence acting on the population growth rate depends on the age-specific population sizes. In a 38-yr dataset of an age-structured great tit (Parus major) population, we find that the age classes, including the youngest breeding females, were the critical age classes for density regulation. These age classes correspond to new breeders that attempt to take a territory and that have the strongest competitive effect on other breeding females. They strongly affected population growth rate and reduced recruitment and survival rates of all breeding females. We also show that depending on their age class, females may differently respond to varying density. In particular, the negative effect of the number of breeding females was stronger on recruitment rate of the youngest breeding females. These findings question the classical assumptions that all the individuals of a population can be treated as having an equal contribution to density regulation and that the effect of the number of individuals is age independent. Our results improve our understanding of density regulation in natural populations.

  20. 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.

  1. Stochastic Time-Dependent Current-Density Functional Theory

    NASA Astrophysics Data System (ADS)

    D'Agosta, Roberto

    2008-03-01

    Static and dynamical density functional methods have been applied with a certain degree of success to a variety of closed quantum mechanical systems, i.e., systems that can be described via a Hamiltonian dynamics. However, the relevance of open quantum systems - those coupled to external environments, e.g., baths or reservoirs - cannot be overestimated. To investigate open quantum systems with DFT methods we have introduced a new theory, we have named Stochastic Time-Dependent Current Density Functional theory (S-TDCDFT) [1]: starting from a suitable description of the system dynamics via a stochastic Schrödinger equation [2], we have proven that given an initial quantum state and the coupling between the system and the environment, there is a one-to-one correspondence between the ensemble-averaged current density and the external vector potential applied to the system.In this talk, I will introduce the stochastic formalism needed for the description of open quantum systems, discuss in details the theorem of Stochastic TD-CDFT, and provide few examples of its applicability like the dissipative dynamics of excited systems, quantum-measurement theory and other applications relevant to charge and energy transport in nanoscale systems.[1] M. Di Ventra and R. D'Agosta, Physical Review Letters 98, 226403 (2007)[2] N.G. van Kampen, Stochastic processes in Physics and Chemistry, (North Holland, 2001), 2nd ed.

  2. Development and application of a density dependent matrix ...

    EPA Pesticide Factsheets

    Ranging along the Atlantic coast from US Florida to the Maritime Provinces of Canada, the Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems. Matrix population models are useful tools for ecological risk assessment because they integrate effects across the life cycle, provide a linkage between endpoints observed in the individual and ecological risk to the population as a whole, and project outcomes for many generations in the future. We developed a density dependent matrix population model for Atlantic killifish by modifying a model developed for fathead minnow (Pimephales promelas) that has proved to be extremely useful, e.g. to incorporate data from laboratory studies and project effects of endocrine disrupting chemicals. We developed a size-structured model (as opposed to one that is based upon developmental stages or age class structure) so that we could readily incorporate output from a Dynamic Energy Budget (DEB) model, currently under development. Due to a lack of sufficient data to accurately define killifish responses to density dependence, we tested a number of scenarios realistic for other fish species in order to demonstrate the outcome of including this ecologically important factor. We applied the model using published data for killifish exposed to dioxin-like compounds, and compared our results to those using

  3. Subcycle dynamics of high-harmonic generation in valence-shell and virtual states of Ar atoms: A self-interaction-free time-dependent density-functional-theory approach

    NASA Astrophysics Data System (ADS)

    Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.

    2015-02-01

    We perform an ab initio all-electron study of the subcycle structure, dynamics, and spectra of high harmonic generation (HHG) processes of Ar atoms in the presence of extreme ultraviolet (XUV) attosecond pulses and near-infrared (NIR) laser fields by means of the self-interaction-free time-dependent density functional theory (TDDFT). The TDDFT equations are solved accurately and efficiently via the time-dependent generalized pseudospectral (TDGPS) method. We focus on the subcycle (with respect to NIR field) temporal behavior of the level shift of the excited energy levels and related dynamics of harmonic photon emission. We observe and identify the subcycle shifts in the harmonic emission spectrum as a function of the time delay between the XUV and NIR pulses. In the region where the two pulses overlap, the photon emission peaks have an oscillatory structure with a period of ˜1.3 fs, which is half of the NIR laser optical cycle. We present and analyze the harmonic emission spectra from 3 s n p0,3 p0n s ,3 p1n d1,3 p1n p1,3 p0n d0,3 p0n p0 , and 3 p0n s excited states and the 3 p04 p0- virtual state as functions of the time delay. In addition, we explore the subcycle a.c. Stark shift phenomenon in NIR fields and its influence on the harmonic emission process. Our analysis reveals several features of the subcycle HHG dynamics and spectra as well as a temporal energy level shift.

  4. 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.

  5. Subcycle dynamics of high-order-harmonic generation of He atoms excited by attosecond pulses and driven by near-infrared laser fields: A self-interaction-free time-dependent density-functional-theory approach

    NASA Astrophysics Data System (ADS)

    Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.

    2014-05-01

    In the framework of the self-interaction-free time-dependent density-functional theory, we have performed three-dimensional (3D) ab initio calculations of He atoms in near-infrared (NIR) laser fields subject to excitation by a single extreme ultraviolet (XUV) attosecond pulse (SAP). We have explored the dynamical behavior of the subcycle high harmonic generation (HHG) for transitions from the excited states to the ground state and found oscillation structures with respect to the time delay between the SAP and NIR fields. The oscillatory pattern in the photon emission spectra has a period of ˜1.3 fs which is half of the NIR laser optical cycle, similar to that recently measured in the experiments on transient absorption of He [M. Chini et al., Sci. Rep. 3, 1105 (2013), 10.1038/srep01105]. We present the photon emission spectra from 1s2p, 1s3p, 1s4p, 1s5p, and 1s6p excited states as functions of the time delay. We explore the subcycle Stark shift phenomenon in NIR fields and its influence on the photon emission process. Our analysis reveals several interesting features of the subcycle HHG dynamics and we identify the mechanisms responsible for the observed peak splitting in the photon emission spectra.

  6. 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.

  7. 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.

  8. Time-dependent density functional theory for many-electron systems interacting with cavity photons.

    PubMed

    Tokatly, I V

    2013-06-07

    Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles. We suggest possible approximations for the exchange-correlation potentials and discuss implications of this approach for the theory of open quantum systems. In particular we show that it naturally leads to time-dependent density functional theory for systems coupled to the Caldeira-Leggett bath.

  9. 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.

  10. Density dependence triggers runaway selection of reduced senescence.

    PubMed

    Seymour, Robert M; Doncaster, C Patrick

    2007-12-01

    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.

  11. Incorporating density dependence into the directed-dispersal hypothesis.

    PubMed

    Spiegel, Orr; Nathan, Ran

    2010-05-01

    The directed-dispersal (DrD) hypothesis, one of the main explanations for the adaptive value of seed dispersal, asserts that enhanced (nonrandom) arrival to favorable establishment sites is advantageous for plant fitness. However, as anticipated by the ideal free distribution theory, enhanced seed deposition may impair site suitability by increasing density-dependent mortality, thus negating the advantage postulated by the DrD hypothesis. Although the role of density effects is thoroughly discussed in the seed-dispersal literature, this DrD paradox remains largely overlooked. The paradox, however, may be particularly pronounced in animal-mediated dispersal systems, in which DrD is relatively common, because animals tend to generate local seed aggregations due to their nonrandom movements. To investigate possible solutions to the DrD paradox, we first introduce a simple analytical model that calculates the optimal DrD level at which seed arrival to favorable establishment sites yields maximal fitness gain in comparison to a null model of random arrival. This model predicts intermediate optimal DrD levels that correspond to various attributes of the plants, the dispersers, and the habitat. We then use a simulation model to explore the temporal dynamics of the invasion process of the DrD strategy in a randomly dispersed population, and the resistance of a DrD population against invasion of other dispersal strategies. This model demonstrates that some properties of the invasion process (e.g., mutant persistence ratio in the population and generations until initial establishment) are facilitated by high DrD levels, and not by intermediate levels as expected from the analytical model. These results highlight the need to revise the DrD hypothesis to include the countering effects of density-dependent mortality inherently imposed by enhanced arrival of seeds to specific sites. We illustrate how the revised hypothesis can elucidate previous results from empirical studies

  12. 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.

  13. 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.

  14. Density-dependent role of an invasive marsh grass, Phragmites australis, on ecosystem service provision

    PubMed Central

    Puckett, Brandon J.; Theuerkauf, Kathrynlynn W.; Theuerkauf, Ethan J.; Eggleston, David B.

    2017-01-01

    Invasive species can positively, neutrally, or negatively affect the provision of ecosystem services. The direction and magnitude of this effect can be a function of the invaders’ density and the service(s) of interest. We assessed the density-dependent effect of an invasive marsh grass, Phragmites australis, on three ecosystem services (plant diversity and community structure, shoreline stabilization, and carbon storage) in two oligohaline marshes within the North Carolina Coastal Reserve and National Estuarine Research Reserve System (NCNERR), USA. Plant species richness was equivalent among low, medium and high Phragmites density plots, and overall plant community composition did not vary significantly by Phragmites density. Shoreline change was most negative (landward retreat) where Phragmites density was highest (-0.40 ± 0.19 m yr-1 vs. -0.31 ± 0.10 for low density Phragmites) in the high energy marsh of Kitty Hawk Woods Reserve and most positive (soundward advance) where Phragmites density was highest (0.19 ± 0.05 m yr-1 vs. 0.12 ± 0.07 for low density Phragmites) in the lower energy marsh of Currituck Banks Reserve, although there was no significant effect of Phragmites density on shoreline change. In Currituck Banks, mean soil carbon content was approximately equivalent in cores extracted from low and high Phragmites density plots (23.23 ± 2.0 kg C m-3 vs. 22.81 ± 3.8). In Kitty Hawk Woods, mean soil carbon content was greater in low Phragmites density plots (36.63 ± 10.22 kg C m-3) than those with medium (13.99 ± 1.23 kg C m-3) or high density (21.61 ± 4.53 kg C m-3), but differences were not significant. These findings suggest an overall neutral density-dependent effect of Phragmites on three ecosystem services within two oligohaline marshes in different environmental settings within a protected reserve system. Moreover, the conceptual framework of this study can broadly inform an ecosystem services-based approach to invasive species management

  15. Density-dependent role of an invasive marsh grass, Phragmites australis, on ecosystem service provision.

    PubMed

    Theuerkauf, Seth J; Puckett, Brandon J; Theuerkauf, Kathrynlynn W; Theuerkauf, Ethan J; Eggleston, David B

    2017-01-01

    Invasive species can positively, neutrally, or negatively affect the provision of ecosystem services. The direction and magnitude of this effect can be a function of the invaders' density and the service(s) of interest. We assessed the density-dependent effect of an invasive marsh grass, Phragmites australis, on three ecosystem services (plant diversity and community structure, shoreline stabilization, and carbon storage) in two oligohaline marshes within the North Carolina Coastal Reserve and National Estuarine Research Reserve System (NCNERR), USA. Plant species richness was equivalent among low, medium and high Phragmites density plots, and overall plant community composition did not vary significantly by Phragmites density. Shoreline change was most negative (landward retreat) where Phragmites density was highest (-0.40 ± 0.19 m yr-1 vs. -0.31 ± 0.10 for low density Phragmites) in the high energy marsh of Kitty Hawk Woods Reserve and most positive (soundward advance) where Phragmites density was highest (0.19 ± 0.05 m yr-1 vs. 0.12 ± 0.07 for low density Phragmites) in the lower energy marsh of Currituck Banks Reserve, although there was no significant effect of Phragmites density on shoreline change. In Currituck Banks, mean soil carbon content was approximately equivalent in cores extracted from low and high Phragmites density plots (23.23 ± 2.0 kg C m-3 vs. 22.81 ± 3.8). In Kitty Hawk Woods, mean soil carbon content was greater in low Phragmites density plots (36.63 ± 10.22 kg C m-3) than those with medium (13.99 ± 1.23 kg C m-3) or high density (21.61 ± 4.53 kg C m-3), but differences were not significant. These findings suggest an overall neutral density-dependent effect of Phragmites on three ecosystem services within two oligohaline marshes in different environmental settings within a protected reserve system. Moreover, the conceptual framework of this study can broadly inform an ecosystem services-based approach to

  16. Time-dependent density functional theory quantum transport simulation in non-orthogonal basis.

    PubMed

    Kwok, Yan Ho; Xie, Hang; Yam, Chi Yung; Zheng, Xiao; Chen, Guan Hua

    2013-12-14

    Basing on the earlier works on the hierarchical equations of motion for quantum transport, we present in this paper a first principles scheme for time-dependent quantum transport by combining time-dependent density functional theory (TDDFT) and Keldysh's non-equilibrium Green's function formalism. This scheme is beyond the wide band limit approximation and is directly applicable to the case of non-orthogonal basis without the need of basis transformation. The overlap between the basis in the lead and the device region is treated properly by including it in the self-energy and it can be shown that this approach is equivalent to a lead-device orthogonalization. This scheme has been implemented at both TDDFT and density functional tight-binding level. Simulation results are presented to demonstrate our method and comparison with wide band limit approximation is made. Finally, the sparsity of the matrices and computational complexity of this method are analyzed.

  17. 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.

  18. 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.

  19. 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.

  20. High-harmonic spectra from time-dependent two-particle reduced-density-matrix theory

    NASA Astrophysics Data System (ADS)

    Lackner, Fabian; Březinová, Iva; Sato, Takeshi; Ishikawa, Kenichi L.; Burgdörfer, Joachim

    2017-03-01

    The ab initio description of the nonlinear response of many-electron systems to strong-laser fields remains a major challenge. In order to address larger systems, alternative methods need to be developed that bypass the exponential scaling with particle number inherent to conventional wave-function-based approaches. In this paper we present a fully three-dimensional implementation of the time-dependent two-particle reduced-density-matrix (TD-2RDM) method for many-electron atoms. We benchmark this approach by a comparison with multiconfigurational time-dependent Hartree-Fock results for the harmonic spectra of beryllium and neon. We show that the TD-2RDM is very well suited to describe the nonlinear atomic response and to reveal the influence of electron-correlation effects.

  1. Density-dependent vulnerability of forest ecosystems to drought

    USGS Publications Warehouse

    Bottero, Alessandra; D'Amato, Anthony W.; Palik, Brian J.; Bradford, John B.; Fraver, Shawn; Battaglia, Mike A.; Asherin, Lance A.

    2017-01-01

    1. Climate models predict increasing drought intensity and frequency for many regions, which may have negative consequences for tree recruitment, growth and mortality, as well as forest ecosystem services. Furthermore, practical strategies for minimizing vulnerability to drought are limited. Tree population density, a metric of tree abundance in a given area, is a primary driver of competitive intensity among trees, which influences tree growth and mortality. Manipulating tree population density may be a mechanism for moderating drought-induced stress and growth reductions, although the relationship between tree population density and tree drought vulnerability remains poorly quantified, especially across climatic gradients.2. In this study, we examined three long-term forest ecosystem experiments in two widely distributed North American pine species, ponderosa pine Pinus ponderosa (Lawson & C. Lawson) and red pine Pinus resinosa (Aiton), to better elucidate the relationship between tree population density, growth and drought. These experiments span a broad latitude and aridity range and include tree population density treatments that have been purposefully maintained for several decades. We investigated how tree population density influenced resistance (growth during drought) and resilience (growth after drought compared to pre-drought growth) of stand-level growth during and after documented drought events.3. Our results show that relative tree population density was negatively related to drought resistance and resilience, indicating that trees growing at lower densities were less vulnerable to drought. This result was apparent in all three forest ecosystems, and was consistent across species, stand age and drought intensity.4. Synthesis and applications. Our results highlighted that managing pine forest ecosystems at low tree population density represents a promising adaptive strategy for reducing the adverse impacts of drought on forest growth in coming decades

  2. Inoculation-density-dependent responses and pathway shifts in Saccharomyces cerevisiae.

    PubMed

    Cheng, Jing-Sheng; Ding, Ming-Zhu; Tian, Hong-Chi; Yuan, Ying-Jin

    2009-10-01

    The cell-density-dependent responses of Saccharomyces cerevisiae to inoculation sizes were explored by a proteomic approach. According to their gene ontology, 100 protein spots with differential expression, corresponding to 67 proteins, were identified and classed into 17 different functional groups. Upregulation of eight heat shock, oxidative response and amino acid biosynthesis-related proteins (e.g. Hsp78p, Ssa1p, Hsp60p, Ctt1p, Sod1p, Ahp1p, Met6p and Met17p), which may jointly maintain the cell redox homeostasis, was dependant on inoculation density. Significant increases in the levels of five proteins involved in glycolysis and alcohol biosynthesis pathways (e.g. Glk1p, Fba1p, Eno1p, Pdc1p and Adh1p) might play critical roles in improving ethanol productivity of the fermentation process and shortening the fermentation time when inoculation sizes were increased. Cell-density-dependent glycolytic variations of proteins involved in trehalose, glycerol biosynthesis and pentose phosphate pathway revealed shifts among metabolic pathways during fermentation with different inoculation sizes. Upregulation of three signal transduction proteins (Bmh1p, Bmh2p and Fpr1p) indicated that adequate cell-cell contacts improved cellular communication at high inoculation sizes. These findings provide insights into yeast responses to inoculation size and optimizing the direct inoculation of active dry yeast fermentation, so as to improve the ethanol production.

  3. 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

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

    PubMed

    Petrenko, Taras; Kossmann, Simone; Neese, Frank

    2011-02-07

    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

  5. Frequency Dependence of the Exact Exchange-Correlation Kernel of Time-Dependent Density-Functional Theory

    NASA Astrophysics Data System (ADS)

    Thiele, M.; Kümmel, S.

    2014-02-01

    We present a scheme for numerically reconstructing the exact and the Kohn-Sham time-dependent density-density response functions, and from their inverse the numerical representation of the exact frequency-dependent exchange-correlation kernel fxc of time-dependent Kohn-Sham density-functional theory. We investigate the exact fxc in detail for a system that is known to show strong memory effects. The reconstructed kernel fulfills the appropriate sum rule. Using it in linear response calculations, we show how the exact fxc, due to its frequency dependence, yields the exact excitation energies, including the ones of double excitation character.

  6. Excitons in solids with non-empirical hybrid time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Ullrich, Carsten; Yang, Zeng-Hui; Sottile, Francesco

    2015-03-01

    The Bethe-Salpeter equation (BSE) accurately describes the optical properties of solids, but is computationally expensive. Time-dependent density-functional theory (TDDFT) is more efficient, but standard functionals do not produce excitons in extended systems. We present a new, non-empirical hybrid TDDFT approach whose computational cost is much less than BSE, while the accuracy for both bound excitons and the continuum spectra is comparable to that of the BSE. Good performance is observed for both small-gap semiconductors and large-gap insulators. Work supported by NSF Grant DMR-1408904.

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

    PubMed

    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.

  8. 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.

  9. Fibroblast PER2 Circadian Rhythmicity Depends on Cell Density

    PubMed Central

    Noguchi, Takako; Wang, Lexie L.; Welsh, David K.

    2013-01-01

    Like neurons in the suprachiasmatic nucleus (SCN), the master circadian pacemaker in the brain, single fibroblasts can function as independent oscillators. In the SCN, synaptic and paracrine signaling among cells creates a robust, synchronized circadian oscillation, whereas there is no evidence for such integration in fibroblast cultures. However, interactions among single-cell fibroblast oscillators cannot be completely excluded, because fibroblasts were not isolated in previous work. In this study, we tested the autonomy of fibroblasts as single-cell circadian oscillators in high and low density culture, by single-cell imaging of cells from PER2::LUC circadian reporter mice. We found greatly reduced PER2::LUC rhythmicity in low density cultures, which could result from lack of either constitutive or rhythmic paracrine signals from neighboring fibroblasts. To discriminate between these two possibilities, we mixed PER2::LUC wild type (WT) cells with non-luminescent, non-rhythmic Bmal1−/− cells, so that density of rhythmic cells was low but overall cell density remained high. In this condition, WT cells showed clear rhythmicity similar to high density cultures. We also mixed PER2::LUC WT cells with non-luminescent, long period Cry2−/− cells. In this condition, WT cells showed a period no different from cells cultured with rhythmic WT cells or non-rhythmic Bmal1−/− cells. In previous work, we found that low K+ suppresses fibroblast rhythmicity, and we and others have found that either low K+ or low Ca2+ suppresses SCN rhythmicity. Therefore, we attempted to rescue rhythmicity of low density fibroblasts with high K+ (21 mM), high Ca2+ (3.6 mM), or conditioned medium. Conditioned medium from high density fibroblast cultures rescued rhythmicity of low density cultures, whereas high K+ or Ca2+ medium did not consistently rescue rhythmicity. These data suggest that fibroblasts require paracrine signals from adjacent cells for normal expression of rhythmicity

  10. 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

  11. 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...

  12. Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach.

    PubMed

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

    2017-02-28

    Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

  13. Spectral densities for Frenkel exciton dynamics in molecular crystals: A TD-DFTB approach

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    Effects of thermal fluctuations on the electronic excitation energies and intermonomeric Coulomb couplings are investigated for a perylene-tetracarboxylic-diimide crystal. To this end, time dependent density functional theory based tight binding (TD-DFTB) in the linear response formulation is used in combination with electronic ground state classical molecular dynamics. As a result, a parametrized Frenkel exciton Hamiltonian is obtained, with the effect of exciton-vibrational coupling being described by spectral densities. Employing dynamically defined normal modes, these spectral densities are analyzed in great detail, thus providing insight into the effect of specific intramolecular motions on excitation energies and Coulomb couplings. This distinguishes the present method from approaches using fixed transition densities. The efficiency by which intramolecular contributions to the spectral density can be calculated is a clear advantage of this method as compared with standard TD-DFT.

  14. The dependence of graphene Raman D-band on carrier density.

    PubMed

    Liu, Junku; Li, Qunqing; Zou, Yuan; Qian, Qingkai; Jin, Yuanhao; Li, Guanhong; Jiang, Kaili; Fan, Shoushan

    2013-01-01

    Raman spectroscopy has been an integral part of graphene research and can provide information about graphene structure, electronic characteristics, and electron-phonon interactions. In this study, the characteristics of the graphene Raman D-band, which vary with carrier density, are studied in detail, including the frequency, full width half-maximum, and intensity. We find the Raman D-band frequency increases for hole doping and decreases for electron doping. The Raman D-band intensity increases when the Fermi level approaches half of the excitation energy and is higher in the case of electron doping than that of hole doping. These variations can be explained by electron-phonon interaction theory and quantum interference between different Raman pathways in graphene. The intensity ratio of Raman D- and G-band, which is important for defects characterization in graphene, shows a strong dependence on carrier density.

  15. Localized operator partitioning method for electronic excitation energies in the time-dependent density functional formalism.

    PubMed

    Nagesh, Jayashree; Frisch, Michael J; Brumer, Paul; Izmaylov, Artur F

    2016-12-28

    We extend the localized operator partitioning method (LOPM) [J. Nagesh, A. F. Izmaylov, and P. Brumer, J. Chem. Phys. 142, 084114 (2015)] to the time-dependent density functional theory framework to partition molecular electronic energies of excited states in a rigorous manner. A molecular fragment is defined as a collection of atoms using Becke's atomic partitioning. A numerically efficient scheme for evaluating the fragment excitation energy is derived employing a resolution of the identity to preserve standard one- and two-electron integrals in the final expressions. The utility of this partitioning approach is demonstrated by examining several excited states of two bichromophoric compounds: 9-((1- naphthyl)- methyl)- anthracene and 4-((2- naphthyl)- methyl)- benzaldehyde. The LOPM is found to provide nontrivial insights into the nature of electronic energy localization that is not accessible using a simple density difference analysis.

  16. 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.

  17. Excursion behaviour of female roe deer may depend on density.

    PubMed

    Bocci, A; Aiello, V; Lovari, S

    2013-07-01

    The excursion behaviour of roe does was studied for two years in a low density population (ca. 6.5 ind./100 ha), in an Apennine-continental forest of Southern Italy, through satellite radiotracking. During the rutting period, our radiotagged does (N=6) moved well outside their summer ranges, with an average exploration area eight times greater than summer ranges. The median duration of excursions was 51 h (range: 10-99 h). One female stayed away for a total of 11 days. In order further to understand this behaviour, we reviewed all studies (N=6) dealing with excursion behaviour of roe does and carried out in areas where population density was assessed through the same method (i.e. drive counts). Out of five ecological parameters included in the analysis, excursion behaviour of roe does was found significantly and negatively associated only to population density: when density was low, the proportion of roaming does increased, probably because of the lower availability of "free" bucks during the short time of female oestrous.

  18. 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

  19. 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.

  20. 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.

  1. Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.

    PubMed

    Rom, Naomi; Zybin, Sergey V; van Duin, Adri C T; Goddard, William A; Zeiri, Yehuda; Katz, Gil; Kosloff, Ronnie

    2011-09-15

    The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (∼30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods.

  2. Extended density-dependent mortality in mature conifer forests: causes and implications for ecosystem management.

    PubMed

    Gendreau-Berthiaume, Benoit; Macdonald, S Ellen; Stadt, J John

    2016-07-01

    Understanding processes driving mortality in forests is important for comprehension of natural stand dynamics and for informing natural disturbance-based ecosystem management. There has been considerable study of mortality in forests during the self-thinning phase but we know much less about processes driving mortality in stands at later successional stages. We addressed this through study of five 1-ha spatially explicit permanent plots in mature (111-186 yr old in 2012) Pinus contorta stands in the Canadian Rocky Mountains using data from repeated measurements over a 45-yr period, dendrochronological information, and point pattern analysis. We tested the hypothesis that these stands had completed the self-thinning/density-dependent mortality stage of succession. Contrary to our expectations, the self-thinning phase can persist for more than 140 yr following stand establishment. Our findings suggest this was attributable to prolonged post-fire establishment periods due to surface fires in three of the plots while in the other two plots moist conditions and slow growth most likely delayed the onset of competition. Several pieces of evidence indicated the importance of density-dependent mortality in these stands over the study period: (1) The diameter distribution of individuals changed from initially right-skewed toward normality as a result of mortality of smaller-diameter stems. (2) Individuals of lower canopy positions were proportionally more affected by mortality. (3) When compared to the pre-mortality pattern, surviving stems in all stands had an increasingly uniform spatial distribution. In two of the plots, recent windthrow and/or ingrowth initially hindered our ability to detect density-dependent mortality but our dendrochronological sampling and permanent plot data allowed us to untangle the different processes at play; in doing so we demonstrate for the first time how density-independent processes can mask underlying density-dependent mortality

  3. 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.

  4. Invasion rate of deer ked depends on spatiotemporal variation in host density.

    PubMed

    Meier, C M; Bonte, D; Kaitala, A; Ovaskainen, O

    2014-06-01

    Invasive parasites are of great global concern. Understanding the factors influencing the spread of invading pest species is a first step in developing effective countermeasures. Growing empirical evidence suggests that spread rates are essentially influenced by spatiotemporal dynamics of host-parasite interactions, yet approaches modelling spread rate have typically assumed static environmental conditions. We analysed invasion history of the deer ked (Lipoptena cervi) in Finland with a diffusion-reaction model, which assumed either the movement rate, the population growth rate, or both rates may depend on spatial and temporal distribution of moose (Alces alces), the main host of deer ked. We fitted the model to the data in a Bayesian framework, and used the Bayesian information criterion to show that accounting for the variation in local moose density improved the model's ability to describe the pattern of the invasion. The highest ranked model predicted higher movement rate and growth rate of deer ked with increasing moose density. Our results suggest that the historic increase in host density has facilitated the spread of the deer ked. Our approach illustrates how information about the ecology of an invasive species can be extracted from the spatial pattern of spread even with rather limited data.

  5. Density dependent polarized secretion of a prostatic epithelial cell line.

    PubMed

    Djakiew, D; Pflug, B; Delsite, R; Lynch, J H; Onoda, M

    1992-01-01

    The polarized secretions (apical/basal) of newly synthesized total protein and proteases from prostatic epithelial sheets of PA-III cells grown in dual compartment chambers were investigated at various cell densities and culture conditions. PA-III cells grown in a serum free defined medium (SFDM) form morphologically polarized monolayers of epithelial cells. These cells secreted their 35S-methionine labeled total protein in a predominantly apical direction (apical/basal ratio, 4-8 fold), with a lesser proportion of protein secreted apically at lower cell densities of the PA-III cell monolayer. PA-III cells grown in 5% fetal calf serum (FCS) are morphologically squamous, comparable to the anaplastic phenotype, and exhibited an inversion of polarized total protein secretion (apical/basal ratio, 0.4-0.9 fold), with an increased proportion of total protein secreted in a basal direction at lower cell densities. Since the culture of PA-III cells in FCS may approximate the anaplastic phenotype we investigated the polarized secretion of proteases from these cells at various cell densities, and compared them with the secretory pattern of protease secretion from polarized PA-III cells cultured in SFDM. At lower cell densities of the PA-III cells grown in FCS the polarity of protease secretion was inverted such that metalloproteinases, tissue type plasminogen activator, and a 72 kD gelatinase were secreted in a predominantly basal direction, as well as urokinase and a gelatinase of 26 kD that were secreted more or less equally into the apical and basal compartments of the chambers. On the other hand, for cultures of PA-III cells grown in SFDM the aforementioned proteases exhibited predominantly an apically directed polarity of secretion. These results suggest that the anaplastic phenotype characterized by a loss of polarized structure may also be characterized by a functional loss or inversion of polarized secretion. The consequences of such a loss or inversion of polarized

  6. Density-dependent dispersal and relative dispersal affect the stability of predator-prey metacommunities.

    PubMed

    Hauzy, Céline; Gauduchon, Mathias; Hulot, Florence D; Loreau, Michel

    2010-10-07

    Although density-dependent dispersal and relative dispersal (the difference in dispersal rates between species) have been documented in natural systems, their effects on the stability of metacommunities are poorly understood. Here we investigate the effects of intra- and interspecific density-dependent dispersal on the regional stability in a predator-prey metacommunity model. We show that, when the dynamics of the populations reach equilibrium, the stability of the metacommunity is not affected by density-dependent dispersal. However, the regional stability, measured as the regional variability or the persistence, can be modified by density-dependent dispersal when local populations fluctuate over time. Moreover these effects depend on the relative dispersal of the predator and the prey. Regional stability is modified through changes in spatial synchrony. Interspecific density-dependent dispersal always desynchronizses local dynamics, whereas intraspecific density-dependent dispersal may either synchronize or desynchronize it depending on dispersal rates. Moreover, intra- and interspecific density-dependent dispersal strengthen the top-down control of the prey by the predator at intermediate dispersal rates. As a consequence the regional stability of the metacommunity is increased at intermediate dispersal rates. Our results show that density-dependent dispersal and relative dispersal of species are keys to understanding the response of ecosystems to fragmentation.

  7. Time-dependent Liouville density functional theory for laser-induced ultrafast demagnetization in ferromagnets

    NASA Astrophysics Data System (ADS)

    Zhang, Guoping; Bai, Yihua; George, Thomas F.

    Abstract: The traditional time-dependent density functional theory is very powerful to simulate the dynamic process, but is very time consuming. When it was first used to understand laser-induced ultrafast demagnetization in ferromagnets, the results were disappointing, with the laser amplitude at least three orders of magnitude larger than the experimental one to achieve the similar spin reduction. We develop a new theory within the density functional theory (DFT) for laser-induced ultrafast demagnetization in ferromagnets. We first solve the Liouville equation in the time domain and then feed the excited state density into the DFT code, so the dynamics proceeds on the excited and constraint potential surface. We test this for several magnetic systems and find a significantly larger demagnetization than the static approach, but is still smaller than the experimental finding. Both the local density approximation and the generalized gradient approximation fail. Our finding strongly suggests that a new functional must be developed. As a first test, we introduce a spin power scaling method. Some primitive results will be presented. This work was solely supported by the U.S. Department of Energy under Contract No. DE-FG02-06ER46304. The research used resources of the National Energy Research Scientific Computing Center.

  8. Validation of density-functional versus density-functional+U approaches for oxide ultrathin films

    NASA Astrophysics Data System (ADS)

    Barcaro, Giovanni; Thomas, Iorwerth Owain; Fortunelli, Alessandro

    2010-03-01

    A comparison between available experimental information and the predictions of density-functional and density-functional+U approaches is presented for oxide ultrathin films grown on single-crystal metal surfaces. Prototypical examples of monolayer phases of an ionic oxide (ZnO), a late transition metal oxide (NiO), and an early transition metal oxide (TiO2) are considered. The aim is to validate the theoretical approaches, focusing on the prediction of structural features and the reproduction of scanning tunneling microscopy images, rationalized in terms of the local density of states of the systems. It is found that it is possible to reasonably estimate the optimal lattice constant of ultrathin supported films and that the inclusion of the Hubbard U term appreciably improves the accuracy of theoretical predictions, especially in the case of nonpolar ultrathin phases of a transition metal oxide. Moreover, the optimal value of U for the oxide layer at the interface with the metal support is found to differ from that appropriate for the bulk oxide, as a consequence of the intermixing of oxide and support electronic states and screening effects.

  9. Charge density-dependent strength of hydration and biological structure.

    PubMed Central

    Collins, K D

    1997-01-01

    Small ions of high charge density (kosmotropes) bind water molecules strongly, whereas large monovalent ions of low charge density (chaotropes) bind water molecules weakly relative to the strength of water-water interactions in bulk solution. The standard heat of solution of a crystalline alkali halide is shown here to be negative (exothermic) only when one ion is a kosmotrope and the ion of opposite charge is a chaotrope; this standard heat of solution is known to become proportionally more positive as the difference between the absolute heats of hydration of the corresponding gaseous anion and cation decreases. This suggests that inner sphere ion pairs are preferentially formed between oppositely charged ions with matching absolute enthalpies of hydration, and that biological organization arises from the noncovalent association of moieties with matching absolute free energies of solution, except where free energy is expended to keep them apart. The major intracellular anions (phosphates and carboxylates) are kosmotropes, whereas the major intracellular monovalent cations (K+; arg, his, and lys side chains) are chaotropes; together they form highly soluble, solvent-separated ion pairs that keep the contents of the cell in solution. PMID:8994593

  10. 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.

  11. 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.

  12. Electronic density of states in sequence dependent DNA molecules

    NASA Astrophysics Data System (ADS)

    de Oliveira, B. P. W.; Albuquerque, E. L.; Vasconcelos, M. S.

    2006-09-01

    We report in this work a numerical study of the electronic density of states (DOS) in π-stacked arrays of DNA single-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T, forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Both structures are constructed starting from a G nucleotide as seed and following their respective inflation rules. Our theoretical method uses Dyson's equation together with a transfer-matrix treatment, within an electronic tight-binding Hamiltonian model, suitable to describe the DNA segments modelled by the quasiperiodic chains. We compared the DOS spectra found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22, with a remarkable concordance, as far as the RS structure is concerned. The electronic spectrum shows several peaks, corresponding to localized states, as well as a striking self-similar aspect.

  13. 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

  14. 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.

  15. Effects of bronchomotor tone and gas density on time dependence of forced expiratory vital capacity maneuver.

    PubMed

    D'Angelo, E; Milic-Emili, J; Marazzini, L

    1996-11-01

    It has been shown that in normal subjects and chronic obstructive pulmonary disease (COPD) patients the maximal expiratory flows and FEV1 are significantly higher if the FVC maneuver is preceded by a rapid inspiration without an end-inspiratory pause (maneuver 1) compared with a slow inspiration with an end-inspiratory pause of approximately 5 s (maneuver 2). This time dependency of FVC was attributed primarily to loss of lung recoil (stress relaxation) during breath-holding at TLC, in association with time constant inequality within the lungs, and changes in bronchomotor tone. To examine the role of bronchomotor tone on time dependency of FVC, 11 COPD and 10 asthmatic patients performed FVC maneuvers 1 and 2 before and after administration of a bronchodilator drug (salbutamol). In addition, using the same approach, the effects of changing airway resistance per se were assessed in another group of 10 COPD patients and 10 normal subjects, while breathing air and after equilibration with 80% helium in oxygen. Main findings were: peak expiratory flow (PEF), FEV1, and maximal midexpiratory flow rate (MMF) were significantly larger with maneuver 1 than 2; after salbutamol administration and during helium-oxygen breathing, all indices increased significantly with both maneuvers but the relative differences between maneuvers 1 and 2 were unchanged. We conclude that time dependency of maximal expiratory flow-volume (MEFV) curves, as indexed by PEF, FEV1, and MMF, is largely independent of bronchomotor tone and gas density, and probably reflects mainly stress relaxation of the respiratory tissues. The relevance of time dependency of FVC maneuver in the assessment of bronchodilator response and density dependence is discussed.

  16. 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.

  17. 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.

  18. 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.

  19. Kinetic modeling of rhamnolipid production by Pseudomonas aeruginosa PAO1 including cell density-dependent regulation.

    PubMed

    Henkel, Marius; Schmidberger, Anke; Vogelbacher, Markus; Kühnert, Christian; Beuker, Janina; Bernard, Thomas; Schwartz, Thomas; Syldatk, Christoph; Hausmann, Rudolf

    2014-08-01

    The production of rhamnolipid biosurfactants by Pseudomonas aeruginosa is under complex control of a quorum sensing-dependent regulatory network. Due to a lack of understanding of the kinetics applicable to the process and relevant interrelations of variables, current processes for rhamnolipid production are based on heuristic approaches. To systematically establish a knowledge-based process for rhamnolipid production, a deeper understanding of the time-course and coupling of process variables is required. By combining reaction kinetics, stoichiometry, and experimental data, a process model for rhamnolipid production with P. aeruginosa PAO1 on sunflower oil was developed as a system of coupled ordinary differential equations (ODEs). In addition, cell density-based quorum sensing dynamics were included in the model. The model comprises a total of 36 parameters, 14 of which are yield coefficients and 7 of which are substrate affinity and inhibition constants. Of all 36 parameters, 30 were derived from dedicated experimental results, literature, and databases and 6 of them were used as fitting parameters. The model is able to describe data on biomass growth, substrates, and products obtained from a reference batch process and other validation scenarios. The model presented describes the time-course and interrelation of biomass, relevant substrates, and products on a process level while including a kinetic representation of cell density-dependent regulatory mechanisms.

  20. 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.

  1. 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})

  2. X-ray absorption spectroscopy of titanium oxide by time dependent density functional calculations.

    PubMed

    Fronzoni, G; De Francesco, R; Stener, M; Causà, M

    2006-05-25

    The potentiality of the time dependent density functional theory (TDDFT) for the description of core excitation spectra (XAS) in transition metal oxides is analyzed, considering the rutile form of TiO(2) as a test case. Cluster models are adopted to mimic the bulk, embedded within an array of point charges to simulate the Madelung potential. All of the edges, titanium and oxygen K and titanium L edges, are considered, and the TDDFT results are compared with the experimental data in order to assess the performance of the theoretical approach in dealing with this complex class of compounds. Satisfactory results have been obtained for the Ti and O K edges, while in the case of the Ti L edge some discrepancies with the experiment are still present. The configuration mixing explicitly included in the TDDFT model strongly influences the distribution of the 2p metal oscillator strength. The origin of the spectral features is investigated with the help of the partial density of the virtual states (PDOS) calculated for each core hole considered, which can be qualitatively compared with the theoretical spectra calculated in the Kohn-Sham one-electron approach.

  3. 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.

  4. Liquid water simulations with the density fragment interaction approach.

    PubMed

    Hu, Xiangqian; Jin, Yingdi; Zeng, Xiancheng; Hu, Hao; Yang, Weitao

    2012-06-07

    We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve the efficiency of the DFI approach and thus enable the calculations for large molecules: the electrostatic interactions between fragments are computed efficiently by means of polarizable electrostatic-potential-fitted atomic charges; and frozen fragment pseudopotentials, similar to the effective fragment potentials that can be fitted from interactions between small molecules, are employed to take into account the Pauli repulsion effect among fragments. Our reformulated and parallelized DFI method demonstrates excellent parallel performance based on the benchmarks for the system of 256 water molecules. Molecular dynamics simulations for the structural properties of liquid water also show a qualitatively good agreement with experimental measurements including the heat capacity, binding energy per water molecule, and the radial distribution functions of atomic pairs of O-O, O-H, and H-H. With this approach, large-scale quantum mechanical simulations for water and other liquids become feasible.

  5. Negative density-dependent emigration of males in an increasing red deer population.

    PubMed

    Loe, Leif Egil; Mysterud, Atle; Veiberg, Vebjørn; Langvatn, Rolf

    2009-07-22

    In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deer Cervus elaphus marked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (37 km) than at low density in 1977 (26 km), possibly caused by increasing saturation of deer in areas surrounding the marking sites. Our study highlights that pattern of density dependence in dispersal rates may differ markedly between sexes in highly polygynous species. Contrasting patterns reported in small-scale studies are suggestive that spatial scale of density variation may affect the pattern of temporal density dependence in emigration rates and distances.

  6. 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.

  7. Disentangling density-dependent dynamics using full annual cycle models and Bayesian model weight updating

    USGS Publications Warehouse

    Robinson, Orin J.; McGowan, Conor; Devers, Patrick K.

    2017-01-01

    Density dependence regulates populations of many species across all taxonomic groups. Understanding density dependence is vital for predicting the effects of climate, habitat loss and/or management actions on wild populations. Migratory species likely experience seasonal changes in the relative influence of density dependence on population processes such as survival and recruitment throughout the annual cycle. These effects must be accounted for when characterizing migratory populations via population models.To evaluate effects of density on seasonal survival and recruitment of a migratory species, we used an existing full annual cycle model framework for American black ducks Anas rubripes, and tested different density effects (including no effects) on survival and recruitment. We then used a Bayesian model weight updating routine to determine which population model best fit observed breeding population survey data between 1990 and 2014.The models that best fit the survey data suggested that survival and recruitment were affected by density dependence and that density effects were stronger on adult survival during the breeding season than during the non-breeding season.Analysis also suggests that regulation of survival and recruitment by density varied over time. Our results showed that different characterizations of density regulations changed every 8–12 years (three times in the 25-year period) for our population.Synthesis and applications. Using a full annual cycle, modelling framework and model weighting routine will be helpful in evaluating density dependence for migratory species in both the short and long term. We used this method to disentangle the seasonal effects of density on the continental American black duck population which will allow managers to better evaluate the effects of habitat loss and potential habitat management actions throughout the annual cycle. The method here may allow researchers to hone in on the proper form and/or strength of

  8. 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.

  9. Time-dependent density functional theory Ehrenfest dynamics: collisions between atomic oxygen and graphite clusters.

    PubMed

    Isborn, Christine M; Li, Xiaosong; Tully, John C

    2007-04-07

    An ab initio direct Ehrenfest dynamics method with time-dependent density functional theory is introduced and applied to collisions of 5 eV oxygen atoms and ions with graphite clusters. Collisions at three different sites are simulated. Kinetic energy transfer from the atomic oxygen to graphite local vibrations is observed and electron-nuclear coupling resulting in electronic excitation within the graphite surface as well as alteration of the atomic charge is first reported in this paper. The three oxygen species studied, O(3P), O-(2P), and O+(4S), deposit different amounts of energy to the surface, with the highest degree of damage to the pi conjugation of the cluster produced by the atomic oxygen cation. Memory of the initial charge state is not lost as the atom approaches, in contrast to the usual assumption.

  10. Counterintuitive density-dependent growth in a long-lived vertebrate after removal of nest predators.

    PubMed

    Spencer, Ricky-John; Janzen, Fredric J; Thompson, Michael B

    2006-12-01

    Examining the phenotypic and genetic underpinnings of life-history variation in long-lived organisms is central to the study of life-history evolution. Juvenile growth and survival are often density dependent in reptiles, and theory predicts the evolution of slow growth in response to low resources (resource-limiting hypothesis), such as under densely populated conditions. However, rapid growth is predicted when exceeding some critical body size reduces the risk of mortality (mortality hypothesis). Here we present results of paired, large-scale, five-year field experiments to identify causes of variation in individual growth and survival rates of an Australian turtle (Emydura macquarii) prior to maturity. To distinguish between these competing hypotheses, we reduced nest predators in two populations and retained a control population to create variation in juvenile density by altering recruitment levels. We also conducted a complementary split-clutch field-transplant experiment to explore the impact of incubation temperature (25 degrees or 30 degrees C), nest predator level (low or high), and clutch size on juvenile growth and survival. Juveniles in high-recruitment (predator removal) populations were not resource limited, growing more rapidly than young turtles in the control populations. Our experiments also revealed a remarkably long-term impact of the thermal conditions experienced during embryonic development on growth of turtles prior to maturity. Moreover, this thermal effect was manifested in turtles approaching maturity, rather than in turtles closer to hatching, and was dependent on population density in the post-hatching rearing environment. This apparent phenotypic plasticity in growth complements our observation of a strong, positive genetic correlation between individual body size in the experimental and control populations over the first five years of life (rG - +0.77). Thus, these Australian pleurodiran turtles have the impressive capacity to

  11. 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.

  12. 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.

  13. Density-dependent population dynamics in larvae of the dragonfly Pachydiplax longipennis: a field experiment.

    PubMed

    Van Buskirk, J

    1987-05-01

    Several features of dragonfly population biology suggest that population regulation occurs in the larval stage. This study was designed to determine if density-dependent interactions among larval odonates can affect survival, growth and emergence. First-instar larvae of the dragonfly Pachydiplax longipennis were raised in outdoor experimental ponds at initial densities of 38, 152, and 608 larvae · m(-2), under two levels of food availability. Food availability was supplemented in half the pools by volumetric addition of zooplankton every other day. Pools in the low food treatment did not receive the zooplankton supplement.There was a strong negative effect of density on the mean growth rate of survivors, which included both emerging tenerals and individuals overwintering in the larval stage. A higher proportion emerged from low density than high density pools. Metamorphs from high density populations were smaller and emerged slightly later than those from low density, but the absolute number of metamorphs did not differ significantly among density treatments. Food supplementation significantly increased the proportion of overwintering larvae. There were no significant food-by-density interactions, indicating that food and density acted independently on larval population dynamics. Density-dependent mechanisms can clearly contribute to odonate population regulation, especially by controlling the number of larvae which emerge and the average age at reproduction. Population-level responses to density may be a result of interference among larvae.

  14. 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

  15. Remarks on the use of projected densities in the density-dependent part of Skyrme or Gogny functionals

    NASA Astrophysics Data System (ADS)

    Robledo, L. M.

    2010-06-01

    I discuss the inadequacy of the 'projected density' prescription to be used in density-dependent forces/functionals when calculations beyond mean field are pursued. The case of calculations aimed at the symmetry restoration of mean fields obtained with effective realistic forces of the Skyrme or Gogny type is considered in detail. It is shown that, at least for the restoration of spatial symmetries like rotations, translations or parity, the above prescription yields catastrophic results for the energy that drive the intrinsic wave-function to configurations with infinite deformation, thereby preventing its use both in projection after and before variation.

  16. Density-Dependent Compensatory Growth in Brown Trout (Salmo trutta) in Nature

    PubMed Central

    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. PMID:23658820

  17. 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.

  18. 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.

  19. Food supply influences offspring provisioning but not density-dependent fecundity in a marine fish.

    PubMed

    Samhouri, Jameal Farouq

    2009-12-01

    Replenishment of many marine populations occurs through the entry of juveniles to adult populations following a pelagic larval stage. Because mortality during the pelagic stage is thought to be high and density independent, larval abundance and traits of individual larvae should have strong effects on overall population dynamics in marine organisms. Surprisingly, few experiments have tested how localized interactions among breeding adults affect the quantity and phenotypic traits of larvae they produce. Here I experimentally test for the influence of food competition, mate limitation, and population density on somatic growth, fecundity, and offspring provisioning (larval length and energy reserves) in a planktivorous, territorial coral reef damselfish, Stegastes partitus. I manipulated food supply and adult S. partitus density on isolated patch reefs in the Bahamas and also made behavioral observations of S. partitus occurring on nearby natural reefs at a range of population densities. On the experimental reefs, females experienced density-dependent growth and fecundity; male reproductive success was density dependent, but male growth was not. Density-dependent growth and reproduction were not moderated by food supplementation, and density-dependent reproduction was not influenced by mate availability. On natural reefs, the frequency of aggressive interactions, particularly involving females, increased with population density, implicating aggression-related energetic costs as the source of both forms of density dependence in the experiments. Food supplementation increased female somatic growth and larval energy reserves, suggesting that females allocated surplus energy to future reproductive potential and enhanced offspring quality. Neither experimental treatment affected larval length. By altering patterns of reproduction, the interplay between spatial variation in food availability and population density may drive population dynamics in a broad range of benthic

  20. 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.

  1. Intraspecific density dependence and a guild of consumers coexisting on one resource.

    PubMed

    McPeek, Mark A

    2012-12-01

    The importance of negative intraspecific density dependence to promoting species coexistence in a community is well accepted. However, such mechanisms are typically omitted from more explicit models of community dynamics. Here I analyze a variation of the Rosenzweig-MacArthur consumer-resource model that includes negative intraspecific density dependence for consumers to explore its effect on the coexistence of multiple consumers feeding on a single resource. This analysis demonstrates that a guild of multiple consumers can easily coexist on a single resource if each limits its own abundance to some degree, and stronger intraspecific density dependence permits a wider variety of consumers to coexist. The mechanism permitting multiple consumers to coexist works in a fashion similar to apparent competition or to each consumer having its own specialized predator. These results argue for a more explicit emphasis on how negative intraspecific density dependence is generated and how these mechanisms combine with species interactions to shape overall community structure.

  2. Time-Dependent Dark Energy Density and Holographic DE Model with Interaction

    NASA Astrophysics Data System (ADS)

    Saadat, H.; Saadat, A. M.

    2011-05-01

    In this article we consider holographic dark energy model with interaction and space curvature. We calculate cosmic scale factor by using the time-dependent dark energy density. Then we obtain phenomenological interaction between holographic dark energy and matter.

  3. 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

  4. Remark on compressible Navier-Stokes equations with density-dependent viscosity and discontinuous initial data

    NASA Astrophysics Data System (ADS)

    Zhang, Ting; Fang, Daoyuan

    2008-03-01

    In this paper, we study the free boundary problem for 1D compressible Navier-Stokes equations with density-dependent viscosity. We focus on the case where the viscosity coefficient vanishes on vacuum. We prove the global existence and uniqueness for discontinuous solutions to the Navier-Stokes equations when the initial density is a bounded variation function, and give a decay result for the density as t-->+[infinity].

  5. Time-Dependent Density of Viscous Modified Chaplygin Gas with Arbitrary α

    NASA Astrophysics Data System (ADS)

    Saadat, H.

    2013-11-01

    In this paper we study modified Chaplygin gas which has viscosity for the case of arbitrary α instead of α=0.5. We obtain behavior of the energy density of modified Chaplygin gas with respect to the constant and time-dependent bulk viscosity. We find also, numerically, effect of α on the energy density.

  6. Time-dependent density functional theory for strong-field ionization by circularly polarized pulses

    NASA Astrophysics Data System (ADS)

    Chirilă, Ciprian C.; Lein, Manfred

    2017-03-01

    By applying time-dependent density functional theory to a two-dimensional multielectron atom subject to strong circularly polarized light pulses, we confirm that the ionization of p orbitals with defined angular momentum depends on the sense of rotation of the applied field. A simple ad-hoc modification of the adiabatic local-density exchange-correlation functional is proposed to remedy its unphysical behavior under orbital depletion.

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

    DOE PAGES

    Stetcu, I.; Bertulani, C. A.; Bulgac, A.; ...

    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

  8. Global strong solution to compressible Navier-Stokes equations with density dependent viscosity and temperature dependent heat conductivity

    NASA Astrophysics Data System (ADS)

    Duan, Ran; Guo, Ai; Zhu, Changjiang

    2017-04-01

    We obtain existence and uniqueness of global strong solution to one-dimensional compressible Navier-Stokes equations for ideal polytropic gas flow, with density dependent viscosity and temperature dependent heat conductivity under stress-free and thermally insulated boundary conditions. Here we assume viscosity coefficient μ (ρ) = 1 +ρα and heat conductivity coefficient κ (θ) =θβ for all α ∈ [ 0 , ∞) and β ∈ (0 , + ∞).

  9. Dependence of the density limit on the toroidal magnetic field on FTU

    NASA Astrophysics Data System (ADS)

    Pucella, G.; Tudisco, O.; Apicella, M. L.; Apruzzese, G.; Artaserse, G.; Belli, F.; Bin, W.; Boncagni, L.; Botrugno, A.; Buratti, P.; Calabrò, G.; Castaldo, C.; Cianfarani, C.; Cocilovo, V.; Dimatteo, L.; Esposito, B.; Frigione, D.; Gabellieri, L.; Giovannozzi, E.; Granucci, G.; Marinucci, M.; Marocco, D.; Martines, E.; Mazzitelli, G.; Mazzotta, C.; Nowak, S.; Ramogida, G.; Romano, A.; Tuccillo, A. A.; Zeng, L.; Zuin, M.

    2013-02-01

    The capability of predicting the density limit of a magnetically confined burning plasma is of crucial importance to establish the ultimate performance of a fusion power plant. The Greenwald density limit, commonly used as an empirical scaling law, predicts that the maximum achievable central line-averaged density is given by the relation \\bar{n}_G = k \\bar{J} , where \\bar{J} is the average plasma current density and k is the plasma elongation. However, several experiments have pointed out that such a limit can be overcome in the presence of peaked density profiles. This paper proposes a new empirical scaling law for a limiter tokamak operating in the low-energy confinement mode (L-mode) concerning the case of peaked density profiles associated with the presence of multifaceted asymmetric radiation from the edges. This result is based on dedicated experiments performed on the Frascati Tokamak Upgrade (FTU) under extremely clean machine conditions (Zeff = 1.0-1.5), in which the high-density domain is explored in a wide range of values of plasma current (Ip = 500-900 kA) and toroidal magnetic field (BT = 4-8 T). It is found that the maximum achievable central line-averaged density essentially depends on the toroidal magnetic field only and does not depend on the average plasma current density: the behaviour is explained in terms of density profile peaking in the high-density domain. As a confirmation that the limit is an edge limit, it is also shown that a Greenwald-like scaling (i.e. depending on the current density) actually holds for the edge line-averaged density (at r/a ≃ 4/5).

  10. Attosecond time delay in valence photoionization and photorecombination of argon: A time-dependent local-density-approximation study

    NASA Astrophysics Data System (ADS)

    Magrakvelidze, Maia; Madjet, Mohamed El-Amine; Dixit, Gopal; Ivanov, Misha; Chakraborty, Himadri S.

    2015-06-01

    We determine and analyze the quantum phases and time delays in photoionization and photorecombination of valence 3 p and 3 s electrons of argon using the Kohn-Sham local-density-functional approach. The time-dependent local-density approximation is used to account for the electron correlation. Resulting attosecond Wigner-Smith time delays show very good agreement with the recent experiment on argon that measured the delay in 3 p photorecombination [S. B. Schoun et al., Phys. Rev. Lett. 112, 153002 (2014), 10.1103/PhysRevLett.112.153002].

  11. 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

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

    PubMed

    Stewart, Kelley M; Walsh, Danielle R; Kie, John G; Dick, Brian L; Bowyer, R Terry

    2015-02-01

    We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 1999-2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20 elk/km(2), and a low-density population at 4 elk/km(2) to test hypotheses relative to timing and duration of sexual segregation and variation in selection of resources. We used multi-response permutation procedures to investigate patterns of sexual segregation, and resource selection functions to document differences in selection of resources by individuals in high- and low-density populations during sexual segregation and aggregation. The duration of sexual segregation was 2 months longer in the high-density population and likely was influenced by individuals in poorer nutritional condition, which corresponded with later conception and parturition, than at low density. Males and females in the high-density population overlapped in selection of resources to a greater extent than in the low-density population, probably resulting from density-dependent effects of increased intraspecific competition and lower availability of resources.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Modeling the doubly excited state with time-dependent Hartree-Fock and density functional theories

    NASA Astrophysics Data System (ADS)

    Isborn, Christine M.; Li, Xiaosong

    2008-11-01

    Multielectron excited states have become a hot topic in many cutting-edge research fields, such as the photophysics of polyenes and in the possibility of multiexciton generation in quantum dots for the purpose of increasing solar cell efficiency. However, obtaining multielectron excited states has been a major obstacle as it is often done with multiconfigurational methods, which involve formidable computational cost for large systems. Although they are computationally much cheaper than multiconfigurational wave function based methods, linear response adiabatic time-dependent Hartree-Fock (TDHF) and density functional theory (TDDFT) are generally considered incapable of obtaining multielectron excited states. We have developed a real-time TDHF and adiabatic TDDFT approach that is beyond the perturbative regime. We show that TDHF/TDDFT is able to simultaneously excite two electrons from the ground state to the doubly excited state and that the real-time TDHF/TDDFT implicitly includes double excitation within a superposition state. We also present a multireference linear response theory to show that the real-time electron density response corresponds to a superposition of perturbative linear responses of the S0 and S2 states. As a result, the energy of the two-electron doubly excited state can be obtained with several different approaches. This is done within the adiabatic approximation of TDDFT, a realm in which the doubly excited state has been deemed missing. We report results on simple two-electron systems, including the energies and dipole moments for the two-electron excited states of H2 and HeH+. These results are compared to those obtained with the full configuration interaction method.

  20. Density-dependent productivity depression in Pyrenean Bearded Vultures: implications for conservation.

    PubMed

    Carrete, Martina; Donázar, José A; Margalida, Antoni

    2006-10-01

    The main objective of many conservation programs is to increase population size by improving a species' survival and reproduction. However, density dependence of demographic parameters may confound this approach. In this study we used a 25-year data set on Bearded Vultures (Gypaetus barbatus) in Spain to evaluate the consequences of population growth on reproductive performance. Unlike its coefficient of variation (cv), mean annual productivity decreased with increasing population size. After controlling for territorial heterogeneity, productivity also was negatively related to the distance to the nearest conspecific breeding pair and to supplementary feeding points where floaters congregate. These results suggest that vulture populations are regulated as posited by the site-dependency hypothesis: as the population increases, average productivity decreases because progressively poorer territories are used. The combined effects of the shrinkage of territories and the presence of floaters around supplementary feeding points seem to be the main causes of productivity decline and are therefore the main determinants of territory quality. This has conservation implications, especially concerning the role of supplementary feeding points. Supplementary feeding should be reviewed given that its usefulness in reducing preadult mortality has not yet been proved and its effect on productivity, as our results suggest, is negative.

  1. Density-dependent outcomes in a digestive mutualism between carnivorous Roridula plants and their associated hemipterans.

    PubMed

    Anderson, Bruce; Midgley, Jeremy J

    2007-05-01

    Recent studies have shown that mutualisms often have variable outcomes in space and time. In particular, the outcomes may be dependent on the density of the partners with unimodal or saturating outcomes providing stability to the mutualism. We examine density-dependent outcomes of an obligate, species-specific mutualism between a South African carnivorous plant (Roridula dentata) and a hemipteran (Pameridea) that facilitates prey digestion, but also sucks plant sap. Plants occur in sandy, leached, nitrogen-poor soils and have no digestive enzymes to digest prey. Instead they rely on obligately dependent hemipterans to supply nitrogen by digesting prey for them and defecating on their leaves. We documented the densities of Pameridea on Roridula in the field. In the greenhouse, we manipulated the hemipteran densities on Roridula and measured the mean relative growth rates of plants with differing hemipteran densities. Plants exhibited a unimodal response to the density of their mutualist partners. Those with no hemipterans had negative growth rates, suggesting that hemipterans are important in facilitating nitrogen absorption. Plants with intermediate hemipteran densities had positive growth rates but growth rates were negative under very high hemipteran densities. Our research provides support for variable and unimodal outcomes in mutualism. Unimodal outcomes may be particularly important in obligate mutualisms and this is one of the few studied outside of pollinating seed parasite mutualisms. In this system, extrinsic factors such as other predators may affect the mutualism by altering the numbers of hemipterans.

  2. Quantum fluid density functional theory of time-dependent phenomena: Ion-atom collisions

    NASA Astrophysics Data System (ADS)

    Deb, B. M.; Chattaraj, P. K.

    1988-07-01

    Using a recently proposed kinetic energy density functional and an amalgamation of density functional theory with quantum fluid dynamics, a time-dependent Kohn-Sham-type equation in three-dimensional space, which is a new non-linear Schrödinger equation, has been derived. The equation is also derived through the stochastic interpretation of quantum mechanics. A molecular "thermodynamic" viewpoint is suggested in terms of space-time-dependent quantities. Numerical solution of the above equation yields the time-dependent charge density, current density, effective potential and chemical potential. Perspective plots of these quantities for the proton-neon 25 keV head-on collision are presented.

  3. Density-dependent regulation of the sex ratio in an annual plant.

    PubMed

    Dorken, Marcel E; Pannell, John R

    2008-06-01

    Sex ratios are subject to strong frequency-dependent selection regulated by the mating system and the relative male versus female investment. In androdioecious plant populations, where males co-occur with hermaphrodites, the sex ratio depends on the rate of self-fertilization by hermaphrodites and on the relative pollen production of males versus hermaphrodites. Here, we report evolutionary changes in the sex ratio from experimental mating arrays of the androdioecious plant Mercurialis annua. We found that the progeny sex ratio depended strongly on density, with fewer males in the progeny of plants grown under low density. This occurred in part because of a plastic adjustment in pollen production by hermaphrodites, which produced more pollen when grown at low density than at high density. Our results provide support for the prediction that environmental conditions govern sex ratios through their effects on the relative fertility of unisexual versus hermaphrodite individuals.

  4. Density dependence of the /s-wave repulsion in pionic atoms

    NASA Astrophysics Data System (ADS)

    Friedman, E.

    2002-11-01

    Several mechanisms of density dependence of the s-wave repulsion in pionic atoms, beyond the conventional model, are tested by parameter fits to a large (106 points) set of data from 16O to 238U, including 'deeply bound' states in 205Pb. Special attention is paid to the proper choice of nuclear density distributions. A density-dependent isovector scattering amplitude suggested recently by Weise to result from a density dependence of the pion decay constant is introduced and found to account for most of the so-called anomalous repulsion. The presence of such an effect might indicate partial chiral symmetry restoration in dense matter. The anomalous repulsion is fully accounted for when an additional relativistic impulse approximation term is included in the potential.

  5. Combined effects of climate, predation, and density dependence on Greater and Lesser Scaup population dynamics.

    PubMed

    Ross, Beth E; Hooten, Mevin B; DeVink, Jean-Michel; Koons, David N

    2015-09-01

    An understanding of species relationships is critical in the management and conservation of populations facing climate change, yet few studies address how climate alters species interactions and other population drivers. We use a long-term, broad-scale data set of relative abundance to examine the influence of climate, predators, and density dependence on the population dynamics of declining scaup (Aythya) species within the core of their breeding range. The state-space modeling approach we use applies to a wide range of wildlife species, especially populations monitored over broad spatiotemporal extents. Using this approach, we found that immediate snow cover extent in the preceding winter and spring had the strongest effects, with increases in mean snow cover extent having a positive effect on the local surveyed abundance of scaup. The direct effects of mesopredator abundance on scaup population dynamics were weaker, but the results still indicated a potentil interactive process between climate and food web dynamics (mesopredators, alternative prey, and scaup). By considering climate variables and other potential effects on population dynamics, and using a rigorous estimation framework, we provide insight into complex ecological processes for guiding. conservation and policy actions aimed at mitigating and reversing the decline of scaup.

  6. 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.

  7. Ecological drivers of guanaco recruitment: variable carrying capacity and density dependence.

    PubMed

    Marino, Andrea; Pascual, Miguel; Baldi, Ricardo

    2014-08-01

    Ungulates living in predator-free reserves offer the opportunity to study the influence of food limitation on population dynamics without the potentially confounding effects of top-down regulation or livestock competition. We assessed the influence of relative forage availability and population density on guanaco recruitment in two predator-free reserves in eastern Patagonia, with contrasting scenarios of population density. We also explored the relative contribution of the observed recruitment to population growth using a deterministic linear model to test the assumption that the studied populations were closed units. The observed densities increased twice as fast as our theoretical populations, indicating that marked immigration has taken place during the recovery phase experienced by both populations, thus we rejected the closed-population assumption. Regarding the factors driving variation in recruitment, in the low- to medium-density setting, we found a positive linear relationship between recruitment and surrogates of annual primary production, whereas no density dependence was detected. In contrast, in the high-density scenario, both annual primary production and population density showed marked effects, indicating a positive relationship between recruitment and per capita food availability above a food-limitation threshold. Our results support the idea that environmental carrying capacity fluctuates in response to climatic variation, and that these fluctuations have relevant consequences for herbivore dynamics, such as amplifying density dependence in drier years. We conclude that including the coupling between environmental variability in resources and density dependence is crucial to model ungulate population dynamics; to overlook temporal changes in carrying capacity may even mask density dependence as well as other important processes.

  8. 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.

  9. 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.

  10. Spectral functions with the density matrix renormalization group: Krylov-space approach for correction vectors

    NASA Astrophysics Data System (ADS)

    Nocera, A.; Alvarez, G.

    2016-11-01

    Frequency-dependent correlations, such as the spectral function and the dynamical structure factor, help illustrate condensed matter experiments. Within the density matrix renormalization group (DMRG) framework, an accurate method for calculating spectral functions directly in frequency is the correction-vector method. The correction vector can be computed by solving a linear equation or by minimizing a functional. This paper proposes an alternative to calculate the correction vector: to use the Krylov-space approach. This paper then studies the accuracy and performance of the Krylov-space approach, when applied to the Heisenberg, the t-J, and the Hubbard models. The cases studied indicate that the Krylov-space approach can be more accurate and efficient than the conjugate gradient, and that the error of the former integrates best when a Krylov-space decomposition is also used for ground state DMRG.

  11. 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.

  12. 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.

  13. 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.

  14. Local control theory using trajectory surface hopping and linear-response time-dependent density functional theory.

    PubMed

    Curchod, Basile F E; Penfold, Thomas J; Rothlisberger, Ursula; Tavernelli, Ivano

    2013-01-01

    The implementation of local control theory using nonadiabatic molecular dynamics within the framework of linear-response time-dependent density functional theory is discussed. The method is applied to study the photoexcitation of lithium fluoride, for which we demonstrate that this approach can efficiently generate a pulse, on-the-fly, able to control the population transfer between two selected electronic states. Analysis of the computed control pulse yields insights into the photophysics of the process identifying the relevant frequencies associated to the curvature of the initial and final state potential energy curves and their energy differences. The limitations inherent to the use of the trajectory surface hopping approach are also discussed.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

    2016-09-09

    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.

  20. 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.

  1. Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments.

    PubMed

    Donohue, K; Pyle, E H; Messiqua, D; Heschel, M S; Schmitt, J

    2000-12-01

    We identified environment-dependent constraints on the evolution of plasticity to density under natural conditions in two natural populations of Impatiens capensis. We also examined the expression of population divergence in genetic variance-covariance matrices in these natural environments. Inbred lines, originally collected from a sunny site with high seedling densities and a woodland site with low seedling densities, were planted in both original sites at natural high densities and at low density. Morphological and life-history characters were measured. More genetic variation for plastic responses to density was expressed in the sun site than in the woodland site, so the evolutionary potential of plasticity was greater in the sun site. Strong genetic correlations between the same character expressed at different densities and correlations among different characters could constrain the evolution of plasticity in both sites. Genetically based trade-offs in meristem allocation to vegetative growth and reproduction were apparent only in the high-resource environment with no overhead canopy and no intraspecific competition. Therefore, genetic constraints on the evolution of plasticity depended on the site and density in which plants were grown, and correlated responses to selection on plastic characters are also expected to differ between sites and densities. Population differentiation in genetic variance-covariance matrices was detected, but matrix structural differences, as opposed to proportional differences, were detected between populations only in the sun site at natural high density. Thus, population divergence in genetic architecture can occur rapidly and on a fine spatial scale, but the expression of such divergence may depend on the environment.

  2. 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.

  3. Restricted dispersal reduces the strength of spatial density dependence in a tropical bird population

    PubMed Central

    Burgess, Malcolm D; Nicoll, Malcolm A.C; Jones, Carl G; Norris, Ken

    2008-01-01

    Spatial processes could play an important role in density-dependent population regulation because the disproportionate use of poor quality habitats as population size increases is widespread in animal populations—the so-called buffer effect. While the buffer effect patterns and their demographic consequences have been described in a number of wild populations, much less is known about how dispersal affects distribution patterns and ultimately density dependence. Here, we investigated the role of dispersal in spatial density dependence using an extraordinarily detailed dataset from a reintroduced Mauritius kestrel (Falco punctatus) population with a territorial (despotic) breeding system. We show that recruitment rates varied significantly between territories, and that territory occupancy was related to its recruitment rate, both of which are consistent with the buffer effect theory. However, we also show that restricted dispersal affects the patterns of territory occupancy with the territories close to release sites being occupied sooner and for longer as the population has grown than the territories further away. As a result of these dispersal patterns, the strength of spatial density dependence is significantly reduced. We conclude that restricted dispersal can modify spatial density dependence in the wild, which has implications for the way population dynamics are likely to be impacted by environmental change. PMID:18285284

  4. Larval density dependence in Anopheles gambiae s.s., the major African vector of malaria.

    PubMed

    Muriu, Simon M; Coulson, Tim; Mbogo, Charles M; Godfray, H Charles J

    2013-01-01

    Anopheles gambiae sensu stricto is the most important vector of malaria in Africa although relatively little is known about the density-dependent processes determining its population size. Mosquito larval density was manipulated under semi-natural conditions using artificial larval breeding sites placed in the field in coastal Kenya; two experiments were conducted: one manipulating the density of a single cohort of larvae across a range of densities and the other employing fewer densities but with the treatments crossed with four treatments manipulating predator access. In the first experiment, larval survival, development rate and the size of the adult mosquito all decreased with larval density (controlling for block effects between 23% and 31% of the variance in the data could be explained by density). In the second experiment, the effects of predator manipulation were not significant, but again we observed strong density dependence in larval survival (explaining 30% of the variance). The results are compared with laboratory studies of A. gambiae larval competition and the few other studies conducted in the field, and the consequences for malaria control are discussed.

  5. Larval density dependence in Anopheles gambiae s.s., the major African vector of malaria

    PubMed Central

    Muriu, Simon M.; Coulson, Tim; Mbogo, Charles M.; Godfray, H. Charles J.

    2017-01-01

    Summary Anopheles gambiae sensu stricto is the most important vector of malaria in Africa although relatively little is known about the density-dependent processes determining its population size.Mosquito larval density was manipulated under semi-natural conditions using artificial larval breeding sites placed in the field in coastal Kenya; two experiments were conducted: one manipulating the density of a single cohort of larvae across a range of densities and the other employing fewer densities but with the treatments crossed with four treatments manipulating predator access.In the first experiment, larval survival, development rate and the size of the adult mosquito all decreased with larval density (controlling for block effects between 23% and 31% of the variance in the data could be explained by density).In the second experiment, the effects of predator manipulation were not significant, but again we observed strong density dependence in larval survival (explaining 30% of the variance).The results are compared with laboratory studies of A. gambiae larval competition and the few other studies conducted in the field, and the consequences for malaria control are discussed PMID:23163565

  6. Effects of hepatocyte growth factor on glutathione synthesis, growth, and apoptosis is cell density-dependent

    SciTech Connect

    Yang Heping; Magilnick, Nathaniel; Xia Meng; Lu, Shelly C.

    2008-01-15

    Hepatocyte growth factor (HGF) is a potent hepatocyte mitogen that exerts opposing effects depending on cell density. Glutathione (GSH) is the main non-protein thiol in mammalian cells that modulates growth and apoptosis. We previously showed that GSH level is inversely related to cell density of hepatocytes and is positively related to growth. Our current work examined whether HGF can modulate GSH synthesis in a cell density-dependent manner and how GSH in turn influence HGF's effects. We found HGF treatment of H4IIE cells increased cell GSH levels only under subconfluent density. The increase in cell GSH under low density was due to increased transcription of GSH synthetic enzymes. This correlated with increased protein levels and nuclear binding activities of c-Jun, c-Fos, p65, p50, Nrf1 and Nrf2 to the promoter region of these genes. HGF acts as a mitogen in H4IIE cells under low cell density and protects against tumor necrosis factor {alpha} (TNF{alpha})-induced apoptosis by limiting JNK activation. However, HGF is pro-apoptotic under high cell density and exacerbates TNF{alpha}-induced apoptosis by potentiating JNK activation. The increase in cell GSH under low cell density allows HGF to exert its full mitogenic effect but is not necessary for its anti-apoptotic effect.

  7. 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...

  8. Delayed density-dependent season length alone can lead to rodent population cycles.

    PubMed

    Smith, Matthew J; White, Andrew; Lambin, Xavier; Sherratt, Jonathan A; Begon, Michael

    2006-05-01

    Studies of cyclic microtine populations (voles and lemmings) have suggested a relationship between the previous year's population density and the subsequent timing of the onset of reproduction by overwintered breeding females. No studies have explored the importance of this relationship in the generation of population cycles. Here we mathematically examine the implications of variation in reproductive season length caused by delayed density-dependent changes in its start date. We demonstrate that when reproductive season length is a function of past population densities, it is possible to get realistic population cycles without invoking any changes in birth rates or survival. When parameterized for field voles (Microtus agrestis) in Kielder Forest (northern England), our most realistic model predicts population cycles of similar periodicity to the Kielder populations. Our study highlights the potential importance of density-dependent reproductive timing in microtine population cycles and calls for investigations into the mechanism(s) underlying this phenomenon.

  9. On the well-posedness of the incompressible density-dependent Euler equations in the L framework

    NASA Astrophysics Data System (ADS)

    Danchin, Raphaël

    The present paper is devoted to the study of the well-posedness issue for the density-dependent Euler equations in the whole space. We establish local-in-time results for the Cauchy problem pertaining to data in the Besov spaces embedded in the set of Lipschitz functions, including the borderline case Bp,1/Np+1(R). A continuation criterion in the spirit of the celebrated one by Beale, Kato and Majda (1984) in [2] for the classical Euler equations, is also proved. In contrast with the previous work dedicated to this system in the whole space, our approach is not restricted to the L framework or to small perturbations of a constant density state: we just need the density to be bounded away from zero. The key to that improvement is a new a priori estimate in Besov spaces for an elliptic equation with nonconstant coefficients.

  10. 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

  11. Density-dependent selection on mate search and evolution of Allee effects.

    PubMed

    Berec, Luděk; Kramer, Andrew M; Bernhauerová, Veronika; Drake, John M

    2017-02-27

    Sexually reproducing organisms require males and females to find each other. Increased difficulty of females finding mates as male density declines is the most frequently reported mechanism of Allee effects in animals. Evolving more effective mate search may alleviate Allee effects, but may depend on density regimes a population experiences. In particular, high density populations may evolve mechanisms that induce Allee effects which become detrimental when populations are reduced and maintained at a low density. We develop an individual-based, eco-genetic model to study how mating systems and fitness trade-offs interact with changes in population density to drive evolution of the rate at which males or females search for mates. Finite mate search rate triggers Allee effects in our model and we explore how these Allee effects respond to such evolution. We allow a population to adapt to several population density regimes and examine whether high-density populations are likely to reverse adaptations attained at low densities. We find density-dependent selection in most of scenarios, leading to search rates that result in lower Allee thresholds in populations kept at lower densities. This mainly occurs when fecundity costs are imposed on mate search, and provides an explanation for why Allee effects are often observed in anthropogenically rare species. Optimizing selection, where the attained trait value minimizes the Allee threshold independent of population density, depended on the trade-off between search and survival, combined with monogamy when females were searching. Other scenarios led to runaway selection on the mate search rate, including evolutionary suicide. Trade-offs involved in mate search may thus be crucial to determining how density influences the evolution of Allee effects. Previous studies did not examine evolution of a trait related to the strength of Allee effects under density variation. We emphasize the crucial role that mating systems, fitness

  12. Population cycles produced by delayed density dependence in an annual plant.

    PubMed

    Gonzalez-Andujar, J L; Fernandez-Quintanilla, C; Navarrete, L

    2006-09-01

    In contrast to insect and animal populations, little attention has been directed to the study of cycles in plant populations. It has been argued on theoretical grounds that plants present stable dynamics. Nevertheless, there are examples where plant populations appear to exhibit oscillatory dynamics, but the oscillatory signal is variable and comes from very short time series data. Using a combination of time series, models, and empirical results, we present evidence of population cycles for Descurania sophia in a 16-year field experiment. Endogenous and exogenous causal mechanisms were studied to identify processes underlying this temporal dynamic. Our results show a 4-year cycle produced by delayed density dependence. We suggest that high nutrient levels might be responsible for the observed dynamics of D. sophia. Our results suggest that although plant population dynamics may be stabilized by direct density dependence, delayed density dependence could destabilize dynamics.

  13. 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.

  14. 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

  15. Density-dependent gastroretentive microparticles motion in human gastric emptying studied using computer simulation.

    PubMed

    Hao, Shilei; Wang, Bochu; Wang, Yazhou

    2015-04-05

    Density-dependent gastroretentive drug delivery systems have been used to prolong the gastric retention time of drugs since the 1960s. The design of density-dependent gastroretentive dosage forms, however, usually focuses on specific parameters rather than combines with the fluid dynamics of dosage form in the gastric emptying. Therefore, the purpose of the present study was to develop a 2-D model of multiple-phase flows for the simulation of gastric emptying and gastroretentive microparticles motion, and the influence of microparticle density, microparticle viscosity, and gastric juice viscosity on the gastric retention were studied. The recirculating flows, formed in the gastric emptying, could mix the conventional-density microparticles and transport them to the pylorus. However, the low-density microparticles remained floating on the surface of gastric juice, while the high-density microparticles could sink and deposit in the bottom of the stomach. The remaining integral area of microparticles was higher than 90% after 18.33min of simulation when the density of microparticles was lower than 550kg/m(3) or higher than 2500kg/m(3), which was higher compared to conventional-density microparticles (67.05%). These results are in good agreement with experimental data previously reported. In addition, the viscosity of microparticle and gastric juice also influenced the remaining integral area of gastroretentive microparticles. This study shows that the multiple-phase computational fluid dynamics models could provide detailed insights into the fluid dynamics of density-dependent gastroretentive microparticles in gastric emptying, which offers a powerful tool to further understand the mechanism of gastric retention for gastroretentive dosage forms and study the influence of different parameters on their ability for gastric retention.

  16. 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

  17. Density-dependent survival and fecundity of hemlock woolly adelgid (Hemiptera: Adelgidae).

    PubMed

    Sussky, Elizabeth M; Elkinton, Joseph S

    2014-10-01

    The hemlock woolly adelgid (Adelges tsugae Annand) has decimated eastern hemlocks (Tsuga canadensis Carrière) in forests throughout the eastern United Sates, but its densities in central New England appear to have stabilized. To find out why, we infested 64 eastern hemlocks with varying densities of adelgid ovisacs in a typical eastern hemlock forest in western Massachusetts. We subsequently documented adelgid density, fecundity, and the amount of new growth on experimental trees over two consecutive years. We used a 2 by 2 randomized block design using previously and newly infested hemlocks that were either 1-m tall saplings or branches of mature trees. There was a density-dependent decline in the survival and fecundity of adelgid in both the spring and winter generations. This response was a function of both previous infestation by adelgid and current year's crawler density in the spring generation. Additionally, the production of sexuparae in the spring generation played a key role in the overall density-dependent survival of adelgid, suggesting that sexuparae production is strongly linked to developing crawler density.

  18. 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.

  19. Density-dependent speciation alters the structure and dynamics of neutral communities.

    PubMed

    Wang, Shaopeng; Chen, Anping; Pacala, Stephen W; Fang, Jingyun

    2015-05-07

    The neutral theory of biodiversity (NTB) provides an individual-based modeling framework to study eco-evolutionary dynamics. Previous NTB models usually assumed the same per capita rate of speciation across lineages. However, population dynamics may induce macroevolutionary feedbacks that can result in variable per capita speciation rates across lineages. In this paper, with analytical and simulation approaches, we explore how different scenarios of density-dependent speciation may impact the diversity and phylogenetic patterns of neutral communities, and compare the results to predictions of the original NTB model with an invariant speciation rate. Our results show that positive per capita speciation rate-abundance relationships could result in higher species richness and evenness, enhanced stability (evidenced by higher post-disturbance recovery rates and lower temporal variability in species diversity), and higher imbalance in phylogenetic trees. The opposite patterns are predicted when per capita speciation rates decrease with abundance. Particularly, strong negative speciation rate-abundance relationships can generate a positive correlation between phylogenetic age and abundance, which has been observed in Panamanian tree species. Our findings demonstrate the importance of eco-evolutionary feedbacks for understanding long-term diversity and phylogenetic patterns in ecological communities.

  20. Linear-scaling time-dependent density-functional theory in the linear response formalism.

    PubMed

    Zuehlsdorff, T J; Hine, N D M; Spencer, J S; Harrison, N M; Riley, D J; Haynes, P D

    2013-08-14

    We present an implementation of time-dependent density-functional theory (TDDFT) in the linear response formalism enabling the calculation of low energy optical absorption spectra for large molecules and nanostructures. The method avoids any explicit reference to canonical representations of either occupied or virtual Kohn-Sham states and thus achieves linear-scaling computational effort with system size. In contrast to conventional localised orbital formulations, where a single set of localised functions is used to span the occupied and unoccupied state manifold, we make use of two sets of in situ optimised localised orbitals, one for the occupied and one for the unoccupied space. This double representation approach avoids known problems of spanning the space of unoccupied Kohn-Sham states with a minimal set of localised orbitals optimised for the occupied space, while the in situ optimisation procedure allows for efficient calculations with a minimal number of functions. The method is applied to a number of medium sized organic molecules and a good agreement with traditional TDDFT methods is observed. Furthermore, linear scaling of computational cost with system size is demonstrated on (10,0) carbon nanotubes of different lengths.

  1. 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.

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

    PubMed

    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 (SO2) in gas and liquid phases.

  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.

  4. On the scaling of avaloids and turbulence with the average density approaching the density limit

    NASA Astrophysics Data System (ADS)

    Antar, G. Y.; Counsell, G.; Ahn, J.-W.

    2005-08-01

    This article is dedicated to the characterization of turbulent transport in the scrape-off layer of the Mega Ampère Spherical Tokamak [A. Sykes et al., Phys. Plasmas 8, 2101 (2001)] as a function of the average density (nL). The aim is to answer a renewed interest in this subject since the bursty character of turbulence in the scrape-off layer was shown to be caused by large-scale events with high radial velocity reaching about 1/10th of the sound speed called avaloids [G. Antar et al., Phys. Rev. Lett 87, 065001 (2001)]. With increasing density, turbulence and transport increase nonlinearly at the midplane while remaining almost unchanged in the target region. Using various and complementary statistical analyses, the existence of a "critical" density, at nL/nG≃0.35 is emphasized; nG is the Greenwald density. Both above and below this density, intermittency decreases and avaloids play a decreasing role in the particle radial transport. This is interpreted as caused by the interplay between avaloids and the surrounding turbulent structures which mix them more efficiently with increasing density as the level of the background turbulence increases. The scaling of the different quantities with respect to the normalized density is obtained. It reveals that not only the level of turbulence and transport increase, but also the radial velocity and length scales. This increases the coupling between the hot plasma edge and the cold scrape-off layer that may explain the disruptive instability occurring at high densities.

  5. On the scaling of avaloids and turbulence with the average density approaching the density limit

    SciTech Connect

    Antar, G.Y.; Counsell, G.; Ahn, J.-W.

    2005-08-15

    This article is dedicated to the characterization of turbulent transport in the scrape-off layer of the Mega Ampere Spherical Tokamak [A. Sykes et al., Phys. Plasmas 8, 2101 (2001)] as a function of the average density (n{sub L}). The aim is to answer a renewed interest in this subject since the bursty character of turbulence in the scrape-off layer was shown to be caused by large-scale events with high radial velocity reaching about 1/10th of the sound speed called avaloids [G. Antar et al., Phys. Rev. Lett 87, 065001 (2001)]. With increasing density, turbulence and transport increase nonlinearly at the midplane while remaining almost unchanged in the target region. Using various and complementary statistical analyses, the existence of a 'critical' density, at n{sub L}/n{sub G}{approx_equal}0.35 is emphasized; n{sub G} is the Greenwald density. Both above and below this density, intermittency decreases and avaloids play a decreasing role in the particle radial transport. This is interpreted as caused by the interplay between avaloids and the surrounding turbulent structures which mix them more efficiently with increasing density as the level of the background turbulence increases. The scaling of the different quantities with respect to the normalized density is obtained. It reveals that not only the level of turbulence and transport increase, but also the radial velocity and length scales. This increases the coupling between the hot plasma edge and the cold scrape-off layer that may explain the disruptive instability occurring at high densities.

  6. The role of weather and density dependence on population dynamics of Alpine-dwelling red deer.

    PubMed

    Bonardi, Anna; Corlatti, Luca; Bragalanti, Natalia; Pedrotti, Luca

    2017-01-01

    The dynamics of red deer Cervus elaphus populations has been investigated across different environmental conditions, with the notable exception of the European Alps. Although the population dynamics of mountain-dwelling ungulates is typically influenced by the interaction between winter severity and density, the increase of temperatures and the reduction of snowpack occurring on the Alps since the 1980s may be expected to alter this pattern, especially in populations dwelling at medium - low elevations. Taking advantage of a 29-year time series of spring count data, we explored the role of weather stochasticity and density dependence on growth rate and vital rates (mortality and weaning success), and the density-dependent variation in body mass in a red deer population of the Italian Alps. The interaction between increasing values of density and snow depth exerted negative and positive effects on growth and mortality rates, respectively, while weaning success was negatively affected by increasing values of density, female-biased sex ratio and snow depth. Body mass of males and females of different age classes declined as population size increased. Our data support the role of winter severity and density dependence as key components of red deer population dynamics, and provide insight into the species' ecology on the European Alps. Despite the recent decline of snowpack on the Alpine Region, the negative impacts of winter severity and population abundance on growth rrate (possibly mediated by the density-dependent decline in body mass) confirms the importance of overwinter mortality in affecting the population dynamics of Alpine-dwelling red deer.

  7. 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

  8. 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

  9. Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study.

    PubMed

    Ma, Haibo; Ma, Jing

    2011-08-07

    Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.

  10. Linear-response time-dependent density-functional theory with pairing fields.

    PubMed

    Peng, Degao; van Aggelen, Helen; Yang, Yang; Yang, Weitao

    2014-05-14

    Recent development in particle-particle random phase approximation (pp-RPA) broadens the perspective on ground state correlation energies [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013), Y. Yang, H. van Aggelen, S. N. Steinmann, D. Peng, and W. Yang, J. Chem. Phys. 139, 174110 (2013); D. Peng, S. N. Steinmann, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 104112 (2013)] and N ± 2 excitation energies [Y. Yang, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 224105 (2013)]. So far Hartree-Fock and approximated density-functional orbitals have been utilized to evaluate the pp-RPA equation. In this paper, to further explore the fundamentals and the potential use of pairing matrix dependent functionals, we present the linear-response time-dependent density-functional theory with pairing fields with both adiabatic and frequency-dependent kernels. This theory is related to the density-functional theory and time-dependent density-functional theory for superconductors, but is applied to normal non-superconducting systems for our purpose. Due to the lack of the proof of the one-to-one mapping between the pairing matrix and the pairing field for time-dependent systems, the linear-response theory is established based on the representability assumption of the pairing matrix. The linear response theory justifies the use of approximated density-functionals in the pp-RPA equation. This work sets the fundamentals for future density-functional development to enhance the description of ground state correlation energies and N ± 2 excitation energies.

  11. 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.

  12. An Extreme Learning Machine Approach to Density Estimation Problems.

    PubMed

    Cervellera, Cristiano; Maccio, Danilo

    2017-01-17

    In this paper, we discuss how the extreme learning machine (ELM) framework can be effectively employed in the unsupervised context of multivariate density estimation. In particular, two algorithms are introduced, one for the estimation of the cumulative distribution function underlying the observed data, and one for the estimation of the probability density function. The algorithms rely on the concept of $F$-discrepancy, which is closely related to the Kolmogorov-Smirnov criterion for goodness of fit. Both methods retain the key feature of the ELM of providing the solution through random assignment of the hidden feature map and a very light computational burden. A theoretical analysis is provided, discussing convergence under proper hypotheses on the chosen activation functions. Simulation tests show how ELMs can be successfully employed in the density estimation framework, as a possible alternative to other standard methods.

  13. Local environment and density-dependent feedbacks determine population growth in a forest herb.

    PubMed

    Dahlgren, Johan P; Ostergård, Hannah; Ehrlén, Johan

    2014-12-01

    Linking spatial variation in environmental factors to variation in demographic rates is essential for a mechanistic understanding of the dynamics of populations. However, we still know relatively little about such links, partly because feedbacks via intraspecific density make them difficult to observe in natural populations. We conducted a detailed field study and investigated simultaneous effects of environmental factors and the intraspecific density of individuals on the demography of the herb Lathyrus vernus. In regression models of vital rates we identified effects associated with spring shade on survival and growth, while density was negatively correlated with these vital rates. Density was also negatively correlated with average individual size in the study plots, which is consistent with self-thinning. In addition, average plant sizes were larger than predicted by density in plots that were less shaded by the tree canopy, indicating an environmentally determined carrying capacity. A size-structured integral projection model based on the vital rate regressions revealed that the identified effects of shade and density were strong enough to produce differences in stable population sizes similar to those observed in the field. The results illustrate how the local environment can determine dynamics of populations and that intraspecific density may have to be more carefully considered in studies of plant demography and population viability analyses of threatened species. We conclude that demographic approaches incorporating information about both density and key environmental factors are powerful tools for understanding the processes that interact to determine population dynamics and abundances.

  14. 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.

  15. Native Birds and Alien Insects: Spatial Density Dependence in Songbird Predation of Invading Oak Gallwasps

    PubMed Central

    Schönrogge, Karsten; Begg, Tracey; Stone, Graham N.

    2013-01-01

    Revealing the interactions between alien species and native communities is central to understanding the ecological consequences of range expansion. Much has been learned through study of the communities developing around invading herbivorous insects. Much less, however, is known about the significance of such aliens for native vertebrate predators for which invaders may represent a novel food source. We quantified spatial patterns in native bird predation of invading gall-inducing Andricus wasps associated with introduced Turkey oak (Quercus cerris) at eight sites across the UK. These gallwasps are available at high density before the emergence of caterpillars that are the principle spring food of native insectivorous birds. Native birds showed positive spatial density dependence in gall attack rates at two sites in southern England, foraging most extensively on trees with highest gall densities. In a subsequent study at one of these sites, positive spatial density dependence persisted through four of five sequential week-long periods of data collection. Both patterns imply that invading galls are a significant resource for at least some native bird populations. Density dependence was strongest in southern UK bird populations that have had longest exposure to the invading gallwasps. We hypothesise that this pattern results from the time taken for native bird populations to learn how to exploit this novel resource. PMID:23342048

  16. Nonadiabatic electron dynamics in time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Ullrich, C. A.; Tokatly, I. V.

    2006-06-01

    Time-dependent density-functional theory (TDDFT) treats dynamical exchange and correlation (xc) via a single-particle potential, Vxc(r,t) , defined as a nonlocal functional of the density n(r',t') . The popular adiabatic local-density approximation (ALDA) for Vxc(r,t) uses only densities at the same space-time point (r,t) . To go beyond the ALDA, two local approximations have been proposed based on quantum hydrodynamics and elasticity theory: (a) using the current as the basic variable (C-TDDFT) [G. Vignale, C. A. Ullrich, and S. Conti, Phys. Rev. Lett. 79, 4847 (1997)], (b) working in a comoving Lagrangian reference frame (L-TDDFT) [I. V. Tokatly, Phys. Rev. B 71, 165105 (2005)]. In this paper we illustrate, compare, and analyze both nonadiabatic theories for simple time-dependent model densities in the linear and nonlinear regime, for a broad range of time and frequency scales. C- and L-TDDFT are identical in certain limits, but, in general, exhibit qualitative and quantitative differences in their respective treatment of elastic and dissipative electron dynamics. In situations where the electronic density rapidly undergoes large deformations, it is found that nonadiabatic effects can become significant, causing the ALDA to break down.

  17. 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.

  18. 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.

  19. Variation in the strength of inbreeding depression across environments: effects of stress and density dependence.

    PubMed

    Yun, Li; Agrawal, Aneil F

    2014-12-01

    In what types of environments should we expect to find strong inbreeding depression? Previous studies indicate that inbreeding depression, δ, is positively correlated with the stressfulness of the environment in which it is measured. However, it remains unclear why stress, per se, should increase δ. To our knowledge, only "competitive stress" has a logical connection to δ. Through competition for resources, better quality (outbred) individuals make the environment worse for lower quality (inbred) individuals, accentuating the differences between them. For this reason, we expect inbreeding depression to be stronger in environments where the fitness of individuals is more sensitive to the presence of conspecifics (i.e., where fitness is more density dependent). Indeed, some studies suggest a role for competition within environments, but this idea has not been tested in the context of understanding variation in δ across environments. Using Drosophila melanogaster, we estimated δ for viability in 22 different environments. These environments were simultaneously characterized for (1) stressfulness and (2) density dependence. Although stress and density dependence are moderately correlated with each other, inbreeding depression is much more strongly correlated with density dependence. These results suggest that mean selection across the genome is stronger in environments where competition is intense, rather than in environments that are stressful for other reasons.

  20. Controlled suppression of the photoluminescence superlinear dependence on excitation density in quantum dots.

    PubMed

    Bietti, Sergio; Sanguinetti, Stefano

    2012-10-04

    : We have shown that it is possible to tune, up to complete suppression, the photoluminescence superlinear dependence on the excitation density in quantum dot samples at high temperatures by annealing treatments. The effect has been attributed to the reduction of the defectivity of the material induced by annealing.

  1. 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…

  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 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...

  4. Density dependence of microscopic nucleon optical potential in first order Brueckner theory

    NASA Astrophysics Data System (ADS)

    Saliem, S. M.; Haider, W.

    2002-06-01

    In the present work we apply the lowest order Brueckner theory of infinite nuclear matter to obtain nucleon-nucleus optical potential for p-40Ca elastic scattering at 200 MeV using Urbana V14 soft core internucleon potential. We have investigated the effect of target density on the calculated nucleon-nucleus optical potential. We find that the calculated optical potentials depend quite sensitively on the density distribution of the target nucleus. The important feature is that the real part of calculated central optical potential for all densities shows a wine-bottle-bottom type behaviour at this energy. We also discuss the effect of our new radial dependent effective mass correction. Finally, we compare the prediction of our calculated nucleon optical potential using V14 with the prediction using older hard core Hamada-Johnston internucleon potential for p-40Ca elastic scattering at 200 MeV.

  5. Cosmological density perturbations with a scale-dependent Newton's constant G

    SciTech Connect

    Hamber, Herbert W.; Toriumi, Reiko

    2010-08-15

    We explore possible cosmological consequences of a running Newton's constant G({open_square}), as suggested by the nontrivial ultraviolet fixed point scenario in the quantum field-theoretic treatment of Einstein gravity with a cosmological constant term. In particular, we focus here on what possible effects the scale-dependent coupling might have on large scale cosmological density perturbations. Starting from a set of manifestly covariant effective field equations derived earlier, we systematically develop the linear theory of density perturbations for a nonrelativistic, pressureless fluid. The result is a modified equation for the matter density contrast, which can be solved and thus provides an estimate for the growth index parameter {gamma} in the presence of a running G. We complete our analysis by comparing the fully relativistic treatment with the corresponding results for the nonrelativistic (Newtonian) case, the latter also with a weakly scale-dependent G.

  6. 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...

  7. Widespread density-dependent seedling mortality promotes species coexistence in a highly diverse Amazonian rain forest.

    PubMed

    Metz, Margaret R; Sousa, Wayne P; Valencia, Renato

    2010-12-01

    Negative density-dependent mortality can promote species coexistence through a spacing mechanism that prevents species from becoming too locally abundant. Negative density-dependent seedling mortality can be caused by interactions among seedlings or between seedlings and neighboring adults if the density of neighbors affects the strength of competition or facilitates the attack of natural enemies. We investigated the effects of seedling and adult neighborhoods on the survival of newly recruited seedlings for multiple cohorts of known age from 163 species in Yasuni National Park, Ecuador, an ever-wet, hyper-diverse lowland Amazonian rain forest. At local scales, we found a strong negative impact on first-year survival of conspecific seedling densities and adult abundance in multiple neighborhood sizes and a beneficial effect of a local tree neighborhood that is distantly related to the focal seedling. Once seedlings have survived their first year, they also benefit from a more phylogenetically dispersed seedling neighborhood. Across species, we did not find evidence that rare species have an advantage relative to more common species, or a community compensatory trend. These results suggest that the local biotic neighborhood is a strong influence on early seedling survival for species that range widely in their abundance and life history. These patterns in seedling survival demonstrate the role of density-dependent seedling dynamics in promoting and maintaining diversity in understory seedling assemblages. The assemblage-wide impacts of species abundance distributions may multiply with repeated cycles of recruitment and density-dependent seedling mortality and impact forest diversity or the abundance of individual species over longer time scales.

  8. 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.

  9. 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.

  10. Collisionality Dependence of Multi-species Density Peaking in Turbulence Simulations of C-Mod Plasmas

    NASA Astrophysics Data System (ADS)

    Mikkelsen, D. R.; Bitter, M.; Delgado-Aparicio, L.; Hill, K. W.; Greenwald, M.; Howard, N.; Podpaly, Y.; Reinke, M.; Rice, J. E.; Hughes, J. W.; Ma, Y.; Candy, J.; Waltz, R. E.

    2012-10-01

    In nonlinear GYRO simulations of C-Mod plasmas, a turbulently driven pinch produces modest density peaking of all species. The ratio of density at r/a=0.44 and 0.74 is 1.2 for the majority and minority D & H (and electrons), and increases with impurity Z: 1.1 for helium, 1.15 for boron, 1.29 for neon, 1.36 for argon, 1.47 for molybdenum. Density peaking is only weakly affected when the ion temperature profile is varied to align the predicted heat flux to the experimental transport analysis. New simulations will extend the collisionality to the lower part of the experimentally accessible range in C-Mod to study the collisionality dependence of density peaking, and to establish whether much stronger peaking is predicted for lower collisionalities. Simulations based on measured I-mode ion and electron temperature profiles will also be presented.

  11. Frequency dependent power and energy flux density equations of the electromagnetic wave

    NASA Astrophysics Data System (ADS)

    Muhibbullah, M.; Haleem, Ashraf M. Abdel; Ikuma, Yasuro

    The calculation of the power and energy of the electromagnetic wave is important for numerous applications. There are some equations to compute the power and energy density of the electromagnetic wave radiation. For instance, the Poynting vector is frequently used to calculate the power density. However those including the Poynting vector are not perfect to represent the actual values because the equations are frequency independent. In the present study we have derived the frequency-dependent equations to calculate the power and energy flux density of the electromagnetic wave by help of the classical electromagnetic theories. It is seems that the Poynting vector with a certain electric and magnetic fields is correct only for a specific frequency. However our equations are perfect to calculate the values of the power and energy flux density for all frequencies of the electromagnetic radiation. The equations may help to develop the applications of the electromagnetic wave radiation.

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

    DOE PAGES

    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

  13. 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

  14. Density-dependent responses of fawn cohort body mass in two contrasting roe deer populations.

    PubMed

    Kjellander, Petter; Gaillard, Jean-Michel; Hewison, A J Mark

    2006-01-01

    We investigated the influence of population density on juvenile body mass in two contrasting roe deer populations, in Sweden (Bogesund) and France (Chizé), in which density was monitored for >or=15 years. We investigated the effect of population density and climatic conditions on cohort performance. We predicted that: (1) body mass of growing fawns should be sensitive to environmental changes, showing marked between-year variation (i.e., cohort effects), (2) fawns in the less productive (weakly seasonal, weakly predictable summer weather) habitat of Chizé should show stronger density-dependent responses due to more severe food competition during summer than fawns in the more productive (markedly seasonal, moderately predictable summer weather) habitat of Bogesund, and (3) fawns at Bogesund should be heavier both in absolute terms and relative to their size than their conspecifics in Chizé due to a higher degree of fat accumulation in northern environments. In both study sites we found marked cohort variation and clear effects of density, with body mass varying by as much as 29% over years. While neither summer nor winter climate influenced fawn body mass at Bogesund, fawns tended to be lighter after summers with high temperatures at Chizé. In addition, fawns were heavier after acorn mast years experienced in utero at Bogesund. As expected, the strength of the density-dependent response of fawn body mass was greater at Chizé than at Bogesund. For a given density, male fawns were consistently heavier than females in both sites. Lastly, both sexes at Bogesund had higher absolute body mass and were larger for a given body size than in Chizé. Our results clearly demonstrate that absolute density is a poor predictor of roe deer performance and supports the view that habitat quality has an overwhelming importance for determining fawn body mass in roe deer populations.

  15. Density- and Size-Dependent Winter Mortality and Growth of Late Chaoborus flavicans Larvae

    PubMed Central

    Schröder, Arne

    2013-01-01

    Winter processes such as overwinter survival and growth of individuals can have wide-ranging consequences for population dynamics and communities within and across seasons. In freshwater organisms winter processes have been mainly studied in fish despite that invertebrates also have substantial impacts on lake and pond food webs. One of the major invertebrate consumers in lake and ponds is the planktonic larvae of the dipteran insect Chaoborus spec. However, while much is known about Chaoborus feeding ecology, behaviour and structuring role in food webs, its winter ecology and how it affects its populations are poorly understood. Here size- and density-dependent winter mortality and body growth of late Chaoborus flavicans larvae were quantified over naturally occurring size and density ranges in autumn and under natural winter conditions using two field enclosure experiments. Winter mortality increased with autumn density but decreased with autumn body size while winter growth rates decreased with autumn density and body sizes. There was also a density- and size-independent background mortality component. The proportion of pupae found in spring decreased strongly and exponentially with autumn density. These results may explain the commonly observed univoltine life cycle and multi-annual density fluctuations in northern Chaoborus populations. They further demonstrate the relevance of winter processes and conditions for freshwater invertebrates and ecosystems. PMID:24124517

  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. Unified approach to nuclear densities from exotic atoms

    NASA Astrophysics Data System (ADS)

    Friedman, E.

    2009-09-01

    Parameters of nuclear density distributions are derived from least-squares fits to strong interaction observables in exotic atoms. Global analyses of antiprotonic and pionic atoms show reasonably good agreement between the two types of probes regarding the average behaviour of root-mean-square radii of the neutron distributions. Apparent conflict regarding the shape of the neutron distribution is attributed to different radial sensitivities of these two probes.

  18. 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.

  19. An evolutionary maximum principle for density-dependent population dynamics in a fluctuating environment.

    PubMed

    Lande, Russell; Engen, Steinar; Saether, Bernt-Erik

    2009-06-12

    The evolution of population dynamics in a stochastic environment is analysed under a general form of density-dependence with genetic variation in r and K, the intrinsic rate of increase and carrying capacity in the average environment, and in sigma(e)(2), the environmental variance of population growth rate. The continuous-time model assumes a large population size and a stationary distribution of environments with no autocorrelation. For a given population density, N, and genotype frequency, p, the expected selection gradient is always towards an increased population growth rate, and the expected fitness of a genotype is its Malthusian fitness in the average environment minus the covariance of its growth rate with that of the population. Long-term evolution maximizes the expected value of the density-dependence function, averaged over the stationary distribution of N. In the theta-logistic model, where density dependence of population growth is a function of N(theta), long-term evolution maximizes E[N(theta)]=[1-sigma(e)(2)/(2r)]K(theta). While sigma(e)(2) is always selected to decrease, r and K are always selected to increase, implying a genetic trade-off among them. By contrast, given the other parameters, theta has an intermediate optimum between 1.781 and 2 corresponding to the limits of high or low stochasticity.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Dispersal, density dependence, and population dynamics of a fungal microbe on leaf surfaces.

    PubMed

    Woody, Scott T; Ives, Anthony R; Nordheim, Erik V; Andrews, John H

    2007-06-01

    Despite the ubiquity and importance of microbes in nature, little is known about their natural population dynamics, especially for those that occupy terrestrial habitats. Here we investigate the dynamics of the yeast-like fungus Aureobasidium pullulans (Ap) on apple leaves in an orchard. We asked three questions. (1) Is variation in fungal population density among leaves caused by variation in leaf carrying capacities and strong density-dependent population growth that maintains densities near carrying capacity? (2) Do resident populations have competitive advantages over immigrant cells? (3) Do Ap dynamics differ at different times during the growing season? To address these questions, we performed two experiments at different times in the growing season. Both experiments used a 2 x 2 factorial design: treatment 1 removed fungal cells from leaves to reveal density-dependent population growth, and treatment 2 inoculated leaves with an Ap strain engineered to express green fluorescent protein (GFP), which made it possible to track the fate of immigrant cells. The experiments showed that natural populations of Ap vary greatly in density due to sustained differences in carrying capacities among leaves. The maintenance of populations close to carrying capacities indicates strong density-dependent processes. Furthermore, resident populations are strongly competitive against immigrants, while immigrants have little impact on residents. Finally, statistical models showed high population growth rates of resident cells in one experiment but not in the other, suggesting that Ap experiences relatively "good" and "bad" periods for population growth. This picture of Ap dynamics conforms to commonly held, but rarely demonstrated, expectations of microbe dynamics in nature. It also highlights the importance of local processes, as opposed to immigration, in determining the abundance and dynamics of microbes on surfaces in terrestrial systems.

  5. Evaluating Systematic Dependencies of Type Ia Supernovae: The Influence of Deflagration to Detonation Density

    NASA Astrophysics Data System (ADS)

    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 56Ni 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 56Ni 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 56Ni and NSE material synthesized for a suite of simulated explosions in which the transition density is varied in the range (1-3) ×107 g cm-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 sun for a 1 Z sun increase in metallicity evaluated about solar metallicity. For the same change in metallicity, this result translates to a 0.067 ± 0.004 M sun decrease in the 56Ni 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.

  6. 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.

  7. 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.

  8. Time-dependent stochastic Bethe-Salpeter approach

    NASA Astrophysics Data System (ADS)

    Rabani, Eran; Baer, Roi; Neuhauser, Daniel

    2015-06-01

    A time-dependent formulation for electron-hole excitations in extended finite systems, based on the Bethe-Salpeter equation (BSE), is developed using a stochastic wave function approach. The time-dependent formulation builds on the connection between time-dependent Hartree-Fock (TDHF) theory and the configuration-interaction with single substitution (CIS) method. This results in a time-dependent Schrödinger-like equation for the quasiparticle orbital dynamics based on an effective Hamiltonian containing direct Hartree and screened exchange terms, where screening is described within the random-phase approximation (RPA). To solve for the optical-absorption spectrum, we develop a stochastic formulation in which the quasiparticle orbitals are replaced by stochastic orbitals to evaluate the direct and exchange terms in the Hamiltonian as well as the RPA screening. This leads to an overall quadratic scaling, a significant improvement over the equivalent symplectic eigenvalue representation of the BSE. Application of the time-dependent stochastic BSE (TDsBSE) approach to silicon and CdSe nanocrystals up to size of ≈3000 electrons is presented and discussed.

  9. Quantum-dot density dependence of power conversion efficiency of intermediate-band solar cells

    NASA Astrophysics Data System (ADS)

    Sakamoto, Katsuyoshi; Kondo, Yasunori; Uchida, Keisuke; Yamaguchi, Koichi

    2012-12-01

    For intermediate-band solar cells containing GaAs/InAs quantum dots (QDs), the QD density dependence of the power conversion efficiency (PCE) was theoretically calculated for various sun concentrations under AM1.5 conditions based on detailed balance principles. A QD density of over 5 × 1013 cm-2 was required to achieve a PCE of more than 50% under 10 000 suns. However, under the photo-filled state and 1 sun, the PCE decreased over a wide total QD density range from about 3 × 1010 to 1 × 1013 cm-2. This reduction was attributed to the negative net carrier generation rate through the intermediate band, which was due to insufficient two-step optical absorption. The short-circuit current density increased as the QD density increased up to about 1 × 1011 cm-2 and it then saturated. In contrast, the open-circuit voltage decreased with increasing QD density. This reduction in the open-circuit voltage was suppressed at high sun concentrations.

  10. Electrode material dependence of two-dimensional electron and vapour density distribution over vacuum arc discharge

    NASA Astrophysics Data System (ADS)

    Inada, Y.; Matsuoka, S.; Kumada, A.; Ikeda, H.; Hidaka, K.

    2017-03-01

    Electrode material dependence of intense-mode vacuum arc behaviour was systematically investigated by using the Shack-Hartmann method capable of simultaneously visualising two-dimensional electron and metal vapour density distributions from single-shot recordings. The electrode materials studied included Cu, CuCr (Cu75Cr25 wt. %), WC, and AgWC (Ag40WC60 wt. %). A comparison between the Cu and CuCr electrodes showed that the metal vapour densities for the CuCr decreased in an even shorter time scale than for the Cu. In the case of the WC electrodes, the widths of the electron density distributions became narrower as the arc current decreased although the electron densities hardly decreased in the decaying process of the arc current. The density measurements conducted at the late stage of the vacuum arcs demonstrated that the metal vapour densities around the anode were maintained at the highest value for the AgWC among the electrode materials in this study.

  11. The density dependence of H-mode access at high magnetic fields

    NASA Astrophysics Data System (ADS)

    Hughes, J. W.; Brunner, D.; Hubbard, A. E.; Labombard, B.; Rice, J.; Terry, J.; Tolman, E.; Cziegler, I.; Edlund, E.

    2016-10-01

    Experimental investigations on Alcator C-Mod explore the power requirements, and local edge threshold conditions, for H-mode transitions, while accessing reactor-relevant plasma densities and toroidal magnetic fields from 2.5T to 8T. As on many tokamaks, the power threshold for H-mode Pth does not increase monotonically with density, but actually rises significantly below a particular value of ne (the so-called `low-density limit' for H-mode). Such behavior can not be reproduced by current scaling laws used to project the power threshold for H-mode on future devices, which tend to assume a power law form, e.g. Pth BTxney . Considerably more complicated dependencies are suggested by experiments, which indicate that the low-density branch moves to higher values of density as BT is increased. We extend this examination to magnetic fields that meet and surpass the ITER design field, and interpret the results in the context of candidate models to explain the upturn in Pth at low density. Supported by USDoE Award DE-FC02-99ER54512.

  12. 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.

  13. 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

  14. Density-dependent prophylaxis in the coral-eating crown-of-thorns sea star, Acanthaster planci

    NASA Astrophysics Data System (ADS)

    Mills, S. C.

    2012-06-01

    The density-dependent prophylaxis hypothesis predicts that individuals at high density will invest more resources into immune defence than individuals at lower densities as a counter-measure to density-dependent pathogen transmission rates. Evidence has been found for this hypothesis in insects, but not in a non-arthropod taxon. To investigate this hypothesis in the coral-eating crown-of-thorns sea star, Acanthaster planci, density treatments were set up over 21 days, and pathogen infection was simulated with bacterial injection. Five immune responses: amoebocyte count, amoebocyte viability, lysosomal membrane integrity, respiratory burst and peroxidase activity were all upregulated at high density. These results demonstrate that immune investment shows phenotypic plasticity with adult population density in agreement with the density-dependent prophylaxis hypothesis. Here I show that the density-dependent prophylaxis hypothesis is neither dependent on larval density nor restricted to insects, and hence may potentially have important consequences on disease dynamics in any species with widely fluctuating population densities. This is the first demonstration of the density-dependent prophylaxis hypothesis outside arthropods.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

    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)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.

  20. An exact solution in a gravitating fluid with a density-dependent viscosity

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Nikhil; Schamel, Hans; Schamel

    2013-12-01

    An exact nonlinear solution for a cold fluid in presence of a gravitational field and viscous dissipation is obtained using Lagrange variable. It is shown that with a density-dependent viscosity the nonlinear equation can be exactly solved. The solution indicates that in absence of viscosity and initial fluid velocity shear, density collapse occurs at time of the order of inverse Jeans frequency. The effect of viscosity is to delay the collapse but it can not halt the collapse. The initial fluid velocity shear can act in both directions: a positive one leads to delay, a negative one to a speeding up of the density collapse. This nonlinear solution may have some bearing with the structure formations in the universe.

  1. Temperature and concentration dependences of density and refraction of aqueous duloxetine solutions

    NASA Astrophysics Data System (ADS)

    Deosarkar, S. D.; Deoraye, S. M.; Kalyankar, T. M.

    2014-07-01

    Present paper reports the measured densities (ρ) and refractive indices ( n D) of aqueous solutions of Duloxetine drug in wide range of molal concentrations ( m = 0.0101-0.1031 mol kg-1) and at different temperatures (297.15, 302.15, and 307.15 K). Apparent molar volumes (φv) of drug were calculated from density data and fitted to Masson's relation and partial molar volumes (φ{v/0}) were evaluated at different temperatures. Concentration dependence of refractive index ( n D = Kc + n {D/0}) at experimental temperature has been studied. Density and refractive index data has been used for the calculation of specific refractions ( R D). Experimental (ρ and n D) and calculated (φv, φ{v/0}, and R D) properties have been interpreted in terms of concentration and temperature effects on structural fittings and drug-water interactions.

  2. Behavioral signature of intraspecific competition and density dependence in colony-breeding marine predators.

    PubMed

    Breed, Greg A; Don Bowen, W; Leonard, Marty L

    2013-10-01

    In populations of colony-breeding marine animals, foraging around colonies can lead to intraspecific competition. This competition affects individual foraging behavior and can cause density-dependent population growth. Where behavioral data are available, it may be possible to infer the mechanism of intraspecific competition. If these mechanics are understood, they can be used to predict the population-level functional response resulting from the competition. Using satellite relocation and dive data, we studied the use of space and foraging behavior of juvenile and adult gray seals (Halichoerus grypus) from a large (over 200,000) and growing population breeding at Sable Island, Nova Scotia (44.0 (o)N 60.0 (o)W). These data were first analyzed using a behaviorally switching state-space model to infer foraging areas followed by randomization analysis of foraging region overlap of competing age classes. Patterns of habitat use and behavioral time budgets indicate that young-of-year juveniles (YOY) were likely displaced from foraging areas near (<10 km) the breeding colony by adult females. This displacement was most pronounced in the summer. Additionally, our data suggest that YOY are less capable divers than adults and this limits the habitat available to them. However, other segregating mechanisms cannot be ruled out, and we discuss several alternate hypotheses. Mark-resight data indicate juveniles born between 1998 and 2002 have much reduced survivorship compared with cohorts born in the late 1980s, while adult survivorship has remained steady. Combined with behavioral observations, our data suggest YOY are losing an intraspecific competition between adults and juveniles, resulting in the currently observed decelerating logistic population growth. Competition theory predicts that intraspecific competition resulting in a clear losing competitor should cause compensatory population regulation. This functional response produces a smooth logistic growth curve as

  3. Behavioral signature of intraspecific competition and density dependence in colony-breeding marine predators

    PubMed Central

    Breed, Greg A; Don Bowen, W; Leonard, Marty L

    2013-01-01

    In populations of colony-breeding marine animals, foraging around colonies can lead to intraspecific competition. This competition affects individual foraging behavior and can cause density-dependent population growth. Where behavioral data are available, it may be possible to infer the mechanism of intraspecific competition. If these mechanics are understood, they can be used to predict the population-level functional response resulting from the competition. Using satellite relocation and dive data, we studied the use of space and foraging behavior of juvenile and adult gray seals (Halichoerus grypus) from a large (over 200,000) and growing population breeding at Sable Island, Nova Scotia (44.0 oN 60.0 oW). These data were first analyzed using a behaviorally switching state-space model to infer foraging areas followed by randomization analysis of foraging region overlap of competing age classes. Patterns of habitat use and behavioral time budgets indicate that young-of-year juveniles (YOY) were likely displaced from foraging areas near (<10 km) the breeding colony by adult females. This displacement was most pronounced in the summer. Additionally, our data suggest that YOY are less capable divers than adults and this limits the habitat available to them. However, other segregating mechanisms cannot be ruled out, and we discuss several alternate hypotheses. Mark–resight data indicate juveniles born between 1998 and 2002 have much reduced survivorship compared with cohorts born in the late 1980s, while adult survivorship has remained steady. Combined with behavioral observations, our data suggest YOY are losing an intraspecific competition between adults and juveniles, resulting in the currently observed decelerating logistic population growth. Competition theory predicts that intraspecific competition resulting in a clear losing competitor should cause compensatory population regulation. This functional response produces a smooth logistic growth curve as carrying

  4. Density Functional Approach and Random Matrix Theory in Proteogenesis

    NASA Astrophysics Data System (ADS)

    Yamanaka, Masanori

    2017-02-01

    We study the energy-level statistics of amino acids by random matrix theory. The molecular orbital and the Kohn-Sham orbital energies are calculated using ab initio and density-functional formalisms for 20 different amino acids. To generate statistical data, we performed a multipoint calculation on 10000 molecular structures produced via a molecular dynamics simulation. For the valence orbitals, the energy-level statistics exhibit repulsion, but the universality in the random matrix cannot be determined. For the unoccupied orbitals, the energy-level statistics indicate an intermediate distribution between the Gaussian orthogonal ensemble and the semi-Poisson statistics for all 20 different amino acids. These amino acids are considered to be in a type of critical state.

  5. 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.

  6. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding.

    PubMed

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

    2016-11-14

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nuclear wavefunction. The theory of vibrationally resolved UV/Vis spectroscopy is first summarized from the viewpoint of TD-DFTB. The method is benchmarked against time-dependent density functional theory (TD-DFT) calculations for strongly dipole allowed excitations in various aromatic and polar molecules. Using the recent 3ob:freq parameter set of Elstner's group, very good agreement with TD-DFT calculations using local functionals was achieved.

  7. 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)

  8. 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.

  9. Angular momentum dependence of the nuclear level density in the A ≈170 -200 region

    NASA Astrophysics Data System (ADS)

    Gohil, M.; Roy, Pratap; Banerjee, K.; Bhattacharya, C.; Kundu, S.; Rana, T. K.; Ghosh, T. K.; Mukherjee, G.; Pandey, R.; Pai, H.; Srivastava, V.; Meena, J. K.; Banerjee, S. R.; Mukhopadhyay, S.; Pandit, D.; Pal, S.; Bhattacharya, S.

    2015-01-01

    Neutron evaporation spectra along with γ multiplicity has been measured from 201Tl*,185Re*, and 169Tm* compound nuclei at the excitation energies of ˜27 and 37 MeV. Statistical model analysis of the experimental data has been carried out to extract the value of the inverse level density parameter k at different angular-momentum (J ) regions corresponding to different γ multiplicities. It is observed that, for the present systems the value of k remains almost constant for different J . The present results for the angular-momentum dependence of the nuclear level density (NLD) parameter a ˜(=A /k ) , for nuclei with A ˜180 are quite different from those obtained in earlier measurements in the case of light- and medium-mass systems. The present study provides useful information to understand the angular-momentum dependence of the NLD at different nuclear mass regions.

  10. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nuclear wavefunction. The theory of vibrationally resolved UV/Vis spectroscopy is first summarized from the viewpoint of TD-DFTB. The method is benchmarked against time-dependent density functional theory (TD-DFT) calculations for strongly dipole allowed excitations in various aromatic and polar molecules. Using the recent 3ob:freq parameter set of Elstner's group, very good agreement with TD-DFT calculations using local functionals was achieved.

  11. Frequency-dependent response of a pinned charge-density wave

    NASA Astrophysics Data System (ADS)

    Vinokur, Valerii; Fogler, Michael

    2003-03-01

    Recent theoretical advances in the theory of collective pinning [M. M. Fogler, Phys. Rev. Lett. 88, 186402 (2002)] enable us to go beyond the usual phenomenology in the theory of a finite-frequency response of a pinned charge-density wave (CDW) and to calculate ω and T dependences of the complex dielectric function without additional assumptions. According to our estimates, in typical electrical experiments on CDW, the dominant process is a thermal activation over atypically shallow barriers. It gives rise to a novel T^3/4-dependence of the linear response, in agreement with the experiment. A close analogy with acoustic attenuation in glassy dielectrics is noted.

  12. 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.

  13. Terrestrial habitat selection and strong density-dependent mortality in recently metamorphosed amphibians.

    PubMed

    Patrick, David A; Harper, Elizabeth B; Hunter, Malcolm L; Calhoun, Aram J K

    2008-09-01

    To predict the effects of terrestrial habitat change on amphibian populations, we need to know how amphibians respond to habitat heterogeneity, and whether habitat choice remains consistent throughout the life-history cycle. We conducted four experiments to evaluate how the spatial distribution of juvenile wood frogs, Rana sylvatica (including both overall abundance and localized density), was influenced by habitat choice and habitat structure, and how this relationship changed with spatial scale and behavioral phase. The four experiments included (1) habitat manipulation on replicated 10-ha landscapes surrounding breeding pools; (2) short-term experiments with individual frogs emigrating through a manipulated landscape of 1 m wide hexagonal patches; and habitat manipulations in (3) small (4-m2); and (4) large (100-m2) enclosures with multiple individuals to compare behavior both during and following emigration. The spatial distribution of juvenile wood frogs following emigration resulted from differences in the scale at which juvenile amphibians responded to habitat heterogeneity during active vs. settled behavioral phases. During emigration, juvenile wood frogs responded to coarse-scale variation in habitat (selection between 2.2-ha forest treatments) but not to fine-scale variation. After settling, however, animals showed habitat selection at much smaller scales (2-4 m2). This resulted in high densities of animals in small patches of suitable habitat where they experienced rapid mortality. No evidence of density-dependent habitat selection was seen, with juveniles typically choosing to remain at extremely high densities in high-quality habitat, rather than occupying low-quality habitat. These experiments demonstrate how prediction of the terrestrial distribution of juvenile amphibians requires understanding of the complex behavioral responses to habitat heterogeneity. Understanding these patterns is important, given that human alterations to amphibian habitats

  14. Remarks on time-dependent [current]-density functional theory for open quantum systems.

    PubMed

    Yuen-Zhou, Joel; Aspuru-Guzik, Alán

    2013-08-14

    Time-dependent [current]-density functional theory for open quantum systems (OQS) has emerged as a formalism that can incorporate dissipative effects in the dynamics of many-body quantum systems. Here, we review and clarify some formal aspects of these theories that have been recently questioned in the literature. In particular, we provide theoretical support for the following conclusions: (1) contrary to what we and others had stated before, within the master equation framework, there is in fact a one-to-one mapping between vector potentials and current densities for fixed initial state, particle-particle interaction, and memory kernel; (2) regardless of the first conclusion, all of our recently suggested Kohn-Sham (KS) schemes to reproduce the current and particle densities of the original OQS, and in particular, the use of a KS closed driven system, remains formally valid; (3) the Lindblad master equation maintains the positivity of the density matrix regardless of the time-dependence of the Hamiltonian or the dissipation operators; (4) within the stochastic Schrödinger equation picture, a one-to-one mapping from stochastic vector potential to stochastic current density for individual trajectories has not been proven so far, except in the case where the vector potential is the same for every member of the ensemble, in which case, it reduces to the Lindblad master equation picture; (5) master equations may violate certain desired properties of the density matrix, such as positivity, but they remain as one of the most useful constructs to study OQS when the environment is not easily incorporated explicitly in the calculation. The conclusions support our previous work as formally rigorous, offer new insights into it, and provide a common ground to discuss related theories.

  15. Exact ensemble density functional theory for excited states in a model system: Investigating the weight dependence of the correlation energy

    NASA Astrophysics Data System (ADS)

    Deur, Killian; Mazouin, Laurent; Fromager, Emmanuel

    2017-01-01

    Ensemble density functional theory (eDFT) is an exact time-independent alternative to time-dependent DFT (TD-DFT) for the calculation of excitation energies. Despite its formal simplicity and advantages in contrast to TD-DFT (multiple excitations, for example, can be easily taken into account in an ensemble), eDFT is not standard, which is essentially due to the lack of reliable approximate exchange-correlation (x c ) functionals for ensembles. Following Smith et al. [Phys. Rev. B 93, 245131 (2016), 10.1103/PhysRevB.93.245131], we propose in this work to construct an exact eDFT for the nontrivial asymmetric Hubbard dimer, thus providing more insight into the weight dependence of the ensemble x c energy in various correlation regimes. For that purpose, an exact analytical expression for the weight-dependent ensemble exchange energy has been derived. The complementary exact ensemble correlation energy has been computed by means of Legendre-Fenchel transforms. Interesting features like discontinuities in the ensemble x c potential in the strongly correlated limit have been rationalized by means of a generalized adiabatic connection formalism. Finally, functional-driven errors induced by ground-state density-functional approximations have been studied. In the strictly symmetric case or in the weakly correlated regime, combining ensemble exact exchange with ground-state correlation functionals gives better ensemble energies than when calculated with the ground-state exchange-correlation functional. However, when approaching the asymmetric equiensemble in the strongly correlated regime, the former approximation leads to highly curved ensemble energies with negative slope which is unphysical. Using both ground-state exchange and correlation functionals gives much better results in that case. In fact, exact ensemble energies are almost recovered in some density domains. The analysis of density-driven errors is left for future work.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Baseggio, Oscar; Fronzoni, Giovanna; Stener, Mauro

    2015-07-01

    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 H2 to [Au147]-). 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.

  18. 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.

  19. Protocol Dependence in Jammed Particulate Media: Statistics of the Density Landscape

    NASA Astrophysics Data System (ADS)

    Sampangiraj, Ashwin S.

    2011-03-01

    The density at which hard-sphere fluids jam into amorphous solids depends strongly on the compression protocol. Extremely fast quenching protocols bring each initial point in configuration space to the closest basin-maximum on the density landscape. In contrast, slower quench protocols allow the system to relax and explore configuration space. The protocol-dependence of the density, other structural quantities, and mechanical properties depends strongly on statistical features of the landscape. In this talk, I describe calculations of the the basin volumes associated with jammed hard sphere packings, and the critical quench rate Γ* above which the probabilities for obtaining jammed packings are determined by their basin volumes. Basin volumes are exponentially distributed; thus, for Γ >Γ* , so are jammed packing probabilities. We discuss the implications of this result on the statistical mechanics of jammed systems. This work was done in collaboration with Corey S O'Hern, Jerzy Blawdziewicz, Mark D. Shattuck. S. S. Ashwin and Corey O'Hern are supported by NSF grant no. CBET-0967262.

  20. 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.

  1. Simulations and Theory of Density-Dependent Dispersion in Weakly Heterogeneous Porous Media

    NASA Astrophysics Data System (ADS)

    Landman, A.; Schotting, R. J.

    2004-12-01

    The effect of density gradients on dispersive mixing of miscible fluids is studied. Density gradients not only affect dispersive transport for unstable flow, but also can significantly affect dispersion under stable conditions. For vertical displacements, laboratory experiments show a reduction of the longitudinal dispersivity under the influence of stabilizing density gradients. Linear Fick's law for the dispersive flux is inadequate to model these experiments. Therefore, alternative theories have been developed that incorporate the effect of density gradients. In this study, accurate numerical simulations of vertical displacements in weakly heterogeneous porous columns are performed. The numerical results confirm experimental observations. Furthermore, the computed concentration profiles are used to validate nonlinear dispersion theories applicable for high density gradients. A comparison is made with the stochastic theory of Welty and Gelhar, with homogenization theory, and with the nonlinear dispersion theory of Hassanizadeh and Leijnse. For small variances in log k, the stochastic and homogenization theory lead to reasonably good predictions of the computed concentration profiles and variances, without any fitting. In the theory of Hassanizadeh and Leijnse a fitting parameter is involved. This nonlinear dispersion parameter is not a true medium parameter, as it is found to be dependent on the flow rate and on the travel distance.

  2. 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.

  3. 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.

  4. Non-swarming grasshoppers exhibit density-dependent phenotypic plasticity reminiscent of swarming locusts.

    PubMed

    Gotham, Steven; Song, Hojun

    2013-11-01

    Locusts are well known for exhibiting an extreme form of density-dependent phenotypic plasticity known as locust phase polyphenism. At low density, locust nymphs are cryptically colored and shy, but at high density they transform into conspicuously colored and gregarious individuals. Most of what we know about locust phase polyphenism come from the study of the desert locust Schistocerca gregaria (Forskål), which is a devastating pest species affecting many countries in North Africa and the Middle East. The desert locust belongs to the grasshopper genus Schistocerca Stål, which includes mostly non-swarming, sedentary species. Recent phylogenetic studies suggest that the desert locust is the earliest branching lineage within Schistocerca, which raises a possibility that the presence of density-dependent phenotypic plasticity may be a plesiomorphic trait for the whole genus. In order to test this idea, we have quantified the effect of rearing density in terms of the resulting behavior, color, and morphology in two non-swarming Schistocerca species native to Florida. When reared in both isolated and crowded conditions, the two non-swarming species, Schistocerca americana (Drury) and Schistocerca serialis cubense (Saussure) clearly exhibited plastic reaction norms in all traits measured, which were reminiscent of the desert locust. Specifically, we found that both species were more active and more attracted to each other when reared in a crowded condition than in isolation. They were mainly bright green in color when isolated, but developed strong black patterns and conspicuous background colors when crowded. We found a strong effect of rearing density in terms of size. There were also more mechanoreceptor hairs on the outer face of the hind femora in the crowded nymphs in both species. Although both species responded similarly, there were some clear species-specific differences in terms of color and behavior. Furthermore, we compare and contrast our findings with

  5. 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.

  6. 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

  7. Experimental examination of intraspecific density-dependent competition during the breeding period in monarch butterflies (Danaus plexippus).

    PubMed

    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.

  8. 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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Yachao

    2014-12-01

    A first-principles study of critical temperatures (Tc) 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 Tc 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 ΔEHL and molecular vibrational frequencies in both spin states, then obtain the temperature dependent enthalpy and entropy changes (ΔH and ΔS), and finally extract Tc 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 Tc of the two phases. This study shows the applicability of the DFT+U approach for predicting Tc of SCO materials, and provides a clear insight into the subtle influence of the crystal packing effects on SCO behavior.

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

    PubMed

    Zhang, Yachao

    2014-12-07

    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.

  12. 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

  13. 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

  14. 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

  15. Time-Resolved Spectroscopy in Time-Dependent Density Functional Theory: An Exact Condition

    NASA Astrophysics Data System (ADS)

    Fuks, Johanna I.; Luo, Kai; Sandoval, Ernesto D.; Maitra, Neepa T.

    2015-05-01

    A fundamental property of a quantum system driven by an external field is that when the field is turned off the positions of its response frequencies are independent of the time at which the field is turned off. We show that this leads to an exact condition for the exchange-correlation potential of time-dependent density functional theory. The Kohn-Sham potential typically continues to evolve after the field is turned off, which leads to time dependence in the response frequencies of the Kohn-Sham response function. The exchange-correlation kernel must cancel out this time dependence. The condition is typically violated by approximations currently in use, as we demonstrate by several examples, which has severe consequences for their predictions of time-resolved spectroscopy.

  16. 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

  17. Density-dependent reduction and induction of milkweed cardenolides by a sucking insect herbivore.

    PubMed

    Martel, John W; Malcolm, Stephen B

    2004-03-01

    The effect of aphid population size on host-plant chemical defense expression and the effect of plant defense on aphid population dynamics were investigated in a milkweed-specialist herbivore system. Density effects of the aposematic oleander aphid, Aphis nerii, on cardenolide expression were measured in two milkweed species, Asclepias curassavica and A. incarnata. These plants vary in constitutive chemical investment with high mean cardenolide concentration in A. curassavica and low to zero in A. incarnata. The second objective was to determine whether cardenolide expression in these two host plants impacts mean A. nerii colony biomass (mg) and density. Cardenolide concentration (microgram/g) of A. curassavica in both aphid-treated leaves and opposite, herbivore-free leaves decreased initially in comparison with aphid-free controls, and then increased significantly with A. nerii density. Thus, A. curassavica responds to aphid herbivory initially with density-dependent phytochemical reduction, followed by induction of cardenolides to concentrations above aphid-free controls. In addition, mean cardenolide concentration of aphid-treated leaves was significantly higher than that of opposite, herbivore-free leaves. Therefore, A. curassavica induction is strongest in herbivore-damage tissue. Conversely, A. incarnata exhibited no such chemical response to aphid herbivory. Furthermore, neither host plant responded chemically to herbivore feeding duration time (days) or to the interaction between herbivore initial density and feeding duration time. There were also no significant differences in mean colony biomass or population density of A. nerii reared on high cardenolide (A. curassavica) and low cardenolide (A. incarnata) hosts.

  18. Density-Dependent Quantized Least Squares Support Vector Machine for Large Data Sets.

    PubMed

    Nan, Shengyu; Sun, Lei; Chen, Badong; Lin, Zhiping; Toh, Kar-Ann

    2017-01-01

    Based on the knowledge that input data distribution is important for learning, a data density-dependent quantization scheme (DQS) is proposed for sparse input data representation. The usefulness of the representation scheme is demonstrated by using it as a data preprocessing unit attached to the well-known least squares support vector machine (LS-SVM) for application on big data sets. Essentially, the proposed DQS adopts a single shrinkage threshold to obtain a simple quantization scheme, which adapts its outputs to input data density. With this quantization scheme, a large data set is quantized to a small subset where considerable sample size reduction is generally obtained. In particular, the sample size reduction can save significant computational cost when using the quantized subset for feature approximation via the Nyström method. Based on the quantized subset, the approximated features are incorporated into LS-SVM to develop a data density-dependent quantized LS-SVM (DQLS-SVM), where an analytic solution is obtained in the primal solution space. The developed DQLS-SVM is evaluated on synthetic and benchmark data with particular emphasis on large data sets. Extensive experimental results show that the learning machine incorporating DQS attains not only high computational efficiency but also good generalization performance.

  19. Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems.

    PubMed

    Ribbe, Jan; Maier, Berenike

    2016-04-12

    Bacterial quorum sensing is usually studied in well-mixed populations residing within closed systems. The latter do not exchange mass with their surroundings; however, in their natural environment, such as the rhizosphere, bacteria live in spatially structured open systems. Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation. We designed a microfluidic device that trapped swimming bacteria within microscopic compartments. The geometry of the traps controlled their diffusive coupling to fluid flow that played a dual role as nutrient source and autoinducer sink. Bacillus subtilis differentiates into a state of competence in response to quorum sensing and nutrient limitation. Using a mutant strain with a high differentiation rate and fluorescent reporters for competence, we found that the cell density required for differentiation was 100-fold higher than that required in closed systems. A direct comparison of strongly and moderately coupled reservoirs showed that strong coupling supported early differentiation but required a higher number of bacteria for its initiation. Weak coupling resulted in retardation of growth and differentiation. We conclude that spatial heterogeneity can promote density-dependent differentiation in open systems, and propose that the minimal quorum is determined by diffusive coupling to the environment through a trade-off between retaining autoinducers and accessing nutrients.

  20. Simulating Regional Groundwater Flow Patterns in South Florida Using Density-Dependent Numerical Models

    NASA Astrophysics Data System (ADS)

    England, S. M.; Stevens, G. T.

    2008-05-01

    Aquifer Storage and Recovery (ASR) is the storage of fresh water in an aquifer via injection during times when water is available, and recovery of the water from the same aquifer via pumping during times when it is needed. ASR is one of the proposed alternatives recommended by the Comprehensive Everglades Restoration Plan (CERP) to help with water supply, storage, and distribution of water in South Florida. To evaluate the numerous design considerations and the variation in aquifer response resulting from CERP ASR, regional density- dependent numerical modeling of the Floridan Aquifer System (FAS) in the southern half of Florida is in progress. This modeling incorporates use of two density-dependent numerical codes, SEAWAT and WASH123D, and the synthesis of regional knowledge of the FAS in terms of geologic parameters, groundwater flow patterns, and salinity influences. Several challenges have been discovered in replicating the existing regional groundwater flow patterns, most notably, that in south-central Florida the simulated heads are considerably lower than observed values. Recent model studies of several factors that could affect south Florida regional flow patterns indicate that the inclusion of preferential flow as well as the effects of temperature on groundwater density yield results that are more consistent with observed values. Future work will focus on the investigation of field data to support the application of preferential flow and the addition of groundwater injection and withdrawal including existing and proposed ASR projects.

  1. Predator effects on reef fish settlement depend on predator origin and recruit density.

    PubMed

    Benkwitt, Cassandra E

    2017-04-01

    During major life-history transitions, animals often experience high mortality rates due to predation, making predator avoidance particularly advantageous during these times. There is mixed evidence from a limited number of studies, however, regarding how predator presence influences settlement of coral-reef fishes and it is unknown how other potentially mediating factors, including predator origin (native vs. nonnative) or interactions among conspecific recruits, mediate the non-consumptive effects of predators on reef fish settlement. During a field experiment in the Caribbean, approximately 52% fewer mahogany snapper (Lutjanus mahogoni) recruited to reefs with a native predator (graysby grouper, Cephalopholis cruentata) than to predator-free control reefs and reefs with an invasive predator (red lionfish, Pterois volitans) regardless of predator diet. These results suggest that snapper recruits do not recognize nonnative lionfish as a threat. However, these effects depended on the density of conspecific recruits, with evidence that competition may limit the response of snapper to even native predators at the highest recruit densities. In contrast, there was no effect of predator presence or conspecific density on the recruitment of bicolor damselfish (Stegastes partitus). These context-dependent responses of coral-reef fishes to predators during settlement may influence individual survival and shape subsequent population and community dynamics.

  2. Invasive leaf resources alleviate density dependence in the invasive mosquito, Aedes albopictus

    PubMed Central

    Zarrabi, Ali A.; Lounibos, L. Philip

    2012-01-01

    Interactions between invasive species can have important consequences for the speed and impact of biological invasions. Containers occupied by the invasive mosquito, Aedes albopictus Skuse, may be sensitive to invasive plants whose leaves fall into this larval habitat. To examine the potential for interactions between invasive leaf species and larval A. albopictus, we conducted a field survey of leaf material found with A. albopictus in containers in Palm Beach County, Florida and measured density dependent responses of A. albopictus larvae to two invasive and one native leaf species in laboratory experiments. We found increased diversity of leaf species, particularly invasive species, in areas further from the urbanized coast, and a significant positive association between the presence of Schinus terebinthifolious (Brazilian pepper) and the abundance of A. albopictus. In laboratory experiments, we determined that larval growth and survivorship were significantly affected by both larval density and leaf species which, in turn, resulted in higher population performance on the most abundant invasive species (Brazilian pepper) relative to the most abundant native species, Quercus virginiana (live oak). These results suggest invasive leaf species can alleviate density dependent reductions in population performance in A. albopictus, and may contribute to its invasion success and potential to spread infectious disease. PMID:22523473

  3. Context-dependent landscape of fear: algal density elicits risky herbivory in a coral reef.

    PubMed

    Gil, Michael A; Zill, Julie; Ponciano, José M

    2017-02-01

    Foraging theory posits that isolation from refuge habitat within a landscape increases perceived predation risk and, thus, suppresses the foraging behavior of prey species. However, these effects may depend fundamentally on resource availability, which could affect prey boldness and can change considerably through bottom-up processes. We conducted a field survey and experiment in a coral reef to test the effects of isolation from refuge habitat (i.e., reef structure) on herbivory by reef fishes and whether these effects depend on resource density. By fitting continuous-time, pure death Markov processes to our data, we found that at both the local and landscape scale distance from refuge habitat reduced herbivory in attractive resource patches of palatable benthic algae. However, our field experiment revealed that higher initial resource densities weakened negative effects of distance from refuge habitat on herbivory. Furthermore, we observed higher bite rates and greater total lengths of herbivorous fishes with greater distance from refuge habitat-responses consistent with higher perceived predation risk. Our results suggest that while the loss or fragmentation of refuge habitat reduces consumer control of resources, greater resource densities can partially counteract this effect by altering landscapes of fear of consumer species. Our findings emphasize the importance of considering the spatial context of species interactions that structure communities.

  4. Is the prevalence of Taenia taeniaeformis in Microtus arvalis dependent on population density?

    PubMed

    Fichet-Calvet, Elisabeth; Giraudoux, Patrick; Quéré, Jean-Pierre; Ashford, Richard William; Delattre, Pierre

    2003-12-01

    Populations of common voles Microtus arvalis were studied as hosts of the tapeworm Taenia taeniaeformis during a 14-yr survey. They were monitored in spring, summer, and autumn in a pastoral ecosystem in eastern France. A total of 7,574 voles were sampled during 2 multiannual population fluctuations. A third fluctuation was sampled during the increase phase only. Overall prevalence was lowest in summer (0.6%), increased by 3 times in autumn (1.5%) and a further 5 times in spring (7.8%). Analysis of prevalence, based on 7,384 voles, by multiple logistic regression revealed that extrinsic factors such as season and intrinsic factors such as host age and host density have a combined effect. In the longer term, host age and host density were positively associated with prevalence in summer. Host density was strongly associated with autumn prevalence. There was no association between the fluctuation phase and prevalence. The study shows that a long timescale (here a multiannual survey) is necessary to demonstrate the positive effect of host density on the prevalence of this indirectly transmitted parasite. The demonstration of this relationship depends on the rodents being intermediate rather than definitive hosts.

  5. Density-Dependent Effects of an Invasive Ant on a Ground-Dwelling Arthropod Community.

    PubMed

    Cooling, M; Sim, D A; Lester, P J

    2015-02-01

    It is frequently assumed that an invasive species that is ecologically or economically damaging in one region, will typically be so in other environments. The Argentine ant Linepithema humile (Mayr) is listed among the world's worst invaders. It commonly displaces resident ant species where it occurs at high population densities, and may also reduce densities of other ground-dwelling arthropods. We investigated the effect of varying Argentine ant abundance on resident ant and nonant arthropod species richness and abundance in seven cities across its range in New Zealand. Pitfall traps were used to compare an invaded and uninvaded site in each city. Invaded sites were selected based on natural varying abundance of Argentine ant populations. Argentine ant density had a significant negative effect on epigaeic ant abundance and species richness, but hypogaeic ant abundance and species richness was unaffected. We observed a significant decrease in Diplopoda abundance with increasing Argentine ant abundance, while Coleoptera abundance increased. The effect on Amphipoda and Isopoda depended strongly on climate. The severity of the impact on negatively affected taxa was reduced in areas where Argentine ant densities were low. Surprisingly, Argentine ants had no effect on the abundance of the other arthropod taxa examined. Morphospecies richness for all nonant arthropod taxa was unaffected by Argentine ant abundance. Species that are established as invasive in one location therefore cannot be assumed to be invasive in other locations based on presence alone. Appropriate management decisions should reflect this knowledge.

  6. 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

    2014-11-07

    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.

  7. 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

  8. 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.

  9. 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.

  10. Time-dependent, lattice approach to atomic collisions

    SciTech Connect

    Schultz, D.R.

    1995-12-31

    Recent progress in developing and applying methods of direct numerical solution of atomic collision problems is described. Various forms of the three-body problem are used to illustrate these techniques. Specifically, the process of ionization in proton-, antiproton-, and electron-impact of atomic hydrogen is considered in applications ranging in computational intensity from collisions simulated in two spatial dimensions to treatment of the three-dimensional, fully correlated two-electron Schroedinger equation. These examples demonstrate the utility and feasibility of treating strongly interacting atomic systems through time-dependent, lattice approaches.

  11. 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.

  12. A density-dependent model of competition for one resource in the chemostat.

    PubMed

    Fekih-Salem, Radhouane; Lobry, Claude; Sari, Tewfik

    2017-04-01

    This paper deals with a two-microbial species model in competition for a single-resource in the chemostat including general intra- and interspecific density-dependent growth rates with distinct removal rates for each species. In order to understand the effects of intra- and interspecific interference, this general model is first studied by determining the conditions of existence and local stability of steady states. With the same removal rate, the model can be reduced to a planar system and then the global stability results for each steady state are derived. The bifurcations of steady states according to interspecific interference parameters are analyzed in a particular case of density-dependent growth rates which are usually used in the literature. The operating diagrams show how the model behaves by varying the operating parameters and illustrate the effect of the intra- and interspecific interference on the disappearance of coexistence region and the occurrence of bi-stability region. Concerning the small enough interspecific interference terms, we would shed light on the global convergence towards the coexistence steady state for any positive initial condition. When the interspecific interference pressure is large enough this system exhibits bi-stability where the issue of the competition depends on the initial condition.

  13. LHC soft physics and transverse momentum dependent gluon density at low x

    NASA Astrophysics Data System (ADS)

    Lipatov, A. V.; Lykasov, G. I.; Zotov, N. P.

    2014-01-01

    We study the unintegrated, or transverse momentum dependent gluon distribution obtained from the best description of the LHC data on the inclusive spectra of hadrons produced in the midrapidity region and at low transverse momenta at the starting scale Q02=1 GeV2. To extend this gluon density to higher Q2 we apply the Catani-Ciafoloni-Fiorani-Marchesini evolution equation. The influence of the initial (starting) nonperturbative gluon distribution is studied. The application of the obtained gluon density to the analysis of the deep inelastic ep scattering allows us to get the results which describe reasonably well the H1 and ZEUS data on the longitudinal proton structure function FL(x ,Q2). So, the connection between the soft processes at the LHC and small-x physics at HERA has been confirmed and extended to a wide kinematical region.

  14. 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.

  15. 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.

  16. 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.

  17. Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.

    PubMed

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-01-14

    Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.

  18. 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.

  19. Excitation energy dependence of the level density parameter close to the doubly magic 208Pb

    NASA Astrophysics Data System (ADS)

    Roy, Pratap; Banerjee, K.; Bhattacharya, C.; Pandey, R.; Sen, A.; Manna, S.; Kundu, S.; Rana, T. K.; Ghosh, T. K.; Mukherjee, G.; Roy, T.; Dhal, A.; Dey, A.; Meena, J. K.; Saha, A. K.; Pandit, Deepak; Mukhopadhyay, S.; Bhattacharya, S.

    2016-12-01

    Neutron evaporation spectra have been measured from 4He+208Pb and 4He+209Bi reactions by using 4He-ion beams of several bombarding energies. Excitation-energy dependence of the level density parameter has been studied for the two systems in the excitation energy range of ˜18 -50 MeV. For both the reactions an overall reduction of the asymptotic level density parameter with increasing excitation energy (temperature) is observed. The trend of the data was compared with the Thomas-Fermi model predictions and found to be in reasonable agreement. The value of the shell damping parameter has been extracted from the lowest-energy data in the case of Po,211210 and At,212211 nuclei close to the Z =82 and N =126 shell closure, and it was found to be consistent with the recent measurement in the vicinity of doubly magic 208Pb nucleus.

  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

    DOE PAGES

    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

  2. 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.

  3. Density-dependent changes in effective area occupied for sea-bottom-associated marine fishes.

    PubMed

    Thorson, James T; Rindorf, Anna; Gao, Jin; Hanselman, Dana H; Winker, Henning

    2016-10-12

    The spatial distribution of marine fishes can change for many reasons, including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model (PDM; no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model (BM; positive abundance-area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes. We fit a spatio-temporal model and estimate changes in effective area occupied and abundance, and combine results to estimate the average abundance-area relationship as well as variability among taxa and regions. The average relationship is weak but significant (0.6% increase in area for a 10% increase in abundance), whereas only a small proportion of species-region combinations show a negative relationship (i.e. shrinking area when abundance increases). Approximately one-third of combinations (34.6%) are predicted to increase in area more than 1% for every 10% increase in abundance. We therefore infer that population density generally changes faster than effective area occupied during abundance changes. Gadiformes have the strongest estimated relationship (average 1.0% area increase for every 10% abundance increase) followed by Pleuronectiformes and Scorpaeniformes, and the Eastern Bering Sea shows a strong relationship between abundance and area occupied relative to other regions. We conclude that the BM explains a small but important portion of spatial dynamics for sea-bottom-associated fishes, and that many individual populations merit cautious management during population declines, because a compressed range may increase the efficiency of harvest.

  4. 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).

  5. Density functional description of size-dependent effects at nucleation on neutral and charged nanoparticles

    NASA Astrophysics Data System (ADS)

    Shchekin, Alexander K.; Lebedeva, Tatiana S.

    2017-03-01

    A numerical study of size-dependent effects in the thermodynamics of a small droplet formed around a solid nanoparticle has been performed within the square-gradient density functional theory. The Lennard-Jones fluid with the Carnahan-Starling model for the hard-sphere contribution to intermolecular interaction in liquid and vapor phases and interfaces has been used for description of the condensate. The intermolecular forces between the solid core and condensate molecules have been taken into account with the help of the Lennard-Jones part of the total molecular potential of the core. The influence of the electric charge of the particle has been considered under assumption of the central Coulomb potential in the medium with dielectric permittivity depending on local condensate density. The condensate density profiles and equimolecular radii for equilibrium droplets at different values of the condensate chemical potential have been computed in the cases of an uncharged solid core with the molecular potential, a charged core without molecular potential, and a core with joint action of the Coulomb and molecular potentials. The appearance of stable equilibrium droplets even in the absence of the electric charge has been commented. As a next step, the capillary, disjoining pressure, and electrostatic contributions to the condensate chemical potential have been considered and compared with the predictions of classical thermodynamics in a wide range of values of the droplet and the particle equimolecular radii. With the help of the found dependence of the condensate chemical potential in droplet on the droplet size, the activation barrier for nucleation on uncharged and charged particles has been computed as a function of the vapor supersaturation. Finally, the work of droplet formation and the work of wetting the particle have been found as functions of the droplet size.

  6. 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.

  7. Extraction of state-resolved information from systems with a fractional number of electrons within the framework of time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Wang, Feng; Yao, Yugui; Calvayrac, Florent; Zhang, Fengshou

    2016-09-01

    The determination of the state-resolved physical information within the framework of time-dependent density functional theory has remained a widely open question. We demonstrated the ability to extract the state-resolved probability from the knowledge of only the time-dependent density, which has been used as the basic variable within the time-dependent density functional theory, with the help of state-resolved single-electron capture experiments for collisions of protons on helium in the energy range of 2-100 keV/amu. The present theoretical results for capture into states of H(1s), H(2s), and H(2p) are in good agreement with the most sophisticated experimental results of H+ + He(1s2) system, validating our approach and numerical implementation.

  8. 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.

  9. 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.

  10. Excitonic effects in solids described by time-dependent density-functional theory.

    PubMed

    Reining, Lucia; Olevano, Valerio; Rubio, Angel; Onida, Giovanni

    2002-02-11

    Starting from the many-body Bethe-Salpeter equation we derive an exchange-correlation kernel f(xc) that reproduces excitonic effects in bulk materials within time-dependent density functional theory. The resulting f(xc) accounts for both self-energy corrections and the electron-hole interaction. It is static, nonlocal, and has a long-range Coulomb tail. Taking the example of bulk silicon, we show that the -alpha/q(2) divergency is crucial and can, in the case of continuum excitons, even be sufficient for reproducing the excitonic effects and yielding excellent agreement between the calculated and the experimental absorption spectrum.

  11. The amplitude of auroral backscatter. I - Model estimates of the dependence on electron density

    NASA Astrophysics Data System (ADS)

    Uspenskii, M. V.; Williams, P. J. S.

    1988-01-01

    A model of the auroral backscatter amplitude, in the form discussed by Uspensky (1985) and Oksman et al. (1986), has been derived for the radar geometry appropriate to joint observations by the PGI auroral radars at Karmaselga and Essoyla and the EISCAT incoherent scatter radar. The model shows how refraction effects cause a strongly nonlinear dependence of backscatter amplitude on electron density in the E-region. It also explains why the macroaspect sensitivity for auroral radar operating at a frequency of about 45 MHz is only 1-2 dB per degree for aspect angles greater than 5 deg.

  12. Depth dependency of neutron density produced by cosmic rays in the lunar subsurface

    NASA Astrophysics Data System (ADS)

    Ota, S.; Sihver, L.; Kobayashi, S.; Hasebe, N.

    2014-11-01

    Depth dependency of neutrons produced by cosmic rays (CRs) in the lunar subsurface was estimated using the three-dimensional Monte Carlo particle and heavy ion transport simulation code, PHITS, incorporating the latest high energy nuclear data, JENDL/HE-2007. The PHITS simulations of equilibrium neutron density profiles in the lunar subsurface were compared with the measurement by Apollo 17 Lunar Neutron Probe Experiment (LNPE). Our calculations reproduced the LNPE data except for the 350-400 mg/cm2 region under the improved condition using the CR spectra model based on the latest observations, well-tested nuclear interaction models with systematic cross section data, and JENDL/HE-2007.

  13. Density dependent mechanical properties and structures of a freeze dried biopharmaceutical excipient--sucrose.

    PubMed

    Devi, Sharmila; Williams, Daryl R

    2014-10-01

    Knowledge of the mechanical behaviour of freeze dried biopharmaceutical products is essential for designing of products with physical robustness that will not to crack, crumble or collapse during processing or transportation. The compressive mechanical deformation behaviour for freeze-dried sucrose cakes has been experimentally studied from a relative density (ρf/ρs) of 0.01-0.30 using a novel in-vial indentation test. Cakes exhibited more open like structures at lower densities and more closed structures at higher densities with some faces being present at all densities, as confirmed by SEM. The reduced elastic modulus Ef/Es=0.0044(ρf/ρs)(1) for all cake densities, indicating that face stretching was the dominant deformation mode assuming Gibson and Ashby's closed cell model. This linear scaling for the reduced elastic modulus is in line with various theoretical treatments based on tetrakaidecahedral cells and other experimental studies. Consistently, the wall thickness to cell diameter ratio scaled ρf/ρs with a power constant of 1.05. The maximum crushing stress was given by σmax=3800(ρf/ρs)(1.48) which agrees with a strut bending failure stress, assuming Gibson and Ashby's open cell model. Overall, the freeze dried cakes behaved as neither classic closed cell nor open cell materials, with their compressive elastic moduli reflecting a closed cell elastic response whilst their failure stresses reflecting an open cell failure mode. It was concluded that the mechanical response of freeze dried cellular materials depends upon their complex cellular structures and morphologies, and they cannot be rationalised using simple limiting case models of open or closed cell solids.

  14. Stimulation of limb cartilage differentiation by cyclic AMP is dependent on cell density.

    PubMed

    Rodgers, B J; Kulyk, W M; Kosher, R A

    1989-12-01

    Cyclic AMP (cAMP) has been implicated in the regulation of limb cartilage differentiation. This study represents an attempt to clarify potential mechanisms by which cAMP might regulate chondrogenesis. We have found that the ability of cAMP to stimulate limb cartilage differentiation in vitro is dependent on cell density. Dibutyryl cAMP (dbcAMP) elicits a striking increase in the accumulation of Alcian blue, pH 1.0-positive cartilage matrix, and a corresponding three- to fourfold increase in the accumulation of 35S-labeled glycosaminoglycans (GAG) by limb mesenchymal cells cultured in low serum medium at densities greater than confluence (i.e. micromass cultures established with 1-2 x 10(5) cells in 10 microliters of medium). Moreover, dbcAMP causes a striking (two- to fourfold) increase in the steady-state cytoplasmic levels of mRNAs for cartilage-characteristic type II collagen and the core protein of cartilage-specific sulfated proteoglycan in these high density, supraconfluent cultures. In contrast, cAMP does not promote the chondrogenesis of limb mesenchymal cells cultured at subconfluent densities (i.e. cultures initiated with 2.5-5 x 10(4) cells in 10 microliters of medium). In these low density cultures, dbcAMP does not promote the formation of cartilage matrix, sulfated GAG accumulation or the accumulation of cartilage-specific mRNAs. These observations suggest that cAMP may exert its regulatory effect in part by facilitating cell-cell communication during the critical condensation phase of chondrogenesis.

  15. 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.

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

    PubMed Central

    Chan, Ying-Chi; Penning, Emma; Cluderay, John; Spaulding, Eric L.; Dekinga, Anne; ten Horn, Job; Brugge, Maarten; Winkler, David W.

    2016-01-01

    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

  17. 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

  18. Anomalous Magnetic Field Dependence of Charge Carrier Density in Ferromagnetic Semiconductors

    NASA Astrophysics Data System (ADS)

    Kuivalainen, P.; Sinkkonen, J.; Stubb, T.

    1980-01-01

    This paper reports calculations of temperature and magnetic field dependent thermal and optical activation energies of a shallow donor state and the energy of the conduction band edge in a ferromagnetic semiconductor. The formation of the bound magnetic polaron (BMP), i.e., a magnetically polarized cluster associated with the donor electron, is taken into account. The solution of a set of coupled equations for the energy of a donor electron and for the local non-uniform magnetization around the donor center indicates that the activation energies have their maxima near the Curie temperature and decrease with the application of a magnetic field. This decrease leads to a strong magnetic field dependence of the charge carrier density nc explains well the giant negative magnetoresistance of EuSe observed experimentally at low temperatures.

  19. Rotochemical heating with a density-dependent superfluid energy gap in neutron stars

    SciTech Connect

    Gonzalez-Jimenez, Nicolas; Petrovich, Cristobal; Reisenegger, Andreas

    2010-08-04

    When a rotating neutron star loses angular momentum, the reduction of the centrifugal force makes it contract. This perturbs each fluid element, raising the local pressure and originating deviations from beta equilibrium, inducing reactions that release heat (rotochemical heating). This effect has previously been studied by Fernandez and Reisenegger for neutron stars of non-superfluid matter and by Petrovich and Reisenegger for superfluid matter, finding that the system in both cases reaches a quasi-steady state, corresponding to a partial equilibration between compression, due to the loss of angular momentum, and reactions that try to restore the equilibrium. However, Petrovich and Reisenegger assumes a constant value of the superfluid energy gap, whereas theoretical models predict density-dependent gap amplitudes, and therefore gaps that depend on the location in the star. In this work, we try to discriminate between several proposed gap models, comparing predicted surface temperatures to the value measured for the nearest millisecond pulsar, J0437-4715.

  20. Surface Structure and Electron Density Dependence of Scattered Ne^+ Ion Fractions From the Si(100)-(2x1) Surface

    NASA Astrophysics Data System (ADS)

    Wolfgang, John; Nordlander, Peter; Vaquilla, Isadora; Lui, K. M.; Rabalais, J. W.

    2000-03-01

    Experimental measurements of ion neutralization rates scattered from semiconductor surfaces have shown strong dependence on local surface structure and charge density. Recent scattering experiments utilizing 4 KeV Ne^+ scattered from a Si(100)-(2x1)surface exhibit strong azmuthal anisotropy, and can be shown to directly correlate to the reconstructed silicon surface geometry. Using a simple rate equation approach, a model based on the local charge density of the silicon surface has been used to determine the final neutral ion fraction from this scattering experiment. This rate equation approach has also been applied to scattering events between 4 KeV Ne^+ and a n- or p-type Si(100)-(2x1) surface. In the case of an n-doped Si surface, little or no change in the final ion neutralization is observed, while p-doping of the Si surface presents a significant decrease in the final neutral ion fractions compared to the undoped case. This effect will be discussed using a rate equation analysis, examining contributions from modification of the valence and conduction bands as a result of Si doping upon the overall charge transfer and ion neutralization.

  1. Nucleus-Dependent Valence-Space Approach to Nuclear Structure

    NASA Astrophysics Data System (ADS)

    Stroberg, S. R.; Calci, A.; Hergert, H.; Holt, J. D.; Bogner, S. K.; Roth, R.; Schwenk, A.

    2017-01-01

    We present a nucleus-dependent valence-space approach for calculating ground and excited states of nuclei, which generalizes the shell-model in-medium similarity renormalization group to an ensemble reference with fractionally filled orbitals. Because the ensemble is used only as a reference, and not to represent physical states, no symmetry restoration is required. This allows us to capture three-nucleon (3 N ) forces among valence nucleons with a valence-space Hamiltonian specifically targeted to each nucleus of interest. Predicted ground-state energies from carbon through nickel agree with results of other large-space ab initio methods, generally to the 1% level. In addition, we show that this new approach is required in order to obtain convergence for nuclei in the upper p and s d shells. Finally, we address the 1+/3+ inversion problem in 22Na and 46V. This approach extends the reach of ab initio nuclear structure calculations to essentially all light- and medium-mass nuclei.

  2. Modified Sediment Rating Curve Approach for Supply-dependent Conditions

    NASA Astrophysics Data System (ADS)

    Wright, S. A.; Topping, D. J.; Rubin, D. M.; Melis, T. S.

    2007-12-01

    particularly suited to such an approach because it is substantially sediment supply-limited such that transport rates are dependent on both flow and sediment supply; also, there is a rich dataset available for constraining the empirical parameters and testing the hybrid model. Though more empirical in nature than the morphodynamic models, this modified sediment rating curve approach may have broad potential application because its simplicity allows for relatively rapid evaluation of long-term sediment budgets under a range of flow regimes and sediment supply conditions.

  3. 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.

  4. Individual differences, density dependence and offspring birth traits in a population of red deer

    PubMed Central

    Stopher, Katie V; Pemberton, Josephine M; Clutton-Brock, Tim H; Coulson, Tim

    2008-01-01

    Variation between individuals is an essential component of natural selection and evolutionary change, but it is only recently that the consequences of persistent differences between individuals on population dynamics have been considered. In particular, few authors have addressed whether interactions exist between individual quality and environmental variation. In part, this is due to the difficulties of collecting sufficient data, but also the challenge of defining individual quality. Using a long-established study population of red deer, Cervus elaphus, inhabiting the North Block of the Isle of Rum, and three quality measures, this paper investigates how differences in maternal quality affect variation in birth body mass and date, as population density varies, and how this differs depending on the sex of the offspring and the maternal quality measure used. Significant interactions between maternal quality, measured as a hind's total contribution to population growth, and population density are reported for birth mass, but only for male calves. Analyses using dominance or age at primiparity to define maternal quality showed no significant interactions with population density, highlighting the difficulties of defining a consistent measure of individual quality. PMID:18522909

  5. 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.

  6. Hippo signaling regulates Microprocessor and links cell density-dependent miRNA biogenesis to cancer

    PubMed Central

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

    2014-01-01

    SUMMARY 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 post-transcriptional 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. PMID:24581491

  7. 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.

  8. Individual differences, density dependence and offspring birth traits in a population of red deer.

    PubMed

    Stopher, Katie V; Pemberton, Josephine M; Clutton-Brock, Tim H; Coulson, Tim

    2008-09-22

    Variation between individuals is an essential component of natural selection and evolutionary change, but it is only recently that the consequences of persistent differences between individuals on population dynamics have been considered. In particular, few authors have addressed whether interactions exist between individual quality and environmental variation. In part, this is due to the difficulties of collecting sufficient data, but also the challenge of defining individual quality. Using a long-established study population of red deer, Cervus elaphus, inhabiting the North Block of the Isle of Rum, and three quality measures, this paper investigates how differences in maternal quality affect variation in birth body mass and date, as population density varies, and how this differs depending on the sex of the offspring and the maternal quality measure used. Significant interactions between maternal quality, measured as a hind's total contribution to population growth, and population density are reported for birth mass, but only for male calves. Analyses using dominance or age at primiparity to define maternal quality showed no significant interactions with population density, highlighting the difficulties of defining a consistent measure of individual quality.

  9. Density-dependent predation influences the evolution and behavior of masquerading prey

    PubMed Central

    Skelhorn, John; Rowland, Hannah M.; Delf, Jon; Speed, Michael P.; Ruxton, Graeme D.

    2011-01-01

    Predation is a fundamental process in the interaction between species, and exerts strong selection pressure. Hence, anti-predatory traits have been intensively studied. Although it has long been speculated that individuals of some species gain protection from predators by sometimes almost-uncanny resemblances to uninteresting objects in the local environment (such as twigs or stones), demonstration of antipredatory benefits to such “masquerade” have only very recently been demonstrated, and the fundamental workings of this defensive strategy remain unclear. Here we use laboratory experiments with avian predators and twig-mimicking caterpillars as masqueraders to investigate (i) the evolutionary dynamics of masquerade; and (ii) the behavioral adaptations associated with masquerade. We show that the benefit of masquerade declines as the local density of masqueraders relative to their models (twigs, in our system) increases. This occurs through two separate mechanisms: increasing model density both decreased predators’ motivation to search for masqueraders, and made masqueraders more difficult to detect. We further demonstrated that masquerading organisms have evolved complex microhabitat selection strategies that allow them to best exploit the density-dependent properties of masquerade. Our results strongly suggest the existence of opportunity costs associated with masquerade. Careful evaluation of such costs will be vital to the development of a fuller understanding of both the distribution of masquerade across taxa and ecosystems, and the evolution of the life history strategies of masquerading prey. PMID:21464318

  10. Density-dependent predation influences the evolution and behavior of masquerading prey.

    PubMed

    Skelhorn, John; Rowland, Hannah M; Delf, Jon; Speed, Michael P; Ruxton, Graeme D

    2011-04-19

    Predation is a fundamental process in the interaction between species, and exerts strong selection pressure. Hence, anti-predatory traits have been intensively studied. Although it has long been speculated that individuals of some species gain protection from predators by sometimes almost-uncanny resemblances to uninteresting objects in the local environment (such as twigs or stones), demonstration of antipredatory benefits to such "masquerade" have only very recently been demonstrated, and the fundamental workings of this defensive strategy remain unclear. Here we use laboratory experiments with avian predators and twig-mimicking caterpillars as masqueraders to investigate (i) the evolutionary dynamics of masquerade; and (ii) the behavioral adaptations associated with masquerade. We show that the benefit of masquerade declines as the local density of masqueraders relative to their models (twigs, in our system) increases. This occurs through two separate mechanisms: increasing model density both decreased predators' motivation to search for masqueraders, and made masqueraders more difficult to detect. We further demonstrated that masquerading organisms have evolved complex microhabitat selection strategies that allow them to best exploit the density-dependent properties of masquerade. Our results strongly suggest the existence of opportunity costs associated with masquerade. Careful evaluation of such costs will be vital to the development of a fuller understanding of both the distribution of masquerade across taxa and ecosystems, and the evolution of the life history strategies of masquerading prey.

  11. Spin- and Parity-Dependent Level Densities in Exotic Calcium Isotopes?

    NASA Astrophysics Data System (ADS)

    Usman, I. T.; Carter, J.; Sideras-Haddad, E.; Jingo, M.; Kureba, C. O.; Donaldson, L.; Latif, M.; Neveling, R.; Smit, F. D.; Swartz, C.; Nemulodi, F.; von Neumann-Cosel, P.; Richter, A.; Fearick, R. W.; Fujita, H.; Fulita, Y.; Tamii, A.

    2015-11-01

    Level densities of 2+ and 1- states in 40Ca have been extracted from high energy-resolution (p,p') experiments performed using the K600 magnetic spectrometer at iThemba LABS, South Africa. The success of the method depends on the accurate determination of various background components underneath the giant resonance. It was found that using the nearly model-independent method of Discrete Wavelet Transform (DWT) background determination using bi-orthogonal wavelets of high order of vanishing moments proved sufficient for the extraction of level density in the excitation energy region of the Isoscalar Giant Quadrupole Resonance (ISGQR) and Isovector Giant Dipole Resonance (IVGDR). Comparison of the experimentally extracted 2+ and 1- level densities with Back-Shifted Fermi Gas Model (BSFG), Hartree-Fock Bogoliubov (HFB) and Hartree-Fock-Bardeen-Cooper Schriffer (HF-BCS) theoretical model predictions were made. Future interests in the use of radioactive-ion beams of different intensities will provide opportunities in elucidating this important property experimentally for more exotic calcium isotopes.

  12. Zoospore density-dependent behaviors of Phytophthora nicotianae are autoregulated by extracellular products.

    PubMed

    Kong, Ping; Hong, Chuanxue

    2010-07-01

    Phytophthora species are destructive fungus-like plant pathogens that use asexual single-celled flagellate zoospores for dispersal and plant infection. Many of the zoospore behaviors are density-dependent although the underlying mechanisms are poorly understood. Here, we use P. nicotianae as a model and demonstrate autoregulation of some zoospore behaviors using signal molecules that zoospores release into the environment. Specifically, zoospore aggregation, plant targeting, and infection required or were enhanced by threshold concentrations of these signal molecules. Below the threshold concentration, zoospores did not aggregate and move toward a cauline leaf of Arabidopsis thaliana (Col-0) and failed to individually attack annual vinca (Catharanthus roseus cv. Little Bright Eye). These processes were reversed when supplemented with zoospore-free fluid (ZFF) prepared from a zoospore suspension above threshold densities but not with calcium chloride at a concentration equivalent to extracellular Ca(2+) in ZFF. These results suggest that Ca(2+) is not a primary signal molecule regulating these communal behaviors. Zoospores coordinated their communal behaviors by releasing, detecting, and responding to signal molecules. This chemical communication mechanism raises the possibility that Phytophthora plant infection may not depend solely on zoospore number in the real world. Single zoospore infection may take place if it is signaled by a common molecule available in the environment which contributes to the destructiveness of these plant pathogens.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Yen, Jian D. L.; Paganin, David M.; Thomson, James R.; Mac Nally, Ralph

    2015-04-01

    Linking our knowledge of organisms to our knowledge of ecological communities and ecosystems is a key challenge for ecology. Individual size distributions (ISDs) link the size of individual organisms to the structure of ecological communities, so that studying ISDs might provide insight into how organism functioning affects ecosystems. Similarly shaped ISDs among ecosystems, coupled with allometric links between organism size and resource use, suggest the possibility of emergent resource-use patterns in ecological communities. We drew on thermodynamics to develop a maximization principle that predicted both organism and community energy use. These predictions highlighted the importance of density-dependent metabolic rates and were able to explain nonlinear relationships between community energy use and community biomass. We analyzed data on fish community energy use and biomass and found evidence of nonlinear scaling, which was predicted by the thermodynamic principle developed here and is not explained by other theories of ISDs. Detailed measurements of organism energy use will clarify the role of density dependence in driving metabolic rates and will further test our derived thermodynamic principle. Importantly, our study highlights the potential for fundamental links between ecology and thermodynamics.

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

    PubMed

    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(n) (+), 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.

  16. 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.

  17. 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.

  18. Plant growth responses to inorganic environmental contaminants are density-dependent: experiments with copper sulfate, barley and lettuce.

    PubMed

    Hansi, Mari; Weidenhamer, Jeffrey D; Sinkkonen, Aki

    2014-01-01

    The density-dependence of terrestrial plant-plant interactions in the presence of toxins has previously been explored using biodegradable compounds. We exposed barley and lettuce to four copper concentrations at four stand densities. We hypothesized that toxin effects would decrease and Cu uptake would increase at increasing plant densities. We analyzed toxin effects by (a) comparing plant biomasses and (b) using a recent regression model that has a separate parameter for the interaction of resource competition and toxin interference. Plant response to Cu was density-dependent in both experiments. Total Cu uptake by barley increased and the dose per plant decreased as plant density increased. This study is the first to demonstrate that plant density mediates plant response to metals in soil in a predictable way. This highlights the need to explore the mechanisms for and consequences of these effects, and to integrate the use of several plant densities into standard ecotoxicological testing.

  19. Accurate Ground-State Energies of Solids and Molecules from Time-Dependent Density-Functional Theory

    NASA Astrophysics Data System (ADS)

    Olsen, Thomas; Thygesen, Kristian S.

    2014-05-01

    We demonstrate that ground-state energies approaching chemical accuracy can be obtained by combining the adiabatic-connection fluctuation-dissipation theorem with time-dependent density-functional theory. The key ingredient is a renormalization scheme, which eliminates the divergence of the correlation hole characteristic of any local kernel. This new class of renormalized kernels gives a significantly better description of the short-range correlations in covalent bonds compared to the random phase approximation (RPA) and yields a fourfold improvement of RPA binding energies in both molecules and solids. We also consider examples of barrier heights in chemical reactions, molecular adsorption, and graphene interacting with metal surfaces, which are three examples where the RPA has been successful. In these cases, the renormalized kernel provides results that are of equal quality or even slightly better than the RPA, with a similar computational cost.

  20. 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

  1. Time-dependent approach to electron pumping in open quantum systems

    NASA Astrophysics Data System (ADS)

    Stefanucci, G.; Kurth, S.; Rubio, A.; Gross, E. K. U.

    2008-02-01

    We use a recently proposed time-dependent approach to investigate the motion of electrons in quantum pump device configurations. The occupied one-particle states are propagated in real time and employed to calculate the local electron density and current. The approach can also be embedded in the framework of time-dependent density functional theory to include electron-electron interactions. An advantage of the present computational scheme is that the same computational effort is required to simulate monochromatic, polychromatic, and nonperiodic drivings. Furthermore, initial-state dependence and history effects are naturally accounted for. We present results for one-dimensional devices exposed to a traveling potential wave. (i) We show that for pumping across a single potential barrier, electrons are transported in pockets and the transport mechanism resembles pumping of water with the Archimedean screw; (ii) we propose a simple model to study pumping through semiconductor nanostructures and we address the phenomenon of the current flowing in the opposite direction to the field propagation; (iii) we present the first numerical evidence of long-lived superimposed oscillations as induced by the presence of bound states and discuss the dependence of their lifetime on the frequency and amplitude of the driving field. By combining Floquet theory with nonequilibrium Green’s functions, we also obtain a general expression for the pumped current in terms of inelastic transmission probabilities. This latter result is used for benchmarking our propagation scheme in the long-time limit. Finally, we discuss the limitations of Floquet-based algorithms and suggest our approach as a possible way to go beyond them.

  2. 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.

  3. Exponential dependence of the vortex pinning potential on current density in high- Tc superconductors

    NASA Astrophysics Data System (ADS)

    Yan, H.; Abdelhadi, M. M.; Jung, J. A.; Willemsen, B. A.; Kihlstrom, K. E.

    2005-08-01

    We investigated the dependence of the vortex pinning potential on current density Ueff(J) in Tl2Ba2CaCu2Oy , Tl2Ba2Ca2Cu3Oy , and YBa2Cu3Oy thin films and single crystals, measured by us and other research groups. In all these cases Ueff(J) was calculated from the magnetic relaxation data using Maley’s procedure [Phys. Rev. B 42, 2639 (1990)]. We explored the exponential dependence of Ueff(J) , first introduced by Thompson [Phys. Rev. B 44, 456 (1991).] to explain long-term nonlogarithmic magnetic relaxations in high-temperature superconductors (HTSC), as an alternative to power-law and logarithmic forms of Ueff(J) . The results revealed that for J larger than approximately 0.4Jc , the energy barrier can be expressed in the following form: Ueff(J)=aIco(1-T/T*)3/2exp(-bJ/Jco) , where the constant b is the same for all samples investigated. This result is independent of the anisotropy (the interplanar coupling). The experimental results were analyzed taking into account the spatial dependence of the pinning potential, proposed by Qin [J. Appl. Phys. 77, 2618 (1995)]. We suggested that the exponential form of Ueff(J) could represent vortex pinning and motion in the a-b planes due to a nanoscopic variation of the order parameter, in agreement with the growing experimental evidence for the presence of nanostructures, stripes (filaments) in HTSC.

  4. 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.

  5. 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.

  6. Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population

    PubMed Central

    Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K

    2014-01-01

    Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong. PMID:25077023

  7. 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

  8. 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.

  9. 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 ...

  10. Presence of a voltage-dependent anion channel 1 in the rat postsynaptic density fraction.

    PubMed

    Moon, J I; Jung, Y W; Ko, B H; De Pinto, V; Jin, I; Moon, I S

    1999-02-25

    Little is known about the molecular organization and functions of the postsynaptic density (PSD), a cytoskeletal specialization on the postsynaptic membrane. In an attempt to elucidate the protein composition of PSD, we have sequenced a 35 kDa protein of the rat forebrain PSD fraction. Amino acid sequence information of the tryptic peptides and immunoblot analyses revealed that the protein is a voltage-dependent anion channel 1 (VDAC1). VDAC1 was enriched in the PSD fraction and was partially soluble in 1% n-octyl glucoside (NOG) or Triton X-100. Our data indicate that VDAC1, which is originally found in the outer mitochondrial membrane, is also present in the central nervous system (CNS) synapses in association with the PSD 'core'.

  11. Density-dependent analysis of nonequilibrium paths improves free energy estimates

    PubMed Central

    Minh, David D. L.

    2009-01-01

    When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities such as free energy differences. Here, we consider analyzing paths generated with one protocol using another one. It is posited that analysis protocols which minimize the lag, the difference between the nonequilibrium and the instantaneous equilibrium densities, will reduce the dissipation of reprocessed trajectories and lead to better free energy estimates. Indeed, when minimal lag analysis protocols based on exactly soluble propagators or relative entropies are applied to several test cases, substantial gains in the accuracy and precision of estimated free energy differences are observed. PMID:19485432

  12. An efficient state-specific scheme of time-dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Chiba, Mahito; Tsuneda, Takao; Hirao, Kimihiko

    2006-03-01

    A state-specific scheme for time-dependent density functional theory (SS-TDDFT) based on the Davidson algorithm is presented. SS-TDDFT is a method devised for speeding up TDDFT calculations by screening transitions that contribute to a specific excitation. By applying this method to calculations of the low-lying excitation energies of test molecules (N 2, CO, H 2CO, C 2H 4 and C 6H 6), water clusters and polyenes, we found that SS-TDDFT accurately reproduced the excitation energies of standard TDDFT while drastically reducing the rank of the TDDFT response matrix without loss of accuracy. We have thus formulated TDDFT that works more efficiently and economically for memory storage.

  13. 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.

  14. Time-dependent density functional study on the photoisomerization mechanism of azobenzene

    NASA Astrophysics Data System (ADS)

    Oyama, Norihisa; Tateyama, Yoshitaka; Miyamoto, Yoshiyuki; Ohno, Takahisa

    2004-03-01

    Photochemical reactions in organic molecules have attracted considerable attention in semiconductor physics and also in bioscience. Azobenzene is a simple molecule which shows the reversible photoisomerization at high quantum yields, and can be used as a light-driven molecular switch and so on. However, the photoisomerization process of azobenzene is still an open question because of its femtosecond ultra-fast reaction. In this talk, we present time-dependent density functional calculations for the azobenzene molecule, and discuss the mechanism of photoisomerization induced by S1 and S2 excitations. This research is partially supported by ACT-JST, and also by FSIS and Special Coordination Funds of MEXT of Japanese Government. The calculations were carried out partly using the Numerical Materials Simulator in National Institute for Materials Science, and partly using the NEC-SX5 at Cybermedia Center of Osaka University.

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

    NASA Astrophysics Data System (ADS)

    Pellegrini, Camilla; Flick, Johannes; Tokatly, Ilya V.; Appel, Heiko; Rubio, Angel

    2015-08-01

    We propose an orbital exchange-correlation functional for applying time-dependent density functional theory to many-electron systems coupled to cavity photons. The time nonlocal equation for the electron-photon optimized effective potential (OEP) is derived. In the static limit our OEP energy functional reduces to the Lamb shift of the ground state energy. We test the new approximation in the Rabi model. It is shown that the OEP (i) reproduces quantitatively the exact ground-state energy from the weak to the deep strong coupling regime and (ii) accurately captures the dynamics entering the ultrastrong coupling regime. The present formalism opens the path to a first-principles description of correlated electron-photon systems, bridging the gap between electronic structure methods and quantum optics for real material applications.

  16. Time-dependent density-functional-theory study of the suppressed tunneling ionization of vanadium

    NASA Astrophysics Data System (ADS)

    Chu, Xi; Groenenboom, Gerrit C.

    2016-11-01

    Using a time-dependent density-functional-theory (TDDFT) method that incorporates the exact exchange, we reproduce the measured ionization suppression for vanadium in 1500-nm lasers of 1.4 to 2.8 ×1013W /cm2 . The calculated ionization yields are 0.07 to 0.5 in 100 fs sin2 pulses. For weaker laser intensities a method with more configurations is needed to properly describe the multiphoton, rather than tunneling, ionization of a transition-metal atom. Our calculations show that the isotropic component of the induced potential increases the binding energy of the electron while the dipole component elevates the potential barrier of tunneling ionization. Both effects suppress the tunneling ionization.

  17. 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.

  18. Time-dependent current-density-functional theory for the linear response of weakly disordered systems

    NASA Astrophysics Data System (ADS)

    Ullrich, C. A.; Vignale, G.

    2002-05-01

    Time-dependent density-functional theory (TDFT) provides a way of calculating, in principle exactly, the linear response of interacting many-electron systems, and thus allows one to obtain their excitation energies. For extended systems, there exist excitations of a collective nature, such as bulk and surface plasmons in metals or intersubband plasmons in doped semiconductor quantum wells. This paper develops a quantitatively accurate first-principles description for the frequency and the linewidth of such excitations in inhomogeneous weakly disordered systems. A finite linewidth in general has intrinsic and extrinsic sources. At low temperatures and outside the region where electron-phonon interaction occurs, the only intrinsic damping mechanism is provided by electron-electron interaction. This kind of intrinsic damping can be described within TDFT, but one needs to go beyond the adiabatic approximation and include retardation effects. It has been shown [G. Vignale, C. A. Ullrich, and S. Conti, Phys. Rev. Lett. 79, 4878 (1997)] that a density-functional response theory that is local in space but nonlocal in time has to be constructed in terms of the currents, rather than the density. This theory will be reviewed in the first part of this paper. For quantitatively accurate linewidths, extrinsic dissipation mechanisms, such as impurities or disorder, have to be included in the response theory. In the second part of this paper, we discuss how extrinsic dissipation can be described within the so-called memory-function formalism. This formalism will first be introduced and reviewed for homogeneous systems. We will then present a synthesis of TDFT with the memory function formalism for inhomogeneous systems, which allows one to simultaneously account for intrinsic and extrinsic damping of collective excitations. As an example where both sources of dissipation are important and where high-quality experimental data are available for comparison, we discuss intersubband

  19. 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.

  20. 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.

  1. Transport efficiency of membrane-anchored kinesin-1 motors depends on motor density and diffusivity.

    PubMed

    Grover, Rahul; Fischer, Janine; Schwarz, Friedrich W; Walter, Wilhelm J; Schwille, Petra; Diez, Stefan

    2016-11-15

    In eukaryotic cells, membranous vesicles and organelles are transported by ensembles of motor proteins. These motors, such as kinesin-1, have been well characterized in vitro as single molecules or as ensembles rigidly attached to nonbiological substrates. However, the collective transport by membrane-anchored motors, that is, motors attached to a fluid lipid bilayer, is poorly understood. Here, we investigate the influence of motors' anchorage to a lipid bilayer on the collective transport characteristics. We reconstituted "membrane-anchored" gliding motility assays using truncated kinesin-1 motors with a streptavidin-binding peptide tag that can attach to streptavidin-loaded, supported lipid bilayers. We found that the diffusing kinesin-1 motors propelled the microtubules in the presence of ATP. Notably, we found the gliding velocity of the microtubules to be strongly dependent on the number of motors and their diffusivity in the lipid bilayer. The microtubule gliding velocity increased with increasing motor density and membrane viscosity, reaching up to the stepping velocity of single motors. This finding is in contrast to conventional gliding motility assays where the density of surface-immobilized kinesin-1 motors does not influence the microtubule velocity over a wide range. We reason that the transport efficiency of membrane-anchored motors is reduced because of their slippage in the lipid bilayer, an effect that we directly observed using single-molecule fluorescence microscopy. Our results illustrate the importance of motor-cargo coupling, which potentially provides cells with an additional means of regulating the efficiency of cargo transport.

  2. 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.

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

    PubMed

    Hu, Chunping; Sugino, Osamu; Watanabe, Kazuyuki

    2014-02-07

    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.

  4. Relaxation and dissipation in time-dependent current-density functional theory

    NASA Astrophysics Data System (ADS)

    D'Agosta, Roberto

    2005-03-01

    In a typical relaxation problem a many-particle system evolves from an initial excited state under the action of its own hamiltonian plus a ``thermal bath", until equilibrium (or the ground-state at T=0) is reached. Due to the presence of the thermal bath the time evolution of the system is not unitary, and an initially pure state will evolve into a statistical mixture of states. Here we show that the time-dependent current density functional theory^1 allows a hamiltonian description of the relaxation process, whereby the quantum state of the system undergoes a unitary time evolution without becoming entangled with a thermal bath. The essential feature that causes the system to eventually settle into a stationary state of the ground-state Kohn-Sham hamiltonian is the presence of an effective electric field, which is determined by the instantaneous values of the current and the density. Our theory is consistent with recent numerical results by Wijewardane and Ullrich^ 2.1. G. Vignale, C. A. Ullrich, and S. Conti, PRL 79, 4878 (1997)2. H. O. Wijewardane and C. A. Ullrich, cond-mat/0411157

  5. Density-dependent effective baryon-baryon interaction from chiral three-baryon forces

    NASA Astrophysics Data System (ADS)

    Petschauer, Stefan; Haidenbauer, Johann; Kaiser, Norbert; Meißner, Ulf-G.; Weise, Wolfram

    2017-01-01

    A density-dependent effective potential for the baryon-baryon interaction in the presence of the (hyper)nuclear medium is constructed, based on the leading (irreducible) three-baryon forces derived within SU(3) chiral effective field theory. We evaluate the contributions from three classes: contact terms, one-pion exchange and two-pion exchange. In the strangeness-zero sector we recover the known result for the in-medium nucleon-nucleon interaction. Explicit expressions for the ΛN in-medium potential in (asymmetric) nuclear matter are presented. Our results are suitable for implementation into calculations of (hyper)nuclear matter. In order to estimate the low-energy constants of the leading three-baryon forces we introduce the decuplet baryons as explicit degrees of freedom and construct the relevant terms in the minimal non-relativistic Lagrangian. With these, the constants are estimated through decuplet saturation. Utilizing this approximation we provide numerical results for the effect of the three-body force in symmetric nuclear matter and pure neutron matter on the ΛN interaction. A moderate repulsion that increases with density is found in comparison to the free ΛN interaction.

  6. 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.

  7. 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.

  8. Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection.

    PubMed

    Ozer, Abdullah; White, Brian S; Lis, John T; Shalloway, David

    2013-08-01

    The non-specific binding of undesired ligands to a target is the primary factor limiting the enrichment of tight-binding ligands in affinity selection. Solution-phase non-specific affinity is determined by the free-energy of ligand binding to a single target. However, the solid-phase affinity might be higher if a ligand bound concurrently to multiple adjacent immobilized targets in a cooperative manner. Cooperativity could emerge in this case as a simple consequence of the relationship between the free energy of binding, localization entropy and the spatial distribution of the immobilized targets. We tested this hypothesis using a SELEX experimental design and found that non-specific RNA aptamer ligands can concurrently bind up to four bead-immobilized peptide targets, and that this can increase their effective binding affinity by two orders-of-magnitude. Binding curves were quantitatively explained by a new statistical mechanical model of density-dependent cooperative binding, which relates cooperative binding to both the target concentration and the target surface density on the immobilizing substrate. Target immobilization plays a key role in SELEX and other ligand enrichment methods, particularly in new multiplexed microfluidic purification devices, and these results have strong implications for optimizing their performance.

  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. Temperature and composition-dependent density of states in organic small-molecule/polymer blend transistors

    NASA Astrophysics Data System (ADS)

    Hunter, Simon; Mottram, Alexander D.; Anthopoulos, Thomas D.

    2016-07-01

    The density of trap states (DOS) in organic p-type transistors based on the small-molecule 2,8-difluoro-5,11-bis(triethylsilylethynyl) anthradithiophene (diF-TES ADT), the polymer poly(triarylamine) and blends thereof are investigated. The DOS in these devices are measured as a function of semiconductor composition and operating temperature. We show that increasing operating temperature causes a broadening of the DOS below 250 K. Characteristic trap depths of ˜15 meV are measured at 100 K, increasing to between 20 and 50 meV at room-temperature, dependent on the semiconductor composition. Semiconductor films with high concentrations of diF-TES ADT exhibit both a greater density of trap states as well as broader DOS distributions when measured at room-temperature. These results shed light on the underlying charge transport mechanisms in organic blend semiconductors and the apparent freezing-out of hole conduction through the polymer and mixed polymer/small molecule phases at temperatures below 225 K.

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

    PubMed

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

    2012-08-07

    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.

  12. Modelling density-dependent flow and solute transport at the Lake Tutchewop saline disposal complex, Victoria

    NASA Astrophysics Data System (ADS)

    Simmons, Craig T.; Narayan, Kumar A.

    1998-05-01

    Intercepted saline groundwaters and drainage effluent from irrigation are commonly stored in both natural and artificial saline disposal basins throughout the Murray-Darling Basin of Australia. Their continued use as wastewater evaporation sites requires an understanding of existing groundwater dynamics. The useful of individual basins, their sustainability and possible environmental impacts remain largely unknown. In this work, the movement of salt to the underlying groundwater system from Lake Tutchewop, a saline disposal complex in north-central Victoria, was modelled in cross-section. Due to the salinity contrast between the hypersaline basin waters and the regional groundwater, it was necessary to simulate density-dependent flow behaviour. Under certain conditions, these density-stratified systems may become unstable leading to the onset of convective behaviour, which greatly increases the movement of salt from the basin to the groundwater system. Modelled concentration profiles in the aquifer system and calculated seepage rates from the basin show that Lake Tutchewop is stable under its present operating regime. The downward movement of salt is mainly controlled by diffusion and dispersion. The calibrated model was used to assess the impact of several management scenarios using time-dependent boundary conditions for lake salinity and water levels. The influence of heterogeneous basin linings on ensuing salt flux rates is examined, and results show that increased solute transport will occur under such conditions. A sensitivity analysis performed on governing variables showed that salt fluxes were most sensitive to lake salinity levels. A solute Rayleigh number defined in terms of basin salinity and hydrogeologic parameters is seen to be an effective tool for predicting the long term behaviour of such saline disposal basins. The models and concepts developed in this work may find application in the design and management of saline disposal complexes.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. A Unifying Probabilistic Bayesian Approach to Derive Electron Density from MRI for Radiation Therapy Treatment Planning

    PubMed Central

    Gudur, Madhu Sudhan Reddy; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang

    2014-01-01

    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 8 patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as ROC's for bone detection (HU>200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p=2×10-4), 283 for the intensity approach (p=2×10-6) and 282 without density correction (p=5×10-6). For 90% sensitivity in bone

  18. 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

    2014-11-07

    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

  19. 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

  20. 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...

  1. Evaluating Systematic Dependence of Type Ia Supernovae: The Influence of Progenitor Central Density

    NASA Astrophysics Data System (ADS)

    Krueger, Brendan K.; Jackson, A. P.; Calder, A. C.; Townsley, D. M.; Brown, E. F.; Timmes, F. X.

    2011-01-01

    We present a study of type Ia supernovae in the single-degenerate scenario, in which a white dwarf accretes mass from a companion star until it approaches the Chandrasekhar limiting mass and an explosion ensues. We investigate progenitor models with a range of central densities to study the influence of this parameter on explosion outcome. We present a suite of simulations from a well-controlled statistical study that allows us to quantify the effects of a variety of initial conditions. We present details of the models, including the mass and distribution of 56Ni, the radioactive decay of which powers the light curve. Our results indicate that progenitors with a higher central density produce less 56Ni and hence a dimmer event. We combine our results with those from previous studies by our collaboration to explore trends in explosion brightness that follow from properties related to the morphology and color of the host galaxy. This work was supported by NASA under grant No. NNX09AD19G and utilized resources at the New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory, which is supported by the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 and by the State of New York.

  2. Impact of numerical artifact of the forward model in the inverse solution of density-dependent flow problem

    NASA Astrophysics Data System (ADS)

    Nassar, Mohamed K.; Ginn, Timothy R.

    2014-08-01

    We investigate the effect of computational error on the inversion of a density-dependent flow and transport model, using SEAWAT and UCODE-2005 in an inverse identification of hydraulic conductivity and dispersivity using head and concentration data from a 2-D laboratory experiment. We investigated inversions using three different solution schemes including variation of number of particles and time step length, in terms of the three aspects: the shape and smoothness of the objective function surface, the consequent impacts to the optimization, and the resulting Pareto analyses. This study demonstrates that the inversion is very sensitive to the choice of the forward model solution scheme. In particular, standard finite difference methods provide the smoothest objective function surface; however, this is obtained at the cost of numerical artifacts that can lead to erroneous warping of the objective function surface. Total variation diminishing (TVD) schemes limit these impacts at the cost of more computation time, while the hybrid method of characteristics (HMOC) approach with increased particle numbers and/or reduced time step gives both smoothed and accurate objective function surface. Use of the most accurate methods (TVD and HMOC) did lead to successful inversion of the two parameters; however, with distinct results for Pareto analyses. These results illuminate the sensitivity of the inversion to a number of aspects of the forward solution of the density-driven flow problem and reveal that parameter values may result that are erroneous but that counteract numerical errors in the solution.

  3. Intra- and interspecific density-dependent effects on growth in helminth parasites of the cormorant, Phalacrocorax carbo sinensis.

    PubMed

    Dezfuli, B S; Volponi, S; Beltrami, I; Poulin, R

    2002-05-01

    The action of intra- and interspecific competition, mediated by density-dependent effects on growth, was investigated among the 3 helminth species found in the alimentary tract of 104 cormorants, Phalacrocorax carbo sinensis. Intraspecific density-dependent effects on worm sizes were observed in the abundant nematode Contracaecum rudolphii, as shown by a negative correlation between mean worm size and intensity of infection. Higher intensities of infection by C. rudolphii were also associated with more variable worm sizes in the nematode Syncuaria squamata, suggesting a one-sided and density-dependent interspecific effect. There was also clear evidence of some form of negative interaction between the nematode S. squamata and the acanthocephalan Southwellina hispida from two fronts. First, there was a strong negative correlation between the intensities of infection of the 2 species across hosts. Second, sizes of worms of 1 species became more variable as the number of worms of the other species per host increased, and vice versa. This interspecific density-dependent effect on growth was thus apparently symmetrical. We also found evidence that worm size is a predictor of egg output in the 3 helminth species, indicating that intra- and interspecific density-dependent effects on growth can affect population dynamics in these worms. These results illustrate the complex nature of density dependence in helminth growth, and how its effects can act both within and among species.

  4. Electrokinetics dependence on water-content: laboratory and field approach

    NASA Astrophysics Data System (ADS)

    Allègre, Vincent; Sénéchal, Pascale; Lehmann, François; Bordes, Clarisse; Jouniaux, Laurence; Sailhac, Pascal; Bano, Maksim

    2010-05-01

    Electrokinetics results from the coupling between the water flow and the electrical current through the electrokinetic coefficient. The Self-Potential (SP) method, which is based on this phenomenon, is currently used to investigate shallow transport in the vadose zone. Thus, the understanding of the electrokinetic coefficient behaviour in unsaturated conditions is crucial to interpret such methods. Empirical and theoretical models proposed in the literature to describe this behaviour are still discussed. Consequently, physical processes involved in the electrokinetic coefficient behaviour in unsaturated conditions need to be futher investigate. We propose here to study the electrokinetics dependence on water content through an experimental approach and the numerical solving of the Richards' equation. We show several continuous records of the electrokinetic coefficient as a function of water saturation. We found that the normalized electrokinetic coefficient behaviour in unsaturated conditions is more complex than it was previously proposed. Indeed, we first observed its increasing with decreasing water saturation. After it reaches a maximum, identified around 80 % of water saturation, it begins to decrease with decreasing saturation. It is an important result since previous works predicted a monotically decreasing of the electrokinetic coefficient with decreasing saturation. We found that the normalized value of the measured electrokinetic coefficient could be two orders of magnitude greater than the classical value in saturated conditions, Csat. We performed several experiments and tried to invert the electrokinetic coefficient data and interpret it in terms of physical processes. We also propose a field study through several geophysical methods, as electrical resistivity tomography, seismoelectrics, and GPR, in order to combine the results in terms of water-content dependence in soils.

  5. 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.

  6. An exponential scaling law for the strain dependence of the Nb3Sn critical current density

    NASA Astrophysics Data System (ADS)

    Bordini, B.; Alknes, P.; Bottura, L.; Rossi, L.; Valentinis, D.

    2013-07-01

    The critical current density of the Nb3Sn superconductor is strongly dependent on the strain applied to the material. In order to investigate this dependence, it is a common practice to measure the critical current of Nb3Sn strands for different values of applied axial strain. In the literature, several models have been proposed to describe these experimental data in the reversible strain region. All these models are capable of fitting the measurement results in the strain region where data are collected, but tend to predict unphysical trends outside the range of data, and especially for large strain values. In this paper we present a model of a new strain function, together with the results obtained by applying the new scaling law on relevant datasets. The data analyzed consisted of the critical current measurements at 4.2 K that were carried out under applied axial strain at Durham University and the University of Geneva on different strand types. With respect to the previous models proposed, the new scaling function does not present problems at large strain values, has a lower number of fitting parameters (only two instead of three or four), and is very stable, so that, starting from few experimental points, it can estimate quite accurately the strand behavior in a strain region where there are no data. A relationship is shown between the proposed strain function and the elastic strain energy, and an analogy is drawn with the exponential form of the McMillan equation for the critical temperature.

  7. 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.

  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. 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.

  10. Δ (1232 ) effects in density-dependent relativistic Hartree-Fock theory and neutron stars

    NASA Astrophysics Data System (ADS)

    Zhu, Zhen-Yu; Li, Ang; Hu, Jin-Niu; Sagawa, Hiroyuki

    2016-10-01

    The density-dependent relativistic Hartree-Fock (DDRHF) theory is extended to include Δ isobars for the study of dense nuclear matter and neutron stars. To this end, we solve the Rarita-Schwinger equation for spin-3/2 particle. Both the direct and exchange terms of the Δ isobars' self-energies are evaluated in detail. In comparison with the relativistic mean field theory (Hartree approximation), a weaker parameter dependence is found for DDRHF. An early appearance of Δ isobars is recognized at ρB˜0.28 fm-3, comparable with that of hyperons. Also, we find that the Δ isobars' softening of the equation of state is mainly due to the reduced Fock contributions from the coupling of the isoscalar mesons, while the pion contributions are negligibly small. We finally conclude that with typical parameter sets, neutron stars with Δ isobars in their interiors could be as heavy as the two massive pulsars whose masses are precisely measured, with slightly smaller radii than normal neutron stars.

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

    DOE PAGES

    Božović, I.; He, X.; Wu, J.; ...

    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

  12. Path integral density matrix dynamics: A method for calculating time-dependent properties in thermal adiabatic and non-adiabatic systems

    NASA Astrophysics Data System (ADS)

    Habershon, Scott

    2013-09-01

    We introduce a new approach for calculating quantum time-correlation functions and time-dependent expectation values in many-body thermal systems; both electronically adiabatic and non-adiabatic cases can be treated. Our approach uses a path integral simulation to sample an initial thermal density matrix; subsequent evolution of this density matrix is equivalent to solution of the time-dependent Schrödinger equation, which we perform using a linear expansion of Gaussian wavepacket basis functions which evolve according to simple classical-like trajectories. Overall, this methodology represents a formally exact approach for calculating time-dependent quantum properties; by introducing approximations into both the imaginary-time and real-time propagations, this approach can be adapted for complex many-particle systems interacting through arbitrary potentials. We demonstrate this method for the spin Boson model, where we find good agreement with numerically exact calculations. We also discuss future directions of improvement for our approach with a view to improving accuracy and efficiency.

  13. Ion-number-density-dependent effects on hyperfine transition of trapped 199Hg+ ions in quadrupole linear ion traps

    NASA Astrophysics Data System (ADS)

    Yang, Zhihui; Chen, Yihe; Yan, Bibo; Wang, Man; Wan, Yongquan; Liu, Hao; She, Lei; Li, Jiaomei

    2017-04-01

    The ion-number-density-dependent frequency offsets and broadening of the ground state hyperfine transition spectra of trapped 199Hg+ ions were measured as a function of the end-cap voltage of the quadrupole linear ion trap. The number density of trapped 199Hg+ ions in the quadrupole linear trap was controlled by the end-cap voltage. The fractional frequency stability of 199Hg+ hyperfine transition to the 1 mV end-cap voltage variation was preliminary estimated to be less than 1 ×10-16. The causes of the ion-number-density-dependent frequency shift and spectrum broadening were analyzed theoretically and explained.

  14. Reconstruction of Layer Densities in a Multilayer Snowpack using a Bayesian Approach to Inverse Modeling

    NASA Astrophysics Data System (ADS)

    Aguayo, M.; Marshall, H.; McNamara, J. P.; Mead, J.; Flores, A. N.

    2013-12-01

    Estimation of snowpack parameters such as depth, density and grain structure is a central focus of hydrology in seasonally snow-covered lands. These parameters are directly estimated by field observations, indirectly estimated from other parameters using statistical correlations, or simulated with a model. Difficulty in sampling thin layers and uncertainty in the transition between layers can cause significant uncertainty in measurements of these parameters. Snow density is one of the most important parameters to measure because it is strictly related with snow water content, an important component of the global water balance. We develop a mathematical framework to estimate snow density from measurements of temperature and thickness of snowpack layers over a particular time period, in conjunction with a physics-based model of snowpack evolution. We formulate a Bayesian approach to estimate the snowpack density profile, using a full range of possible simulations that incorporate key sources of uncertainty to build in prior snowpack knowledge. The posterior probability density function of the snow density, conditioned on snowpack temperature measurements, is computed by multiplying the likelihoods and assumed prior distribution function. Random sampling is used to generate a range of densities with same probability when prior uniform probability function is assumed. A posterior probability density function calculated directly via Bayes' theorem is used to calculate the probability of every sample generated. The forward model is a 1D, multilayer snow energy and mass balance model, which solves for snow temperature, density, and liquid water content on a finite element mesh. The surface and ground temperature data of snowpack (boundary conditions), are provided by the Center for Snow and Avalanche Studies (CSAS), Silverton CO, from snow pits made at Swamp Angel and Senator Beck study plot sites. Standard errors between field observations and results computed denote the

  15. Weakening density dependence from climate change and agricultural intensification triggers pest outbreaks: a 37-year observation of cotton bollworms.

    PubMed

    Ouyang, Fang; Hui, Cang; Ge, Saiying; Men, Xin-Yuan; Zhao, Zi-Hua; Shi, Pei-Jian; Zhang, Yong-Sheng; Li, Bai-Lian

    2014-09-01

    Understanding drivers of population fluctuation, especially for agricultural pests, is central to the provision of agro-ecosystem services. Here, we examine the role of endogenous density dependence and exogenous factors of climate and human activity in regulating the 37-year population dynamics of an important agricultural insect pest, the cotton bollworm (Helicoverpa armigera), in North China from 1975 to 2011. Quantitative time-series analysis provided strong evidence explaining long-term population dynamics of the cotton bollworm and its driving factors. Rising temperature and declining rainfall exacerbated the effect of agricultural intensification on continuously weakening the negative density dependence in regulating the population dynamics of cotton bollworms. Consequently, ongoing climate change and agricultural intensification unleashed the tightly regulated pest population and triggered the regional outbreak of H. armigera in 1992. Although the negative density dependence can effectively regulate the population change rate to fluctuate around zero at stable equilibrium levels before and after outbreak in the 1992, the population equilibrium jumped to a higher density level with apparently larger amplitudes after the outbreak. The results highlight the possibility for exogenous factors to induce pest outbreaks and alter the population regulating mechanism of negative density dependence and, thus, the stable equilibrium of the pest population, often to a higher level, posing considerable risks to the provision of agro-ecosystem services and regional food security. Efficient and timely measures of pest management in the era of Anthropocene should target the strengthening and revival of weakening density dependence caused by climate change and human activities.

  16. 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.

  17. 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…

  18. Inhibition of osteoclast differentiation by polycyclic aryl hydrocarbons is dependent on cell density and RANKL concentration.

    PubMed

    Voronov, I; Heersche, J N M; Casper, R F; Tenenbaum, H C; Manolson, M F

    2005-07-15

    We investigated the effect of representative polycyclic aryl hydrocarbons (PAHs), benzo[a]pyrene (BaP), and 7,12-dimethylbenz[a]anthracene (DMBA) on osteoclast differentiation and function by using dispersed cancellous bone derived rabbit osteoclasts and the RAW264.7 cells. These cells differentiate into osteoclasts when exposed to receptor activator of NF-kappaB ligand (RANKL). The rabbit osteoclasts were exposed to 10(-6) to 10(-9)M BaP or DMBA and the tartrate-resistant acid phosphatase (TRAP)-positive cells were counted. The effect of PAHs on osteoclast differentiation in dispersed rabbit osteoclast-containing stromal cell populations was cell density dependent, suggesting that the cell density of stromal cells, osteoclast precursors, and/or mature osteoclasts are factors regulating the effect of PAHs. To investigate the direct effect of BaP on osteoclast differentiation, RAW264.7 cells were exposed to 10(-5) to 10(-6) M BaP. Treatment of RAW264.7 cells cultured with 25 ng/ml soluble RANKL and 10(-5)M BaP for 5 days decreased osteoclast differentiation, TRAP activity levels, and resorption of bone-like substrata. The inhibition was prevented by 10(-6) to 10(-7) M resveratrol, an aryl hydrocarbon receptor (AhR) antagonist, and by higher concentrations of RANKL. To investigate the ability of RANKL to reverse BaP-mediated inhibition, gene expression was determined by RT-PCR. Cytochrome P450 1B1 (CYP1B1) mRNA, one of the genes activated by BaP, was present only in the groups exposed to BaP; the levels of CYP1B1 mRNA decreased in the presence of increasing concentrations of RANKL. These results suggest that the inhibitory effects of PAHs on osteoclastogenesis are direct and likely involve interaction of the RANKL and PAH signaling pathways.

  19. 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}.

  20. THE COLUMN DENSITY VARIANCE IN TURBULENT INTERSTELLAR MEDIA: A FRACTAL MODEL APPROACH

    SciTech Connect

    Seon, Kwang-Il

    2012-12-20

    Fractional Brownian motion structures are used to investigate the dependency of column density variance ({sigma}{sup 2}{sub lnN}) in the turbulent interstellar medium on the variance of three-dimensional density ({sigma}{sup 2}{sub ln{rho}}) and the power-law slope of the density power spectrum. We provide quantitative expressions to infer the three-dimensional density variance, which is not directly observable, from the observable column density variance and spectral slope. We also investigate the relationship between the column density variance and sonic Mach number (M{sub s}) in the hydrodynamic (HD) regime by assuming the spectral slope and density variance to be functions of sonic Mach number, as obtained from the HD turbulence simulations. They are related by the expression {sigma}{sup 2}{sub lnN} = A{sigma}{sub ln{rho}} {sup 2} = Aln (1 + b {sup 2} M{sup 2}{sub s}), suggested by Burkhart and Lazarian for the magnetohydrodynamic case. The proportional constant A varies from Almost-Equal-To 0.2 to Almost-Equal-To 0.4 in the HD regime as the turbulence forcing parameter b increases from 1/3 (purely solenoidal forcing) to 1 (purely compressive forcing). It is also discussed that the parameter A is lowered in the presence of a magnetic field.

  1. Accuracy of estimated geometric parameters of trees depending on the LIDAR data density

    NASA Astrophysics Data System (ADS)

    Hadas, Edyta; Estornell, Javier

    2015-04-01

    The estimation of dendrometric variables has become important for spatial planning and agriculture projects. Because classical field measurements are time consuming and inefficient, airborne LiDAR (Light Detection and Ranging) measurements are successfully used in this area. Point clouds acquired for relatively large areas allows to determine the structure of forestry and agriculture areas and geometrical parameters of individual trees. In this study two LiDAR datasets with different densities were used: sparse with average density of 0.5pt/m2 and the dense with density of 4pt/m2. 25 olive trees were selected and field measurements of tree height, crown bottom height, length of crown diameters and tree position were performed. To determine the tree geometric parameters from LiDAR data, two independent strategies were developed that utilize the ArcGIS, ENVI and FUSION software. Strategy a) was based on canopy surface model (CSM) slicing at 0.5m height and in strategy b) minimum bounding polygons as tree crown area were created around detected tree centroid. The individual steps were developed to be applied also in automatic processing. To assess the performance of each strategy with both point clouds, the differences between the measured and estimated geometric parameters of trees were analyzed. As expected, the tree height were underestimated for both strategies (RMSE=0.7m for dense dataset and RMSE=1.5m for sparse) and tree crown height were overestimated (RMSE=0.4m and RMSE=0.7m for dense and sparse dataset respectively). For dense dataset, strategy b) allows to determine more accurate crown diameters (RMSE=0.5m) than strategy a) (RMSE=0.8m), and for sparse dataset, only strategy a) occurs to be relevant (RMSE=1.0m). The accuracy of strategies were also examined for their dependency on tree size. For dense dataset, the larger the tree (height or crown longer diameter), the higher was the error of estimated tree height, and for sparse dataset, the larger the tree

  2. Effect of measurement error on tests of density dependence of catchability for walleyes in northern Wisconsin angling and spearing fisheries

    USGS Publications Warehouse

    Hansen, M.J.; Beard, T.D.; Hewett, S.W.

    2005-01-01

    We sought to determine how much measurement errors affected tests of density dependence of spearing and angling catchability for walleye Sander vitreus by quantifying relationships between spearing and angling catch rates (catch/h) and walleye population density (number/acre) in northern Wisconsin lakes. The mean measurement error of spearing catch rates was 43.5 times greater than the mean measurement error of adult walleye population densities, whereas the mean measurement error of angling catch rates was only 5.6 times greater than the mean measurement error of adult walleye population densities. The bias-corrected estimate of the relationship between spearing catch rate and adult walleye population density was similar to the ordinary-least-squares regression estimate but differed significantly from the geometric mean (GM) functional regression estimate. In contrast, the bias-corrected estimate of the relationship between angling catch rate and total walleye population density was intermediate between ordinary-least-squares and GM functional regression estimates. Catch rates of walleyes in both spearing and angling fisheries were not linearly related to walleye population density, which indicated that catch rates in both fisheries were hyperstable in relation to walleye population density. For both fisheries, GM functional regression overestimated the degree of hyperdepletion in catch rates and ordinary-least-squares regression overestimated the degree of hyperstability in catch rates. However, ordinary-least-squares regression induced significantly less bias in tests of density dependence than GM functional regression, so it may be suitable for testing the degree of density dependence in fisheries for which fish population density is estimated with mark-recapture methods similar to those used in our study. ?? Copyright by the American Fisheries Society 2005.

  3. Flowing afterglow measurements of the density dependence of gas-phase ion-ion mutual neutralization reactions

    SciTech Connect

    Shuman, Nicholas S.; Viggiano, Albert A.; Johnsen, Rainer

    2013-05-28

    We have studied the dependence of several ion-ion mutual neutralization (MN) reactions on helium density in the range from 1.6 Multiplication-Sign 10{sup 16} to 1.5 Multiplication-Sign 10{sup 17} cm{sup -3} at 300 K, using the Variable Electron and Neutral Density Attachment Mass Spectrometry method. The rate coefficients of the reactions Ar{sup +}+ Br{sub 2}{sup -}, Ar{sup +}+ SF{sub 6}{sup -}, and Ar{sup +}+ C{sub 7}F{sub 14}{sup -} were found to be independent of gas density over the range studied, in disagreement with earlier observations that similar MN reactions are strongly enhanced at the same gas densities. The cause of the previous enhancement with density is traced to the use of 'orbital-motion-limit' theory to infer ion densities from the currents collected by ion-attracting Langmuir probes in a region where it is not applicable.

  4. Flowing afterglow measurements of the density dependence of gas-phase ion-ion mutual neutralization reactions

    NASA Astrophysics Data System (ADS)

    Shuman, Nicholas S.; Viggiano, Albert A.; Johnsen, Rainer

    2013-05-01

    We have studied the dependence of several ion-ion mutual neutralization (MN) reactions on helium density in the range from 1.6 × 1016 to 1.5 × 1017 cm-3 at 300 K, using the Variable Electron and Neutral Density Attachment Mass Spectrometry method. The rate coefficients of the reactions Ar+ + Br2-, Ar+ + SF6-, and Ar+ + C7F14- were found to be independent of gas density over the range studied, in disagreement with earlier observations that similar MN reactions are strongly enhanced at the same gas densities. The cause of the previous enhancement with density is traced to the use of "orbital-motion-limit" theory to infer ion densities from the currents collected by ion-attracting Langmuir probes in a region where it is not applicable.

  5. Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

    NASA Technical Reports Server (NTRS)

    He, Guowei; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

  6. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets.

    PubMed

    Thorvaldsen, Andreas J; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-07

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  7. A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets

    NASA Astrophysics Data System (ADS)

    Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

    2008-12-01

    A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

  8. Does cancellous screw insertion torque depend on bone mineral density and/or microarchitecture?

    PubMed

    Ab-Lazid, Rosidah; Perilli, Egon; Ryan, Melissa K; Costi, John J; Reynolds, Karen J

    2014-01-22

    During insertion of a cancellous bone screw, the torque level reaches a plateau, at the engagement of all the screw threads prior to the screw head contact. This plateau torque (T(Plateau)) was found to be a good predictor of the insertion failure torque (stripping) and also exhibited strong positive correlations with areal bone mineral density (aBMD) in ovine bone. However, correlations between T(Plateau) and aBMD, as well as correlations between T(Plateau) and bone microarchitecture, have never been explored in human bone. The aim of this study was to determine whether T(Plateau), a predictor of insertion failure torque, depends on aBMD and/or bone microarchitecture in human femoral heads. Fifty-two excised human femoral heads were obtained. The aBMD and microarchitecture of each specimen were evaluated using dual X-ray Absorptiometry and micro-computed tomography. A cancellous screw was inserted into specimens using an automated micro-mechanical test device, and T(Plateau) was calculated from the insertion profile. T(Plateau) exhibited the strongest correlation with the structure model index (SMI, R=-0.82, p<0.001), followed by bone volume fraction (BV/TV, R=0.80, p<0.01) and aBMD (R=0.76, p<0.01). Stepwise forward regression analysis showed an increase for the prediction of T(Plateau) when aBMD was combined with microarchitectural parameters, i.e., aBMD combined with SMI (R(2) increased from 0.58 to 0.72) and aBMD combined with BV/TV and BS/TV (R(2) increased from 0.58 to 0.74). In conclusion, T(Plateau), a strong predictor for insertion failure torque, is significantly dependent on bone microarchitecture (particularly SMI and BV/TV) and aBMD.

  9. Spin-dependent electron momentum density in the Ni2MnSn Heusler alloy

    NASA Astrophysics Data System (ADS)

    Deb, Aniruddha; Hiraoka, N.; Itou, M.; Sakurai, Y.; Onodera, M.; Sakai, N.

    2001-05-01

    The spin-dependent electron momentum distribution in Ni2MnSn Heusler alloy single crystals was studied using 270 keV circularly polarized synchrotron radiation, through magnetic Compton profile measurements, on the high energy inelastic scattering beamline at SPring-8. The experiments were carried out for the three principal crystallographic directions [100], [110], and [111] at 10 K. The results show that the conduction electrons have a negative spin polarization of 0.34μB the 3d spin moment on the nickel site was found to be negligible. A band structure calculation was performed including a hyperfine field study using the full potential linearized augmented plane wave (FLAPW) method, with the generalized gradient approximation (GGA) for the electronic exchange and correlation. The spin moment on the Mn site at 10 K was observed as 4.39μB. The spin-dependent Compton profiles for the [100], [110], and [111] directions reported here show anisotropy in the momentum density, which is in good agreement with the FLAPW-GGA results, based on a ferromagnetic ground state. The hyperfine fields calculated were compared with previously calculated hyperfine field of Cu2MnAl and Co2FeGa Heusler alloys. From the comparison it is seen that the value of Hval (valence contribution to the hyperfine field) is roughly proportional to the spin polarization (ms) of the s electrons at the X (Ni,Cu,Co) and Y (Mn of Ni2MnSn and Cu2MnAl, Fe of Co2FeGa) atom positions.

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

    SciTech Connect

    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) 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.

  11. Two-electron Rabi oscillations in real-time time-dependent density-functional theory.

    PubMed

    Habenicht, Bradley F; Tani, Noriyuki P; Provorse, Makenzie R; Isborn, Christine M

    2014-11-14

    We investigate the Rabi oscillations of electrons excited by an applied electric field in several simple molecular systems using time-dependent configuration interaction (TDCI) and real-time time-dependent density-functional theory (RT-TDDFT) dynamics. While the TDCI simulations exhibit the expected single-electron Rabi oscillations at a single resonant electric field frequency, Rabi oscillations in the RT-TDDFT simulations are a two-electron process. The existence of two-electron Rabi oscillations is determined both by full population inversion between field-free molecular orbitals and the behavior of the instantaneous dipole moment during the simulations. Furthermore, the Rabi oscillations in RT-TDDFT are subject to an intensity threshold of the electric field, below which Rabi oscillations do not occur and above which the two-electron Rabi oscillations occur at a broad range of frequencies. It is also shown that at field intensities near the threshold intensity, the field frequency predicted to induce Rabi oscillations by linear response TDDFT only produces detuned Rabi oscillations. Instead, the field frequency that yields the full two-electron population inversion and Rabi oscillation behavior is shown to be the average of single-electron transition frequencies from the ground S0 state and the doubly-excited S2 state. The behavior of the two-electron Rabi oscillations is rationalized via two possible models. The first model is a multi-photon process that results from the electric field interacting with the three level system such that three level Rabi oscillations may occur. The second model suggests that the mean-field nature of RT-TDDFT induces paired electron propagation.

  12. Forced canonical thermalization in a hadronic transport approach at high density

    NASA Astrophysics Data System (ADS)

    Oliinychenko, Dmytro; Petersen, Hannah

    2017-03-01

    Hadronic transport approaches based on an effective solution of the relativistic Boltzmann equation are widely applied for the dynamical description of heavy ion reactions at low beam energies. At high densities, the assumption of binary interactions often used in hadronic transport approaches may not be applicable anymore. Therefore, we effectively simulate the high-density regime using the local forced canonical thermalization. This framework provides the opportunity to interpolate in a dynamical way between two different limits of kinetic theory: the dilute gas approximation and the ideal fluid case. This approach will be important for studies of the dynamical evolution of heavy ion collisions at low and intermediate energies as experimentally investigated at the beam energy scan program at RHIC, and in the future at FAIR and NICA. On the other hand, this new way of modeling hot and dense strongly interacting matter might be relevant for small systems at high energies (LHC and RHIC) as well.

  13. Lianas escape self-thinning: Experimental evidence of positive density dependence in temperate lianas Celastrus orbiculatus and C. scandens

    USGS Publications Warehouse

    Leicht-Young, S. A.; Latimer, A.M.; Silander, J.A.

    2011-01-01

    The neighborhood density of plants strongly affects their growth, reproduction, and survival. In most cases, high density increases competition and negatively affects a focal plant in predictable ways, leading to the self-thinning law. There are, however, situations in which high densities of plants facilitate focal plant performance, resulting in positive density dependence. Despite their importance in forest gap dynamics and distinctive growth form, there have been very few studies of the effect of density on lianas or vines. We grew an invasive (Celastrus orbiculatus) and a native (Celastrus scandens) liana species together in three different density treatments, while also manipulating the light and support availability. We found that across treatment conditions, C. orbiculatus always out-performed C. scandens, showing greater relative growth rate in height and diameter, greater biomass and higher survival. Both species responded similarly to the density treatments: with plants in high density not showing a decrease in relative height growth rate compared to medium density. Aboveground biomass for C. scandens was not affected by density, while for C. orbiculatus, the most massive plants were growing in medium density without support. More surprisingly, survival analysis indicated that the two species both had significantly lower mortality rates in the highest density treatment; this trend held true across the other treatments of light and supports. More generally, this study demonstrates that these lianas can escape the consequences of high density and thus the self-thinning law that affects self-supporting plants. This suggests a broader hypothesis about lianas in general: their greater flexibility in allocating growth resources allows them to grow taller and thinner without collapsing and thereby potentially escape shading and mortality even at high densities.

  14. Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns.

    PubMed

    Liu, Quan-Xing; Rietkerk, Max; Herman, Peter M J; Piersma, Theunis; Fryxell, John M; van de Koppel, Johan

    2016-12-01

    Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn-Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems.

  15. How to test different density-dependent fecundity hypotheses in an increasing or stable population.

    PubMed

    Ferrer, Miguel; Newton, Ian; Casado, Eva

    2006-01-01

    1. We report on a simulation study of increasing and stable populations working under two different hypotheses of density dependence of fecundity: the habitat heterogeneity hypothesis (HHH) and the individual adjustment hypothesis (IAH). Our aim is to find critical differences between the two regulatory hypotheses in natural populations. 2. Populations under HHH show a strong negative relationship between fecundity and the coefficient of variation of fecundity. We also found a strong negative relationship between fecundity and skewness, demonstrating that, as fecundity decreases, the form of the distribution of brood sizes changes, being more left-skewed due to more territories failing to produce any offspring. 3. This strong relationship was found only in the simulations of populations under HHH; whether increasing or stable, and under different ratios of good: poor territories and different population sizes. In contrast, no relationship between mean fecundity and skewness was found among simulations under IAH. 4. Populations under IAH also showed a significant relationship between mean fecundity and the coefficient of variation of fecundity, but with a lower slope than in populations under HHH. 5. In conclusion, skewness was found to be an adequate critical test that showed significant and strong relationships with mean fecundity only in populations under HHH, whether increasing or stable. This test is useful for species with a discrete distribution of offspring with a small number of integer categories, including most of the bird and mammal species.

  16. Modeling Changing Morphology and Density Dependent Groundwater Flow in a Dynamic Environment: case study

    NASA Astrophysics Data System (ADS)

    Huizer, S.; Bierkens, M. F.; Oude Essink, G.

    2014-12-01

    In many coastal regions around the world climate change will lead to a sea level rise and an increase in extreme weather conditions. This prospect has resulted in a new focus on coastal protection in the Netherlands, resulting in the initiation of an innovative coastal defence project called the Sand Motor. In this project a large body of sand or so-called mega-nourishment has been constructed along the Dutch coast. This body of sand will be distributed slowly along the coastline by wind, waves and currents. Keeping the coastal defence structures in place and creating a unique, dynamic environment with changing morphology over time. Because of the large size of the body of sand (21.5 million m3) and the position at the coastline and near coastal dunes, the Sand Motor might cause a substantial increase of the fresh water availability by increasing the volume fresh water lens underneath the dunes. This creates an opportunity to combine coastal protection with an increase of fresh water resources in coastal regions. With a three dimensional, density dependent, groundwater model the effects of changing morphology over time and the potential increase in fresh water availability have been studied.

  17. Modeling Changing Morphology and Density Dependent Groundwater Flow in a Dynamic Environment: case study

    NASA Astrophysics Data System (ADS)

    Huizer, Sebastian; Bierkens, Marc; Oude Essink, Gualbert

    2015-04-01

    The prospect of sea level rise and increase in extreme weather conditions has led to a new focus on coastal defense in the Netherlands. As an innovative solution for coastal erosion a mega-nourishment named the Sand Motor (or Sand Engine) has been constructed at the Dutch coast. This body of sand will be distributed slowly along the coastline by wind, waves and currents; keeping the coastal defense structures in place and creating a unique, dynamic environment with changing morphology over time. The large size and position of the Sand Motor might lead to a substantial increase of fresh ground water resources. This creates an opportunity to combine coastal protection with an increase of fresh water resources in coastal regions. With a three dimensional, density dependent, groundwater model the effects of changing morphology over time and the potential increase in fresh water availability have been studied. The preliminary model calculations show that in a period of 20 years volume of fresh water gradually increases to ca. 12 Mm3. In the nearby dune area 7-8 Mm3 is abstracted yearly, therefore the first results are promising in increasing fresh groundwater resources. More model calculations will be performed to investigate the sensitivity of the change in the fresh, brackish and salt water distribution.

  18. Phagocytosis of aggregated lipoprotein by macrophages: Low density lipoprotein receptor-dependent foam-cell formation

    SciTech Connect

    Suits, A.G.; Chait, A.; Aviram, M.; Heinecke, J.W. )

    1989-04-01

    Low density lipoprotein (LDL) modified by incubation with phospholipase C (PLC-LDL) aggregates in solution and is rapidly taken up and degraded by human and mouse macrophages, producing foam cells in vitro. Human, mouse, and rabbit macrophages degraded {sup 125}I-labeled PLC-LDL ({sup 125}I-PLC-LDL) more rapidly than native {sup 125}I-labeled LDL ({sup 125}I-LDL), while nonphagocytic cells such as human fibroblasts and bovine aortic endothelial cells degraded {sup 125}I-PLC-LDL more slowly than {sup 125}I-LDL. This suggested the mechanism for internalization of PLC-LDL was phagocytosis. When examined by electron microscopy, mouse peritoneal macrophages appeared to be phagocytosing PLC-LDL. The uptake and degradation of {sup 125}I-PLC-LDL by human macrophages was inhibited >80% by the monoclonal antibody C7 (IgG2b) produced by hybridoma C7, which blocks the ligand binding domain of the LDL receptor. Similarly, methylation of {sup 125}I-LDL ({sup 125}I-MeLDL) prior to treatment with phospholipase C decreased its subsequent uptake and degradation by human macrophages by >90%. The uptake and degradation of phospholipase C-modified {sup 125}I-MeLDL by macrophages could be restored by incubation of the methylated lipoprotein with apoprotein E, a ligand recognized by the LDL receptor. These results indicate that macrophages internalize PLC-LDL by LDL receptor-dependent phagocytosis.

  19. Recent developments in time-dependent density-functional theory within and beyond linear response

    NASA Astrophysics Data System (ADS)

    Gross, E. K. U.

    2013-03-01

    Time-dependent density functional theory (TDDFT) is a popular and rather successful method in the description of photo-absorption spectra of atoms and molecules in the linear response regime. In extended solids, however, a satisfactory description of excitonic effects has become possible only recently with the advent of advanced approximations for the exchange-correlation kernel fxc. One of these advanced approximations is the so-called bootstrap kernel [S. Sharma et al, PRL 107, 186401 (2011)]. We shall explore the performance of this kernel in the long-wavelength limit and for finite values of q, looking at electron-loss as well as photo-absorption spectra. We find, in particular, that excitonic effects in LiF and Ar are enhanced for values of q away from the Γ-point [S. Sharma et al, New J Phys 14, 053052 (2012)]. Then we present two recent developments in TDDFT beyond the linear-response regime: (i) By using a geometrical partitioning, we calculate the angle and energy resolved photo-electron spectra of finite systems including multi-photon effects [De Giovannini, et al, A. Rubio, PRA 86, 062515 (2012)]. (ii) Finally we show how the dynamics of many-electron systems can be controlled with lasers by marrying TDDFT with optimal control theory [A. Castro et al, PRL 109, 153603 (2012)].

  20. Absorption Spectra and Photoreactivity of p-Aminobenzophenone by Time-dependent Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Cheng, Xue-mei; Huang, Yao; Ma, Jian-yi; Li, Xiang-yuan

    2007-06-01

    The absorption spectral properties of para-aminobenzophenone (p-ABP) were investigated in gas phase and in solution by time-dependent density functional theory. Calculations suggest that the singlet states vary greatly with the solvent polarities. In various polar solvents, including acetonitrile, methanol, ethanol, dimethyl sulfoxide, and dimethyl formamide, the excited S1 states with charge transfer character result from π → π* transitions. However, in nonpolar solvents, cyclohexane, and benzene, the S1 states are the result of n → π* transitions related to local excitation in the carbonyl group. The excited T1 states were calculated to have ππ* character in various solvents. From the variation of the calculated excited states, the band due to π → π* transition undergoes a redshift with an increase in solvent polarity, while the band due to n → π* transition undergoes a blueshift with an increase in solvent polarity. In addition, the triplet yields and the photoreactivities of p-ABP in various solvents are discussed.

  1. Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis.

    PubMed

    Tavernelli, Ivano; Gaigeot, Marie-Pierre; Vuilleumier, Rodolphe; Stia, Carlos; Hervé du Penhoat, Marie-Anne; Politis, Marie-Françoise

    2008-10-06

    The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD-DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B(1), 3A(1), 1B(2) and 2A(1) in turn. We show that the doubly charged H(2)O(2+) molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.

  2. Negative Density Dependence Regulates Two Tree Species at Later Life Stage in a Temperate Forest

    PubMed Central

    Piao, Tiefeng; Chun, Jung Hwa; Yang, Hee Moon; Cheon, Kwangil

    2014-01-01

    Numerous studies have demonstrated that tree survival is influenced by negative density dependence (NDD) and differences among species in shade tolerance could enhance coexistence via resource partitioning, but it is still unclear how NDD affects tree species with different shade-tolerance guilds at later life stages. In this study, we analyzed the spatial patterns for trees with dbh (diameter at breast height) ≥2 cm using the pair-correlation g(r) function to test for NDD in a temperate forest in South Korea after removing the effects of habitat heterogeneity. The analyses were implemented for the most abundant shade-tolerant (Chamaecyparis obtusa) and shade-intolerant (Quercus serrata) species. We found NDD existed for both species at later life stages. We also found Quercus serrata experienced greater NDD compared with Chamaecyparis obtusa. This study indicates that NDD regulates the two abundant tree species at later life stages and it is important to consider variation in species' shade tolerance in NDD study. PMID:25058660

  3. Negative density dependence regulates two tree species at later life stage in a temperate forest.

    PubMed

    Piao, Tiefeng; Chun, Jung Hwa; Yang, Hee Moon; Cheon, Kwangil

    2014-01-01

    Numerous studies have demonstrated that tree survival is influenced by negative density dependence (NDD) and differences among species in shade tolerance could enhance coexistence via resource partitioning, but it is still unclear how NDD affects tree species with different shade-tolerance guilds at later life stages. In this study, we analyzed the spatial patterns for trees with dbh (diameter at breast height) ≥2 cm using the pair-correlation g(r) function to test for NDD in a temperate forest in South Korea after removing the effects of habitat heterogeneity. The analyses were implemented for the most abundant shade-tolerant (Chamaecyparis obtusa) and shade-intolerant (Quercus serrata) species. We found NDD existed for both species at later life stages. We also found Quercus serrata experienced greater NDD compared with Chamaecyparis obtusa. This study indicates that NDD regulates the two abundant tree species at later life stages and it is important to consider variation in species' shade tolerance in NDD study.

  4. Thickness dependent charge transfer states and dark carriers density in vacuum deposited small molecule organic photocell

    NASA Astrophysics Data System (ADS)

    Shekhar, Himanshu; Tzabari, Lior; Solomeshch, Olga; Tessler, Nir

    2016-10-01

    We have investigated the influence of the active layer thickness on the balance of the internal mechanisms affecting the efficiency of copper phthalocyanine - fullerene (C60) based vacuum deposited bulk heterojunction organic photocell. We fabricated a range of devices for which we varied the thickness of the active layer from 40 to 120 nm and assessed their performance using optical and electrical characterization techniques. As reported previously for phthalocyanine:C60, the performance of the device is highly dependent on the active layer thickness and of all the thicknesses we tried, the 40 nm thin active layer device showed the best solar cell characteristic parameters. Using the transfer matrix based optical model, which includes interference effects, we calculated the optical power absorbed in the active layers for the entire absorption band, and we found that this cannot explain the trend with thickness. Measurement of the cell quantum efficiency as a function of light intensity showed that the relative weight of the device internal processes changes when going from 40 nm to 120 nm thick active layer. Electrical modeling of the device, which takes different internal processes into account, allowed to quantify the changes in the processes affecting the generation - recombination balance. Sub gap external quantum efficiency and morphological analysis of the surface of the films agree with the model's result. We found that as the thickness grows the density of charge transfer states and of dark carriers goes up and the uniformity in the vertical direction is reduced.

  5. Adiabatic approximation in time-dependent reduced-density-matrix functional theory

    SciTech Connect

    Requist, Ryan; Pankratov, Oleg

    2010-04-15

    With the aim of describing real-time electron dynamics, we introduce an adiabatic approximation for the equation of motion of the one-body reduced density matrix (one-matrix). The eigenvalues of the one-matrix, which represent the occupation numbers of single-particle orbitals, are obtained from the constrained minimization of the instantaneous ground-state energy functional rather than from their dynamical equations. The performance of the approximation vis-a-vis nonadiabatic effects is assessed in real-time simulations of a two-site Hubbard model. Due to Landau-Zener-type transitions, the system evolves into a nonstationary state with persistent oscillations in the observables. The amplitude of the oscillations displays a strongly nonmonotonic dependence on the strength of the electron-electron interaction and the rate of variation of the external potential. We interpret an associated resonance behavior in the phase of the oscillations in terms of 'scattering' with spectator energy levels. To clarify the motivation for the minimization condition, we derive a sequence of energy functionals E{sub v}{sup (n)}, for which the corresponding sequence of minimizing one-matrices is asymptotic to the exact one-matrix in the adiabatic limit.

  6. The electronic absorption study of imide anion radicals in terms of time dependent density functional theory.

    PubMed

    Andrzejak, Marcin; Sterzel, Mariusz; Pawlikowski, Marek T

    2005-07-01

    The absorption spectra of the N-(2,5-di-tert-butylphenyl) phthalimide (1-), N-(2,5-di-tert-butylphenyl)-1,8-naphthalimide (2-) and N-(2,5-di-tert-butylphenyl)-perylene-3,4-dicarboximide (3-) anion radicals are studied in terms of time dependent density functional theory (TDDFT). For these anion radicals a large number electronic states (from 30 to 60) was found in the visible and near-IR regions (5000-45,000 cm(-1)). In these regions the TD/B3LYP treatment at the 6-1+G* level is shown to reproduce satisfactorily the empirical absorption spectra of all three anion radicals studied. The most apparent discrepancies between purely electronic theory and the experiment could be found in the excitation region corresponding to D0-->D1 transitions in the 2- and 3- molecules. For these species we argue that the structures seen in the lowest energy part of the absorptions of the 2- and 3- species are very likely due to Franck-Condon (FC) activity of the totally symmetric vibrations not studied in this Letter.

  7. Vertical Singlet Excitations on Adenine Dimer: A Time Dependent Density Functional Study

    NASA Astrophysics Data System (ADS)

    Crespo-Hernández, Carlos E.; Marai, Christopher N. J.

    2007-12-01

    The condense phase, excited state dynamics of the adenylyl(3'→5')adenine (ApA) dinucleotide has been previously studied using transient absorption spectroscopy with femtosecond time resolution (Crespo-Hernández et al. Chem. Rev. 104, 1977-2019 (2004)). An ultrafast and a long-lived component were observed with time constants of <1 ps and 60±16 ps, respectively. Comparison of the time constants measured for the dinucleotide with that for the adenine nucleotide suggested that the fast component observed in ApA could be assigned to monomer dynamics. The long-lived component observed in ApA was assigned to an excimer state that originates from a fraction of base stacked conformations present at the time of excitation. In this contribution, supermolecule calculations using the time dependent implementation of density functional theory is used to provide more insights on the origin of the initial Franck-Condon excitations. Monomer-like, localized excitations are observed for conformations having negligible base stacking interactions, whereas delocalized excitations are predicted for conformations with significant vertical base-base overlap.

  8. The electronic absorption study of imide anion radicals in terms of time dependent density functional theory

    NASA Astrophysics Data System (ADS)

    Andrzejak, Marcin; Sterzel, Mariusz; Pawlikowski, Marek T.

    2005-07-01

    The absorption spectra of the N-(2,5-di- tert-butylphenyl) phthalimide ( 1-), N-(2,5-di- tert-butylphenyl)-1,8-naphthalimide ( 2-) and N-(2,5-di- tert-butylphenyl)-perylene-3,4-dicarboximide ( 3-) anion radicals are studied in terms of time dependent density functional theory (TDDFT). For these anion radicals a large number electronic states (from 30 to 60) was found in the visible and near-IR regions (5000-45000 cm -1). In these regions the TD/B3LYP treatment at the 6-1+G* level is shown to reproduce satisfactorily the empirical absorption spectra of all three anion radicals studied. The most apparent discrepancies between purely electronic theory and the experiment could be found in the excitation region corresponding to D0→ D1 transitions in the 2- and 3- molecules. For these species we argue that the structures seen in the lowest energy part of the absorptions of the 2- and 3- species are very likely due to Franck-Condon (FC) activity of the totally symmetric vibrations not studied in this Letter.

  9. 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…

  10. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

    PubMed

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie; Aspuru-Guzik, Alán; Kleinekathöfer, Ulrich

    2015-08-06

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna-Matthews-Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbital (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.

  11. Agricultural irrigation mediates climatic effects and density dependence in population dynamics of Chinese striped hamster in North China Plain.

    PubMed

    Yan, Chuan; Xu, Lei; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shoushen; Yang, Hefang; Zhang, Zhibin

    2013-03-01

    Several studies show that climatic (extrinsic) factors can interact with density-dependent (intrinsic) factors to alter long-term population dynamics, yet there is a surprising lack of investigations of how anthropogenic disturbance modifies such dynamics. Such interactions could be especially important in agricultural systems subject to climate change. We investigated the effects of density dependence, climate, recurrent disturbance from flood irrigation and their interactions on the population dynamics of an important rodent pest, the Chinese striped hamster (Cricetulus barabensis), over 27 years in the croplands of the North China Plain. Strong density-dependent feedbacks occurred at both annual and seasonal scales. While warmer weather increased population sizes in nonbreeding seasons, this effect was counteracted by the negative effect of flood irrigation in breeding seasons. Precipitation showed significant positive effects in nonbreeding seasons, but negative effects in breeding seasons. There were important interactions between intrinsic dynamics, extrinsic dynamics and disturbance. Low temperature significantly increased the strength of density dependence in nonbreeding seasons, whereas intensification of flood irrigation area significantly increased the strength of density dependence but reduced the effect of summer prec