NASA Technical Reports Server (NTRS)
Hoffman, David K.; Sharafeddin, Omar; Judson, Richard S.; Kouri, Donald J.
1990-01-01
The time-dependent form of the Lippmann-Schwinger integral equation is used as the basis of several new wave packet propagation schemes. These can be formulated in terms of either the time-dependent wave function or a time-dependent amplitude density. The latter is nonzero only in the region of configuratiaon space for which the potential is nonzero, thereby in principle obviating the necessity of large grids or the use of complex absorbing potentials when resonances cause long collision times (leading, consequently, to long propagation times). Transition amplitudes are obtained in terms of Fourier transforms of the amplitude density from the time to the energy domain. The approach is illustrated by an application to a standard potential scattering model problem where, as in previous studies, the action of the kinetic energy operator is evaluated by fast Fourier transform (FFT) techniques.
NASA Astrophysics Data System (ADS)
Steinke, I.; Hoose, C.; Möhler, O.; Connolly, P.; Leisner, T.
2015-04-01
Deposition nucleation experiments with Arizona Test Dust (ATD) as a surrogate for mineral dusts were conducted at the AIDA cloud chamber at temperatures between 220 and 250 K. The influence of the aerosol size distribution and the cooling rate on the ice nucleation efficiencies was investigated. Ice nucleation active surface site (INAS) densities were calculated to quantify the ice nucleation efficiency as a function of temperature, humidity and the aerosol surface area concentration. Additionally, a contact angle parameterization according to classical nucleation theory was fitted to the experimental data in order to relate the ice nucleation efficiencies to contact angle distributions. From this study it can be concluded that the INAS density formulation is a very useful tool to describe the temperature- and humidity-dependent ice nucleation efficiency of ATD particles. Deposition nucleation on ATD particles can be described by a temperature- and relative-humidity-dependent INAS density function ns(T, Sice) with ns(xtherm) = 1.88 ×105 · exp(0.2659 · xtherm) [m-2] , (1) where the temperature- and saturation-dependent function xtherm is defined as xtherm = -(T-273.2)+(Sice-1) ×100, (2) with the saturation ratio with respect to ice Sice >1 and within a temperature range between 226 and 250 K. For lower temperatures, xtherm deviates from a linear behavior with temperature and relative humidity over ice. Also, two different approaches for describing the time dependence of deposition nucleation initiated by ATD particles are proposed. Box model estimates suggest that the time-dependent contribution is only relevant for small cooling rates and low number fractions of ice-active particles.
Size dependence of yield strength simulated by a dislocation-density function dynamics approach
NASA Astrophysics Data System (ADS)
Leung, P. S. S.; Leung, H. S.; Cheng, B.; Ngan, A. H. W.
2015-04-01
The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ∼4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ∼4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ∼2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.
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.
A consumer-resource approach to the density-dependent population dynamics of mutualism
Holland, J. Nathaniel; DeAngelis, Donald L.
2010-01-01
Like predation and competition, mutualism is now recognized as a consumer resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant- mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.
Guido, Ciro A; Jacquemin, Denis; Adamo, Carlo; Mennucci, Benedetta
2015-12-01
We critically analyze the performances of continuum solvation models when coupled to time-dependent density functional theory (TD-DFT) to predict solvent effects on both absorption and emission energies of chromophores in solution. Different polarization schemes of the polarizable continuum model (PCM), such as linear response (LR) and three different state specific (SS) approaches, are considered and compared. We show the necessity of introducing a SS model in cases where large electron density rearrangements are involved in the excitations, such as charge-transfer transitions in both twisted and quadrupolar compounds, and underline the very delicate interplay between the selected polarization method and the chosen exchange-correlation functional. This interplay originates in the different descriptions of the transition and ground/excited state multipolar moments by the different functionals. As a result, the choice of both the DFT functional and the solvent polarization scheme has to be consistent with the nature of the studied electronic excitation. PMID:26642990
Zhang, Xing; Herbert, John M.
2015-02-14
We revisit the formalism for analytic derivative couplings between excited states in time-dependent density functional theory (TDDFT). We derive and implement these couplings using quadratic response theory, then numerically compare this response-theory formulation to couplings implemented previously based on a pseudo-wavefunction formalism and direct differentiation of the Kohn-Sham determinant. Numerical results, including comparison to full configuration interaction calculations, suggest that the two approaches perform equally well for many molecular systems, provided that the underlying DFT method affords accurate potential energy surfaces. The response contributions are found to be important for certain systems with high symmetry, but can be calculated with only a moderate increase in computational cost beyond what is required for the pseudo-wavefunction approach. In the case of spin-flip TDDFT, we provide a formal proof that the derivative couplings obtained using response theory are identical to those obtained from the pseudo-wavefunction formulation, which validates our previous implementation based on the latter formalism.
NASA Astrophysics Data System (ADS)
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.
Sakko, Arto; Hakala, Mikko; Haemaelaeinen, Keijo; Rubio, Angel
2010-11-07
We apply time-dependent density functional theory to study the valence electron excitations of molecules and generalize the typically used time-propagation scheme and Casida's method to calculate the full wavevector dependent response function. This allows the computational study of dipole-forbidden valence electron transitions and the dispersion of spectral weight as a function of the wavevector. The method provides a novel analysis tool for spectroscopic methods such as inelastic x-ray scattering and electron energy loss spectroscopy. We present results for benzene and CF{sub 3}Cl and make a comparison with experimental results.
Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel
2015-12-15
The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715
Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel
2015-01-01
The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe 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
Rüger, Robert; van Lenthe, Erik; Heine, Thomas; Visscher, Lucas
2016-05-14
We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB. PMID:27179467
NASA Astrophysics Data System (ADS)
Rüger, Robert; van Lenthe, Erik; Heine, Thomas; Visscher, Lucas
2016-05-01
We propose a new method of calculating electronically excited states that combines a density functional theory based ground state calculation with a linear response treatment that employs approximations used in the time-dependent density functional based tight binding (TD-DFTB) approach. The new method termed time-dependent density functional theory TD-DFT+TB does not rely on the DFTB parametrization and is therefore applicable to systems involving all combinations of elements. We show that the new method yields UV/Vis absorption spectra that are in excellent agreement with computationally much more expensive TD-DFT calculations. Errors in vertical excitation energies are reduced by a factor of two compared to TD-DFTB.
NASA Astrophysics Data System (ADS)
Tawfik, Sherif A.; El-Sheikh, S. M.; Salem, N. M.
2011-05-01
We introduce a new simplified method for computing the electron field emission current in short carbon nanotubes and graphene sheets using ab-initio computation in slab-periodic simulation cells. The evolution of the wave functions using Time-Dependent Density Functional Theory is computed by utilizing the Crank-Nicholson propagator and using the Octopus code (Castro et al., 2006 [1]), where we skip the wave function relaxation step elaborated by Han et al. (2002) [2], and apply a norm-conserving wave propagation method instead of the norm-nonconserving seventh-order Taylor Expansion method used by Araidai et al. (2004) [3]. Our method is mainly geared towards reducing the time it takes to compute the wave function propagation and enhancing the calculation precision. We found that in pristine carbon nanotubes, the emitted charge tends to emerge mostly from electrons that are concentrated at the nanotube tip region. The charge beam concentrates into specific channel structures, showing the utility of carbon nanotubes in precision emission applications.
Density-dependent covariant energy density functionals
Lalazissis, G. A.
2012-10-20
Relativistic nuclear energy density functionals are applied to the description of a variety of nuclear structure phenomena at and away fromstability line. Isoscalar monopole, isovector dipole and isoscalar quadrupole giant resonances are calculated using fully self-consistent relativistic quasiparticle randomphase approximation, based on the relativistic Hartree-Bogoliubovmodel. The impact of pairing correlations on the fission barriers in heavy and superheavy nuclei is examined. The role of pion in constructing desnity functionals is also investigated.
A density-dependent Leslie matrix model.
Allen, L J
1989-08-01
A density-dependent Leslie matrix model introduced in 1948 by Leslie is mathematically analyzed. It is shown that the behavior is similar to that of the constant Leslie matrix. In the primitive case, the density-dependent Leslie matrix model has an asymptotic distribution corresponding to the logistic equation. However, in the imprimitive case, the asymptotic distribution is periodic, with period depending on the imprimitivity index. PMID:2520184
Pseudospectral time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Ko, Chaehyuk; Malick, David K.; Braden, Dale A.; Friesner, Richard A.; Martínez, Todd J.
2008-03-01
Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.
Density-dependent adjustment of inducible defenses
Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C.; Laforsch, Christian; Kopp, Michael
2015-01-01
Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators’ densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428
Density-dependent adjustment of inducible defenses.
Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C; Laforsch, Christian; Kopp, Michael
2015-01-01
Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators' densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428
Fragment-Based Time-Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Mosquera, Martín A.; Jensen, Daniel; Wasserman, Adam
2013-07-01
Using the Runge-Gross theorem that establishes the foundation of time-dependent density functional theory, we prove that for a given electronic Hamiltonian, choice of initial state, and choice of fragmentation, there is a unique single-particle potential (dubbed time-dependent partition potential) which, when added to each of the preselected fragment potentials, forces the fragment densities to evolve in such a way that their sum equals the exact molecular density at all times. This uniqueness theorem suggests new ways of computing the time-dependent properties of electronic systems via fragment-time-dependent density functional theory calculations. We derive a formally exact relationship between the partition potential and the total density, and illustrate our approach on a simple model system for binary fragmentation in a laser field.
Size-dependent density of zirconia nanoparticles
Opalinska, Agnieszka; Dzwolak, Wojciech; Chudoba, Tadeusz; Presz, Adam; Lojkowski, Witold
2015-01-01
Summary The correlation between density and specific surface area of ZrO2 nanoparticles (NPs) was studied. The NPs were produced using a hydrothermal process involving microwave heating. The material was annealed at 1100 C which resulted in an increase in the average grain size of the ZrO2 NPs from 11 to 78 nm and a decrease in the specific surface area from 97 to 15 m2/g. At the same time, the density increased from 5.22 g/m3 to 5.87 g/m3. This effect was interpreted to be the result of the presence of a hydroxide monolayer on the NP surface. A smaller ZrO2 grain size was correlated with a larger contribution of the low density surface layer to the average density. To prove the existence of such a layer, the material was synthesized using 50% heavy water. Fourier transform infrared spectroscopy (FTIR) permitted the identification of the OD groups created during synthesis. It was found that the OD groups persisted on the ZrO2 surface even after annealing at 1100 C. This hydroxide layer is responsible for the decrease in the average density of the NPs as their size decreases. This study of the correlation between particle size and density may be used to assess the quality of the NPs. In most cases, the technological aim is to avoid an amorphous layer and to obtain fully crystalline nanoparticles with the highest density possible. However, due to the effect of the surface layers, there is a maximum density which can be achieved for a given average NP diameter. The effect of the surface layer on the NP density becomes particularly evident for NPs smaller than 50 nm, and thus, the density of nanoparticles is size dependent. PMID:25671149
Effective pairing interactions with isospin density dependence
Margueron, J.; Sagawa, H.; Hagino, K.
2008-05-15
We perform Hartree-Fock-Bogoliubov (HFB) calculations for semi-magic calcium, nickel, tin, and lead isotopes and N=20,28,50, and 82 isotones using density-dependent pairing interactions recently derived from a microscopic nucleon-nucleon interaction. These interactions have an isovector component so that the pairing gaps in symmetric and neutron matter are reproduced. Our calculations well account for the experimental data for the neutron number dependence of binding energy, two-neutron separation energy, and odd-even mass staggering of these isotopes. This result suggests that by introducing the isovector term in the pairing interaction, one can construct a global effective pairing interaction that is applicable to nuclei in a wide range of the nuclear chart. It is also shown with the local density approximation that the pairing field deduced from the pairing gaps in infinite matter reproduces qualitatively well the pairing field for finite nuclei obtained with the HFB method.
Density dependence: an ecological Tower of Babel.
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. PMID:22648068
Evolution of density-dependent cooperation.
Seppänen, Anne; Parvinen, Kalle
2014-12-01
Cooperation is surprisingly common in life despite of its vulnerability to selfish cheating, i.e. defecting. Defectors do not contribute to common resources but take the advantage of cooperators' investments. Therefore, the emergence and maintenance of cooperation have been considered irrational phenomena. In this study, we focus on plastic, quantitative cooperation behaviour, especially on its evolution. We assume that individuals are capable to sense the population density in their neighbourhood and adjust their real-valued investments on public goods based on that information. The ecological setting is described with stochastic demographic events, e.g. birth and death, occurring at individual level. Individuals form small populations, which further constitute a structured metapopulation. For evolutionary investigations, we apply the adaptive dynamics framework. The cost of cooperative investment is incorporated into the model in two ways, by decreasing the birth rate or by increasing the death rate. In the first case, density-dependent cooperation evolves to be a decreasing function of population size as expected. In the latter case, however, the density-dependent cooperative investment can have a qualitatively different form as it may evolve to be highest in intermediate-sized populations. Indeed, we emphasize that some details in modelling may have a significant impact on the results obtained. PMID:25213153
Density-dependent diversification in North American wood warblers.
Rabosky, Daniel L; Lovette, Irby J
2008-10-22
Evidence from both molecular phylogenies and the fossil record suggests that rates of species diversification often decline through time during evolutionary radiations. One proposed explanation for this pattern is ecological opportunity, whereby an initial abundance of resources and lack of potential competitors facilitate rapid diversification. This model predicts density-dependent declines in diversification rates, but has not been formally tested in any species-level radiation. Here we develop a new conceptual framework that distinguishes density dependence from alternative processes that also produce temporally declining diversification, and we demonstrate this approach using a new phylogeny of North American Dendroica wood warblers. We show that explosive lineage accumulation early in the history of this avian radiation is best explained by a density-dependent diversification process. Our results suggest that the tempo of wood warbler diversification was mediated by ecological interactions among species and that lineage and ecological diversification in this group are coupled, as predicted under the ecological opportunity model. PMID:18611849
Sublinear scaling for time-dependent stochastic density functional theory
Gao, Yi; Neuhauser, Daniel; Baer, Roi; Rabani, Eran
2015-01-21
A stochastic approach to time-dependent density functional theory is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves time-propagation of a small set of stochastic orbitals which are first projected on the occupied space and then propagated in time according to the time-dependent Kohn-Sham equations. The evolving electron density is exactly represented when the number of random orbitals is infinite, but even a small number (≈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.
Density-Dependent Cladogenesis in Birds
Phillimore, Albert B; Price, Trevor D
2008-01-01
A characteristic signature of adaptive radiation is a slowing of the rate of speciation toward the present. On the basis of molecular phylogenies, studies of single clades have frequently found evidence for a slowdown in diversification rate and have interpreted this as evidence for density dependent speciation. However, we demonstrated via simulation that large clades are expected to show stronger slowdowns than small clades, even if the probability of speciation and extinction remains constant through time. This is a consequence of exponential growth: clades, which, by chance, diversify at above the average rate early in their history, will tend to be large. They will also tend to regress back to the average diversification rate later on, and therefore show a slowdown. We conducted a meta-analysis of the distribution of speciation events through time, focusing on sequence-based phylogenies for 45 clades of birds. Thirteen of the 23 clades (57%) that include more than 20 species show significant slowdowns. The high frequency of slowdowns observed in large clades is even more extreme than expected under a purely stochastic constant-rate model, but is consistent with the adaptive radiation model. Taken together, our data strongly support a model of density-dependent speciation in birds, whereby speciation slows as ecological opportunities and geographical space place limits on clade growth. PMID:18366256
Selective fishing induces density-dependent growth.
Svedng, Henrik; Hornborg, Sara
2014-01-01
Over the last decades, views on fisheries management have oscillated between alarm and trust in management progress. The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort. Here we report a case study on how striving for higher yields from the Eastern Baltic cod stock by increasing selectivity has become exceedingly detrimental for its productivity. Although there is a successive increase in numbers of undersized fish, growth potential is severely reduced, and fishing mortality in fishable size has increased. Once density-dependent growth is introduced, the process is self-enforcing as long as the recruitment remains stable. Our findings suggest that policies focusing on maximum yield while targeting greater sizes are risky and should instead prioritize catch rates over yield. Disregarding the underlying population structure may jeopardize stock productivity, with dire consequences for the fishing industry and ecosystem structure and function. PMID:24920387
Selective fishing induces density-dependent growth
Svedäng, Henrik; Hornborg, Sara
2014-01-01
Over the last decades, views on fisheries management have oscillated between alarm and trust in management progress. The predominant policy for remedying the world fishing crisis aims at maximum sustainable yield (MSY) by adjusting gear selectivity and fishing effort. Here we report a case study on how striving for higher yields from the Eastern Baltic cod stock by increasing selectivity has become exceedingly detrimental for its productivity. Although there is a successive increase in numbers of undersized fish, growth potential is severely reduced, and fishing mortality in fishable size has increased. Once density-dependent growth is introduced, the process is self-enforcing as long as the recruitment remains stable. Our findings suggest that policies focusing on maximum yield while targeting greater sizes are risky and should instead prioritize catch rates over yield. Disregarding the underlying population structure may jeopardize stock productivity, with dire consequences for the fishing industry and ecosystem structure and function. PMID:24920387
NASA Astrophysics Data System (ADS)
Timrov, Iurii; Vast, Nathalie; Gebauer, Ralph; Baroni, Stefano
2015-11-01
We introduce turboEELS, an implementation of the Liouville-Lanczos approach to linearized time-dependent density-functional theory, designed to simulate electron energy loss and inelastic X-ray scattering spectra in periodic solids. turboEELS is open-source software distributed under the terms of the GPL as a component of QUANTUM ESPRESSO. As with other components, turboEELS is optimized to run on a variety of different platforms, from laptops to massively parallel architectures, using native mathematical libraries (LAPACK and FFTW) and a hierarchy of custom parallelization layers built on top of MPI.
Ohlberger, Jan; Rogers, Lauren A.; Stenseth, Nils Chr.
2014-01-01
A persistent debate in population ecology concerns the relative importance of environmental stochasticity and density dependence in determining variability in adult year-class strength, which contributes to future reproduction as well as potential yield in exploited populations. Apart from the strength of the processes, the timing of density regulation may affect how stochastic variation, for instance through climate, translates into changes in adult abundance. In this study, we develop a life-cycle model for the population dynamics of a large marine fish population, Northeast Arctic cod, to disentangle the effects of density-independent and density-dependent processes on early life-stages, and to quantify the strength of compensatory density dependence in the population. The model incorporates information from scientific surveys and commercial harvest, and dynamically links multiple effects of intrinsic and extrinsic factors on all life-stages, from eggs to spawners. Using a state-space approach we account for observation error and stochasticity in the population dynamics. Our findings highlight the importance of density-dependent survival in juveniles, indicating that this period of the life cycle largely determines the compensatory capacity of the population. Density regulation at the juvenile life-stage dampens the impact of stochastic processes operating earlier in life such as environmental impacts on the production of eggs and climate-dependent survival of larvae. The timing of stochastic versus regulatory processes thus plays a crucial role in determining variability in adult abundance. Quantifying the contribution of environmental stochasticity and compensatory mechanisms in determining population abundance is essential for assessing population responses to climate change and exploitation by humans. PMID:24893001
NASA Astrophysics Data System (ADS)
Iakovlev, Anton; Bedrov, Dmitry; Müller, Marcus
2015-12-01
Motivated by growing interest in interfacial properties of liquid mercury we investigate by atomistic Molecular Dynamics simulation the ability of density-independent, empiric density-dependent, and recently proposed embedded-atom force fields to predict the surface tension and coexistence density of liquid mercury at room temperature, 293 K. The effect of the density dependence of the studied models on the liquid-vapor coexistence and surface tension is discussed in detail and our results are corroborated by Monte Carlo simulations and semi-analytic liquid-state theory. The latter approach is particularly useful to identify and rationalize artifacts that arise from an ad-hoc generalization of density-independent potentials by introducing density-dependent coefficients. In view of computational efficiency and thermodynamic robustness of density-independent model we optimize its functional form to obtain higher surface tension values in order to improve agreement with experiment.
Statistical approach to nuclear level density
Sen'kov, R. A.; Horoi, M.; Zelevinsky, V. G.
2014-10-15
We discuss the level density in a finite many-body system with strong interaction between the constituents. Our primary object of applications is the atomic nucleus but the same techniques can be applied to other mesoscopic systems. We calculate and compare nuclear level densities for given quantum numbers obtained by different methods, such as nuclear shell model (the most successful microscopic approach), our main instrument - moments method (statistical approach), and Fermi-gas model; the calculation with the moments method can use any shell-model Hamiltonian excluding the spurious states of the center-of-mass motion. Our goal is to investigate statistical properties of nuclear level density, define its phenomenological parameters, and offer an affordable and reliable way of calculation.
Simulating density-dependent flows using the lattice Boltzmann method
NASA Astrophysics Data System (ADS)
Bardsley, K. J.; Sukop, M. C.
2008-12-01
Seawater intrusion is a classic density-dependent problem in hydrogeology. It must be fully understood in order to be able to predict and prevent groundwater deterioration in coastal areas. All of the current programs used to study this issue are either finite difference or finite element methods. Density-dependent flow problems are exceptionally challenging for conventional numerical methods due to inherent non-linearity; definitive solutions are often elusive and a completely different modeling approach may be advantageous. The lattice Boltzmann method (LBM) represents such a numerical tool because it is not based on discretization of a series of differential equations. Instead, its foundation lies in the kinetic theory of gasses as proposed by Boltzmann. A key advantage of lattice Boltzmann method is that it has the ability to solve the Navier-Stokes equations in larger conduits and pores. Recent advances in lattice Boltzmann modeling permit simulation of large-scale density-dependent ground water flow and heat/solute transport. These simulations can be accomplished while retaining the advantages of 'regular' lattice Boltzmann methods, such as solute/heat transport at high Reynolds numbers. Hence it allows for eddy diffusion brought on by inertial components of flow at higher Reynolds numbers, which may occur in some coastal aquifers. This may prove to be an advantage for freshwater/seawater interface simulations especially given the highly macroporous nature of the aquifers underlying south Florida. Simulation of these phenomena is not possible with traditional Darcy's law-based groundwater models. Some geologists and engineers have been able to successfully apply LBM to fluid flow and contaminant transport problems. There are only a handful of scientists attempting to apply LBM to density-dependent flows in general; even fewer have considered seawater intrusion. We show how this method can be applied to density-dependent flows. We present two sets of results. The first are the results for the Horton-Rogers-Lapwood problem, where heat is the cause of varying density. The second are our results for a seawater intrusion simulation, a Henry-like problem.
THE DEPENDENCE OF STAR FORMATION EFFICIENCY ON GAS SURFACE DENSITY
Burkert, Andreas; Hartmann, Lee E-mail: lhartm@umich.edu
2013-08-10
Studies by Lada et al. and Heiderman et al. have suggested that star formation mostly occurs above a threshold in gas surface density {Sigma} of {Sigma}{sub c} {approx} 120 M{sub Sun} pc{sup -2} (A{sub K} {approx} 0.8). Heiderman et al. infer a threshold by combining low-mass star-forming regions, which show a steep increase in the star formation rate per unit area {Sigma}{sub SFR} with increasing {Sigma}, and massive cores forming luminous stars which show a linear relation. We argue that these observations do not require a particular density threshold. The steep dependence of {Sigma}{sub SFR}, approaching unity at protostellar core densities, is a natural result of the increasing importance of self-gravity at high densities along with the corresponding decrease in evolutionary timescales. The linear behavior of {Sigma}{sub SFR} versus {Sigma} in massive cores is consistent with probing dense gas in gravitational collapse, forming stars at a characteristic free-fall timescale given by the use of a particular molecular tracer. The low-mass and high-mass regions show different correlations between gas surface density and the area A spanned at that density, with A {approx} {Sigma}{sup -3} for low-mass regions and A {approx} {Sigma}{sup -1} for the massive cores; this difference, along with the use of differing techniques to measure gas surface density and star formation, suggests that connecting the low-mass regions with massive cores is problematic. We show that the approximately linear relationship between dense gas mass and stellar mass used by Lada et al. similarly does not demand a particular threshold for star formation and requires continuing formation of dense gas. Our results are consistent with molecular clouds forming by galactic hydrodynamic flows with subsequent gravitational collapse.
Alternative Approaches to High Energy Density Fusion
NASA Astrophysics Data System (ADS)
Hammer, J.
2016-03-01
This paper explores selected approaches to High Energy Density (HED) fusion, beginning with discussion of ignition requirements at the National Ignition Facility (NIF). The needed improvements to achieve ignition are closely tied to the ability to concentrate energy in the implosion, manifested in the stagnation pressure, Pstag . The energy that must be assembled in the imploded state to ignite varies roughly as Pstag -2, so among other requirements, there is a premium on reaching higher Pstag to achieve ignition with the available laser energy. The U.S. inertial confinement fusion program (ICF) is pursuing higher Pstag on NIF through improvements to capsule stability and symmetry. One can argue that recent experiments place an approximate upper bound on the ultimate ignition energy requirement. Scaling the implosions consistently in spatial, temporal and energy scales shows that implosions of the demonstrated quality ignite robustly at 9-15 times the current energy of NIF. While lasers are unlikely to reach that bounding energy, it appears that pulsed-power sources could plausibly do so, giving a range of paths forward for ICF depending on success in improving energy concentration. In this paper, I show the scaling arguments then discuss topics from my own involvement in HED fusion. The recent Viewfactor experiments at NIF have shed light on both the observed capsule drive deficit and errors in the detailed modelling of hohlraums. The latter could be important factors in the inability to achieve the needed symmetry and energy concentration. The paper then recounts earlier work in Fast Ignition and the uses of pulsed- power for HED and fusion applications. It concludes with a description of a method for improving pulsed-power driven hohlraums that could potentially provide a factor of 10 in energy at NIF-like drive conditions and reach the energy bound for indirect drive ICF.
Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen
2014-09-01
The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation. PMID:26588541
Extension and parametrization of high-order density dependence in Skyrme forces
NASA Astrophysics Data System (ADS)
Xiong, X. Y.; Pei, J. C.; Chen, W. J.
2016-02-01
The three-body force is indispensable in nuclear energy density functionals, which leads to a density-dependent two-body term in the Hartree-Fock approach. Usually, a single fractional power of density dependency is adopted. We consider the possibility of an additional higher-order density dependence in extended Skyrme forces. As a result, new extended Skyrme parametrizations based on the SLy4 force have been obtained and the improvements in descriptions of global nuclei have been demonstrated. The higher-order term can also substantially affect nuclear properties in the high-density region in general ways.
Elevational variation in density dependence in a subtropical forest.
Xu, Meng; Yu, Shixiao
2014-07-01
Density-dependent mortality has been recognized as an important mechanism that underpins tree species diversity, especially in tropical forests. However, few studies have attempted to explore how density dependence varies with spatial scale and even fewer have attempted to identify why there is scale-dependent differentiation. In this study, we explore the elevational variation in density dependence. Three 1-ha permanent plots were established at low and high elevations in the Heishiding subtropical forest, southern China. Using data from 1200 1 m(2) seedling quadrats, comprising of 200 1 m(2) quadrats located in each 1-ha plot, we examined the variation in density dependence between elevations using a generalized linear mixed model with crossed random effects. A greenhouse experiment also investigated the potential effects of the soil biota on density-dependent differentiation. Our results demonstrated that density-dependent seedling mortality can vary between elevations in subtropical forests. Species found at a lower elevation suffered stronger negative density dependence than those found at a higher elevation. The greenhouse experiment indicated that two species that commonly occur at both elevations suffered more from soilborne pathogens during seed germination and seedling growth when they grew at the lower elevation, which implied that soil pathogens may play a crucial role in density-dependent spatial variation. PMID:25165522
Density-dependent growth in invasive Lionfish (Pterois volitans).
Benkwitt, Cassandra E
2013-01-01
Direct demographic density dependence is necessary for population regulation and is a central concept in ecology, yet has not been studied in many invasive species, including any invasive marine fish. The red lionfish (Pterois volitans) is an invasive predatory marine fish that is undergoing exponential population growth throughout the tropical western Atlantic. Invasive lionfish threaten coral-reef ecosystems, but there is currently no evidence of any natural population control. Therefore, a manipulative field experiment was conducted to test for density dependence in lionfish. Juvenile lionfish densities were adjusted on small reefs and several demographic rates (growth, recruitment, immigration, and loss) were measured throughout an 8-week period. Invasive lionfish exhibited direct density dependence in individual growth rates, as lionfish grew slower at higher densities throughout the study. Individual growth in length declined linearly with increasing lionfish density, while growth in mass declined exponentially with increasing density. There was no evidence, however, for density dependence in recruitment, immigration, or loss (mortality plus emigration) of invasive lionfish. The observed density-dependent growth rates may have implications for which native species are susceptible to lionfish predation, as the size and type of prey that lionfish consume is directly related to their body size. The absence of density-dependent loss, however, contrasts with many native coral-reef fish species and suggests that for the foreseeable future manual removals may be the only effective local control of this invasion. PMID:23825604
Density-Dependent Growth in Invasive Lionfish (Pterois volitans)
Benkwitt, Cassandra E.
2013-01-01
Direct demographic density dependence is necessary for population regulation and is a central concept in ecology, yet has not been studied in many invasive species, including any invasive marine fish. The red lionfish (Pterois volitans) is an invasive predatory marine fish that is undergoing exponential population growth throughout the tropical western Atlantic. Invasive lionfish threaten coral-reef ecosystems, but there is currently no evidence of any natural population control. Therefore, a manipulative field experiment was conducted to test for density dependence in lionfish. Juvenile lionfish densities were adjusted on small reefs and several demographic rates (growth, recruitment, immigration, and loss) were measured throughout an 8-week period. Invasive lionfish exhibited direct density dependence in individual growth rates, as lionfish grew slower at higher densities throughout the study. Individual growth in length declined linearly with increasing lionfish density, while growth in mass declined exponentially with increasing density. There was no evidence, however, for density dependence in recruitment, immigration, or loss (mortality plus emigration) of invasive lionfish. The observed density-dependent growth rates may have implications for which native species are susceptible to lionfish predation, as the size and type of prey that lionfish consume is directly related to their body size. The absence of density-dependent loss, however, contrasts with many native coral-reef fish species and suggests that for the foreseeable future manual removals may be the only effective local control of this invasion. PMID:23825604
Density dependence of the nuclear symmetry energy: A microscopic perspective
Vidana, Isaac; Providencia, Constanca; Polls, Artur; Rios, Arnau
2009-10-15
We perform a systematic analysis of the density dependence of nuclear symmetry energy within the microscopic Brueckner-Hartree-Fock (BHF) approach using the realistic Argonne V18 nucleon-nucleon potential plus a phenomenological three-body force of Urbana type. Our results are compared thoroughly with those arising from several Skyrme and relativistic effective models. The values of the parameters characterizing the BHF equation of state of isospin asymmetric nuclear matter fall within the trends predicted by those models and are compatible with recent constraints coming from heavy ion collisions, giant monopole resonances, or isobaric analog states. In particular we find a value of the slope parameter L=66.5 MeV, compatible with recent experimental constraints from isospin diffusion, L=88{+-}25 MeV. The correlation between the neutron skin thickness of neutron-rich isotopes and the slope L and curvature K{sub sym} parameters of the symmetry energy is studied. Our BHF results are in very good agreement with the correlations already predicted by other authors using nonrelativistic and relativistic effective models. The correlations of these two parameters and the neutron skin thickness with the transition density from nonuniform to {beta}-stable matter in neutron stars are also analyzed. Our results confirm that there is an inverse correlation between the neutron skin thickness and the transition density.
NASA Astrophysics Data System (ADS)
Kimura, Y.; Yoshimura, Y.; Nakahara, M.
1989-08-01
We studied the dimerization equilibrium of 2-methyl-2-nitrosopropane in argon at 25.0 C from about 500 to 1200 kg m-3. It is clarified that in the simplest solvent, argon, there exists a definite difference in the density dependence of the equilibrium constant between the high and medium density regions. In the high density region, the equilibrium constant shows a sizable increase with the solvent density as in the liquid phase. Near the critical density, however, the equilibrium constant shows little density dependence.
Prevalence and strength of density-dependent tree recruitment.
Zhu, Kai; Woodall, Christopher W; Monteiro, Joao V D; Clark, James S
2015-09-01
Density dependence could maintain diversity in forests, but studies continue to disagree on its role. Part of the disagreement results from the fact that different studies have evaluated different responses (survival, recruitment, or growth) of different stages (seeds, seedlings, or adults) to different inputs (density of seedlings, density or distance to adults). Most studies are conducted on a single site and thus are difficult to generalize. Using USDA Forest Service's Forest Inventory and Analysis data, we analyzed over a million seedling-to-sapling recruitment observations of 50 species from the eastern United States, controlling for the effects of climate. We focused on the per-seedling recruitment rate, because it is most likely to promote diversity and to be identified in observational or experimental data. To understand the prevalence of density dependence, we quantified the number of species with significant positive or negative effects. To understand the strength of density dependence, we determined the magnitude of effects among con- and heterospecifics, and how it changes with overall species abundance. We found that density dependence is pervasive among the 50 species, as the majority of them have significant effects and mostly negative. Density-dependence effects are stronger from conspecific than heterospecfic adult neighbors, consistent with the predictions of the Janzen-Connell hypothesis. Contrary to recent reports, density-dependence effects are more negative for common than rare species, suggesting disproportionately stronger population regulation in common species. We conclude that density dependence is pervasive, and it is strongest from conspecific neighbors of common species. Our analysis provides direct evidence that density dependence reaulates opulation dynamics of tree species in eastern U.S. forests. PMID:26594690
Density-dependent acoustic properties of PBX 9502
Brown, Geoffrey W; Thompson, Darla G; Deluca, Racci; Hartline, Ernest L; Hagelberg, Stephanie I
2009-07-31
We have measured the longitudinal and shear acoustic velocities of PBX 9502 as a function of density for die-pressed samples over the range 1.795 g/cc to 1.888 g/cc. The density dependence of the velocities is linear. Thermal cycling of PBX 9502 is known to induce irreversible volume growth. We have measured this volume growth dependence on density for a subset of the pressed parts and find that the most growth occurs for the samples with lowest initial density. The acoustic velocity changes due to the volume growth are significant and reflect damage in the samples.
Kobryn, Alexander E; Yamaguchi, Tsuyoshi; Hirata, Fumio
2005-05-01
We present results of the theoretical study and numerical calculation of the dynamics of molecular liquids based on the combination of the memory equation formalism and the reference interaction site model (RISM). Memory equations for the site-site intermediate scattering functions are studied in the mode-coupling approximation for the first-order memory kernels, while equilibrium properties such as site-site static structure factors are deduced from RISM. The results include the temperature-density (pressure) dependence of translational diffusion coefficients D and orientational relaxation times tau for acetonitrile in water, methanol in water, and methanol in acetonitrile--all in the limit of infinite dilution. Calculations are performed over the range of temperatures and densities employing the extended simple point charge model for water and optimized site-site potentials for acetonitrile and methanol. The theory is able to reproduce qualitatively all main features of temperature and density dependences of D and tau observed in real and computer experiments. In particular, anomalous behavior, i.e, the increase in mobility with density, is observed for D and tau of methanol in water, while acetonitrile in water and methanol in acetonitrile do not show deviations from the ordinary behavior. The variety exhibited by the different solute-solvent systems in the density dependence of the mobility is interpreted in terms of the two competing origins of friction, which interplay with each other as density increases: the collisional and dielectric frictions which, respectively, increase and decrease with increasing density. PMID:15918733
Density dependence of reactor performance with thermal confinement scalings
Stotler, D.P.
1992-03-01
Energy confinement scalings for the thermal component of the plasma published thus far have a different dependence on plasma density and input power than do scalings for the total plasma energy. With such thermal scalings, reactor performance (measured by Q, the ratio of the fusion power to the sum of the ohmic and auxiliary input powers) worsens with increasing density. This dependence is the opposite of that found using scalings based on the total plasma energy, indicating that reactor operation concepts may need to be altered if this density dependence is confirmed in future research.
Density-potential mapping in time-dependent density-functional theory
Maitra, N. T.; Todorov, T. N.; Woodward, C.; Burke, K.
2010-04-15
The key questions of uniqueness and existence in time-dependent density-functional theory are usually formulated only for potentials and densities that are analytic in time. Simple examples, standard in quantum mechanics, lead, however, to nonanalyticities. We reformulate these questions in terms of a nonlinear Schroedinger equation with a potential that depends nonlocally on the wave function.
Seasonality, density dependence, and population cycles in Hokkaido voles
Stenseth, Nils Chr.; Viljugrein, Hildegunn; Saitoh, Takashi; Hansen, Thomas F.; Kittilsen, Marte O.; Bølviken, Erik; Glöckner, Fredrik
2003-01-01
Voles and lemmings show extensive variation in population dynamics regulated across and within species. In an attempt to develop and test generic hypotheses explaining these differences, we studied 84 populations of the gray-sided vole (Clethrionomys rufocanus) in Hokkaido, Japan. We show that these populations are limited by a combination of density-independent factors (such as climate) and density-dependent processes (such as specialist predators). We show that density-dependent regulation primarily occurs in winter months, so that populations experiencing longer winters tend to have a stronger delayed density-dependence and, as a result, exhibit regular density cycles. Altogether, we demonstrate that seasonality plays a key role in determining whether a vole population is cyclic or not. PMID:14504382
Dynamical instabilities in density-dependent hadronic relativistic models
Santos, A. M.; Brito, L.; Providencia, C.
2008-04-15
Unstable modes in asymmetric nuclear matter (ANM) at subsaturation densities are studied in the framework of relativistic mean-field density-dependent hadron models. The size of the instabilities that drive the system are calculated and a comparison with results obtained within the nonlinear Walecka model is presented. The distillation and antidistillation effects are discussed.
Evolution of positive and negative density-dependent dispersal
Rodrigues, Antnio M. M.; Johnstone, Rufus A.
2014-01-01
Understanding the evolution of density-dependent dispersal strategies has been a major challenge for evolutionary ecologists. Some existing models suggest that selection should favour positive and others negative density-dependence in dispersal. Here, we develop a general model that shows how and why selection may shift from positive to negative density-dependence in response to key ecological factors, in particular the temporal stability of the environment. We find that in temporally stable environments, particularly with low dispersal costs and large group sizes, habitat heterogeneity selects for negative density-dependent dispersal, whereas in temporally variable environments, particularly with high dispersal costs and small group sizes, habitat heterogeneity selects for positive density-dependent dispersal. This shift reflects the changing balance between the greater competition for breeding opportunities in more productive patches, versus the greater long-term value of offspring that establish themselves there, the latter being very sensitive to the temporal stability of the environment. In general, dispersal of individuals out of low-density patches is much more sensitive to habitat heterogeneity than is dispersal out of high-density patches. PMID:25100700
Walsh, Rachael K.; Aguilar, Cristobal L.; Facchinelli, Luca; Valerio, Laura; Ramsey, Janine M.; Scott, Thomas W.; Lloyd, Alun L.; Gould, Fred
2013-01-01
Transgenic strains of Aedes aegypti have been engineered to help control transmission of dengue virus. Although resources have been invested in developing the strains, we lack data on the ecology of mosquitoes that could impact the success of this approach. Although studies of intra-specific competition have been conducted using Ae. aegypti larvae, none of these studies examine mixed age cohorts at densities that occur in the field, with natural nutrient levels. Experiments were conducted in Mexico to determine the impact of direct and delayed density dependence on Ae. aegypti populations. Natural water, food, and larval densities were used to estimate the impacts of density dependence on larval survival, development, and adult body size. Direct and delayed density-dependent factors had a significant impact on larval survival, larval development, and adult body size. These results indicate that control methods attempting to reduce mosquito populations may be counteracted by density-dependent population regulation. PMID:23669230
Walsh, Rachael K; Aguilar, Cristobal L; Facchinelli, Luca; Valerio, Laura; Ramsey, Janine M; Scott, Thomas W; Lloyd, Alun L; Gould, Fred
2013-07-01
Transgenic strains of Aedes aegypti have been engineered to help control transmission of dengue virus. Although resources have been invested in developing the strains, we lack data on the ecology of mosquitoes that could impact the success of this approach. Although studies of intra-specific competition have been conducted using Ae. aegypti larvae, none of these studies examine mixed age cohorts at densities that occur in the field, with natural nutrient levels. Experiments were conducted in Mexico to determine the impact of direct and delayed density dependence on Ae. aegypti populations. Natural water, food, and larval densities were used to estimate the impacts of density dependence on larval survival, development, and adult body size. Direct and delayed density-dependent factors had a significant impact on larval survival, larval development, and adult body size. These results indicate that control methods attempting to reduce mosquito populations may be counteracted by density-dependent population regulation. PMID:23669230
Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird.
Dunn, Jenny C; Hamer, Keith C; Benton, Tim G
2015-01-01
Land management intrinsically influences the distribution of animals and can consequently alter the potential for density-dependent processes to act within populations. For declining species, high densities of breeding territories are typically considered to represent productive populations. However, as density-dependent effects of food limitation or predator pressure may occur (especially when species are dependent upon separate nesting and foraging habitats), high territory density may limit per-capita productivity. Here, we use a declining but widespread European farmland bird, the yellowhammer Emberiza citrinella L., as a model system to test whether higher territory densities result in lower fledging success, parental provisioning rates or nestling growth rates compared to lower densities. Organic landscapes held higher territory densities, but nests on organic farms fledged fewer nestlings, translating to a 5 times higher rate of population shrinkage on organic farms compared to conventional. In addition, when parental provisioning behaviour was not restricted by predation risk (i.e., at times of low corvid activity), nestling provisioning rates were higher at lower territory densities, resulting in a much greater increase in nestling mass in low density areas, suggesting that food limitation occurred at high densities. These findings in turn suggest an ecological trap, whereby preferred nesting habitat does not provide sufficient food for rearing nestlings at high population density, creating a population sink. Habitat management for farmland birds should focus not simply on creating a high nesting density, but also on ensuring heterogeneous habitats to provide food resources in close proximity to nesting birds, even if this occurs through potentially restricting overall nest density but increasing population-level breeding success. PMID:26431173
Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird
Dunn, Jenny C.; Hamer, Keith C.; Benton, Tim G.
2015-01-01
Land management intrinsically influences the distribution of animals and can consequently alter the potential for density-dependent processes to act within populations. For declining species, high densities of breeding territories are typically considered to represent productive populations. However, as density-dependent effects of food limitation or predator pressure may occur (especially when species are dependent upon separate nesting and foraging habitats), high territory density may limit per-capita productivity. Here, we use a declining but widespread European farmland bird, the yellowhammer Emberiza citrinella L., as a model system to test whether higher territory densities result in lower fledging success, parental provisioning rates or nestling growth rates compared to lower densities. Organic landscapes held higher territory densities, but nests on organic farms fledged fewer nestlings, translating to a 5 times higher rate of population shrinkage on organic farms compared to conventional. In addition, when parental provisioning behaviour was not restricted by predation risk (i.e., at times of low corvid activity), nestling provisioning rates were higher at lower territory densities, resulting in a much greater increase in nestling mass in low density areas, suggesting that food limitation occurred at high densities. These findings in turn suggest an ecological trap, whereby preferred nesting habitat does not provide sufficient food for rearing nestlings at high population density, creating a population sink. Habitat management for farmland birds should focus not simply on creating a high nesting density, but also on ensuring heterogeneous habitats to provide food resources in close proximity to nesting birds, even if this occurs through potentially restricting overall nest density but increasing population-level breeding success. PMID:26431173
DSA planarization approach to solve pattern density issue
NASA Astrophysics Data System (ADS)
Pimenta Barros, P.; Gharbi, A.; Sarrazin, A.; Tiron, R.; Posseme, N.; Barnola, S.; Bos, S.; Tallaron, C.; Claveau, G.; Chevalier, X.; Argoud, M.; Servin, I.; Navarro, C.; Nicolet, C.; Lapeyre, C.; Monget, C.
2015-03-01
Directed Self-Assembly (DSA) of Block Copolymers (BCP) is one of the most promising solutions for sub-10 nm nodes. However, some challenges need to be addressed for a complete adoption of DSA in manufacturing such as achieving DSA-friendly design, low defectivity and accurate pattern placement. In this paper, we propose to discuss the DSA integration flows using graphoepitaxy for contact-hole patterning application. DSA process dependence on guiding pattern density has been studied and solved thanks to a new approach called "DSA planarization". The capabilities of this new approach have been evaluated in terms of defectivity, Critical Dimension (CD) control and uniformity before and after DSA etching transfer.
An Infrastructureless Approach to Estimate Vehicular Density in Urban Environments
Sanguesa, Julio A.; Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J.; Cano, Juan-Carlos; Calafate, Carlos T.; Manzoni, Pietro
2013-01-01
In Vehicular Networks, communication success usually depends on the density of vehicles, since a higher density allows having shorter and more reliable wireless links. Thus, knowing the density of vehicles in a vehicular communications environment is important, as better opportunities for wireless communication can show up. However, vehicle density is highly variable in time and space. This paper deals with the importance of predicting the density of vehicles in vehicular environments to take decisions for enhancing the dissemination of warning messages between vehicles. We propose a novel mechanism to estimate the vehicular density in urban environments. Our mechanism uses as input parameters the number of beacons received per vehicle, and the topological characteristics of the environment where the vehicles are located. Simulation results indicate that, unlike previous proposals solely based on the number of beacons received, our approach is able to accurately estimate the vehicular density, and therefore it could support more efficient dissemination protocols for vehicular environments, as well as improve previously proposed schemes. PMID:23435054
An infrastructureless approach to estimate vehicular density in urban environments.
Sanguesa, Julio A; Fogue, Manuel; Garrido, Piedad; Martinez, Francisco J; Cano, Juan-Carlos; Calafate, Carlos T; Manzoni, Pietro
2013-01-01
In Vehicular Networks, communication success usually depends on the density of vehicles, since a higher density allows having shorter and more reliable wireless links. Thus, knowing the density of vehicles in a vehicular communications environment is important, as better opportunities for wireless communication can show up. However, vehicle density is highly variable in time and space. This paper deals with the importance of predicting the density of vehicles in vehicular environments to take decisions for enhancing the dissemination of warning messages between vehicles. We propose a novel mechanism to estimate the vehicular density in urban environments. Our mechanism uses as input parameters the number of beacons received per vehicle, and the topological characteristics of the environment where the vehicles are located. Simulation results indicate that, unlike previous proposals solely based on the number of beacons received, our approach is able to accurately estimate the vehicular density, and therefore it could support more efficient dissemination protocols for vehicular environments, as well as improve previously proposed schemes. PMID:23435054
Female elk contacts are neither frequency nor density dependent
Cross, 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.
Dependence of polar hole density on magnetic and solar conditions
NASA Technical Reports Server (NTRS)
Hoegy, W. R.; Grebowsky, J. M.
1991-01-01
Electron densities from the Langmuir probes on the Atmospheric Explorer C and Dynamics Explorer 2 are used for analyzing the behavior of the high-altitude night-side F region polar hole as a function of solar and magnetic activity and of universal time (UT). The polar region of invariant latitude from 70 deg to 80 deg and MLT from 22 to 03 hours is examined. The strongest dependencies are observed in F10.7 and UT; a strong hemispherical difference due to the offset of the magnetic poles from the earth's rotation axis is observed in the UT dependence of the ionization hole. A seasonal variation in the dependence of ion density on solar flux is indicated, and an overall asymmetry in the density level between hemispheres is revealed, with the winter-hole density about a factor of 10 greater in the north than in the south.
Transverse momentum dependent quark densities from Lattice QCD
Bernhard Musch,Philipp Hagler,John Negele,Andreas Schafer
2011-10-01
We study transverse momentum dependent parton distribution functions (TMDs) with non-local operators in lattice QCD, using MILC/LHPC lattices. We discuss the basic concepts of the method, including renormalization of the gauge link. Results obtained with a simplified operator geometry show visible dipole deformations of spin-dependent quark momentum densities.
Competition and the density dependence of metabolic rates.
DeLong, John P; Hanley, Torrance C; Vasseur, David A
2014-01-01
Although mass and temperature are strong predictors of metabolic rates, there is considerable unexplained variation in metabolic rates both within and across species after body size and temperature are taken into account. Some of this variation may be due to changes in the rate of food intake with population density, as metabolism depends on the throughput of food to fuel biochemical reactions. Using data collected from the literature, we show that individual metabolic rates are negatively correlated with population density for a wide range of organisms including primary producers and consumers. Using new data for the zooplankter Daphnia ambigua, we also find genotypic variation in the relationship between metabolic rate and population density. The relationship between metabolic rate and population density generally follows a power law scaling, and within a population, density-correlated variation in metabolism can span two orders of magnitude. We suggest that density-dependent metabolic rates arise via competitive effects on foraging rates (both exploitation and interference competition), combined with an activity response to accommodate the resource constraint induced by competition. Standard ecological models predict the kind of density-dependent foraging patterns that could give rise to density-dependent metabolic rates, but this has generally not been investigated. Our results indicate that after body mass and temperature, population density represents an important third axis that may account for a large amount of unexplained variance in metabolic rates within and among species. The effect of population density on metabolism has implications for the scaling of metabolic rates from individuals to populations and the relative performance of species and genotypes and therefore also for community assembly and evolution. PMID:23565624
p53 mediates density-dependent growth arrest.
Meerson, A; Milyavsky, M; Rotter, V
2004-02-13
While the stress-response-associated importance of the p53 tumor suppressor is well established, recent studies have also linked p53 with several basic parameters in the normal behavior of cells. Here, we present evidence that basal p53 expression in WI38 human embryonic lung fibroblasts restricts growth rate and mediates density-dependent inhibition of growth and the associated G1 phase arrest of the cell cycle by affecting the density-dependent regulation of p16/INK4a. Additionally, we show that prolonged culturing of hTert-immortalized WI38 cells leads to a loss of density-dependent growth inhibition that correlates with p27/KIP deregulation as well as the previously shown INK4a locus silencing, and to an onset of contact-induced, p53-dependent cell death. PMID:14960324
Transverse momentum dependent quark densities from Lattice QCD
Bernhard Musch,Philipp Hagler,John Negele,Andreas Schafer
2011-02-01
We study transverse momentum dependent parton distribution functions (TMDs) with non-local operators in lattice QCD, using MILC/LHPC lattices. Results obtained with a simpli?ed operator geometry show visible dipole de- formations of spin-dependent quark momentum densities. We discuss the basic concepts of the method, including renormalization of the gauge link, and an ex- tension to a more elaborate operator geometry that would allow us to analyze process-dependent TMDs such as the Sivers-function.
Action formalism of time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Mosquera, Martín A.
2013-08-01
The Runge-Gross [E. Runge and E. K. U. Gross, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.52.997 52, 997 (1984)] action functional of time-dependent density-functional theory leads to a well-known causality paradox; that is, a perturbation of the electronic density in the future affects the response of the system in the present. This paradox is known to be caused by an inconsistent application of the Dirac-Frenkel variational principle. In view of the recent solutions to this problem, the action functional employed by Runge and Gross in their formulation of time-dependent density-functional theory is analyzed in the context of the Keldysh contour technique. The time-dependent electronic density and the concept of causality are extended to the contour. We derive a variational equation that obeys causality and relates the exchange-correlation potential with its kernel and the functional derivative of the exchange-correlation action functional with respect to the density. It is shown that the adiabatic local-density approximation is a consistent solution of this equation and that the time-dependent optimized potential method can also be derived from it. The formalism presented here can be used to find new approximation methods for the exchange-correlation potential and to avoid the causality dilemma.
Time-dependent density fluctuations in liquid water
NASA Astrophysics Data System (ADS)
Waldron, Conor J.; English, Niall J.
2016-04-01
Temporal system-mass-density fluctuation analysis was performed on liquid-water molecular-dynamics simulations at ambient pressure and 200 and 300 K, in three increasingly-large systems. A prominent mode in system-density fluctuations was observed at molecular-librational frequencies of ∼600-800 cm-1 (with pronounced temperature dependence). This mode displayed marked system-size dependence, disappearing for larger systems. Persistent system-density fluctuations were clearly evident at 10-11 cm-1 for all systems and temperatures, with lower-amplitude 'overtones' evident only in larger systems. It is conjectured that this reflects ∼3 ps timescales observed in earlier studies for dissipation of local-density fluctuations in liquid water in this 200-300 K temperature range.
Parity dependence of level densities in sup 49 V
York, B.W.
1991-01-01
In this research, we have studied {sup 48}Ti(p, p{sub 1}) and {sup 48}(p, p{sub 1}{gamma}) in an effort to determine the dependence of level densities on parity in the compound nucleus {sup 49}V. This nuclide was chosen because of the high level density of the {sup 49}V system (leading to good statistical accuracy) and because the target is zero spin (making the assignment of J easier). 5 refs., 3 figs.
Density dependence of nuclear neutrino-pair production
Horowitz, C.J. )
1992-11-02
Nuclear decay via neutrino-pair production is found to have a large density dependence because of intermediate electromagnetic couplings to electrons. These are calculated in a relativistic random phase approximation. The decay rate for vector (Fermi) transitions producing electron type neutrino pairs can be enhanced by 10{sup 5} or more at densities relevant for stellar collapse. Axial-vector (Gamow-Teller) transitions are not enhanced.
Nonlinear Density Dependence of Singlet Fission Rate in Tetracene Films.
Zhang, Bo; Zhang, Chunfeng; Wang, Rui; Tan, Zhanao; Liu, Yunlong; Guo, Wei; Zhai, Xiaoling; Cao, Yi; Wang, Xiaoyong; Xiao, Min
2014-10-16
Singlet fission holds the potential to dramatically improve the efficiency of solar energy conversion by creating two triplet excitons from one photoexcited singlet exciton in organic semiconductors. It is generally assumed that the singlet-fission rate is linearly dependent on the exciton density. Here we experimentally show that the rate of singlet fission has a nonlinear dependence on the density of photoexcited singlet excitons in tetracene films with small crystalline grains. We disentangle the spectrotemporal features of singlet and triplet dynamics from ultrafast spectroscopic data with the algorithm of singular value decomposition. The correlation between their temporal dynamics indicates a superlinear dependence of fission rate on the density of singlet excitons, which may arise from excitonic interactions. PMID:26278594
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.
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.
Ringelman, Kevin M; Eadie, John M; Ackerman, Joshua T
2012-07-01
When nest predation levels are very high or very low, the absolute range of observable nest success is constrained (a floor/ceiling effect), and it may be more difficult to detect density-dependent nest predation. Density-dependent nest predation may be more detectable in years with moderate predation rates, simply because there can be a greater absolute difference in nest success between sites. To test this, we replicated a predation experiment 10 years after the original study, using both natural and artificial nests, comparing a year when overall rates of nest predation were high (2000) to a year with moderate nest predation (2010). We found no evidence for density-dependent predation on artificial nests in either year, indicating that nest predation is not density-dependent at the spatial scale of our experimental replicates (1-ha patches). Using nearest-neighbor distances as a measure of nest dispersion, we also found little evidence for "dispersion-dependent" predation on artificial nests. However, when we tested for dispersion-dependent predation using natural nests, we found that nest survival increased with shorter nearest-neighbor distances, and that neighboring nests were more likely to share the same nest fate than non-adjacent nests. Thus, at small spatial scales, density-dependence appears to operate in the opposite direction as predicted: closer nearest neighbors are more likely to be successful. We suggest that local nest dispersion, rather than larger-scale measures of nest density per se, may play a more important role in density-dependent nest predation. PMID:22179311
Watching excitons move: the time-dependent transition density matrix
NASA Astrophysics Data System (ADS)
Ullrich, Carsten
2012-02-01
Time-dependent density-functional theory allows one to calculate excitation energies and the associated transition densities in principle exactly. The transition density matrix (TDM) provides additional information on electron-hole localization and coherence of specific excitations of the many-body system. We have extended the TDM concept into the real-time domain in order to visualize the excited-state dynamics in conjugated molecules. The time-dependent TDM is defined as an implicit density functional, and can be approximately obtained from the time-dependent Kohn-Sham orbitals. The quality of this approximation is assessed in simple model systems. A computational scheme for real molecular systems is presented: the time-dependent Kohn-Sham equations are solved with the OCTOPUS code and the time-dependent Kohn-Sham TDM is calculated using a spatial partitioning scheme. The method is applied to show in real time how locally created electron-hole pairs spread out over neighboring conjugated molecular chains. The coupling mechanism, electron-hole coherence, and the possibility of charge separation are discussed.
Density dependence and density independence during the early life stages of four marine fish stocks.
Dingsør, Gjert E; Ciannelli, Lorenzo; Chan, Kung-Sik; Ottersen, Geir; Stenseth, Nils Chr
2007-03-01
Recruitment variability caused by density-dependent and density-independent processes is an important area within the study of fish dynamics. These processes can exhibit nonlinearities and nonadditive properties that may have profound dynamic effects. We investigate the importance of population density (i.e., density dependence) and environmental forcing (i.e., density independence) on the age-0 and age-1 abundance of capelin (Mallotus villosus), northeast Arctic cod (Gadus morhua), northeast Arctic haddock (Melanogrammus aeglefinus), and Norwegian spring spawning herring (Clupea harengus) in the Barents Sea. We use statistical methods that explicitly account for nonlinearities and nonadditive interactions between internal and external variables in the abundance of these two pre-recruitment stages. Our results indicate that, during their first five months of life, cod, haddock, and herring experience higher density-dependent survival than capelin. The abundance of age-0 cod depends on the mean age and biomass of the spawning stock, a result which has implications for the management of the entire cod stock. Temperature is another important factor influencing the abundance at age-0 and age-1 of all four species, except herring at age-1. Between age-0 and age-1, there is an attenuation of density-dependent survival for cod and herring, while haddock and capelin experience density dependence at high and low temperatures, respectively. Predation by subadult cod is important for both capelin and cod at age-1. We found strong indications for interactions among the studied species, pointing to the importance of viewing the problem of species recruitment variability as a community, rather than as a population phenomenon. PMID:17503591
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.
Cuticular antifungals in spiders: density- and condition dependence.
González-Tokman, Daniel; Ruch, Jasmin; Pulpitel, Tamara; Ponton, Fleur
2014-01-01
Animals living in groups face a high risk of disease contagion. In many arthropod species, cuticular antimicrobials constitute the first protective barrier that prevents infections. Here we report that group-living spiders produce cuticular chemicals which inhibit fungal growth. Given that cuticular antifungals may be costly to produce, we explored whether they can be modulated according to the risk of contagion (i.e. under high densities). For this purpose, we quantified cuticular antifungal activity in the subsocial crab spider Diaea ergandros in both natural nests and experimentally manipulated nests of varying density. We quantified the body-condition of spiders to test whether antifungal activity is condition dependent, as well as the effect of spider density on body-condition. We predicted cuticular antifungal activity to increase and body-condition to decrease with high spider densities, and that antifungal activity would be inversely related to body-condition. Contrary to our predictions, antifungal activity was neither density- nor condition-dependent. However, body-condition decreased with density in natural nests, but increased in experimental nests. We suggest that pathogen pressure is so important in nature that it maintains high levels of cuticular antifungal activity in spiders, impacting negatively on individual energetic condition. Future studies should identify the chemical structure of the isolated antifungal compounds in order to understand the physiological basis of a trade-off between disease prevention and energetic condition caused by group living, and its consequences in the evolution of sociality in spiders. PMID:24637563
Cuticular Antifungals in Spiders: Density- and Condition Dependence
González-Tokman, Daniel; Ruch, Jasmin; Pulpitel, Tamara; Ponton, Fleur
2014-01-01
Animals living in groups face a high risk of disease contagion. In many arthropod species, cuticular antimicrobials constitute the first protective barrier that prevents infections. Here we report that group-living spiders produce cuticular chemicals which inhibit fungal growth. Given that cuticular antifungals may be costly to produce, we explored whether they can be modulated according to the risk of contagion (i.e. under high densities). For this purpose, we quantified cuticular antifungal activity in the subsocial crab spider Diaea ergandros in both natural nests and experimentally manipulated nests of varying density. We quantified the body-condition of spiders to test whether antifungal activity is condition dependent, as well as the effect of spider density on body-condition. We predicted cuticular antifungal activity to increase and body-condition to decrease with high spider densities, and that antifungal activity would be inversely related to body-condition. Contrary to our predictions, antifungal activity was neither density- nor condition-dependent. However, body-condition decreased with density in natural nests, but increased in experimental nests. We suggest that pathogen pressure is so important in nature that it maintains high levels of cuticular antifungal activity in spiders, impacting negatively on individual energetic condition. Future studies should identify the chemical structure of the isolated antifungal compounds in order to understand the physiological basis of a trade-off between disease prevention and energetic condition caused by group living, and its consequences in the evolution of sociality in spiders. PMID:24637563
Time-dependent Partition Density-functional Theory
NASA Astrophysics Data System (ADS)
Mosquera, Martin; Wasserman, Adam
2012-02-01
We present an extension of time-dependent density functional theory that allows to partition the time-dependent external potential in terms of localized molecular fragment potentials. As a consequence, localized time-dependent densities arise for each molecular fragment. To enforce the condition that the sum of fragments must add up to the exact total density, a new quantity termed ``time-dependent partition potential'' is introduced. The Runge-Gross theorem is employed to show that there is a quasi one-to-one correspondence between the partition potential and the electronic density. The corresponding quantum-mechanical actions are derived by using the van Leeuwen's action and are used to derive a decomposition of the partition potential which allows for practical approximations. Linear response formulas are deduced to obtain the transition energies, and an approximation is suggested to obtain localized excitations in large molecular systems. Finally, numerical illustration of our theory is shown for one-dimensional fermions under the influence of a laser field.
NASA Astrophysics Data System (ADS)
Ruggenthaler, Michael; Penz, Markus; van Leeuwen, Robert
2015-05-01
In this work we review the mapping from densities to potentials in quantum mechanics, which is the basic building block of time-dependent density-functional theory and the Kohn-Sham construction. We first present detailed conditions such that a mapping from potentials to densities is defined by solving the time-dependent 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.
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. PMID:25921322
Energy dependence with the number of particles: Density and reduced density matrices functionals
NASA Astrophysics Data System (ADS)
Miranda-Quintana, Ramón A.; Bochicchio, Roberto C.
2014-02-01
The energy of a physical domain within a molecular system considered as a quantum open system is analyzed as a functional of the electron distribution dependence with the number of particles. Our attention is focused upon the constrained-search functionals of the electron density, the 1- and 2-reduced density matrices (1-, 2-RDMs) for grand-canonical states. It is shown that functionals of the 2-RDM depend on the number of particles if the ground state energy is not a convex function of them.
Modelling the effect of autotoxicity on density-dependent phytotoxicity.
Sinkkonen, A
2007-01-21
An established method to separate resource competition from chemical interference is cultivation of monospecific, even-aged stands. The stands grow at several densities and they are exposed to homogenously spread toxins. Hence, the dose received by individual plants is inversely related to stand density. This results in distinguishable alterations in dose-response slopes. The method is often recommended in ecological studies of allelopathy. However, many plant species are known to release autotoxic compounds. Often, the probability of autotoxicity increases as sowing density increases. Despite this, the possibility of autotoxicity is ignored when experiments including monospecific stands are designed and when their results are evaluated. In this paper, I model mathematically how autotoxicity changes the outcome of dose-response slopes as different densities of monospecific stands are grown on homogenously phytotoxic substrata. Several ecologically reasonable relations between plant density and autotoxin exposure are considered over a range of parameter values, and similarities between different relations are searched for. The models indicate that autotoxicity affects the outcome of density-dependent dose-response experiments. Autotoxicity seems to abolish the effects of other phytochemicals in certain cases, while it may augment them in other cases. Autotoxicity may alter the outcome of tests using the method of monospecific stands even if the dose of autotoxic compounds per plant is a fraction of the dose of non-autotoxic phytochemicals with similar allelopathic potential. Data from the literature support these conclusions. A faulty null hypothesis may be accepted if the autotoxic potential of a test species is overlooked in density-response experiments. On the contrary, if test species are known to be non-autotoxic, the method of monospecific stands does not need fine-tuning. The results also suggest that the possibility of autotoxicity should be investigated in many density-response bioassays that are made with even-aged plants, and that measure plant growth or germination. PMID:16989866
Hard scale dependent gluon density, saturation, and forward-forward dijet production at the LHC
NASA Astrophysics Data System (ADS)
Kutak, Krzysztof
2015-02-01
We propose a method to introduce Sudakov effects to the unintegrated gluon density, promoting it to be hard scale dependent. The advantage of the approach is that it guarantees that the gluon density is positive definite and that the Sudakov effects cancel on the integrated level. As a case study, we apply the method to calculate angular correlations and the Rp A ratio for p +p vs p +Pb collision in the production of forward-forward dijets.
Modelling interactions of toxicants and density dependence in wildlife populations
Schipper, Aafke M.; Hendriks, Harrie W.M.; Kauffman, Matthew J.; Hendriks, A. Jan; Huijbregts, Mark A.J.
2013-01-01
1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 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 toxicant impacts until a critical threshold is crossed. In our study population, toxicant-induced changes were observed in the equilibrium number of nonbreeding rather than breeding birds, suggesting that monitoring efforts including both life stages are needed to timely detect population declines. Further, by combining quantitative exposure–response relationships with a wildlife demographic model, we provided a method to quantify critical toxicant thresholds for wildlife population persistence.
Floater dynamics can explain positive patterns of density-dependent fecundity in animal populations.
Penteriani, Vincenzo; Otalora, Fermín; Ferrer, Miguel
2006-11-01
After some 70 years of debate on density-dependent regulation of animal populations, there is still poor understanding of where spatial and temporal density dependence occurs. Clearly defining the portion of the population that shapes density-dependent patterns may help to solve some of the ambiguities that encircle density dependence and its patterns. In fact, individuals of the same species and population can show different dynamics and behaviors depending on their locations (e.g., breeding vs. dispersal areas). Considering this form of intrapopulation heterogeneity may improve our understanding of density dependence and population dynamics in general. We present the results of individual-based simulations on a metapopulation of the Spanish imperial eagle Aquila adalberti. Our results suggest that high rates of floater mortality within settlement areas can determine a shift in the classical relationship (from negative to positive) between the fecundity (i.e., fledglings per pair) and density (i.e., number of pairs) of the breeding population. Finally, we proved that different initial conditions affecting the breeder portion of the population can lead to the same values of fecundity. Our results can represent a starting point for new and more complex approaches studying the regulation of animal populations, where the forgotten and invisible component--the floater--is taken into account. PMID:17080366
Cycles, stochasticity and density dependence in pink salmon population dynamics
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
Cycles, stochasticity and density dependence in pink salmon population dynamics.
Krkosek, Martin; Hilborn, Ray; Peterman, Randall M; Quinn, Thomas P
2011-07-01
Complex dynamics of animal populations often involve deterministic and stochastic components. A fascinating example is the variation in magnitude of 2-year cycles in abundances of pink salmon (Oncorhynchus gorbuscha) stocks along the North Pacific rim. Pink salmon have a 2-year anadromous and semelparous life cycle, resulting in odd- and even-year lineages that occupy the same habitats but are reproductively isolated in time. One lineage is often much more abundant than the other in a given river, and there are phase switches in dominance between odd- and even-year lines. In some regions, the weak line is absent and in others both lines are abundant. Our analysis of 33 stocks indicates that these patterns probably result from stochastic perturbations of damped oscillations owing to density-dependent mortality caused by interactions between lineages. Possible mechanisms are cannibalism, disease transmission, food depletion and habitat degradation by which one lineage affects the other, although no mechanism has been well-studied. Our results provide comprehensive empirical estimates of lagged density-dependent mortality in salmon populations and suggest that a combination of stochasticity and density dependence drives cyclical dynamics of pink salmon stocks. PMID:21147806
Estimating the functional form for the density dependence from life history data.
Coulson, T; Ezard, T H G; Pelletier, F; Tavecchia, G; Stenseth, N C; Childs, D Z; Pilkington, J G; Pemberton, J M; Kruuk, L E B; Clutton-Brock, T H; Crawley, M J
2008-06-01
Two contrasting approaches to the analysis of population dynamics are currently popular: demographic approaches where the associations between demographic rates and statistics summarizing the population dynamics are identified; and time series approaches where the associations between population dynamics, population density, and environmental covariates are investigated. In this paper, we develop an approach to combine these methods and apply it to detailed data from Soay sheep (Ovis aries). We examine how density dependence and climate contribute to fluctuations in population size via age- and sex-specific demographic rates, and how fluctuations in demographic structure influence population dynamics. Density dependence contributes most, followed by climatic variation, age structure fluctuations and interactions between density and climate. We then simplify the density-dependent, stochastic, age-structured demographic model and derive a new phenomenological time series which captures the dynamics better than previously selected functions. The simple method we develop has potential to provide substantial insight into the relative contributions of population and individual-level processes to the dynamics of populations in stochastic environments. PMID:18589530
Does spacecraft potential depend on the ambient electron density?
NASA Astrophysics Data System (ADS)
Lai, S. T.; Martinez-Sanchez, M.; Cahoy, K.; Thomsen, M. F.; Shprits, Y.; Lohmeyer, W. Q.; Wong, F.
2014-12-01
In a Maxwellian space plasma model, the onset of spacecraft charging at geosynchronous altitudes is due to the ambient electron, ambient ions, and secondary electrons. By using current balance, one can show that the onset of spacecraft charging depends not on the ambient electron density but instead on the critical temperature of the ambient electrons. If the ambient plasma deviates significantly from equilibrium, a non-Maxwellian electron distribution results. For a kappa distribution, the onset of spacecraft charging remains independent of ambient electron density. However, for double Maxwellian distributions, the densities do have a role in the onset of spacecraft charging. For a dielectric spacecraft in sunlight, the trapping of photoelectrons on the sunlit side enhances the local electron density. Using the coordinated environmental satellite data from the Los Alamos National Laboratory geosynchronous satellites, we have obtained results that confirm that the observed spacecraft potential is independent of the ambient electron density during eclipse and that in sunlight charging the low-energy population around the sunlit side of the spacecraft is enhanced by photoelectrons trapped inside the potential barrier.
Quark matter at high density based on an extended confined isospin-density-dependent mass model
NASA Astrophysics Data System (ADS)
Qauli, A. I.; Sulaksono, A.
2016-01-01
We investigate the effect of the inclusion of relativistic Coulomb terms in a confined-isospin-density-dependent-mass (CIDDM) model of strange quark matter (SQM). We found that if we include the Coulomb term in scalar density form, the SQM equation of state (EOS) at high densities is stiffer but if we include the Coulomb term in vector density form it is softer than that of the standard CIDDM model. We also investigate systematically the role of each term of the extended CIDDM model. Compared with what was reported by Chu and Chen [Astrophys. J. 780, 135 (2014)], we found the stiffness of SQM EOS is controlled by the interplay among the oscillator harmonic, isospin asymmetry and Coulomb contributions depending on the parameter's range of these terms. We have found that the absolute stable condition of SQM and the mass of 2 M⊙ pulsars can constrain the parameter of oscillator harmonic κ1≈0.53 in the case the Coulomb term is excluded. If the Coulomb term is included, for the models with their parameters are consistent with SQM absolute stability condition, the 2.0 M⊙ constraint more prefers the maximum mass prediction of the model with the scalar Coulomb term than that of the model with the vector Coulomb term. On the contrary, the high densities EOS predicted by the model with the vector Coulomb is more compatible with the recent perturbative quantum chromodynamics result [1] than that predicted by the model with the scalar Coulomb. Furthermore, we also observed the quark composition in a very high density region depends quite sensitively on the kind of Coulomb term used.
Density dependence and cooperation: theory and a test with bacteria.
Ross-Gillespie, Adin; Gardner, Andy; Buckling, Angus; West, Stuart A; Griffin, Ashleigh S
2009-09-01
Although cooperative systems can persist in nature despite the potential for exploitation by noncooperators, it is often observed that small changes in population demography can tip the balance of selective forces for or against cooperation. Here we consider the role of population density in the context of microbial cooperation. First, we account for conflicting results from recent studies by demonstrating theoretically that: (1) for public goods cooperation, higher densities are relatively unfavorable for cooperation; (2) in contrast, for self-restraint-type cooperation, higher densities can be either favorable or unfavorable for cooperation, depending on the details of the system. We then test our predictions concerning public goods cooperation using strains of the pathogenic bacterium Pseudomonas aeruginosa that produce variable levels of a public good-iron-scavenging siderophore molecules. As predicted, we found that the relative fitness of cheats (under-producers) was greatest at higher population densities. Furthermore, as assumed by theory, we show that this occurs because cheats are better able to exploit the cooperative siderophore production of other cells when they are physically closer to them. PMID:19453724
Nuclear structure calculations in the density-dependent relativistic Hartree theory
Ineichen, F.; Weigel, M.K.; Von-Eiff, D.
1996-05-01
In this study we appraise the capability of the relativistic density-dependent Hartree theory to reproduce the properties of finite nuclei by using parametrizations of relativistic Brueckner-Hartree-Fock calculations for infinite nuclear matter, performed in the full Dirac space. We apply the density-dependent relativistic Hartree approach of Brockmann and Toki as well as its covariant extension including rearrangement contributions, recently developed by Lenske and Fuchs. Within this parameter-free theory the results for finite systems are satisfactory. We used the one-boson-exchange potentials {ital A} and {ital B} constructed by Brockmann and Machleidt. {copyright} {ital 1996 The American Physical Society.}
Exploration of a modified density dependence in the Skyrme functional
Erler, J.; Reinhard, P.-G.; Kluepfel, P.
2010-10-15
A variant of the basic Skyrme-Hartree-Fock functional is considered dealing with a new form of density dependence. It employs only integer powers and thus will allow a more sound basis for projection schemes (particle number, angular momentum). We optimize the new functional with exactly the same adjustment strategy as used in an earlier study with a standard Skyrme functional. This allows direct comparisons of the performance of the new functional relative to the standard one. We discuss various observables: bulk properties of finite nuclei, nuclear matter, giant resonances, superheavy elements, and energy systematics. The new functional performs at least as well as the standard one, but offers a wider range of applicability (e.g., for projection) and more flexibility in the regime of high densities.
Large area photonic crystal cavities: a local density approach.
Dobbelaar, M C F; Greveling, S; van Oosten, D
2015-03-23
Large area photonic crystal cavities are devices of interest for photovoltaics, optoelectronics, and solid-state lighting. However, depending on their dimensions they pose a large computational challenge. Here, we use a local density approach to avoid direct simulation of the device. We capture the effect of both ideal and distorted photonic crystals in an effective mass and an effective potential. We use these to map the problem of calculating the electromagnetic field modes to solving a simple time-independent Schrdinger equation. We show that, in the case that the hole radius varies quadratically as a function of position, the eigenmodes of the photonic crystals can be described by the corresponding eigenmodes of the quantum harmonic oscillator with typical agreements well above 90%. PMID:25837088
Effective local potentials for orbital-dependent density functionals
NASA Astrophysics Data System (ADS)
Staroverov, Viktor N.; Scuseria, Gustavo E.; Davidson, Ernest R.
2006-08-01
Practicality of the Kohn-Sham density functional scheme for orbital-dependent functionals hinges on the availability of an efficient procedure for constructing local exchange-correlation potentials in finite basis sets. We have shown recently that the optimized effective potential (OEP) method, commonly used for this purpose, is not free from difficulties. Here we propose a robust alternative to OEPs, termed effective local potentials (ELPs), based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart. The ELP method is applied to the exact-exchange-only problem and shown to be promising for overcoming troubles with OEPs.
Understanding bacteriophage therapy as a density-dependent kinetic process.
Payne, R J; Jansen, V A
2001-01-01
Studies of bacteriophage as therapeutic agents have had mixed and unpredictable outcomes. We argue that interpretation of these apparently paradoxical results requires appreciation of various density-dependent threshold effects. We use a mathematical model to delineate different categories of outcome, including therapy by simple inundation, by active biocontrol, and by delayed active biocontrol. Counter-intuitively, there are situations in which earlier inoculation can be less efficacious, and simultaneous inoculation with antibiotics can be detrimental. Predictions of therapeutic responses are made using formulae dependent on biologically meaningful parameters; experimental measurement of the parameters will be a prerequisite of application of the model to particular study systems. Such modelling can point to which aspects of phage biology might most fruitfully be engineered so as to enhance the viability of bacteriophage therapy. PMID:11162051
The linear pressure dependence of the viscosity at high densities
NASA Astrophysics Data System (ADS)
Gulik, P. S. van der
Over the years, experimental data of the viscosity coefficient of simple dense fluids at high pressures have been obtained both in our laboratory and elsewhere. These data show that, at high densities, i.e. roughly in the last third of the density range from vacuum to the melting transition, for constant temperature the viscosity coefficient is a linear function of the pressure in a few different but neighbouring ranges, each with different slope and intersection with the pressure axis. The slope appears to be a time of picoseconds. The intersection with the pressure axis can be considered to be a value for the internal pressure. Thus, the viscosity coefficient is directly proportional to the thermal pressure, i.e. the combination of the experimental pressure and the internal pressure, in these ranges. It is shown that such a linear pressure dependence of the viscosity occurs in large ranges of the liquid state and at high densities in the fluid state of simple molecules. We subsequently call attention to old ideas of Maxwell on the equivalence of elasticity and viscosity and the modern basis of it given by Zwanzig and Mountain. This concept leads to Maxwell’s relaxation time. On account thereof, the slope of the linear viscosity-pressure relation is interpreted as the relaxation time, i.e. the time in which a disturbance to the Maxwellian equilibrium state decreases to 1/e of its original value, and as the ideal collision interval. The similarity of the present solution and the case of electrical conductivity in an n-type semiconductor is also pointed out. This leads to a simple view on the transport mechanism and gives reason to consider the temperature dependence of the relaxation times.
Time-Dependent Electronic Populations in Fragment-Based Time-Dependent Density Functional Theory.
Mosquera, Martín A; Wasserman, Adam
2015-08-11
Conceiving a molecule as being composed of smaller molecular fragments, or subunits, is one of the pillars of the chemical and physical sciences and leads to productive methods in quantum chemistry. Using a fragmentation scheme, efficient algorithms can be proposed to address problems in the description of chemical bond formation and breaking. We present a formally exact time-dependent density functional theory for the electronic dynamics of molecular fragments with a variable number of electrons. This new formalism is an extension of previous work [Phys. Rev. Lett. 111, 023001 (2013)]. We also introduce a stable density-inversion method that is applicable to time-dependent and ground-state density functional theories and their extensions, including those discussed in this work. PMID:26574438
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.
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.
Current density partitioning in time-dependent current density functional theory
Mosquera, Martín A.; Wasserman, Adam; Department of Physics, Purdue University, West Lafayette, Indiana 47907
2014-05-14
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Current density partitioning in time-dependent current density functional theory
NASA Astrophysics Data System (ADS)
Mosquera, Martín A.; Wasserman, Adam
2014-05-01
We adapt time-dependent current density functional theory to allow for a fragment-based solution of the many-electron problem of molecules in the presence of time-dependent electric and magnetic fields. Regarding a molecule as a set of non-interacting subsystems that individually evolve under the influence of an auxiliary external electromagnetic vector-scalar potential pair, the partition 4-potential, we show that there are one-to-one mappings between this auxiliary potential, a sharply-defined set of fragment current densities, and the total current density of the system. The partition electromagnetic (EM) 4-potential is expressed in terms of the real EM 4-potential of the system and a gluing EM 4-potential that accounts for exchange-correlation effects and mutual interaction forces between fragments that are required to yield the correct electron dynamics. We prove the zero-force theorem for the fragmented system, establish a variational formulation in terms of action functionals, and provide a simple illustration for a charged particle in a ring.
Leirs, H.; Stenseth, N.C.; Nichols, J.D.; Hines, J.E.; Verhagen, R.; Verheyen, W.
1997-01-01
Ecology has long been troubled by the controversy over how populations are regulated. Some ecologists focus on the role of environmental effects, whereas others argue that density-dependent feedback mechanisms are central. The relative importance of both processes is still hotly debated, but clear examples of both processes acting in the same population are rare. Keyfactor analysis (regression of population changes on possible causal factors) and time-series analysis are often used to investigate the presence of density dependence, but such approaches may be biased and provide no information on actual demographic rates. Here we report on both density-dependent and density-independent effects in a murid rodent pest species, the multimammate rat Mastomys natalensis (Smith, 1834), using statistical capture-recapture models. Both effects occur simultaneously, but we also demonstrate that they do not affect all demographic rates in the same way. We have incorporated the obtained estimates of demographic rates in a population dynamics model and show that the observed dynamics are affected by stabilizing nonlinear density-dependent components coupled with strong deterministic and stochastic seasonal components.
Time-dependent local density measurements in unsteady flows
NASA Technical Reports Server (NTRS)
Mckenzie, R. L.; Monson, D. J.; Exberger, R. J.
1979-01-01
A laser-induced fluorescence technique for measuring the relative time-dependent density fluctuations in unsteady or turbulent flows is demonstrated. Using a 1.5-W continuous-wave Kr(+) laser, measurements have been obtained in 0.1-mm diameter by 1-mm-long sampling volumes in a Mach 3 flow of N2 seeded with biacetyl vapor. A signal amplitude resolution of 2% was achieved for a detection frequency bandwidth of 10 kHz. The measurement uncertainty was found to be dominated by noise behaving as photon statistical noise. The practical limits of signal-to-noise ratios have been characterized for a wide range of detection frequency bandwidths that encompasses those of interest in supersonic turbulence measurements.
Time-dependent local density measurements in unsteady flows
NASA Technical Reports Server (NTRS)
Mckenzie, R. L.; Monson, D. J.; Exberger, R. J.
1979-01-01
A laser-induced fluorescence technique for measuring the relative time-dependent density fluctuations in unsteady or turbulent flows is demonstrated. Using a 1.5-W continuous-wave Kr(+) laser, measurements have been obtained in 0.1-mm-diameter by 1-mm-long sampling volumes in a Mach 3 flow of N2 seeded with biacetyl vapor. A signal amplitude resolution of 2% was achieved for a detection frequency bandwidth of 10 kHz. The measurement uncertainty was found to be dominated by noise behaving as photon statistical noise. The practical limits of signal-to-noise ratios have been characterized for a wide range of detection frequency bandwidths that encompasses those of interest in supersonic turbulence measurements.
Disease transmission models with density-dependent demographics.
Gao, L Q; Hethcote, H W
1992-01-01
The models considered for the spread of an infectious disease in a population are of SIRS or SIS type with a standard incidence expression. The varying population size is described by a modification of the logistic differential equation which includes a term for disease-related deaths. The models have density-dependent restricted growth due to a decreasing birth rate and an increasing death rate as the population size increases towards its carrying capacity. Thresholds, equilibria and stability are determined for the systems of ordinary differential equations for each model. The persistence of the infectious disease and disease-related deaths can lead to a new equilibrium population size below the carrying capacity and can even cause the population to become extinct. PMID:1522393
Density-dependent migratory waves in the marine pelagic ecosystem.
Fauchald, Per; Mauritzen, Mette; Gjøsaeter, Harald
2006-11-01
The migration of large aggregations of animals that sweep through the landscape is a phenomenon with large consequences in many ecosystems. It has been suggested that such migrations are mediated by resource depletion. Under this hypothesis it has been shown that simple foraging rules may generate density-dependent migratory waves (DDMW) in which the speed and amplitude increase with animal abundance. We tested these predictions on a 32-year data set of the spatial distribution of the two youngest age groups of a small pelagic schooling fish, the capelin (Mallotus villosus), by the end of their annual feeding migration in the Barents Sea. Our data suggest that the two age groups divided the Barents Sea by forming migratory waves that moved in opposite directions. The aggregation and spatial displacement of these waves increased with increasing age-specific abundance. However, possibly through social interactions, migratory pattern was modified by the abundance of the other age group. PMID:17168035
Time-dependent local-density approximation in real time
Yabana, K.; Bertsch, G.F.
1996-08-01
We study the dipole response of atomic clusters by solving the equations of the time-dependent local-density approximation in real time. The method appears to be more efficient than matrix or Green{close_quote}s function methods for large clusters modeled with realistic ionic pseudopotentials. As applications of the method, we exhibit results for sodium and lithium clusters and for C{sub 60} molecules. The calculated Mie resonance in Na{sub 147} is practically identical to that obtained in the jellium approximation, leaving the origin of the redshift unresolved. The pseudopotential effects are strong in lithium and act to broaden the Mie resonance and give it a substantial redshift, confirming earlier studies. There is also a large broadening due to Landau damping in the calculated C{sub 60} response, again confirming earlier studies. {copyright} {ital 1996 The American Physical Society.}
NASA Astrophysics Data System (ADS)
Zahn, Jochen
2015-11-01
In the framework of quantum electrodynamics (QED) in external potentials, we introduce a method to compute the time-dependence of the expectation value of the current density for time-dependent homogeneous external electric fields. We apply it to the so-called Sauter pulse. For late times, our results agree with the asymptotic value due to electron-positron pair production. We correct a general expression derived by Serber for the expectation value of the current, linearized in the external field, and compare with our results for the Sauter pulse. Based on the properties of the current density, we argue that the appearance of enhanced quasi-particle densities at intermediate times in slowly varying sub-critical potentials is generic. Also an alternative approach, which circumvents these difficulties, is sketched.
The dependence of ZnO photoluminescence efficiency on excitation conditions and defect densities
Simmons, Jay G.; Liu, Jie; Foreman, John V.; Everitt, Henry O.
2013-11-11
The quantum efficiencies of both the band edge and deep-level defect emission from annealed ZnO powders were measured as a function of excitation fluence and wavelength from a tunable sub-picosecond source. A simple model of excitonic decay reproduces the observed excitation dependence of rate constants and associated trap densities for all radiative and nonradiative processes. The analysis explores how phosphor performance deteriorates as excitation fluence and energy increase, provides an all-optical approach for estimating the number density of defects responsible for deep-level emission, and yields new insights for designing efficient ZnO-based phosphors.
Linear-response calculation in the time-dependent density functional theory
Nakatsukasa, Takashi; Inakura, Tsunenori; Avogadro, Paolo; Ebata, Shuichiro; Sato, Koichi; Yabana, Kazuhiro
2012-11-12
Linear response calculations based on the time-dependent density-functional theory are presented. Especially, we report results of the finite amplitude method which we have recently proposed as an alternative and feasible approach to the (quasiparticle-)random-phase approximation. Calculated properties of the giant resonances and low-energy E1 modes are discussed. We found a universal linear correlation between the low-energy E1 strength and the neutron skin thickness.
Testing the Standard Approach for Density-Functional Transport Calculations
NASA Astrophysics Data System (ADS)
Smith, Justin; Liu, Zhenfei; Burke, Kieron
2014-03-01
Conductance across a single molecular junction can be calculated via the Landauer formalism. This is the standard approach for density-functional theory calculations of transport, but it requires extremely accurate Kohn-Sham potentials that can only be achieved under certain conditions using accurate functionals. Recent work has shown an example where the standard approach works remarkably well for a site model. In this work, we test the standard approach for one dimension in real space where we can extract numerically exact potentials using density-matrix renormalization group. DE-FG02-08ER46496.
Time-dependent approach to atomic autoionization
NASA Astrophysics Data System (ADS)
Schultz, D. R.; Bottcher, C.; Madison, D. H.; Peacher, J. L.; Buffington, G.; Pindzola, M. S.; Gorczyca, T. W.; Gavras, P.; Griffin, D. C.
1994-08-01
A time-dependent approach to the study of atomic autoionization in two-electron systems is formulated. In the first step a two-dimensional (2D) model ``He'' atom is constructed by replacing the full 3D electrostatic interaction with a 1D soft-core interaction. The autoionization decay of doubly excited states constructed within the model is calculated by both standard perturbation theory and direct solution of the time-dependent Schrödinger equation. Configuration-interaction theory is invoked to obtain correlated resonance states, and strong laser fields are found to alter the decay rates. In the second step the full 6D wave function for the He atom is expanded in coupled spherical harmonics using a procedure as described by C. Bottcher, D. R. Schultz, and D. H. Madison [Phys. Rev. A 49, 1714 (1994)]. Solution of the time-dependent Schrödinger equation reduces to solving the propagator equations for the 3D expansion coefficients on a B-spline collocation lattice. Autoionizing decay rate calculations using product resonance states are found to be in qualitative agreement with the 2D model results.
Density dependence in marine fish populations revealed at small and large spatial scales.
Johnson, Darren W
2006-02-01
Experimental manipulation of population density has frequently been used to demonstrate demographic density dependence. However, such studies are usually small scale and typically provide evidence of spatial (within-generation) density dependence. It is often unclear whether small-scale, experimental tests of spatial density dependence will accurately describe temporal (between-generation) density dependence required for population regulation. Understanding the mechanisms generating density dependence may provide a link between spatial experiments and temporal regulation of populations. In this study, I manipulated the density of recently settled kelp rockfish (Sebastes atrovirens) in both the presence and absence of predators to test for density-dependent mortality and whether predation was the mechanism responsible. I also examined mortality of rockfish cohorts within kelp beds throughout central California to evaluate temporal (between-generation) density dependence in mortality. Experiments suggested that short-term behavioral responses of predators and/or a shortage of prey refuges caused spatial density dependence. Temporal density dependence in mortality was also detected at larger spatial scales for several species of rockfish. It is likely that short-term responses of predators generated both spatial and temporal density dependence in mortality. Spatial experiments that describe the causal mechanisms generating density dependence may therefore be valuable in describing temporal density dependence and population regulation. PMID:16637357
A discrete model with density dependent fast migration.
Bravo de la Parra, R; Sánchez, E; Arino, O; Auger, P
1999-03-15
The aim of this work is to develop an approximate aggregation method for certain non-linear discrete models. Approximate aggregation consists in describing the dynamics of a general system involving many coupled variables by means of the dynamics of a reduced system with a few global variables. We present discrete models with two different time scales, the slow one considered to be linear and the fast one non-linear because of its transition matrix depends on the global variables. In our discrete model the time unit is chosen to be the one associated to the slow dynamics, and then we approximate the effect of fast dynamics by using a sufficiently large power of its corresponding transition matrix. In a previous work the same system is treated in the case of fast dynamics considered to be linear, conservative in the global variables and inducing a stable frequency distribution of the state variables. A similar non-linear model has also been studied which uses as time unit the one associated to the fast dynamics and has the non-linearity in the slow part of the system. In the present work we transform the system to make the global variables explicit, and we justify the quick derivation of the aggregated system. The local asymptotic behaviour of the aggregated system entails that of the general system under certain conditions, for instance, if the aggregated system has a stable hyperbolic fixed point then the general system has one too. The method is applied to aggregate a multiregional Leslie model with density dependent migration rates. PMID:10194925
Density of States for Gue Through Supersymmetric Approach
NASA Astrophysics Data System (ADS)
Disertori, M.
The supersymmetric approach has proved to be a powerful tool for the study of random systems where classical techniques do not seem to apply. It also seems promising for rigorous analysis. In this context, we consider the GUE density of states, and show that, using the supersymmetric approach, we can rigorously re-derive the results obtained by classical techniques (orthogonal polynomials), in all energy regions (inside the spectrum, at the edge and outside the spectrum).
Time-dependent density functional theory quantum transport simulation in non-orthogonal basis
Kwok, Yan Ho; Xie, Hang; Yam, Chi Yung; Chen, Guan Hua; Zheng, Xiao
2013-12-14
Basing on the earlier works on the hierarchical equations of motion for quantum transport, we present in this paper a first principles scheme for time-dependent quantum transport by combining time-dependent density functional theory (TDDFT) and Keldysh's non-equilibrium Green's function formalism. This scheme is beyond the wide band limit approximation and is directly applicable to the case of non-orthogonal basis without the need of basis transformation. The overlap between the basis in the lead and the device region is treated properly by including it in the self-energy and it can be shown that this approach is equivalent to a lead-device orthogonalization. This scheme has been implemented at both TDDFT and density functional tight-binding level. Simulation results are presented to demonstrate our method and comparison with wide band limit approximation is made. Finally, the sparsity of the matrices and computational complexity of this method are analyzed.
A real-space stochastic density matrix approach for density functional electronic structure.
Beck, Thomas L
2015-12-21
The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches. PMID:25969148
Towards time-dependent current-density-functional theory in the non-linear regime
Escartín, J. M.; Vincendon, M.; 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.
Towards time-dependent current-density-functional theory in the non-linear regime
NASA Astrophysics Data System (ADS)
Escartín, J. M.; Vincendon, M.; Romaniello, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.
2015-02-01
Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT. This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na2. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.
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.
The multi-configurational time-dependent Hartree approach revisited.
Manthe, Uwe
2015-06-28
The multi-configurational time-dependent Hartree (MCTDH) approach facilitates accurate high-dimensional quantum dynamics simulations. In the approach, the wavefunction is expanded in a direct product of self-adapting time-dependent single-particle functions (SPFs). The equations of motion for the expansion coefficients and the SPFs are obtained via the Dirac-Frenkel variational principle. While this derivation yields well-defined differential equations for the motion of occupied SPFs, singularities in the working equations resulting from unoccupied SPFs have to be removed by a regularization procedure. Here, an alternative derivation of the MCTDH equations of motion is presented. It employs an analysis of the time-dependence of the single-particle density matrices up to second order. While the analysis of the first order terms yields the known equations of motion for the occupied SPFs, the analysis of the second order terms provides new equations which allow one to identify optimal choices for the unoccupied SPFs. The effect of the optimal choice of the unoccupied SPFs on the structure of the MCTDH equations of motion and their regularization is discussed. Generalized equations applicable in the multi-layer MCTDH framework are presented. Finally, the effects resulting from the initial choice of the unoccupied SPFs are illustrated by a simple numerical example. PMID:26133412
NASA Astrophysics Data System (ADS)
Petrenko, Taras; Kossmann, Simone; Neese, Frank
2011-02-01
In this paper, we present the implementation of efficient approximations to time-dependent density functional theory (TDDFT) within the Tamm-Dancoff approximation (TDA) for hybrid density functionals. For the calculation of the TDDFT/TDA excitation energies and analytical gradients, we combine the resolution of identity (RI-J) algorithm for the computation of the Coulomb terms and the recently introduced "chain of spheres exchange" (COSX) algorithm for the calculation of the exchange terms. It is shown that for extended basis sets, the RIJCOSX approximation leads to speedups of up to 2 orders of magnitude compared to traditional methods, as demonstrated for hydrocarbon chains. The accuracy of the adiabatic transition energies, excited state structures, and vibrational frequencies is assessed on a set of 27 excited states for 25 molecules with the configuration interaction singles and hybrid TDDFT/TDA methods using various basis sets. Compared to the canonical values, the typical error in transition energies is of the order of 0.01 eV. Similar to the ground-state results, excited state equilibrium geometries differ by less than 0.3 pm in the bond distances and 0.5° in the bond angles from the canonical values. The typical error in the calculated excited state normal coordinate displacements is of the order of 0.01, and relative error in the calculated excited state vibrational frequencies is less than 1%. The errors introduced by the RIJCOSX approximation are, thus, insignificant compared to the errors related to the approximate nature of the TDDFT methods and basis set truncation. For TDDFT/TDA energy and gradient calculations on Ag-TB2-helicate (156 atoms, 2732 basis functions), it is demonstrated that the COSX algorithm parallelizes almost perfectly (speedup ˜26-29 for 30 processors). The exchange-correlation terms also parallelize well (speedup ˜27-29 for 30 processors). The solution of the Z-vector equations shows a speedup of ˜24 on 30 processors. The parallelization efficiency for the Coulomb terms can be somewhat smaller (speedup ˜15-25 for 30 processors), but their contribution to the total calculation time is small. Thus, the parallel program completes a Becke3-Lee-Yang-Parr energy and gradient calculation on the Ag-TB2-helicate in less than 4 h on 30 processors. We also present the necessary extension of the Lagrangian formalism, which enables the calculation of the TDDFT excited state properties in the frozen-core approximation. The algorithms described in this work are implemented into the ORCA electronic structure system.
The dependence of cylindrical resonator natural frequencies on the fluid density
NASA Astrophysics Data System (ADS)
Rudachenko, V.; Filushin, V.; Korotchenko, T.
2015-11-01
The article examines the dependence of cylindrical resonator natural frequencies (sensitive element) on the density (mass) of different fluids flowing through it. The cylindrical resonators are being widely applied in automatic control systems of technological processes as oscillating transducer density meter. The article presents the experimental results that prove the dependence of natural frequencies and vibration amplitude on the fluid density.
Ion upflow dependence on ionospheric density and solar photoionization
NASA Astrophysics Data System (ADS)
Cohen, I. J.; Lessard, M. R.; Varney, R. H.; Oksavik, K.; Zettergren, M.; Lynch, K. A.
2015-11-01
Motivated by rocket observations showing a variety of different ionospheric responses to precipitation, this paper explores the influence of the background ionospheric density on upflow resulting from auroral precipitation. Simulations of upflow driven by auroral precipitation were conducted using a version of the Varney et al. (2014) model driven by precipitation characterized by observations made during the 2012 Magnetosphere-Ionosphere Coupling in the Alfvén resonator rocket mission and using a variety of different initial electron density profiles. The simulation results show that increased initial density before the onset of precipitation leads to smaller electron temperature increases, longer ionospheric heating timescales, weaker ambipolar electric fields, lower upflow speeds, and longer upflow timescales but larger upflow fluxes. The upflow flux can increase even when the ambipolar electric field strength decreases due to the larger number of ions that are accelerated. Long-term observations from the European Incoherent Scatter (EISCAT) Svalbard radar taken during the International Polar Year support the effects seen in the simulations. This correlation between ionospheric density and ion upflows emphasizes the important role of photoionization from solar ultraviolet radiation, which the EISCAT observations show can increase ionospheric density by as much as an order of magnitude during the summer months.
Density dependent stopping power and muon sticking in muon catalyzed D-T fusion
Rafelski, H.E.; Mueller, B.
1988-12-27
The origin of the experimentally observed (1) density dependence of the muon alpha sticking fraction ..omega../sub s/ in muon catalyzed deuterium- tritium fusion is investigated. We show that the reactivation probability depends sensitively on the target stopping power at low ion velocities. The density dependence of the stopping power for a singly charged projectile in liquid heavy hydrogen is parametrized to simulate possible screening effects and a density dependent effective ionization potential. We find that, in principle, a description of the measured density dependence is possible, but the required parameters appear too large. Also, the discrepancy with observed (He..mu..) X-ray data widens.
Density dependence, whitebark pine, and vital rates of grizzly bears
van Manen, Frank T.; Haroldson, Mark A.; Bjornlie, Daniel D; Ebinger, Michael R.; Thompson, Daniel J.; Costello, Cecily M; White, Gary C.
2016-01-01
Understanding factors influencing changes in population trajectory is important for effective wildlife management, particularly for populations of conservation concern. Annual population growth of the grizzly bear (Ursus arctos) population in the Greater Yellowstone Ecosystem, USA has slowed from 4.2–7.6% 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 index of whitebark pine mortality. The results of our study support the interpretation that slowing of population growth during the last decade was associated more with increasing grizzly bear density than the decline in whitebark pine. Grizzly bear density and its potential effect on vital rates and population trajectory warrant consideration for management of the grizzly bear population in the Greater Yellowstone Ecosystem.
Density dependence of quasifree single-nucleon knockout reactions
Ryckebusch, Jan; Cosyn, Wim; Vanhalst, Maarten
2011-05-15
We address the issue of whether quasifree single-nucleon knockout measurements carry sufficient information about the nuclear interior. To this end, we present comparisons of the reaction probability densities for A(e,e{sup '}p) and A(p,2p) in quasifree kinematics for the target nuclei {sup 4}He, {sup 12}C, {sup 56}Fe, and {sup 208}Pb. We adopt a comprehensive framework based on the impulse approximation and on a relativized extension of Glauber multiple-scattering reaction theory in which the medium effects related to short-range correlations (SRCs) are implemented. It is demonstrated that SRCs weaken the effect of attenuation. For light target nuclei, both the quasifree (p,2p) and (e,e{sup '}p) can probe average densities of the same order as nuclear saturation density {rho}{sub 0}. For heavy nuclei such as {sup 208}Pb, the probed average densities are smaller than 0.1{rho}{sub 0} and the (e,e{sup '}p) reaction is far more efficient in probing the bulk regions than (p,2p).
Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors
The interaction between density dependence (DD) and environmental stressors can result in a compensatory or synergistic response in population growth, and population models that use density-independent demographic rates or generic DD functions may be introducing bias into managem...
Relativistic Coulomb excitation within the time dependent superfluid local density approximation
Stetcu, I.; Bertulani, C. A.; Bulgac, A.; Magierski, P.; Roche, K. J.
2015-01-06
Within the framework of the unrestricted time-dependent density functional theory, we present for the first time an analysis of the relativistic Coulomb excitation of the heavy deformed open shell nucleus ^{238}U. The approach is based on the superfluid local density approximation formulated on a spatial lattice that can take into account coupling to the continuum, enabling self-consistent studies of superfluid dynamics of any nuclear shape. We compute the energy deposited in the target nucleus as a function of the impact parameter, finding it to be significantly larger than the estimate using the Goldhaber-Teller model. The isovector giant dipole resonance, the dipole pygmy resonance, and giant quadrupole modes are excited during the process. As a result, the one-body dissipation of collective dipole modes is shown to lead a damping width Γ↓≈0.4 MeV and the number of preequilibrium neutrons emitted has been quantified.
Attarian Shandiz, M. Gauvin, R.
2014-10-28
The temperature and pressure dependency of the volume plasmon energy of solids was investigated by density functional theory calculations. The volume change of crystal is the major factor responsible for the variation of valence electron density and plasmon energy in the free electron model. Hence, to introduce the effect of temperature and pressure for the density functional theory calculations of plasmon energy, the temperature and pressure dependency of lattice parameter was used. Also, by combination of the free electron model and the equation of state based on the pseudo-spinodal approach, the temperature and pressure dependency of the plasmon energy was modeled. The suggested model is in good agreement with the results of density functional theory calculations and available experimental data for elements with the free electron behavior.
BRIEF REPORT: Nuclear incompressibility using the density-dependent M3Y effective interaction
NASA Astrophysics Data System (ADS)
Basu, D. N.
2004-06-01
A density-dependent M3Y effective nucleon nucleon (NN) interaction is used to determine the incompressibility of infinite nuclear matter. The equilibrium density of the nuclear matter is determined by minimizing the energy per nucleon. The density dependence parameters are chosen to reproduce the saturation energy per nucleon and the saturation density of spin and isospin symmetric cold infinite nuclear matter. The result of such calculations for nuclear incompressibility using the density-dependent M3Y effective interaction predicts a value of about 300 MeV for nuclear incompressibility.
How important is self-consistency for the dDsC density dependent dispersion correction?
Brémond, Éric; Golubev, Nikolay; Steinmann, Stephan N; Corminboeuf, Clémence
2014-05-14
The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation. PMID:24832324
How important is self-consistency for the dDsC density dependent dispersion correction?
Brémond, Éric; Corminboeuf, Clémence; Golubev, Nikolay; Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991 ; Steinmann, Stephan N.
2014-05-14
The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term summed over all atom pairs to standard density functional approximations. These corrections were originally based on atom pairwise parameters and, hence, had a strong touch of empiricism. To overcome such limitations, we recently proposed a robust system-dependent dispersion correction, dDsC, that is computed from the electron density and that provides a balanced description of both weak inter- and intramolecular interactions. From the theoretical point of view and for the sake of increasing reliability, we here verify if the self-consistent implementation of dDsC impacts ground-state properties such as interaction energies, electron density, dipole moments, geometries, and harmonic frequencies. In addition, we investigate the suitability of the a posteriori scheme for molecular dynamics simulations, for which the analysis of the energy conservation constitutes a challenging tests. Our study demonstrates that the post-SCF approach in an excellent approximation.
Estimation of neural firing rate: the wavelet density estimation approach.
Khorasani, Abed; Daliri, Mohammad Reza
2013-08-01
The computation of neural firing rates based on spike sequences has been introduced as a useful tool for extraction of an animal's behavior. Different estimating methods of such neural firing rates have been developed by neuroscientists, and among these methods, time histogram and kernel estimators have been used more than other approaches. In this paper, the problem in the estimation of firing rates using wavelet density estimators has been considered. The results of simulation study in estimation of underlying rates based on spike sequences sampled from two different variable firing rates show that the proposed wavelet density method provides better and more accurate estimation of firing rates with smooth results compared to two other classical approaches. Furthermore, the performance of a different family of wavelet density estimators in the estimation of the underlying firing rate of biological data have been compared with results of both time histogram and kernel estimators. All in all, the results show that the proposed method can be useful in the estimation of firing rate of neural spike trains. PMID:23924519
NASA Astrophysics Data System (ADS)
Showalter, Rachel Hodges
The nuclear symmetry energy, which is important for asymmetric nuclear systems including rare isotopes and neutron stars, has been studied through both experimental and theoretical approaches, spanning a range of densities from below and above normal nuclear matter density. In the past decade, significant constraints on the density dependence have been obtained in the subsaturation density region, from Heavy Ion Collision (HIC) experiments as well as experiments probing nuclear structure. On the other hand, very little has been determined about the symmetry energy at suprasaturation densities; experimentally, this density region is only accessible in HICs. It is therefore important to understand how to extract nuclear symmetry energy information from HIC at high energies where high density nuclear matter is created in a very brief instant. Symmetry energy constraints from HICs are determined by comparing experimental observables with those calculated using transport models. The goals of this dissertation are to identify the observables most sensitive to the symmetry energy strength, the effective mass splitting, and the in-medium nucleon-nucleon cross sections, sigmaNN, at the region just above saturation density which can be created with heavy ion beams available at NSCL. With better constraints in place, the predictive power of transport models will improve. Recent constraints from HIC experiments have relied on symmetric systems, which are predicted to be sensitive to both the density- and the momentum-dependence of the symmetry potentials. In the study of the nuclear equation of state, asymmetric systems have proven to be more effective at low energy in exploring sensitivities to nucleon-nucleon collisions, which is an important input to any transport model. In this work, particles that were emitted from Ca+Sn systems, with a 48Ca beam impinging on 112Sn or 124Sn targets are measured. The experimental data were compared to predictions from the Improved Molecular Dynamics model with Skyrme interactions (ImQMD-Sky). Four Skyrme parameter sets were chosen that span current constraints on the density dependence of the symmetry energy and on the nucleon effective mass splitting, m*n≠m* p, which results from the momentum dependent interaction potentials. ImQMD-Sky calculations were repeated using an alternate form for sigma NN.. The yields and ratios of both free and coalescence invariant experimental spectra, constructed as a function of the transverse momentum, were contrasted to those simulated by ImQMD-Sky. To select the overlap region between beam and target nuclei, a mid-rapidity cut was taken in the analysis. The parameter sets included in this analysis did not show a significant sensitivity to the symmetry energy strength, but do suggest that the neutron-to-proton ratio bears a large sensitivity both to the nucleon effective mass splitting and the sigmaNN forms used in the calculations. Comparison to the measured coalescence invariant spectra suggests a better agreement with calculations employing effective masses that are greater for neutrons than for protons and a set of isospin-dependent sigma NN. The results in this analysis for the asymmetric Ca+Sn reaction are compared with previous results for a symmetric Sn+Sn reaction at 120 AMeV, which shows an opposite conclusion for low energy particles.
Using time-dependent density functional theory in real time for calculating electronic transport
NASA Astrophysics Data System (ADS)
Schaffhauser, Philipp; Kümmel, Stephan
2016-01-01
We present a scheme for calculating electronic transport within the propagation approach to time-dependent density functional theory. Our scheme is based on solving the time-dependent Kohn-Sham equations on grids in real space and real time for a finite system. We use absorbing and antiabsorbing boundaries for simulating the coupling to a source and a drain. The boundaries are designed to minimize the effects of quantum-mechanical reflections and electrical polarization build-up, which are the major obstacles when calculating transport by applying an external bias to a finite system. We show that the scheme can readily be applied to real molecules by calculating the current through a conjugated molecule as a function of time. By comparing to literature results for the conjugated molecule and to analytic results for a one-dimensional model system we demonstrate the reliability of the concept.
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.
Modeling density dependent flow in the sedimentary basin of Thuringia
NASA Astrophysics Data System (ADS)
Zech, A.; Zehner, B.; Fischer, T.; Kolditz, O.; Attinger, S.
2012-04-01
Salty groundwater reaching the surface or coming close to it is a phenomena that can be observed in many places of the Thuringian Basin. However, it is not obvious, why denser brine overlays lighter fresh water in this region. The hydrogeological processes which cause the rising of saltwater plumes from deeper geological layers to the surface are not yet fully understood. The goal of this modeling project is to investigate the mechanism of brine transport within the aquifers of sedimentary basins in general and of Thuringian Basin in particular. In this study we focus at investigating the fluid dynamics of the basin and how the fluid convection of the deep horizons interacts with groundwater flow near the surface. By gradually increasing the complexity of our model we analyze the major mechanism influencing the flow pattern: geology and hydraulic properties, fluid density differences caused by temperature and salt concentration gradients, fractures and faults as well as boundary conditions of the model, like inflow, outflow and groundwater recharge. For our numerical investigations we use a cross section of the Thuringian basin of approximately 80km length and maximal 800m height. The hydrogeological model is based on the major stratigraphical units from upper Perm (Zechstein) to upper Triassic (Keuper) with the lower Triassic (Bundsandstein) formations representing the main aquifer. The structural model as well as aquifer parameters are provided by geological partner groups of the University of Jena, Germany. To investigate hydrogeological scenarios we use the groundwater simulation program OpenGeoSys, which allows us to calculate thermally, hydrologically and chemically coupled processes. The challenge for us is to include density driven flow as a numerically very sensitive process on a grid that represents a large scale geologically realistic setting. With this work we contribute to the understanding of fluid convection processes influenced by density differences and local geological characteristics, especially for the local conditions in the sedimentary basin of Thuringia.
Gilles, J R L; Lees, R S; Soliban, S M; Benedict, M Q
2011-03-01
Anopheles arabiensis Patton (Diptera: Culicidae) larvae were reared from hatching to the adult stage in the laboratory under a range of diet and larval concentrations using a factorial design. The range circumscribed most of the larval densities and diet concentrations that would allow larval growth and survival using the particular diet formulation and water volume we tested. We determined how these variables affected three outcomes, as follows: larval development rate, survival, and wing length. As has been reported previously, negative density dependence of survival as a function of increased larval density was the prevalent effect on all outcomes when diet was limiting. When diet was not limiting, density dependence was not observed, and three cases of overcompensatory survival were seen. We discuss these results in the context of diet and larval densities for mass rearing and the effect of larval competition on control strategies. PMID:21485365
Charge density-dependent strength of hydration and biological structure.
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
Density-dependence of functional spiking networks in vitro
Ham, Michael I; Gintautuas, Vadas; Rodriguez, Marko A; Bettencourt, Luis M A; Bennett, Ryan; Santa Maria, Cara L
2008-01-01
During development, the mammalian brain differentiates into specialized regions with unique functional abilities. While many factors contribute to this functional specialization, we explore the effect neuronal density can have on neuronal interactions. Two types of networks, dense (50,000 neurons and glia support cells) and sparse (12,000 neurons and glia support cells), are studied. A competitive first response model is applied to construct activation graphs that represent pairwise neuronal interactions. By observing the evolution of these graphs during development in vitro we observe that dense networks form activation connections earlier than sparse networks, and that link-!llltropy analysis of the resulting dense activation graphs reveals that balanced directional connections dominate. Information theoretic measures reveal in addition that early functional information interactions (of order 3) are synergetic in both dense and sparse networks. However, during development in vitro, such interactions become redundant in dense, but not sparse networks. Large values of activation graph link-entropy correlate strongly with redundant ensembles observed in the dense networks. Results demonstrate differences between dense and sparse networks in terms of informational groups, pairwise relationships, and activation graphs. These differences suggest that variations in cell density may result in different functional specialization of nervous system tissue also in vivo.
Time-Dependent Density Functional Theory for Universal Quantum Computation
NASA Astrophysics Data System (ADS)
Tempel, David
2015-03-01
In this talk, I will discuss how the theorems of TDDFT can be applied to a class of qubit Hamiltonians that are universal for quantum computation. The theorems of TDDFT applied to universal Hamiltonians imply that single-qubit expectation values can be used as the basic variables in quantum computation and information theory, rather than wavefunctions. From a practical standpoint this opens the possibility of approximating observables of interest in quantum computations directly in terms of single-qubit quantities (i.e. as density functionals). Additionally, I will discuss how TDDFT provides an exact prescription for simulating universal Hamiltonians with other universal Hamiltonians that have different, and possibly easier-to-realize two-qubit interactions.
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. PMID:17584378
Pharmacotherapy for alcohol dependence: A stratified approach.
Thompson, A; Owens, L; Pushpakom, S P; Faizal, M; Pirmohamed, M
2015-09-01
Alcohol dependence is a common disorder in many societies worldwide, and remains difficult to identify and treat. It is also a risk factor for many secondary non-communicable diseases. Pharmacotherapy is one available treatment option, but appears to be underutilised in practice. Major barriers to use of medications in this area include lack of clinical guidance and questionable efficacy. However, for each medication there appears to be a subpopulation that responds positively, and understanding the moderating factors to treatment efficacy is an important research goal. Thus, this review provides a narrative regarding potential stratification techniques in pharmacological treatment of alcohol dependence, with a specific focus on typologies and pharmacogenetics. In addition, we discuss the basic background of stratified medicine and recent studies on genetic predisposition to alcohol dependence. A growing repository of data exists for both approved and non-approved pharmacotherapies, but failure to replicate findings, inadequate sample sizes, and insufficient funding has resulted in a translational gap. Implementing evidence-based stratified/personalised therapy and identifying new therapeutic agents may lead to improved clinical outcomes and reduced financial burden. Despite some promising findings to date, much work is still required. PMID:25985735
A likelihood approach to estimating animal density from binary acoustic transects.
Horrocks, Julie; Hamilton, David C; Whitehead, Hal
2011-09-01
We propose an approximate maximum likelihood method for estimating animal density and abundance from binary passive acoustic transects, when both the probability of detection and the range of detection are unknown. The transect survey is purposely designed so that successive data points are dependent, and this dependence is exploited to simultaneously estimate density, range of detection, and probability of detection. The data are assumed to follow a homogeneous Poisson process in space, and a second-order Markov approximation to the likelihood is used. Simulations show that this method has small bias under the assumptions used to derive the likelihood, although it performs better when the probability of detection is close to 1. The effects of violations of these assumptions are also investigated, and the approach is found to be sensitive to spatial trends in density and clustering. The method is illustrated using real acoustic data from a survey of sperm and humpback whales. PMID:21039393
High temperature intensifies negative density dependence of fitness in red flour beetles
Halliday, William D; Thomas, Alison S; Blouin-Demers, Gabriel
2015-01-01
Competition for food, space, or other depletable resources has strong impacts on the fitness of organisms and can lead to a pattern known as negative density dependence, where fitness decreases as population density increases. Yet, many resources that have strong impacts on fitness are nondepletable (e.g., moisture or temperature). How do these nondepletable resources interact with depletable resources to modify negative density dependence? We tested the hypothesis that negative density dependence is modulated by temperature in red flour beetles and tested the prediction that the strength of negative density dependence should decrease as temperature decreases. We measured the number of eggs laid, offspring development time, and the number of offspring that reached maturity at three temperatures and two food treatment combinations as we simultaneously manipulated adult population density. We demonstrated that low temperatures weaken negative density dependence in the number of eggs laid; this pattern was most evident when food was abundant. Density had no effect on development time, but low temperatures increased development time. The percent of eggs that emerged as adults decreased with both density and temperature and increased with food. Temperature, an abiotic driver, can thus modulate density-dependent processes in ectotherms. Therefore, models of population growth for ectotherms should incorporate the effects of temperature. PMID:25798223
Density-dependent effects on group size are sex-specific in a gregarious ungulate.
Vander Wal, Eric; van Beest, Floris M; Brook, Ryan K
2013-01-01
Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km(2) between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km(2) and we found evidence for a minimum group size at population density ≤0.70 elk/km(2). Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission. PMID:23326502
Density-Dependent Effects on Group Size Are Sex-Specific in a Gregarious Ungulate
Vander Wal, Eric; van Beest, Floris M.; Brook, Ryan K.
2013-01-01
Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km2 between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km2 and we found evidence for a minimum group size at population density ≤0.70 elk/km2. Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission. PMID:23326502
Time-Dependent Density Functional Theory for Extreme Environments
NASA Astrophysics Data System (ADS)
Baczewski, Andrew; Magyar, Rudolph; Shulenburger, Luke
2013-10-01
In recent years, DFT-MD has been shown to be a powerful tool for calculating the equation of state and constitutive properties of warm dense matter (WDM). These studies are validated through a number of experiments, including recently developed X-Ray Thomson Scattering (XRTS) techniques. Here, electronic temperatures and densities of WDM are accessible through x-ray scattering data, which is related to the system's dynamic structure factor (DSF)-a quantity that is accessible through DFT-MD calculations. Previous studies predict the DSF within the Born-Oppenheimer approximation, with the electronic state computed using Mermin DFT. A capability for including more general coupled electron-ion dynamics is desirable, to study both the effect on XRTS observables and the broader problem of electron-ion energy transfer in extreme WDM conditions. Progress towards such a capability will be presented, in the form of an Ehrenfest MD framework using TDDFT. Computational challenges and open theoretical questions will be discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Security Administration under contract DE-AC04-94AL85000.
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.
Reduced density matrix hybrid approach: Application to electronic energy transfer
Berkelbach, Timothy C.; Reichman, David R.; Markland, Thomas E.
2012-02-28
Electronic energy transfer in the condensed phase, such as that occurring in photosynthetic complexes, frequently occurs in regimes where the energy scales of the system and environment are similar. This situation provides a challenge to theoretical investigation since most approaches are accurate only when a certain energetic parameter is small compared to others in the problem. Here we show that in these difficult regimes, the Ehrenfest approach provides a good starting point for a dynamical description of the energy transfer process due to its ability to accurately treat coupling to slow environmental modes. To further improve on the accuracy of the Ehrenfest approach, we use our reduced density matrix hybrid framework to treat the faster environmental modes quantum mechanically, at the level of a perturbative master equation. This combined approach is shown to provide an efficient and quantitative description of electronic energy transfer in a model dimer and the Fenna-Matthews-Olson complex and is used to investigate the effect of environmental preparation on the resulting dynamics.
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.
Bassar, Ronald D; Lopez-Sepulcre, Andres; Reznick, David N; Travis, Joseph
2013-01-01
Recent study of feedbacks between ecological and evolutionary processes has renewed interest in population regulation and density-dependent selection because they represent black-box descriptions of these feedbacks. The roles of population regulation and density-dependent selection in life-history evolution have received a significant amount of theoretical attention, but there are few empirical examples demonstrating their importance. We address this challenge in natural populations of the Trinidadian guppy (Poecilia reticulata) that differ in their predation regimes. First, we tested whether natural populations of guppies are regulated by density dependence and quantified in which phases of the life cycle the effects of density are important. We found that guppies from low-predation (LP) environments are tightly regulated and that the density-dependent responses disproportionately affected some size classes. Second, we tested whether there are differences in density-dependent selection between guppies from LP or high-predation (HP) environments. We found that the fitness of HP guppies is more sensitive to the depressant effects of density than the fitness of LP guppies. Finally, we used an evolutionary invasion analysis to show that, depending on the effect of density on survival of the HP phenotype, this greater sensitivity of the HP phenotype to density can partially explain the evolution of the LP phenotype. We discuss the relevance of these findings to the study of feedbacks between ecology and evolution. PMID:23234843
Temperature and electron density dependence of spin relaxation in GaAs/AlGaAs quantum well.
Han, Lifen; Zhu, Yonggang; Zhang, Xinhui; Tan, Pingheng; Ni, Haiqiao; Niu, Zhichuan
2011-01-01
Temperature and carrier density-dependent spin dynamics for GaAs/AlGaAs quantum wells (QWs) with different structural symmetries have been studied by using time-resolved Kerr rotation technique. The spin relaxation time is measured to be much longer for the symmetrically designed GaAs QW comparing with the asymmetrical one, indicating the strong influence of Rashba spin-orbit coupling on spin relaxation. D'yakonov-Perel' mechanism has been revealed to be the dominant contribution for spin relaxation in GaAs/AlGaAs QWs. The spin relaxation time exhibits non-monotonic-dependent behavior on both temperature and photo-excited carrier density, revealing the important role of non-monotonic temperature and density dependence of electron-electron Coulomb scattering. Our experimental observations demonstrate good agreement with recently developed spin relaxation theory based on microscopic kinetic spin Bloch equation approach. PMID:21711611
Temperature and electron density dependence of spin relaxation in GaAs/AlGaAs quantum well
2011-01-01
Temperature and carrier density-dependent spin dynamics for GaAs/AlGaAs quantum wells (QWs) with different structural symmetries have been studied by using time-resolved Kerr rotation technique. The spin relaxation time is measured to be much longer for the symmetrically designed GaAs QW comparing with the asymmetrical one, indicating the strong influence of Rashba spin-orbit coupling on spin relaxation. D'yakonov-Perel' mechanism has been revealed to be the dominant contribution for spin relaxation in GaAs/AlGaAs QWs. The spin relaxation time exhibits non-monotonic-dependent behavior on both temperature and photo-excited carrier density, revealing the important role of non-monotonic temperature and density dependence of electron-electron Coulomb scattering. Our experimental observations demonstrate good agreement with recently developed spin relaxation theory based on microscopic kinetic spin Bloch equation approach. PMID:21711611
Hwang, Jungseek
2016-01-01
We investigate temperature smearing effects on the electron-boson spectral density function (I(2)χ(ω)) obtained from optical data using a maximum entropy inversion method. We start with two simple model input I(2)χ(ω), calculate the optical scattering rates at selected temperatures using the model input spectral density functions and a generalized Allen's formula, then extract back I(2)χ(ω) at each temperature from the calculated optical scattering rate using the maximum entropy method (MEM) which has been used for analysis of optical data of high-temperature superconductors including cuprates, and finally compare the resulting I(2)χ(ω) with the input ones. From this approach we find that the inversion process can recover the input I(2)χ(ω) almost perfectly when the quality of fits is good enough and also temperature smearing (or thermal broadening) effects appear in the I(2)χ(ω) when the quality of fits is not good enough. We found that the coupling constant and the logarithmically averaged frequency are robust to the temperature smearing effects and/or the quality of fits. We use these robust properties of the two quantities as criterions to check whether experimental data have intrinsic temperature-dependent evolutions or not. We carefully apply the MEM to two material systems (one optimally doped and the other underdoped cuprates) and conclude that the I(2)χ(ω) extracted from the optical data contain intrinsic temperature-dependent evolutions. PMID:27029840
Hwang, Jungseek
2016-01-01
We investigate temperature smearing effects on the electron-boson spectral density function (I2χ(ω)) obtained from optical data using a maximum entropy inversion method. We start with two simple model input I2χ(ω), calculate the optical scattering rates at selected temperatures using the model input spectral density functions and a generalized Allen’s formula, then extract back I2χ(ω) at each temperature from the calculated optical scattering rate using the maximum entropy method (MEM) which has been used for analysis of optical data of high-temperature superconductors including cuprates, and finally compare the resulting I2χ(ω) with the input ones. From this approach we find that the inversion process can recover the input I2χ(ω) almost perfectly when the quality of fits is good enough and also temperature smearing (or thermal broadening) effects appear in the I2χ(ω) when the quality of fits is not good enough. We found that the coupling constant and the logarithmically averaged frequency are robust to the temperature smearing effects and/or the quality of fits. We use these robust properties of the two quantities as criterions to check whether experimental data have intrinsic temperature-dependent evolutions or not. We carefully apply the MEM to two material systems (one optimally doped and the other underdoped cuprates) and conclude that the I2χ(ω) extracted from the optical data contain intrinsic temperature-dependent evolutions. PMID:27029840
Population-Level Density Dependence Influences the Origin and Maintenance of Parental Care
Reyes, Elijah; Thrasher, Patsy; Bonsall, Michael B.; Klug, Hope
2016-01-01
Parental care is a defining feature of animal breeding systems. We now know that both basic life-history characteristics and ecological factors influence the evolution of care. However, relatively little is known about how these factors interact to influence the origin and maintenance of care. Here, we expand upon previous work and explore the relationship between basic life-history characteristics (stage-specific rates of mortality and maturation) and the fitness benefits associated with the origin and the maintenance of parental care for two broad ecological scenarios: the scenario in which egg survival is density dependent and the case in which adult survival is density dependent. Our findings suggest that high offspring need is likely critical in driving the origin, but not the maintenance, of parental care regardless of whether density dependence acts on egg or adult survival. In general, parental care is more likely to result in greater fitness benefits when baseline adult mortality is low if 1) egg survival is density dependent or 2) adult mortality is density dependent and mutant density is relatively high. When density dependence acts on egg mortality, low rates of egg maturation and high egg densities are less likely to lead to strong fitness benefits of care. However, when density dependence acts on adult mortality, high levels of egg maturation and increasing adult densities are less likely to maintain care. Juvenile survival has relatively little, if any, effect on the origin and maintenance of egg-only care. More generally, our results suggest that the evolution of parental care will be influenced by an organism’s entire life history characteristics, the stage at which density dependence acts, and whether care is originating or being maintained. PMID:27093056
Population-Level Density Dependence Influences the Origin and Maintenance of Parental Care.
Reyes, Elijah; Thrasher, Patsy; Bonsall, Michael B; Klug, Hope
2016-01-01
Parental care is a defining feature of animal breeding systems. We now know that both basic life-history characteristics and ecological factors influence the evolution of care. However, relatively little is known about how these factors interact to influence the origin and maintenance of care. Here, we expand upon previous work and explore the relationship between basic life-history characteristics (stage-specific rates of mortality and maturation) and the fitness benefits associated with the origin and the maintenance of parental care for two broad ecological scenarios: the scenario in which egg survival is density dependent and the case in which adult survival is density dependent. Our findings suggest that high offspring need is likely critical in driving the origin, but not the maintenance, of parental care regardless of whether density dependence acts on egg or adult survival. In general, parental care is more likely to result in greater fitness benefits when baseline adult mortality is low if 1) egg survival is density dependent or 2) adult mortality is density dependent and mutant density is relatively high. When density dependence acts on egg mortality, low rates of egg maturation and high egg densities are less likely to lead to strong fitness benefits of care. However, when density dependence acts on adult mortality, high levels of egg maturation and increasing adult densities are less likely to maintain care. Juvenile survival has relatively little, if any, effect on the origin and maintenance of egg-only care. More generally, our results suggest that the evolution of parental care will be influenced by an organism's entire life history characteristics, the stage at which density dependence acts, and whether care is originating or being maintained. PMID:27093056
Roy, Justin; Yannic, Glenn; Côté, Steeve D; Bernatchez, Louis
2012-01-01
Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432
Roy, Justin; Yannic, Glenn; Côté, Steeve D; Bernatchez, Louis
2012-03-01
Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults. PMID:22822432
Negative density-dependent emigration of males in an increasing red deer population
Loe, Leif Egil; Mysterud, Atle; Veiberg, Vebjørn; Langvatn, Rolf
2009-01-01
In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deer Cervus elaphus marked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (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. PMID:19364736
Density-dependent nucleon-nucleon interaction from three-nucleon forces
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.
2011-05-15
Microscopic calculations based on realistic nuclear Hamiltonians, while yielding accurate results for the energies of the ground and low-lying excited states of nuclei with A{<=}12, fail to reproduce the empirical equilibrium properties of nuclear matter, that are known to be significantly affected by three-nucleon forces. We discuss a scheme suitable to construct a density-dependent two-nucleon potential, in which the effects of n-particle interactions can be included by integrating out the degrees of freedom of (n-2) nucleons. Our approach, based on the formalism of correlated basis function and state-of-the-art models of the two- and three-nucleon potentials, leads to an effective interaction that can be easily employed in nuclear matter calculations, yielding results in good agreement with those obtained from the underlying three-body potential.
Density-dependent nucleon-nucleon interaction from three-nucleon forces
NASA Astrophysics Data System (ADS)
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu.; Schmidt, Kevin E.
2011-05-01
Microscopic calculations based on realistic nuclear Hamiltonians, while yielding accurate results for the energies of the ground and low-lying excited states of nuclei with A?12, fail to reproduce the empirical equilibrium properties of nuclear matter, that are known to be significantly affected by three-nucleon forces. We discuss a scheme suitable to construct a density-dependent two-nucleon potential, in which the effects of n-particle interactions can be included by integrating out the degrees of freedom of (n-2) nucleons. Our approach, based on the formalism of correlated basis function and state-of-the-art models of the two- and three-nucleon potentials, leads to an effective interaction that can be easily employed in nuclear matter calculations, yielding results in good agreement with those obtained from the underlying three-body potential.
Physical Origin of Density Dependent Force of the Skyrme Type within the Quark Meson Coupling Model
Pierre Guichon; Hrayr Matevosyan; N. Sandulescu; Anthony Thomas
2006-03-17
A density dependent, effective nucleon-nucleon force of the Skyrme type is derived from the quark-meson coupling model--a self-consistent, relativistic quark level description of nuclear matter. This new formulation requires no assumption that the mean scalar field is small and hence constitutes a significant advance over earlier work. The similarity of the effective interaction to the widely used SkM* force encourages us to apply it to a wide range of nuclear problems, beginning with the binding energies and charge distributions of doubly magic nuclei. Finding impressive results in this conventional arena, we apply the same effective interaction, within the Hartree-Fock-Bogoliubov approach, to the properties of nuclei far from stability. The resulting two neutron drip lines and shell quenching are quite satisfactory. Finally, we apply the relativistic formulation to the properties of dense nuclear matter in anticipation of future application to the properties of neutron stars.
Switching from negative to positive density-dependence among populations of a cobble beach plant.
Goldenheim, William M; Irving, Andrew D; Bertness, Mark D
2008-12-01
Interactions among species occur across a continuum from negative to positive and can have a critical role in shaping population and community dynamics. Growing evidence suggests that inter- and intra-specific interactions can vary in strength or even switch direction (i.e., negative to positive) depending on environmental conditions, consumer pressure, and also among life-history stages. We tested the hypothesis that seedlings and adults of the intertidal annual forb Suaeda linearis growing on New England shores exhibit positive density-dependence under physically stressful conditions high on the shore (i.e., greater temperatures, evaporative stress), but negative density-dependence under physically milder conditions low on the shore. Among experimental treatments of plant density (dense versus sparse) at each shore height, plant biomass, length, and number of leaves/branches were greater in dense stands high on the shore (positive density-dependence), but greater in sparse stands low on the shore (negative density-dependence). Such responses were consistent among life-history stages and generally consistent between sites. As a more direct measure of fitness, per capita seed production was also positively density-dependent high on the shore, but negatively density-dependent low on the shore. These results support the current theory predicting an increase in the frequency of positive interactions with increasing environmental stress and further emphasize the previously understated role of positive interactions in shaping and maintaining populations and communities. PMID:18843509
Estimation of Density-Dependent Mortality of Juvenile Bivalves in the Wadden Sea
Andresen, Henrike; Strasser, Matthias; van der Meer, Jaap
2014-01-01
We investigated density-dependent mortality within the early months of life of the bivalves Macoma balthica (Baltic tellin) and Cerastoderma edule (common cockle) in the Wadden Sea. Mortality is thought to be density-dependent in juvenile bivalves, because there is no proportional relationship between the size of the reproductive adult stocks and the numbers of recruits for both species. It is not known however, when exactly density dependence in the pre-recruitment phase occurs and how prevalent it is. The magnitude of recruitment determines year class strength in bivalves. Thus, understanding pre-recruit mortality will improve the understanding of population dynamics. We analyzed count data from three years of temporal sampling during the first months after bivalve settlement at ten transects in the Sylt-Rømø-Bay in the northern German Wadden Sea. Analyses of density dependence are sensitive to bias through measurement error. Measurement error was estimated by bootstrapping, and residual deviances were adjusted by adding process error. With simulations the effect of these two types of error on the estimate of the density-dependent mortality coefficient was investigated. In three out of eight time intervals density dependence was detected for M. balthica, and in zero out of six time intervals for C. edule. Biological or environmental stochastic processes dominated over density dependence at the investigated scale. PMID:25105293
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.
New Approaches To Nuclear Level Densities Through Particle Emission Measurements
Haight, R.C.; Rochman, D.; O'Donnell, J.M.; Devlin, M.
2003-08-26
With the intense spallation neutron source at the Los Alamos Neutron Science Center (LANSCE), new approaches to nuclear level densities are being explored through neutron-induced reactions and measurements of the resultant particle emission. This continuous-in-energy neutron source has been used to study Ericson fluctuations, charged-particle emission cross sections and spectra, gamma-ray production and, recently, neutron emission. Examples of each will be discussed. The FIGARO array of neutron and gamma-ray detectors has been developed in the past year to allow measurement of neutron emission in a 'double time-of-flight' experiment. The incident neutron energy is determined by time-of-flight over a 21-meter flight path with gamma rays from the induced reaction. Neutron emission spectra from this reaction are then measured by time-of-flight over a flight path of typically 1 meter. Data on 28Si(n,n') are presented, and the relevance to determination of nuclear level densities is discussed.
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 theories that closely couple to the microscopic structure and dynamics.
NASA Astrophysics Data System (ADS)
Hernandez, Samuel
Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) are powerful methods for solving a variety of problems, including ground state electronic structure, electron dynamics, and the absorbance cross section of molecules and materials. DFT is used to calculate the ground state electron configuration, whereas TDDFT is used to solve for the absorption cross section of excited systems. These techniques are not without their challenges. DFT requires the solution of Kohn-Sham orbitals through the diagonalization of the one electron Hamiltonian, which scales as O(N3) where N signifies the number of orbitals in a simulation. TDDFT has its challenges as well. Each orbital must be propagated every time step, but since a single TDDFT simulation requires thousands of time steps, it is very costly. In this dissertation, we present methods that were developed to circumvent the limitations of DFT and TDDFT. One method for decreasing the cost of DFT and TDDFT is direct delocalization, which was used to calculate the electron transfer of rate of a fullerene derivative dimer. Specifically, a common way of determining the electron transfer rate is through the use of Marcus theory, which relies on the dimer having symmetric environments. In nature this is usually the case because the dimer is surrounded by other molecules, thus creating a locally homogeneous environment. In theoretical simulations this is much more difficult to achieve. One way is to add solvating molecules, but this can be extremely costly. Instead we were able to use, in Chapter 1, a modified version of Marcus theory, which applies a bias across the Fock-matrix. This modified version of the Marcus theory allows us to solve for the electron transfer rate using one DFT calculation, because it eliminates the need to solvate the dimer to balance out the environments. The electron transfer rate was calculated to qualitatively determine the factors which lead to a good acceptor in an organic solar cell, as is important for creating an efficient solar cell. In Chapter 2, we present a method for solving for the coupling constant of a dimer without having to balance the environments with solvating molecules. The coupling constant is used in Marcus theory to determine the electron transfer rate. To avoid the balancing we apply an electric field to the system, mimicing the effect that the solvating molecules have on the dimer. The method presented in Chapter 2 is cheaper than the preceding approaches as it limits the size of the system. The final method we developed was the stochastic paradigm for DFT and TDDFT. The stochastic methods that are described in Chapters 3 and 4 reduce the cost of large-scale calculations by replacing the Kohn-Sham orbitals with stochastic orbitals. The density function is determined by a statistical average of the stochastic orbitals. This method enables the calculation of the absorption cross section of large systems such as 9-(4-Mercaptaphenylehtylnyl)anthracene (MPEA) chemisorbed onto a gold surface, and large gold nanoclusters. Both these systems, which contain thousands of electrons, are expensive to simulate using conventional TDDFT, but the stochastic approach we use, stochastic TDDFT (TDsDFT) makes these calculations feasible since it scales moderately (sublinearly) with the number of electrons in the system.
A high-performance Fortran code to calculate spin- and parity-dependent nuclear level densities
NASA Astrophysics Data System (ADS)
Sen'kov, R. A.; Horoi, M.; Zelevinsky, V. G.
2013-01-01
A high-performance Fortran code is developed to calculate the spin- and parity-dependent shell model nuclear level densities. The algorithm is based on the extension of methods of statistical spectroscopy and implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The proton-neutron formalism is used. We have applied the method for calculating the level densities for a set of nuclei in the sd-, pf-, and pf+g- model spaces. Examples of the calculations for 28Si (in the sd-model space) and 64Ge (in the pf+g-model space) are presented. To illustrate the power of the method we estimate the ground state energy of 64Ge in the larger model space pf+g, which is not accessible to direct shell model diagonalization due to the prohibitively large dimension, by comparing with the nuclear level densities at low excitation energy calculated in the smaller model space pf. Program summaryProgram title: MM Catalogue identifier: AENM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 193181 No. of bytes in distributed program, including test data, etc.: 1298585 Distribution format: tar.gz Programming language: Fortran 90, MPI. Computer: Any architecture with a Fortran 90 compiler and MPI. Operating system: Linux. RAM: Proportional to the system size, in our examples, up to 75Mb Classification: 17.15. External routines: MPICH2 (http://www.mcs.anl.gov/research/projects/mpich2/) Nature of problem: Calculating of the spin- and parity-dependent nuclear level density. Solution method: The algorithm implies exact calculation of the first and second Hamiltonian moments for different configurations at fixed spin and parity. The code is parallelized using the Message Passing Interface and a master-slaves dynamical load-balancing approach. Restrictions: The program uses two-body interaction in a restricted single-level basis. For example, GXPF1A in the pf-valence space. Running time: Depends on the system size and the number of processors used (from 1 min to several hours).
Block, G L; Allen, L J
2000-03-01
Density-independent and density-dependent, stochastic and deterministic, discrete-time, structured models are formulated, analysed and numerically simulated. A special case of the deterministic, density-independent, structured model is the well-known Leslie age-structured model. The stochastic, density-independent model is a multitype branching process. A review of linear, density-independent models is given first, then nonlinear, density-dependent models are discussed. In the linear, density-independent structured models, transitions between states are independent of time and state. Population extinction is determined by the dominant eigenvalue lambda of the transition matrix. If lambda < or = 1, then extinction occurs with probability one in the stochastic and deterministic models. However, if lambda > 1, then the deterministic model has exponential growth, but in the stochastic model there is a positive probability of extinction which depends on the fixed point of the system of probability generating functions. The linear, density-independent, stochastic model is generalized to a nonlinear, density-dependent one. The dependence on state is in terms of a weighted total population size. It is shown for small initial population sizes that the density-dependent, stochastic model can be approximated by the density-independent, stochastic model and thus, the extinction behavior exhibited by the linear model occurs in the nonlinear model. In the deterministic models there is a unique stable equilibrium. Given the population does not go extinct, it is shown that the stochastic model has a quasi-stationary distribution with mean close to the stable equilibrium, provided the population size is sufficiently large. For small values of the population size, complete extinction can be observed in the simulations. However, the persistence time increases rapidly with the population size. PMID:10824427
Fronhofer, Emanuel A; Kropf, Tabea; Altermatt, Florian
2015-05-01
Movement and dispersal are critical processes for almost all organisms in natural populations. Understanding their causes and consequences is therefore of high interest. While both theoretical and empirical work suggest that dispersal, more exactly emigration, is plastic and may be a function of local population density, the functional relationship between the underlying movement strategies and population density has received less attention. We here present evidence for the shape of this reaction norm and are able to differentiate between three possible cues: the relative number of individuals, the presence of metabolites (chemical cues) and resource availability. We performed microcosm experiments with the ciliate model organism Tetrahymena in order to understand the plasticity of movement strategies with respect to local density while controlling for possible confounding effects mediated by the availability of different cues. In addition, we investigated how an Allee effect can influence movement and dispersal plasticity. Our findings suggest that movement strategies in Tetrahymena are plastic and density-dependent. The observed movement reaction norm was U-shaped. This may be due to an Allee effect which led to negative density dependence at low population densities and generally positive density dependence at high population densities due to local competition. This possibly adaptive density-dependent movement strategy was likely mediated by chemical cues. Our experimental work in highly controlled conditions indicates that both environmental cues as well as inherent population dynamics must be considered to understand movement and dispersal. PMID:25376344
Density-Dependent Compensatory Growth in Brown Trout (Salmo trutta) in Nature
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
Sex-based differences in density-dependent sociality: an experiment with a gregarious ungulate.
Vander Wal, E; Yip, H; McLoughlin, P D
2012-01-01
For animals living in natural or semi-natural settings, empirical data on how sociality changes in response to increasing population density are few, especially with respect to true conspecific density and not group size. However, insight into this line of research may be far-reaching--from understanding density dependence in sexual selection to improving models of disease transmission. Using elk (Cervus elaphus Linnaeus) held in enclosures, we conducted sex-stratified experiments to test how the frequency of dyadic pairings (interaction rate) and their quality (duration) responded to manipulations in exposure to density. Using proximity-logging radio collars we recorded when and for how long individuals shared a space within 1.4 m of each other. As predicted, males increased their interaction rate as density increased. Female interaction rates, however, increased initially as density increased but soon declined to become indistinguishable from rates at low density. Females interacted for longer periods at medium densities, whereas male interaction length clearly decreased as density increased. We highlight a sexually dichotomous, density-dependent response in sociality that has yet to be reported. In addition to furthering our understanding of sociobiology (e.g., implications of time constraints presented by density on dyadic interactions), our results have implications for managing communicable disease in gregarious species of livestock and wildlife. PMID:22486100
Rotella, J.J.; Link, W.A.; Nichols, J.D.; Hadley, G.L.; Garrott, R.A.; Proffitt, K.M.
2009-01-01
Much of the existing literature that evaluates the roles of density-dependent and density-independent factors on population dynamics has been called into question in recent years because measurement errors were not properly dealt with in analyses. Using state-space models to account for measurement errors, we evaluated a set of competing models for a 22-year time series of mark-resight estimates of abundance for a breeding population of female Weddell seals (Leptonychotes weddellii) studied in Erebus Bay, Antarctica. We tested for evidence of direct density dependence in growth rates and evaluated whether equilibrium population size was related to seasonal sea-ice extent and the Southern Oscillation Index (SOI). We found strong evidence of negative density dependence in annual growth rates for a population whose estimated size ranged from 438 to 623 females during the study. Based on Bayes factors, a density-dependence-only model was favored over models that also included en! vironmental covariates. According to the favored model, the population had a stationary distribution with a mean of 497 females (SD = 60.5), an expected growth rate of 1.10 (95% credible interval 1.08-1.15) when population size was 441 females, and a rate of 0.90 (95% credible interval 0.87-0.93) for a population of 553 females. A model including effects of SOI did receive some support and indicated a positive relationship between SOI and population size. However, effects of SOI were not large, and including the effect did not greatly reduce our estimate of process variation. We speculate that direct density dependence occurred because rates of adult survival, breeding, and temporary emigration were affected by limitations on per capita food resources and space for parturition and pup-rearing. To improve understanding of the relative roles of various demographic components and their associated vital rates to population growth rate, mark-recapture methods can be applied that incorporate both environmental covariates and the seal abundance estimates that were developed here. An improved understanding of why vital rates change with changing population abundance will only come as we develop a better understanding of the processes affecting marine food resources in the Southern Ocean.
Influence of field dependent critical current density on flux profiles in high Tc superconductors
NASA Technical Reports Server (NTRS)
Takacs, S.
1990-01-01
The field distribution for superconducting cylinders and slabs with field dependent critical current densities in combined DC and AC magnetic fields and the corresponding magnetic fluxes are calculated. It is shown that all features of experimental magnetic-field profile measurements can be explained in the framework of field dependent critical current density. Even the quantitative agreement between the experimental and theoretical results using Kim's model is very good.
Relativistic Coulomb excitation within the time dependent superfluid local density approximation
Stetcu, I.; Bertulani, C. A.; Bulgac, A.; Magierski, P.; Roche, K. J.
2015-01-06
Within the framework of the unrestricted time-dependent density functional theory, we present for the first time an analysis of the relativistic Coulomb excitation of the heavy deformed open shell nucleus 238U. The approach is based on the superfluid local density approximation formulated on a spatial lattice that can take into account coupling to the continuum, enabling self-consistent studies of superfluid dynamics of any nuclear shape. We compute the energy deposited in the target nucleus as a function of the impact parameter, finding it to be significantly larger than the estimate using the Goldhaber-Teller model. The isovector giant dipole resonance, 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
An Experimental Field Study of Delayed Density Dependence in Natural Populations of Aedes albopictus
Walsh, Rachael K.; Bradley, Caitlin; Apperson, Charles S.; Gould, Fred
2012-01-01
Aedes albopictus, a species known to transmit dengue and chikungunya viruses, is primarily a container-inhabiting mosquito. The potential for pathogen transmission by Ae. albopictus has increased our need to understand its ecology and population dynamics. Two parameters that we know little about are the impact of direct density-dependence and delayed density-dependence in the larval stage. The present study uses a manipulative experimental design, under field conditions, to understand the impact of delayed density dependence in a natural population of Ae. albopictus in Raleigh, North Carolina. Twenty liter buckets, divided in half prior to experimentation, placed in the field accumulated rainwater and detritus, providing oviposition and larval production sites for natural populations of Ae. albopictus. Two treatments, a larvae present and larvae absent treatment, were produced in each bucket. After five weeks all larvae were removed from both treatments and the buckets were covered with fine mesh cloth. Equal numbers of first instars were added to both treatments in every bucket. Pupae were collected daily and adults were frozen as they emerged. We found a significant impact of delayed density-dependence on larval survival, development time and adult body size in containers with high larval densities. Our results indicate that delayed density-dependence will have negative impacts on the mosquito population when larval densities are high enough to deplete accessible nutrients faster than the rate of natural food accumulation. PMID:22563428
Field tests of density-and frequency-dependent selection in Erigeron annuus (Compositae).
Bennington, C; Stratton, D
1998-04-01
Selection may maintain genetic diversity in natural populations if the physical or biotic environment is variable over space and-or time. Because density and genotype frequencies can be heterogeneous, and because genotypes may differ in competitive ability, both density-and frequency-dependent selection have been considered to be potentially important evolutionary processes. To address the possibility that intraspecific interactions among plants are a source of fitness variation in Erigeron annuus, we conducted field experiments over 2 yr that were designed to examine the potential of population density, genotype frequency, and their interaction to act as selective agents. In both experiments, apomictic genotypes of Erigeron were paired. Seedlings were planted into plots that differed in density and the identity of minority and majority genotype. There was evidence for a differential effect of density among genotypes for only one year's experiment, suggesting that density-dependent selection is either weak or temporally variable. Genotype frequency had no effect on fitness in either year, and thus there was no evidence for frequency-dependent selection. In addition, the lack of a frequency ;ts density interaction demonstrates that resource partitioning, one mechanism for frequency dependence, is not strong among Erigeron genotypes. If frequency-dependent selection does occur in this species, it is either too weak to detect even in large field experiments, or occurs only in the presence of a selective agent (e.g., pathogens) that was lacking in our experiments. PMID:21684937
Size selectivity of predation by brown bears depends on the density of their sockeye salmon prey.
Cunningham, Curry J; Ruggerone, Gregory T; Quinn, Thomas P
2013-05-01
Can variation in prey density drive changes in the intensity or direction of selective predation in natural systems? Despite ample evidence of density-dependent selection, the influence of prey density on predatory selection patterns has seldom been investigated empirically. We used 20 years of field data on brown bears (Ursus arctos) foraging on sockeye salmon (Oncorhynchus nerka) in Alaska, to test the hypothesis that salmon density affects the strength of size-selective predation. Measurements from 41,240 individual salmon were used to calculate variance-standardized selection differentials describing the direction and magnitude of selection. Across the time series, the intensity of predatory selection was inversely correlated with salmon density; greater selection for smaller salmon occurred at low salmon densities as bears' tendency to kill larger-than-average salmon was magnified. This novel connection between density dependence and selective predation runs contrary to some aspects of optimal foraging theory and differs from many observations of density-dependent selection because (1) the direction of selection remains constant while its magnitude changes as a function of density and (2) stronger selection is observed at low abundance. These findings indicate that sockeye salmon may be subject to fishery-induced size selection from both direct mechanisms and latent effects of altered predatory selection patterns on the spawning grounds, resulting from reduced salmon abundance. PMID:23594549
Impacts of poor food availability on positive density dependence in a highly colonial seabird
Ashbrook, Kate; Wanless, Sarah; Harris, Mike P.; Hamer, Keith C.
2010-01-01
For species with positive density dependence, costs and benefits of increasing density may depend on environmental conditions, but this has seldom been tested. By examining a colonial seabird (common guillemot) over a period of unprecedented poor food availability, we test two contrasting hypotheses suggesting that birds breeding at high density have: (i) greater leeway to increase foraging effort owing to more effective defence of unattended chicks against predators; and (ii) less leeway, owing to more attacks on unattended chicks by neighbouring adults. Supporting hypothesis 1, birds at high density increased provisioning rates and hence survival of chicks by foraging simultaneously with their partners, whereas at low density, unattended chicks were liable to be killed by predatory gulls and, unexpectedly, razorbills. Simultaneously, supporting hypothesis 2, heightened aggression towards unattended chicks at high density frequently resulted in infanticide, undermining benefits from collective defence against predators. Consequently, over 25 years, the magnitude of positive density dependence was independent of mean breeding success. These data indicate previously unsuspected trade-offs between costs and benefits of increasing density under changing environments. Previous generalizations about the importance of high density for reproductive success have so far remained robust, but such trade-offs could have unpredictable consequences for future population dynamics. PMID:20335206
NASA Astrophysics Data System (ADS)
Magrakvelidze, Maia; Madjet, Mohamed El-Amine; Dixit, Gopal; Ivanov, Misha; Chakraborty, Himadri S.
2015-06-01
We determine and analyze the quantum phases and time delays in photoionization and photorecombination of valence 3 p and 3 s electrons of argon using the Kohn-Sham local-density-functional approach. The time-dependent local-density approximation is used to account for the electron correlation. Resulting attosecond Wigner-Smith time delays show very good agreement with the recent experiment on argon that measured the delay in 3 p photorecombination [S. B. Schoun et al., Phys. Rev. Lett. 112, 153002 (2014), 10.1103/PhysRevLett.112.153002].
Demographic variability and density-dependent dynamics of a free-ranging rhesus macaque population
Hernández-Pacheco, Raisa; Rawlins, Richard G.; Kessler, Matthew J.; Williams, Lawrence E.; Ruiz-Maldonado, Tagrid M.; González-Martínez, Janis; Ruiz-Lambides, Angelina V.; Sabat, Alberto M.
2014-01-01
Density-dependence is hypothesized as the major mechanism of population regulation. However, the lack of long-term demographic data has hampered the use of density-dependent models in nonhuman primates. In this study, we make use of the long-term demographic data from Cayo Santiago’s rhesus macaques to parameterize and analyze both a density-independent and a density-dependent population matrix model, and compare their projections with the observed population changes. We also employ a retrospective analysis to determine how variance in vital rates, and covariance among them, contributed to the observed variation in long-term fitness across different levels of population density. The population exhibited negative density-dependence in fertility and the model incorporating this relationship accounted for 98% of the observed population dynamics. Variation in survival and fertility of sexually active individuals contributed the most to the variation in long-term fitness, while vital rates displaying high temporal variability exhibited lower sensitivities. Our findings are novel in describing density-dependent dynamics in a provisioned primate population, and in suggesting that selection is acting to lower the variance in the population growth rate by minimizing the variation in adult survival at high density. Because density-dependent mechanisms may become stronger in wild primate populations due to increasing habitat loss and food scarcity, our study demonstrates it is important to incorporate variation in population size, as well as demographic variability into population viability analyses for a better understanding of the mechanisms regulating the growth of primate populations. PMID:23847126
Sexual segregation in North American elk: the role of density dependence
Stewart, Kelley M; Walsh, Danielle R; Kie, John G; Dick, Brian L; Bowyer, R Terry
2015-01-01
We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 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
Lall, Upmanu; Devineni, Naresh; Kaheil, Yasir
2016-01-01
Multivariate simulations of a set of random variables are often needed for risk analysis. Given a historical data set, the goal is to develop simulations that reproduce the dependence structure in that data set so that the risk of potentially correlated factors can be evaluated. A nonparametric, copula-based simulation approach is developed and exemplified. It can be applied to multiple variables or to spatial fields with arbitrary dependence structures and marginal densities. The nonparametric simulator uses logspline density estimation in the univariate setting, together with a sampling strategy to reproduce dependence across variables or spatial instances, through a nonparametric numerical approximation of the underlying copula function. The multivariate data vectors are assumed to be independent and identically distributed. A synthetic example is provided to illustrate the method, followed by an application to the risk of livestock losses in Mongolia. PMID:26177987
Spatial, Temporal, and Density-Dependent Components of Habitat Quality for a Desert Owl
Flesch, Aaron D.; Hutto, Richard L.; van Leeuwen, Willem J. D.; Hartfield, Kyle; Jacobs, Sky
2015-01-01
Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches that consider habitat resources, stochastic factors, and conspecifics are necessary to accurately assess habitat quality. PMID:25786257
Spatial, temporal, and density-dependent components of habitat quality for a desert owl.
Flesch, Aaron D; Hutto, Richard L; van Leeuwen, Willem J D; Hartfield, Kyle; Jacobs, Sky
2015-01-01
Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches that consider habitat resources, stochastic factors, and conspecifics are necessary to accurately assess habitat quality. PMID:25786257
Role of prey and intraspecific density dependence on the population growth of an avian top predator
NASA Astrophysics Data System (ADS)
Fernandez-de-Simon, Javier; Díaz-Ruiz, Francisco; Cirilli, Francesca; Tortosa, Francisco S.; Villafuerte, Rafael; Ferreras, Pablo
2014-10-01
Exploring predator-prey systems in diverse ecosystems increases our knowledge about ecological processes. Predator population growth may be positive when conspecific density is low but predators also need areas with prey availability, associated with competition, which increases the risk of suffering losses but stabilises populations. We studied relationships between European rabbits Oryctolagus cuniculus (prey) and adult eagle owls Bubo bubo (predators) in south-western Europe. We assessed models explaining the predator population growth and stability. We estimated the abundance of rabbits and adult eagle owls during three years in eight localities of central-southern Spain. We explored models including rabbit and adult eagle owl abundance, accounting for yearly variations and including the locality as a random variable. We found that population growth of adult eagle owls was positive in situations with low conspecific abundance and tended to be negative but approaching equilibrium in situations of higher conspecific abundance. Population growth was also positively related to previous summer rabbit density when taking into account eagle owl conspecific abundance, possibly indicating that rabbits may support recruitment. Furthermore, abundance stability of adult eagle owls was positively related to previous winter-spring rabbit density, which could suggest predator population stabilisation through quick territory occupation in high-quality areas. These results exemplify the trade-off between prey availability and abundance of adult predators related to population growth and abundance stability in the eagle owl-rabbit system in south-western Europe. Despite rabbits have greatly declined during the last decades and eagle owls locally specialise on them, eagle owls currently have a favourable conservation status. As eagle owls are the only nocturnal raptor with such dependence on rabbits, this could point out that predators may overcome prey decreases in areas with favourable climate and prey in the absence of superior competitors with similar foraging mode.
Density-dependent habitat selection by brown-headed cowbirds (Molothrus ater) in tallgrass prairie
Jensen, W.E.; Cully, J.F., Jr.
2005-01-01
Local distributions of avian brood parasites among their host habitats may depend upon conspecific parasite density. We used isodar analysis to test for density-dependent habitat selection in brown-headed cowbirds (Molothrus ater) among tallgrass prairie adjacent to wooded edges, and prairie interior habitat (>100 m from wooded edges) with and without experimental perches. Eight study sites containing these three habitat treatments were established along a geographical gradient in cowbird abundance within the Flint Hills region of Eastern Kansas and Oklahoma, USA. The focal host species of our study, the dickcissel (Spiza americana), is the most abundant and preferred cowbird host in the prairie of this region. Cowbird relative abundance and cowbird:host abundance ratios were used as estimates of female cowbird density, whereas cowbird egg density was measured as parasitism frequency (percent of dickcissel nests parasitized), and parasitism intensity (number of cowbird eggs per parasitized nest). Geographical variation in cowbird abundance was independent of host abundance. Within study sites, host abundance was highest in wooded edge plots, intermediate in the experimental perch plots, and lowest in prairie interior. Cowbirds exhibited a pattern of density-dependent selection of prairie edge versus experimental perch and interior habitats. On sites where measures of cowbird density were lowest, all cowbird density estimates (female cowbirds and their eggs) were highest near (???100 m) wooded edges, where host and perch availability are highest. However, as overall cowbird density increased geographically, these density estimates increased more rapidly in experimental perch plots and prairie interiors. Variation in cowbird abundance and cowbird:host ratios suggested density-dependent cowbird selection of experimental perch over prairie interior habitat, but parasitism levels on dickcissel nests were similar among these two habitats at all levels of local cowbird parasitism. The density-dependent pattern of cowbird distribution among prairie edge and interior suggested that density effects on perceived cowbird fitness are greatest at wooded edges. A positive relationship between daily nest mortality rates of parasitized nests during the nestling period with parasitism intensity levels per nest suggested a density-dependent effect on cowbird reproductive success. However, this relationship was similar among habitats, such that all habitats should have been perceived as being equally suitable to cowbirds at all densities. Other unmeasured effects on cowbird habitat suitability (e.g., reduced cowbird success in edge-dwelling host nests, cowbird despotism at edges) might have affected cowbird habitat selection. Managers attempting to minimize cowbird parasitism on sensitive cowbird hosts should consider that hosts in otherwise less-preferred cowbird habitats (e.g., habitat interiors) are at greater risk of being parasitized where cowbirds become particularly abundant. ?? Springer-Verlag 2004.
Modeling the doubly excited state with time-dependent Hartree-Fock and density functional theories.
Isborn, Christine M; Li, Xiaosong
2008-11-28
Multielectron excited states have become a hot topic in many cutting-edge research fields, such as the photophysics of polyenes and in the possibility of multiexciton generation in quantum dots for the purpose of increasing solar cell efficiency. However, obtaining multielectron excited states has been a major obstacle as it is often done with multiconfigurational methods, which involve formidable computational cost for large systems. Although they are computationally much cheaper than multiconfigurational wave function based methods, linear response adiabatic time-dependent Hartree-Fock (TDHF) and density functional theory (TDDFT) are generally considered incapable of obtaining multielectron excited states. We have developed a real-time TDHF and adiabatic TDDFT approach that is beyond the perturbative regime. We show that TDHF/TDDFT is able to simultaneously excite two electrons from the ground state to the doubly excited state and that the real-time TDHF/TDDFT implicitly includes double excitation within a superposition state. We also present a multireference linear response theory to show that the real-time electron density response corresponds to a superposition of perturbative linear responses of the S(0) and S(2) states. As a result, the energy of the two-electron doubly excited state can be obtained with several different approaches. This is done within the adiabatic approximation of TDDFT, a realm in which the doubly excited state has been deemed missing. We report results on simple two-electron systems, including the energies and dipole moments for the two-electron excited states of H(2) and HeH(+). These results are compared to those obtained with the full configuration interaction method. PMID:19045852
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.
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.
Ross, Beth E; Hooten, Mevin B; DeVink, Jean-Michel; Koons, David N
2015-09-01
An understanding of species relationships is critical in the management and conservation of populations facing climate change, yet few studies address how climate alters species interactions and other population drivers. We use a long-term, broad-scale data set of relative abundance to examine the influence of climate, predators, and density dependence on the population dynamics of declining scaup (Aythya) species within the core of their breeding range. The state-space modeling approach we use applies to a wide range of wildlife species, especially populations monitored over broad spatiotemporal extents. Using this approach, we found that immediate snow cover extent in the preceding winter and spring had the strongest effects, with increases in mean snow cover extent having a positive effect on the local surveyed abundance of scaup. The direct effects of mesopredator abundance on scaup population dynamics were weaker, but the results still indicated a potentil interactive process between climate and food web dynamics (mesopredators, alternative prey, and scaup). By considering climate variables and other potential effects on population dynamics, and using a rigorous estimation framework, we provide insight into complex ecological processes for guiding. conservation and policy actions aimed at mitigating and reversing the decline of scaup. PMID:26552268
Density Dependence of Charge-4 Vortex Splitting in Bose–Einstein Condensates
NASA Astrophysics Data System (ADS)
Shibayama, Hitoshi; Tsukada, Akinori; Yoshihara, Takahisa; Kuwamoto, Takeshi
2016-05-01
We studied the axial-direction density dependence of the splitting of a charge-4 vortex created in 87Rb Bose–Einstein condensates. Vortices were generated by topological phase imprinting, and the axial density of the condensates was controlled by an optical potential. Linear and triangular arrangements of four single-charged vortices that emerged through the charge-4 vortex collapse were observed. The splitting of the charge-4 vortices was suppressed by maintaining the density outside the l = 2 unstable mode regions where linear arrangements were formed. In addition, we studied vortex dynamics in a high density region for which investigations have not been previously performed.
A coarse-grain force field for RDX: Density dependent and energy conserving
NASA Astrophysics Data System (ADS)
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Density-dependent immune responses against the gastrointestinal nematode Strongyloides ratti
Bleay, Colin; Wilkes, Clare P.; Paterson, Steve; Viney, Mark E.
2007-01-01
Negative density-dependent effects on the fitness of parasite populations are an important force in their population dynamics. For the parasitic nematode Strongyloides ratti, density-dependent fitness effects require the rat host immune response. By analysis of both measurements of components of parasite fitness and of the host immune response to different doses of S. ratti infection, we have identified specific parts of the host immune response underlying the negative density-dependent effects on the fitness of S. ratti. The host immune response changes both qualitatively from an inflammatory Th1- to a Th2-type immune profile and the Th2-type response increases quantitatively, as the density of S. ratti infection increases. Parasite survivorship was significantly negatively related to the concentration of parasite-specific IgG1 and IgA, whereas parasite fecundity was significantly negatively related to the concentration of IgA only. PMID:17597133
NASA Astrophysics Data System (ADS)
Erdinc, Ozgur; Willett, Peter; Bar-Shalom, Yaakov
2006-05-01
The probability hypothesis density (PHD) filter, an automatically track-managed multi-target tracker, is attracting increasing but cautious attention. Its derivation is elegant and mathematical, and thus of course many engineers fear it; perhaps that is currently limiting the number of researchers working on the subject. In this paper, we explore a physical-space approach - a bin model - which leads us to arrive the same filter equations as the PHD. Unlike the original derivation of the PHD filter, the concepts used are the familiar ones of conditional probability. The original PHD suffers from a "target-death" problem in which even a single missed detection can lead to the apparent disappearance of a target. To obviate this, PHD originator Mahler has recently developed a new "cardinalized" version of PHD (CPHD). We are able to extend our physical-space derivation to the CPHD case as well. We stress that the original derivations are mathematically correct, and need no embellishment from us; our contribution here is to offer an alternative derivation, one that we find appealing.
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.
Density-dependent effects on hatching success of the olive ridley turtle, Lepidochelys olivacea.
Honarvar, Shaya; O'Connor, Michael P; Spotila, James R
2008-08-01
Historically, the olive ridley arribada at Playa Nancite, Costa Rica, was one of the largest olive ridley arribadas in the eastern Pacific with 70,000 nesting females in a year. Recently the Nancite arribada drastically declined. We hypothesized that the population decline at Playa Nancite could have been due to low hatching success as a result of the high density of nests on the beach, such that recruitment to the population was insufficient to balance losses. To test this hypothesis, we examined density-dependent effects on hatching success and their underlying mechanisms by experimentally manipulating nest densities in experimental plots on the nesting beach. We set up four nest-density treatments in five experimental blocks. We measured effects of density on hatching success, CO(2) and O(2) concentrations and temperature both within nests and in sand adjacent to nests frequently during incubation. Experimental nest densities affected hatching success with the highest density having the lowest hatching success. Higher nest density led to lower O(2) levels and higher CO(2) levels in the nest with greater changes in the latter part of the incubation. Highest temperatures occurred in high-density areas. Temperatures were lower in sand surrounding the nest than in the nest. Effects of density on temperature, CO(2) and O(2) were confirmed at a naturally high-density nesting beach, Playa La Flor, Nicaragua. Long-term failure in production of hatchlings due to historic high densities may have contributed to the decline of arribadas on Playa Nancite. Thus, density-dependent population control would have operated at the embryonic life stage in this population of olive ridley turtles. PMID:18481091
Cascading effects of belowground predators on plant communities are density-dependent.
Thakur, Madhav Prakash; Herrmann, Martina; Steinauer, Katja; Rennoch, Saskia; Cesarz, Simone; Eisenhauer, Nico
2015-10-01
Soil food webs comprise a multitude of trophic interactions that can affect the composition and productivity of plant communities. Belowground predators feeding on microbial grazers like Collembola could decelerate nutrient mineralization by reducing microbial turnover in the soil, which in turn could negatively influence plant growth. However, empirical evidences for the ecological significance of belowground predators on nutrient cycling and plant communities are scarce. Here, we manipulated predator density (Hypoaspis aculeifer: predatory mite) with equal densities of three Collembola species as a prey in four functionally dissimilar plant communities in experimental microcosms: grass monoculture (Poa pratensis), herb monoculture (Rumex acetosa), legume monoculture (Trifolium pratense), and all three species as a mixed plant community. Density manipulation of predators allowed us to test for density-mediated effects of belowground predators on Collembola and lower trophic groups. We hypothesized that predator density will reduce Collembola population causing a decrease in nutrient mineralization and hence detrimentally affect plant growth. First, we found a density-dependent population change in predators, that is, an increase in low-density treatments, but a decrease in high-density treatments. Second, prey suppression was lower at high predator density, which caused a shift in the soil microbial community by increasing the fungal: bacterial biomass ratio, and an increase of nitrification rates, particularly in legume monocultures. Despite the increase in nutrient mineralization, legume monocultures performed worse at high predator density. Further, individual grass shoot biomass decreased in monocultures, while it increased in mixed plant communities with increasing predator density, which coincided with elevated soil N uptake by grasses. As a consequence, high predator density significantly increased plant complementarity effects indicating a decrease in interspecific plant competition. These results highlight that belowground predators can relax interspecific plant competition by increasing nutrient mineralization through their density-dependent cascading effects on detritivore and soil microbial communities. PMID:26664680
Spatially heterogeneous populations with mixed negative and positive local density dependence.
Knipl, Diána; Röst, Gergely
2016-06-01
Identifying the steady states of a population is a key issue in theoretical ecology, that includes the study of spatially heterogeneous populations. There are several examples of real ecosystems in patchy environments where the habitats are heterogeneous in their local density dependence. We investigate a multi-patch model of a single species with spatial dispersal, where the growth of the local population is logistic in some localities (negative density dependence) while other patches exhibit a strong Allee effect (positive density dependence). When the local dynamics is logistic in each patch and the habitats are interconnected by dispersal then the total population has only the extinction steady state and a componentwise positive equilibrium, corresponding to persistence in each patch. We show that animal populations in patchy environments can have a large number of steady states if local density dependence varies over the locations. It is demonstrated that, depending on the network topology of migration routes between the patches, the interaction of spatial dispersal and local density dependence can create a variety of coexisting stable positive equilibria. We give a detailed description of the multiple ways dispersal can rescue local populations from extinction. PMID:26801607
Representing the thermal state in time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Modine, N. A.; Hatcher, R. M.
2015-05-01
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble.
Representing the thermal state in time-dependent density functional theory.
Modine, N A; Hatcher, R M
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble. PMID:26026438
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wavefunctions are fixed by the initial state in TDDFT. We work to address this puzzle by (A) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (B) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble.
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.
Negative density dependence of seed dispersal and seedling recruitment in a neotropical palm.
Jansen, Patrick A; Visser, Marco D; Joseph Wright, S; Rutten, Gemma; Muller-Landau, Helene C
2014-09-01
Negative density dependence (NDD) of recruitment is pervasive in tropical tree species. We tested the hypotheses that seed dispersal is NDD, due to intraspecific competition for dispersers, and that this contributes to NDD of recruitment. We compared dispersal in the palm Attalea butyracea across a wide range of population density on Barro Colorado Island in Panama and assessed its consequences for seed distributions. We found that frugivore visitation, seed removal and dispersal distance all declined with population density of A. butyracea, demonstrating NDD of seed dispersal due to competition for dispersers. Furthermore, as population density increased, the distances of seeds from the nearest adult decreased, conspecific seed crowding increased and seedling recruitment success decreased, all patterns expected under poorer dispersal. Unexpectedly, however, our analyses showed that NDD of dispersal did not contribute substantially to these changes in the quality of the seed distribution; patterns with population density were dominated by effects due solely to increasing adult and seed density. PMID:25039608
A comprehensive approach for the assessment of in-situ pavement density using GPR technique
NASA Astrophysics Data System (ADS)
Plati, Christina; Georgiou, Panos; Loizos, Andreas
2013-04-01
Proper construction of the asphalt pavement is a prerequisite to developing a long lasting roadway that does not require extensive future maintenance. This goal is achieved by verifying that design specifications are met through the use of quality assurance (QA) practices. The in-situ density is regarded as one of the most important controls used to ensure that a pavement being placed is of high quality because it is a good indicator of future performance. In-situ density is frequently assessed utilizing one or more of the following three methods: cores, nuclear density gauge measurements or non-nuclear density gauge measurements. Each of the above mentioned methods, however, have their distinct disadvantages. Cores, for example, are generally considered to be the most accurate means of measuring in-situ density, however, they are a time consuming and destructive test that introduces a defect into asphalt pavements. Because of the destructive nature associated with coring, contractors and agencies have alternatively used non-destructive nuclear and non-nuclear density gauges for quality control purposes. These instruments allow for a more rapid assessment of the in-situ density, allowing measurements to be taken even during the pavement's construction. The disadvantage of these gauges are that they provide density readings only at discrete locations of the asphalt pavement mat, while no consensus exists among pavement researchers on the proper correlation between the gauges and core density. In recent years, numerous alternative methods have been introduced for the assessment of in-situ density, both during asphalt pavement construction and afterwards. These methods include, amongst others, intelligent compaction, thermal imaging and ground penetrating radar (GPR). Among these methods, GPR has been defined as both a technically feasible and promising method for the nondestructive, rapid, and continuous evaluation of in-situ asphalt pavement density based on electromagnetic mixing (EM) theory, through the utilization of proper models. These models enable the prediction of asphalt mixture density dependent on its bulk dielectric constant as measured by the GPR, the dielectric properties of the asphalt mix materials, as well as other material information. The goal of the present study is to attempt to verify the prediction performance of various density models. To accomplish this goal GPR surveys were carried out in the field during asphalt pavement construction to evaluate the density results due to different compaction modes. The GPR data was analyzed to calculate the appropriate asphalt mix dielectric properties needed for the activation of the considered density prediction models. Predicted densities were compared with densities of the field cores extracted from the as-built asphalt pavement prior to trafficking. It was found that the predicted density values were significantly lower when compared to the ground truth data. A further investigation of the effect of temperature on GPR readings showed that GPR seems to overestimate the in-situ density. However, this approach could be used effectively to evaluate the performance of different compaction methods and set up the compaction pattern that is needed to achieve the desired asphalt pavement density.
Dependence of SOL Widths on Plasma Current and Density in NSTX H-mode Plasmas
Ahn, J W; Maingi, Rajesh; Boedo, J.; Soukhanovskii, V. A.
2009-01-01
The dependence of various SOL widths on the line-averaged density ((n) over bar (e)) and plasma current (I(p)) for the quiescent H-mode plasmas with Type-V ELMs in the National Spherical Torus Experiment (NSTX) was investigated. It is found that the heat flux SOL width (lambda(q)), measured by the IR camera, is virtually insensitive to (n) over bar (e) and has a strong negative dependence on I(p). This insensitivity of lambda(q) to (n) over bare is consistent with the scaling law from JET H-mode plasmas that shows a very weak dependence on the upstream density. The electron temperature, ion saturation current density, electron density, and electron pressure decay lengths (lambda(Te), lambda(jsat), lambda(ne), and lambda(pe), respectively) measured by the probe showed that lambda(Te) and lambda(jsat) have strong negative dependence on I(p), whereas lambda(ne) and lambda(pe) revealed only a little or no dependence. The dependence of lambda(Te) on I(p) is consistent with the scaling law in the literature, while lambda(ne) and lambda(pe) dependence shows a different trend. (C) 2009 Elsevier B.V. All rights reserved.
Dependence of various SOL widths on plasma current and density in NSTX H-mode plasmas
Ahn, J; Maingi, R; Boedo, J; Soukhanovskii, V A
2009-02-12
The dependence of various SOL widths on the line-averaged density ({ovr n}{sub e}) and plasma current (l{sub p}) for the quiescent H-mode plasmas with Type-V ELMs in the National Spherical Torus Experiment (NSTX) was investigated. It is found that the heat flux SOL width ({lambda}{sub q}), measured by the IR camera, is virtually insensitive to {ovr n}{sub e} and has a strong negative dependence on l{sub p}. This insensitivity of {lambda}{sub q} to {ovr n}{sub e} is consistent with the scaling law from JET H-mode plasmas that shows a very weak dependence on the upstream density. The electron temperature, ion saturation current density, electron density, and electron pressure decay lengths ({lambda}{sub Te}, {lambda}{sub jsat}, {lambda}{sub ne}, and {lambda}{sub pe}, respectively) measured by the probe showed that {lambda}{sub Te} and {lambda}{sub jsat} have strong negative dependence on l{sub p}, whereas {lambda}{sub ne} and {lambda}{sub pe} revealed only a little or no dependence. The dependence of {lambda}{sub Te} on l{sub p} is consistent with the scaling law in the literature while {lambda}{sub ne} and {lambda}{sub pe} dependence shows a different trend.
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.
NASA Astrophysics Data System (ADS)
Wang, RuLin; Zheng, Xiao; Kwok, YanHo; Xie, Hang; Chen, GuanHua; Yam, ChiYung
2015-04-01
Understanding electronic dynamics on material surfaces is fundamentally important for applications including nanoelectronics, inhomogeneous catalysis, and photovoltaics. Practical approaches based on time-dependent density functional theory for open systems have been developed to characterize the dissipative dynamics of electrons in bulk materials. The accuracy and reliability of such approaches depend critically on how the electronic structure and memory effects of surrounding material environment are accounted for. In this work, we develop a novel squared-Lorentzian decomposition scheme, which preserves the positive semi-definiteness of the environment spectral matrix. The resulting electronic dynamics is guaranteed to be both accurate and convergent even in the long-time limit. The long-time stability of electronic dynamics simulation is thus greatly improved within the current decomposition scheme. The validity and usefulness of our new approach are exemplified via two prototypical model systems: quasi-one-dimensional atomic chains and two-dimensional bilayer graphene.
Cubaynes, Sarah; MacNulty, Daniel R; Stahler, Daniel R; Quimby, Kira A; Smith, Douglas W; Coulson, Tim
2014-11-01
Understanding the population dynamics of top-predators is essential to assess their impact on ecosystems and to guide their management. Key to this understanding is identifying the mechanisms regulating vital rates. Determining the influence of density on survival is necessary to understand the extent to which human-caused mortality is compensatory or additive. In wolves (Canis lupus), empirical evidence for density-dependent survival is lacking. Dispersal is considered the principal way in which wolves adjust their numbers to prey supply or compensate for human exploitation. However, studies to date have primarily focused on exploited wolf populations, in which density-dependent mechanisms are likely weak due to artificially low wolf densities. Using 13 years of data on 280 collared wolves in Yellowstone National Park, we assessed the effect of wolf density, prey abundance and population structure, as well as winter severity, on age-specific survival in two areas (prey-rich vs. prey-poor) of the national park. We further analysed cause-specific mortality and explored the factors driving intraspecific aggression in the prey-rich northern area of the park. Overall, survival rates decreased during the study. In northern Yellowstone, density dependence regulated adult survival through an increase in intraspecific aggression, independent of prey availability. In the interior of the park, adult survival was less variable and density-independent, despite reduced prey availability. There was no effect of prey population structure in northern Yellowstone, or of winter severity in either area. Survival was similar among yearlings and adults, but lower for adults older than 6 years. Our results indicate that density-dependent intraspecific aggression is a major driver of adult wolf survival in northern Yellowstone, suggesting intrinsic density-dependent mechanisms have the potential to regulate wolf populations at high ungulate densities. When low prey availability or high removal rates maintain wolves at lower densities, limited inter-pack interactions may prevent density-dependent survival, consistent with our findings in the interior of the park. PMID:24749694
Investigations of turbulent scalar fields using probability density function approach
NASA Technical Reports Server (NTRS)
Gao, Feng
1991-01-01
Scalar fields undergoing random advection have attracted much attention from researchers in both the theoretical and practical sectors. Research interest spans from the study of the small scale structures of turbulent scalar fields to the modeling and simulations of turbulent reacting flows. The probability density function (PDF) method is an effective tool in the study of turbulent scalar fields, especially for those which involve chemical reactions. It has been argued that a one-point, joint PDF approach is the one to choose from among many simulation and closure methods for turbulent combustion and chemically reacting flows based on its practical feasibility in the foreseeable future for multiple reactants. Instead of the multi-point PDF, the joint PDF of a scalar and its gradient which represents the roles of both scalar and scalar diffusion is introduced. A proper closure model for the molecular diffusion term in the PDF equation is investigated. Another direction in this research is to study the mapping closure method that has been recently proposed to deal with the PDF's in turbulent fields. This method seems to have captured the physics correctly when applied to diffusion problems. However, if the turbulent stretching is included, the amplitude mapping has to be supplemented by either adjusting the parameters representing turbulent stretching at each time step or by introducing the coordinate mapping. This technique is still under development and seems to be quite promising. The final objective of this project is to understand some fundamental properties of the turbulent scalar fields and to develop practical numerical schemes that are capable of handling turbulent reacting flows.
A New Approach of Designing Superalloys for Low Density
NASA Technical Reports Server (NTRS)
MacKay, Rebecca A.; Gabb, Timothy P.; Smialek, James L.; Nathal, Michael V.
2010-01-01
New low-density single-crystal (LDS) alloy, have bee. developed for turbine blade applications, which have the potential for significant improvements in the thrust-to-weight ratio over current production superalloys. An innovative alloying strategy was wed to achieve alloy density reductions, high-temperature creep resistance, microstructural stability, and cyclic oxidation resistance. The alloy design relies on molybdenum as a potent. lower-density solid-solution strengthener in the nickel-based superalloy. Low alloy density was also achieved with modest rhenium levels tmd the absence of tungsten. Microstructural, physical mechanical, and environmental testing demonstrated the feasibility of this new LDS superalloy design.
Population dynamics of Norwegian red deer: density-dependence and climatic variation.
Forchhammer, M C; Stenseth, N C; Post, E; Langvatn, R
1998-01-01
We present a model on plant-deer climate interactions developed for improving our understanding of the temporal dynamics of deer abundance and, in particular, how intrinsic (density-dependent) and extrinsic (plants, climate) factors influence these dynamics. The model was tested statistically by analysing the dynamics of five Norwegian red deer populations between 1964 and 1993. Direct and delayed density-dependence significantly influenced the development of the populations: delayed density-dependence primarily operated through female density, whereas direct density-dependence acted through both female and male densities. Furthermore, population dynamics of Norwegian red deer were significantly affected by climate (as measured by the global weather phenomenon, the North Atlantic Oscillation: NAO). Warm, snowy winters (high NAO) were associated with decreased deer abundance, whereas the delayed (two-year) effect of warm, snowy winters had a positive effect on deer abundance. Our analyses are argued to have profound implications for the general understanding of climate change and terrestrial ecosystem functioning. PMID:9523435
Electronic excitations: density-functional versus many-body Green's-function approaches
NASA Astrophysics Data System (ADS)
Onida, Giovanni; Reining, Lucia; Rubio, Angel
2002-04-01
Electronic excitations lie at the origin of most of the commonly measured spectra. However, the first-principles computation of excited states requires a larger effort than ground-state calculations, which can be very efficiently carried out within density-functional theory. On the other hand, two theoretical and computational tools have come to prominence for the description of electronic excitations. One of them, many-body perturbation theory, is based on a set of Green's-function equations, starting with a one-electron propagator and considering the electron-hole Green's function for the response. Key ingredients are the electron's self-energy Σ and the electron-hole interaction. A good approximation for Σ is obtained with Hedin's GW approach, using density-functional theory as a zero-order solution. First-principles GW calculations for real systems have been successfully carried out since the 1980s. Similarly, the electron-hole interaction is well described by the Bethe-Salpeter equation, via a functional derivative of Σ. An alternative approach to calculating electronic excitations is the time-dependent density-functional theory (TDDFT), which offers the important practical advantage of a dependence on density rather than on multivariable Green's functions. This approach leads to a screening equation similar to the Bethe-Salpeter one, but with a two-point, rather than a four-point, interaction kernel. At present, the simple adiabatic local-density approximation has given promising results for finite systems, but has significant deficiencies in the description of absorption spectra in solids, leading to wrong excitation energies, the absence of bound excitonic states, and appreciable distortions of the spectral line shapes. The search for improved TDDFT potentials and kernels is hence a subject of increasing interest. It can be addressed within the framework of many-body perturbation theory: in fact, both the Green's functions and the TDDFT approaches profit from mutual insight. This review compares the theoretical and practical aspects of the two approaches and their specific numerical implementations, and presents an overview of accomplishments and work in progress.
Adaptive nest clustering and density-dependent nest survival in dabbling ducks
Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.
2014-01-01
Density-dependent population regulation is observed in many taxa, and understanding the mechanisms that generate density dependence is especially important for the conservation of heavily-managed species. In one such system, North American waterfowl, density dependence is often observed at continental scales, and nest predation has long been implicated as a key factor driving this pattern. However, despite extensive research on this topic, it remains unclear if and how nest density influences predation rates. Part of this confusion may have arisen because previous studies have studied density-dependent predation at relatively large spatial and temporal scales. Because the spatial distribution of nests changes throughout the season, which potentially influences predator behavior, nest survival may vary through time at relatively small spatial scales. As such, density-dependent nest predation might be more detectable at a spatially- and temporally-refined scale and this may provide new insights into nest site selection and predator foraging behavior. Here, we used three years of data on nest survival of two species of waterfowl, mallards and gadwall, to more fully explore the relationship between local nest clustering and nest survival. Throughout the season, we found that the distribution of nests was consistently clustered at small spatial scales (˜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.
Density-dependent habitat selection and partitioning between two sympatric ungulates.
van Beest, Floris M; McLoughlin, Philip D; Vander Wal, Eric; Brook, Ryan K
2014-08-01
Theory on density-dependent habitat selection predicts that as population density of a species increases, use of higher quality (primary) habitat by individuals declines while use of lower quality (secondary) habitat rises. Habitat partitioning is often considered the primary mechanism for coexistence between similar species, but how this process evolves with changes in population density remains to be empirically tested for free-ranging ungulates. We used resource-selection functions to quantify density effects on landscape-scale habitat selection of two sympatric species of ungulates [moose (Alces alces) and elk (Cervus canadensis manitobensis)] in Riding Mountain National Park, Manitoba, Canada (2000-2011). The density of elk was actively reduced from 1.2 to 0.4 elk km(-2) through increased hunting effort during the period of study, while moose density decreased without additional human influence from 1.6-0.7 moose km(-2). Patterns of habitat selection during winter by both species changed in accordance to expectations from density-dependent habitat-selection theory. At low intraspecific density, moose and elk did not partition habitat, as both species selected strongly for mixed forest (primary habitat providing both food and cover), but did so in different areas segregated across an elevational gradient. As intraspecific density increased, selection for primary habitat by both species decreased, while selection for secondary, lower quality habitat such as agricultural fields (for elk) and built-up areas (for moose) increased. We show that habitat-selection strategies during winter for moose and elk, and subsequent effects on habitat partitioning, depend heavily on the position in state space (density) of both species. PMID:24913777
Yang Heping; Magilnick, Nathaniel; Xia Meng; Lu, Shelly C.
2008-01-15
Hepatocyte growth factor (HGF) is a potent hepatocyte mitogen that exerts opposing effects depending on cell density. Glutathione (GSH) is the main non-protein thiol in mammalian cells that modulates growth and apoptosis. We previously showed that GSH level is inversely related to cell density of hepatocytes and is positively related to growth. Our current work examined whether HGF can modulate GSH synthesis in a cell density-dependent manner and how GSH in turn influence HGF's effects. We found HGF treatment of H4IIE cells increased cell GSH levels only under subconfluent density. The increase in cell GSH under low density was due to increased transcription of GSH synthetic enzymes. This correlated with increased protein levels and nuclear binding activities of c-Jun, c-Fos, p65, p50, Nrf1 and Nrf2 to the promoter region of these genes. HGF acts as a mitogen in H4IIE cells under low cell density and protects against tumor necrosis factor {alpha} (TNF{alpha})-induced apoptosis by limiting JNK activation. However, HGF is pro-apoptotic under high cell density and exacerbates TNF{alpha}-induced apoptosis by potentiating JNK activation. The increase in cell GSH under low cell density allows HGF to exert its full mitogenic effect but is not necessary for its anti-apoptotic effect.
Predicting Fish Densities in Lotic Systems: a Simple Modeling Approach
Fish density models are essential tools for fish ecologists and fisheries managers. However, applying these models can be difficult because of high levels of model complexity and the large number of parameters that must be estimated. We designed a simple fish density model and te...
Sorption on deformable solids. Density functional theory approach.
Berim, Gersh O; Ruckenstein, Eli
2011-11-17
A modified density functional theory is proposed to describe fluid adsorption and absorption by a solid, the density of which is nonhomogeneous near the interface. The density distribution of the solid is not provided by apriori assumptions, but is obtained via the minimization of an appropriate thermodynamic potential. The theory considers a mixture of two components in a slitlike pore. One of them, the fluid, is in contact with a reservoir containing the same kind of molecules and can be described through a grand canonical ensemble. The other component has strong interactions between its molecules. As a consequence, it forms a solid in the slit which can be treated as a canonical ensemble of a fixed number of molecules. The theory predicts both an intrinsic (in the absence of fluid) change in the solid density near the interface and a solid density variation as the fluid density in the reservoir is changed. In addition, it reveals that the oscillations that occur in the fluid density when the solid density is uniform are damped by the nonuniform solid. The theory provides the amounts of fluid adsorbed as well as absorbed by the solid. PMID:21985615
Nowicki, Piotr; Bonelli, Simona; Barbero, Francesca; Balletto, Emilio
2009-08-01
The relative contribution of density-dependent regulation and environmental stochasticity to the temporal dynamics of animal populations is one of the central issues of ecology. In insects, the primary role of the latter factor, typically represented by weather patterns, is widely accepted. We have evaluated the impact of density dependence as well as density-independent factors, including weather and mowing regime, on annual fluctuations of butterfly populations. As model species, we used Maculinea alcon and M. teleius living in sympatry and, consequently, we also analysed the effect of their potential competition. Density dependence alone explained 62 and 42% of the variation in the year-to-year trends of M. alcon and M. teleius, respectively. The cumulative Akaike weight of models with density dependence, which can be interpreted as the probability that this factor should be contained in the most appropriate population dynamics model, exceeded 0.97 for both species. In contrast, the impacts of inter-specific competition, mowing regime and weather were much weaker, with their cumulative weights being in the range of 0.08-0.21; in addition, each of these factors explained only 2-5% of additional variation in Maculinea population trends. Our results provide strong evidence for density-dependent regulation in Maculinea, while the influence of environmental stochasticity is rather minor. In the light of several recent studies on other butterflies that detected significant density-dependent effects, it would appear that density-dependent regulation may be more widespread in this group than previously thought, while the role of environmental stochasticity has probably been overestimated. We suggest that this misconception is the result of deficiencies in the design of most butterfly population studies in the past, including (1) a strong focus on adults and a neglect of the larval stage in which density-dependent effects are most likely to occur; (2) an almost exclusive reliance on transect count results that may confound the impact of environmental stochasticity on butterfly numbers with its impact on adult longevity. PMID:19484269
Stochastic models of classical particle pumps : Density dependence of directed current
NASA Astrophysics Data System (ADS)
Chaudhuri, Debasish
2015-09-01
We present and compare different versions of a simple particle pump-model that describes average directed current of repulsively interacting particles in a narrow channel, due to time-varying local potentials. We analyze the model on discrete lattice with particle exclusion, using three choices of potential-dependent hopping rates that obey microscopic reversibility. Treating the strength of the external potential as a small parameter with respect to thermal energy, we present a perturbative calculation to obtain the expression for average directed current. This depends on driving frequency, phase, and particle density. The directed current vanishes as density goes to zero or close packing. For two choices of hopping rates, it reaches maximum at intermediate densities, while for a third choice, it shows a curious current reversal with increasing density. This can be interpreted in terms of a particle-hole symmetry. Stochastic simulations of the model show good agreement with our analytic predictions.
Exposing extinction risk analysis to pathogens: Is disease just another form of density dependence?
Gerber, L.R.; McCallum, H.; Lafferty, K.D.; Sabo, J.L.; Dobson, A.
2005-01-01
In the United States and several other countries, the development of population viability analyses (PVA) is a legal requirement of any species survival plan developed for threatened and endangered species. Despite the importance of pathogens in natural populations, little attention has been given to host-pathogen dynamics in PVA. To study the effect of infectious pathogens on extinction risk estimates generated from PVA, we review and synthesize the relevance of host-pathogen dynamics in analyses of extinction risk. We then develop a stochastic, density-dependent host-parasite model to investigate the effects of disease on the persistence of endangered populations. We show that this model converges on a Ricker model of density dependence under a suite of limiting assumptions, including a high probability that epidemics will arrive and occur. Using this modeling framework, we then quantify: (1) dynamic differences between time series generated by disease and Ricker processes with the same parameters; (2) observed probabilities of quasi-extinction for populations exposed to disease or self-limitation; and (3) bias in probabilities of quasi-extinction estimated by density-independent PVAs when populations experience either form of density dependence. Our results suggest two generalities about the relationships among disease, PVA, and the management of endangered species. First, disease more strongly increases variability in host abundance and, thus, the probability of quasi-extinction, than does self-limitation. This result stems from the fact that the effects and the probability of occurrence of disease are both density dependent. Second, estimates of quasi-extinction are more often overly optimistic for populations experiencing disease than for those subject to self-limitation. Thus, although the results of density-independent PVAs may be relatively robust to some particular assumptions about density dependence, they are less robust when endangered populations are known to be susceptible to disease. If potential management actions involve manipulating pathogens, then it may be useful to model disease explicitly. ?? 2005 by the Ecological Society of America.
A Simplified Approach to the Density Functional Theory of Molecules
NASA Astrophysics Data System (ADS)
Kollmar, Christian
1999-02-01
A simplified molecular orbital (MO) formalism based on density functional theory is developed. Starting from the same energy expression as Kohn-Sham theory the electronic density is expanded in terms of atomic mono-center densities. Application of the variational principle leads to a secular matrix with a particularly transparent structure which allows the definition of a resonance integral taking into account the effect of interference in a natural way. The construction of the secular matrix scales formally as N2 instead of N3 in the Kohn-Sham formalism with N being the dimension of the atomic orbital (AO) basis set.
Time-dependent first-principles approaches to PV materials
Miyamoto, Yoshiyuki
2013-12-10
Computational scheme for designing photovoltaic (PV) materials is presented. First-principles electron dynamics of photo-excitation and subsequent electron-hole splitting is performed based on the time-dependent density functional theory. Photo-induced enhancement of dipole moment was observed in a polar crystal and a donor-acceptor molecular pair. These experiences will pave a way to design PV material from first-principles simulations.
Steele, Mark A.; Forrester, Graham E.
2005-01-01
Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats. PMID:16150721
Steele, Mark A; Forrester, Graham E
2005-09-20
Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats. PMID:16150721
Explaining the dark energy, baryon and dark matter coincidence via domain-dependent random densities
McDonald, John
2013-05-01
The dark energy, dark matter and baryon densities in the Universe are observed to be similar, with a factor of no more than 20 between the largest and smallest densities. We show that this coincidence can be understood via superhorizon domains of randomly varying densities when the baryon density at initial collapse of galaxy-forming perturbations is determined by anthropic selection. The baryon and dark matter densities are assumed to be dependent on random variables θ{sub d} and θ{sub b} according to ρ{sub dm}∝θ{sub d}{sup α} and ρ{sub b}∝θ{sub b}{sup β}, while the effectively constant dark energy density is dependent upon a random variable φ{sub Q} according to ρ{sub Q}∝φ{sub Q}{sup n}. The ratio of the baryon density to the dark energy density at initial collapse, r{sub Q}, and the baryon-to-dark matter ratio, r, are then determined purely statistically, with no dependence on the anthropically-preferred baryon density. We compute the probability distribution for r{sub Q} and r and show that the observed values of r{sub Q} and r can be naturally understood within this framework. In particular, for the case α = 2, β = 1 and n = 4, which can be physically realized via a combination of axion dark matter, Affleck-Dine baryogenesis and frozen quintessence with a φ{sub Q}{sup 4} potential, the range of r{sub Q} and r which corresponds to the observed Universe is a quite natural, with a probability which is broadly similar to other ranges of r{sub Q} and r.
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
Lonely hearts or sex in the city? Density-dependent effects in mating systems
Kokko, Hanna; Rankin, Daniel J
2006-01-01
Two very basic ideas in sexual selection are heavily influenced by numbers of potential mates: the evolution of anisogamy, leading to sex role differentiation, and the frequency dependence of reproductive success that tends to equalize primary sex ratios. However, being explicit about the numbers of potential mates is not typical to most evolutionary theory of sexual selection. Here, we argue that this may prevent us from finding the appropriate ecological equilibria that determine the evolutionary endpoints of selection. We review both theoretical and empirical advances on how population density may influence aspects of mating systems such as intrasexual competition, female choice or resistance, and parental care. Density can have strong effects on selective pressures, whether or not there is phenotypic plasticity in individual strategies with respect to density. Mating skew may either increase or decrease with density, which may be aided or counteracted by changes in female behaviour. Switchpoints between alternative mating strategies can be density dependent, and mate encounter rates may influence mate choice (including mutual mate choice), multiple mating, female resistance to male mating attempts, mate searching, mate guarding, parental care, and the probability of divorce. Considering density-dependent selection may be essential for understanding how populations can persist at all despite sexual conflict, but simple models seem to fail to predict the diversity of observed responses in nature. This highlights the importance of considering the interaction between mating systems and population dynamics, and we strongly encourage further work in this area. PMID:16612890
Temperature and density dependence of XANES spectra in warm dense aluminum plasmas
Recoules, V.; Mazevet, S.
2009-08-01
Using ab initio molecular-dynamics simulations combined with linear-response theory, we calculate the density and temperature dependence of the x-ray absorption near-edge structure (XANES) of a dense aluminum plasma. At solid density and for temperatures increasing up to 6 eV, we see that the XANES spectrum loses its well-known room-temperature structure, first due to melting and second due to loss of correlation in the liquid. Similarly, as the density decreases and the system evolves from a liquid to a plasma, the XANES spectrum becomes less structured. As the density is further lowered and the system turns into an atomic fluid, a pre-edge forms as the 3p state becomes bound. We suggest that direct measurements of the XANES spectra in this density region is a unique opportunity to validate pressure ionization models routinely used in plasma physics modeling.
A novel approach to evaluating breast density using ultrasound tomography
NASA Astrophysics Data System (ADS)
Glide, Carri K.
2007-12-01
Women with high mammographic breast density have a 4- to 5-fold increased breast cancer risk compared to women with fatty breasts. Current breast density estimation involves mammography, although a mammogram is a 2-D projection which does not provide an accurate volumetric density estimate due to breast thickness not being taken into account. Presumably, breast cancer risk would have a stronger relationship to the volume of dense tissue as opposed to projected area. The purpose of this work was to investigate the feasibility of assessing breast density with ultrasound tomography. First, we evaluated a breast-mimicking phantom, and sound speed measurements were well-correlated with mass density and CT number of the phantom material. Approximately 40 m/s difference in sound speed was observed between fatty and fibroglandular components, a critical result for breast density characterization. Next, we investigated the extension of our results in vivo for a sample of ˜100 patients. We observed significant differences in global sound speed between every BI-RADS compositional category, showing that our technique was consistent with the current standard of care. A strong, positive association was revealed between breast sound speed and quantitative mammographic percent density (MPD). We also assessed volumetric ultrasound percent density (USPD) using sound speed tomograms. The USPD results were also consistent with BI-RADS Categories. Further, an increase in USPD was observed with increased MPD for both mammographic views. Next, we introduced texture analysis, and moderate negative associations between sound speed skewness and MPD, and fractal dimension and MPD, were observed. This work suggests that non-invasive and non-ionizing evaluation of breast density is achievable, and global sound speed and USPD appear to be the most promising indicators of breast density. These applications may play an integral role in monitoring treatment, tracking chemoprevention response, and identifying high-risk patients. Overall, potential benefits of quantifying a relationship between acoustical properties and breast density introduce a novel application of clinical ultrasound, one that be significant in breast cancer risk assessment.
Jiang Weizhou
2010-04-15
Effects of the density dependence of the nuclear symmetry energy on ground-state properties of superheavy nuclei are studied in the relativistic mean-field theory. It is found that the softening of the symmetry energy plays an important role in the empirical shift [Phys. Rev. C 67, 024309 (2003)] of spherical orbitals in superheavy nuclei. The calculation based on the relativistic mean-field models NL3 and FSUGold supports the double shell closure in {sup 292}120 with the softening of the symmetry energy. In addition, the significant effect of the density dependence of the symmetry energy on the neutron skin thickness in superheavy nuclei is investigated.
Density-dependent nucleon-nucleon interaction from Urbana UIX three-nucleon force
NASA Astrophysics Data System (ADS)
Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Illarionov, Alexey Yu; Schmidt, Kevin E.
2011-12-01
A density-dependent two-nucleon potential has been derived within the formalism of correlated basis function. The effects of three-particle interactions has been included by integrating out the degrees of freedom of the third nucleon. The potential can be easily employed in nuclear matter calculations. It yields results in agreement with those obtained from the underlying three-body potential. Using the density dependent potential, we have carried out a study of the effects of three-nucleon interactions in symmetric nuclear matter within the Auxiliary Field Diffusion Monte Carlo (AFDMC) computational scheme.
NASA Technical Reports Server (NTRS)
Chen, A.-B.; Weisz, G.; Sher, A.
1972-01-01
A model calculation of the temperature dependence of the electronic density of states and the electrical conductivity of disordered binary alloys, based on the coherent-potential approximation is made by introducing thermal disorder in the single-band model (Velicky and others). Thermal disorder is found to broaden and smear the static-alloy density of states. The electrical resistivity in weak-scattering alloys always increases with temperature. However, in the strong-scattering case, the temperature coefficient of resistivity can be positive, zero, or negative, depending on the location of the Fermi energy.-
Growth rate dependent trap density in polythiophene-fullerene solar cells and its implications
NASA Astrophysics Data System (ADS)
Nalwa, Kanwar S.; Mahadevapuram, Rakesh C.; Chaudhary, Sumit
2011-02-01
To understand the effect of processing conditions such as spin coating speed and drying rate on the density of defects; poly(3-hexylthiophene):fullerene-derivative solar cells A, B, and C were fabricated with solvent drying times of ˜40 min, 7 min, and 1 min, respectively. We show that slowest grown device A has one order of magnitude less subband gap traps than device C. The open circuit voltage and its light intensity dependence was strongly affected by interfacial recombination of carriers at subgap defect states. The losses due to trap-assisted recombination can even dominate over bimolecular recombination, depending on the density of defect states
NASA Astrophysics Data System (ADS)
Franco de Carvalho, F.; Tavernelli, I.
2015-12-01
In this work, we derive a method to perform trajectory-based nonadiabatic dynamics that is able to describe both nonadiabatic transitions and intersystem crossing events (transitions between states of different spin-multiplicity) at the same level of theory, namely, time-dependent density functional theory (TDDFT). To this end, we combined our previously developed TDDFT-based trajectory surface hopping scheme with an accurate and efficient algorithm for the calculation of the spin-orbit coupling (SOC) matrix elements. More specifically, we designed two algorithms for the calculation of intersystem crossing transitions, one based on an extended Tully's surface hopping scheme including SOC and the second based on a Landau-Zener approximation applied to the spin sector of the electronic Hilbert space. This development allows for the design of an efficient on-the-fly nonadiabatic approach that can handle, on an equal footing, nonadiabatic and intersystem crossing transitions. The method is applied to the study of the photophysics of sulfur dioxide (SO2) in gas and liquid phases.
NASA Astrophysics Data System (ADS)
Zoia, Andrea; Latrille, Christelle; Beccantini, Alberto; Cartadale, Alain
2009-10-01
We investigate the spatial and temporal features of variable-density contaminant plumes migration in porous materials. Our analysis is supported by novel experimental results concerning concentration profiles inside a vertical column setup that has been conceived at CEA to this aim. The experimental method relies on X-ray spectrometry, which allows determining solute profiles as a function of time at several positions along the column. The salient outcomes of the measurements are elucidated, with focus on miscible fluids in homogeneous saturated media. The role of the injected solution molarity is evidenced. As molarity increases, the solutes plume transport progressively deviates from the usual Fickian behavior, and pollutants distribution becomes skewed in the direction dictated by gravity. By resorting to a finite elements approach, we numerically solve the nonlinear equations that rule the pollutants migration: a good agreement is found between the simulated profiles and the experimental data. At high molarity, a strong dependence on initial conditions is found. Finally, we qualitatively explore the (unstable) interfacial dynamics between the dense contaminant plume and the lighter resident fluid that saturates the column, and detail its evolution for finite-duration contaminant injections.
Prediction of Iron K-Edge Absorption Spectra Using Time-Dependent Density Functional Theory
George, S.DeBeer; Petrenko, T.; Neese, F.
2009-05-14
Iron K-edge X-ray absorption pre-edge features have been calculated using a time-dependent density functional approach. The influence of functional, solvation, and relativistic effects on the calculated energies and intensities has been examined by correlation of the calculated parameters to experimental data on a series of 10 iron model complexes, which span a range of high-spin and low-spin ferrous and ferric complexes in O{sub h} to T{sub d} geometries. Both quadrupole and dipole contributions to the spectra have been calculated. We find that good agreement between theory and experiment is obtained by using the BP86 functional with the CP(PPP) basis set on the Fe and TZVP one of the remaining atoms. Inclusion of solvation yields a small improvement in the calculated energies. However, the inclusion of scalar relativistic effects did not yield any improved correlation with experiment. The use of these methods to uniquely assign individual spectral transitions and to examine experimental contributions to backbonding is discussed.
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.
Density dependence in group dynamics of a highly social mongoose, Suricata suricatta.
Bateman, Andrew W; Ozgul, Arpat; Coulson, Tim; Clutton-Brock, Tim H
2012-05-01
1.?For social species, the link between individual behaviour and population dynamics is mediated by group-level demography. 2.?Populations of obligate cooperative breeders are structured into social groups, which may be subject to inverse density dependence (Allee effects) that result from a dependence on conspecific helpers, but evidence for population-wide Allee effects is rare. 3.?We use field data from a long-term study of cooperative meerkats (Suricata suricatta; Schreber, 1776) - a species for which local Allee effects are not reflected in population-level dynamics - to empirically model interannual group dynamics. 4.?Using phenomenological population models, modified to incorporate environmental conditions and potential Allee effects, we first investigate overall patterns of group dynamics and find support only for conventional density dependence that increases after years of low rainfall. 5.?To explain the observed patterns, we examine specific demographic rates and assess their contributions to overall group dynamics. Although per-capita meerkat mortality is subject to a component Allee effect, it contributes relatively little to observed variation in group dynamics, and other (conventionally density dependent) demographic rates - especially emigration - govern group dynamics. 6.?Our findings highlight the need to consider demographic processes and density dependence in subpopulations before drawing conclusions about how behaviour affects population processes in socially complex systems. PMID:22117843
Structural Implications of Reciprocal Exchange: A Power-Dependence Approach
ERIC Educational Resources Information Center
Bonacich, Phillip; Bienenstock, Elisa Jayne
2009-01-01
This paper presents and tests a general model to predict emergent exchange patterns and power differences in reciprocal exchange networks when individual actors follow the norm of reciprocity. With an interesting qualification, the experimental results reported here support the power-dependence approach (Emerson 1972a, b): those who acquire the…
NASA Astrophysics Data System (ADS)
Davari, Nazanin; Åstrand, Per-Olof; Unge, Mikael
2015-02-01
A recent method based on constrained density functional theory (CDFT) has been used to calculate the field-dependent ionization potential by determining the dissociation barrier for the interaction between a cation and an electron in an electric field. In the CDFT model, we rely on that the barrier is located somewhere outside the cation, which has limited the applicability for polyaromatic molecules where the barrier is located closer to the cation than for other molecules. Different density functionals, basis sets and choices of constraints in the CDFT calculations are tested for benzene as a case study. The field-dependent ionization potential calculated by constraining the charge with the B3LYP functional and the cc-pVDZ basis set shows a good agreement with our previous work and has a low computational cost for the larger aromatic molecules included here. In addition, field-dependent excitation energies are investigated using time-dependent DFT.
NASA Astrophysics Data System (ADS)
Chizhov, Anton V.; Graham, Lyle J.
2007-01-01
We propose a macroscopic approach toward realistic simulations of the population activity of hippocampal pyramidal neurons, based on the known refractory density equation with a different hazard function and on a different single-neuron threshold model. The threshold model is a conductance-based model taking into account adaptation-providing currents, which is reduced by omitting the fast sodium current and instead using an explicit threshold criterion for action potential events. Compared to the full pyramidal neuron model, the threshold model well approximates spike-time moments, postspike refractory states, and postsynaptic current integration. The dynamics of a neural population continuum are described by a set of one-dimensional partial differential equations in terms of the distributions of the refractory density (where the refractory state is defined by the time elapsed since the last action potential), the membrane potential, and the gating variables of the voltage-dependent channels, across the entire population. As the source term in the density equation, the probability density of firing, or hazard function, is derived from the Fokker-Planck (FP) equation, assuming that a single neuron is governed by a deterministic average-across-population input and a noise term. A self-similar solution of the FP equation in the subthreshold regime is obtained. Responses of the ensemble to stimulation by a current step and oscillating current are simulated and compared with individual neuron simulations. An example of interictal-like activity of a population of all-to-all connected excitatory neurons is presented.
Density-Dependent Natal Dispersal Patterns in a Leopard Population Recovering from Over-Harvest
Fattebert, Julien; Balme, Guy; Dickerson, Tristan; Slotow, Rob; Hunter, Luke
2015-01-01
Natal dispersal enables population connectivity, gene flow and metapopulation dynamics. In polygynous mammals, dispersal is typically male-biased. Classically, the ‘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 leopard populations over a larger landscape. PMID:25875293
Schrader, Matthew; Jarrett, Benjamin J M; Kilner, Rebecca M
2015-01-01
Studies of siblings have focused mainly on their competitive interactions and to a lesser extent on their cooperation. However, competition and cooperation are at opposite ends on a continuum of possible interactions and the nature of these interactions may be flexible with ecological factors tipping the balance toward competition in some environments and cooperation in others. Here we show that the presence of parental care and the density of larvae on the breeding carcass change the outcome of sibling interactions in burying beetle broods. With full parental care there was a strong negative relationship between larval density and larval mass, consistent with sibling competition for resources. In the absence of care, initial increases in larval density had beneficial effects on larval mass but further increases in larval density reduced larval mass. This likely reflects a density-dependent shift between cooperation and competition. In a second experiment, we manipulated larval density and removed parental care. We found that the ability of larvae to penetrate the breeding carcass increased with larval density and that feeding within the carcass resulted in heavier larvae than feeding outside the carcass. However, larval density did not influence carcass decay. PMID:25648525
Equation of state of dense matter from a density dependent relativistic mean field model
NASA Astrophysics Data System (ADS)
Shen, G.; Horowitz, C. J.; Teige, S.
2010-07-01
We calculate the equation of state (EOS) of dense matter using a relativistic mean field (RMF) model with a density dependent coupling that is a slightly modified form of the original NL3 interaction. For nonuniform nuclear matter we approximate the unit lattice as a spherical Wigner-Seitz cell, wherein the meson mean fields and nucleon Dirac wave functions are solved fully self-consistently. We also calculate uniform nuclear matter for a wide range of temperatures, densities, and proton fractions, and match them to nonuniform matter as the density decreases. The calculations took over 6000 CPU days in Indiana University’s supercomputer clusters. We tabulate the resulting EOS at over 107,000 grid points in the proton fraction range YP=0 to 0.56. For the temperature range T=0.16 to 15.8 MeV, we cover the density range nB=10-4 to 1.6 fm-3; and for the higher temperature range T=15.8 to 80 MeV, we cover the larger density range nB=10-8 to 1.6 fm-3. In the future we plan to study low density, low temperature (T<15.8 MeV), nuclear matter using a Virial expansion, and we will match the low-density and high-density results to generate a complete EOS table for use in astrophysical simulations of supernova and neutron star mergers.
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.
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
Sjödin, Henrik; Brännström, Ke; Söderquist, Mårten; Englund, Göran
2014-02-01
In this paper we elucidate how small-scale movements, such as those associated with searching for food and avoiding predators, affect the stability of predator-prey dynamics. We investigate an individual-based Lotka-Volterra model with density-dependent movement, in which the predator and prey populations live in a very large number of coupled patches. The rates at which individuals leave patches depend on the local densities of heterospecifics, giving rise to one reaction norm for each of the two species. Movement rates are assumed to be much faster than demographics rates. A spatial structure of predators and prey emerges which affects the global population dynamics. We derive a criterion which reveals how demographic stability depends on the relationships between the per capita covariance and densities of predators and prey. Specifically, we establish that a positive relationship with prey density and a negative relationship with predator density tend to be stabilizing. On a more mechanistic level we show how these relationships are linked to the movement reaction norms of predators and prey. Numerical results show that these findings hold both for local and global movements, i.e., both when migration is biased towards neighbouring patches and when all patches are reached with equal probability. PMID:24060621
Koons, David N; Colchero, Fernando; Hersey, Kent; Gimenez, Olivier
2015-06-01
Understanding the relative effects of climate, harvest, and density dependence on population dynamics is critical for guiding sound population management, especially for ungulates in arid and semiarid environments experiencing climate change. To address these issues for bison in southern Utah, USA, we applied a Bayesian state-space model to a 72-yr time series of abundance counts. While accounting for known harvest (as well as live removal) from the population, we found that the bison population in southern Utah exhibited a strong potential to grow from low density (β0 = 0.26; Bayesian credible interval based on 95% of the highest posterior density [BCI] = 0.19-0.33), and weak but statistically significant density dependence (β1 = -0.02, BCI = -0.04 to -0.004). Early spring temperatures also had strong positive effects on population growth (Pfat1 = 0.09, BCI = 0.04-0.14), much more so than precipitation and other temperature-related variables (model weight > three times more than that for other climate variables). Although we hypothesized that harvest is the primary driving force of bison population dynamics in southern Utah, our elasticity analysis indicated that changes in early spring temperature could have a greater relative effect on equilibrium abundance than either harvest or. the strength of density dependence. Our findings highlight the utility of incorporating elasticity analyses into state-space population models, and the need to include climatic processes in wildlife management policies and planning. PMID:26465036
Le Galliard, J-F; Paquet, M; Mugabo, M
2015-05-01
Temperament traits are seen in many animal species, and recent evolutionary models predict that they could be maintained by heterogeneous selection. We tested this prediction by examining density-dependent selection in juvenile common lizards Zootoca vivipara scored for activity, boldness and sociability at birth and at the age of 1 year. We measured three key life-history traits (juvenile survival, body growth rate and reproduction) and quantified selection in experimental populations at five density levels ranging from low to high values. We observed consistent individual differences for all behaviours on the short term, but only for activity and one boldness measure across the first year of life. At low density, growth selection favoured more sociable lizards, whereas viability selection favoured less active individuals. A significant negative correlational selection on activity and boldness existed for body growth rate irrespective of density. Thus, behavioural traits were characterized by limited ontogenic consistency, and natural selection was heterogeneous between density treatments and fitness traits. This confirms that density-dependent selection plays an important role in the maintenance of individual differences in exploration-activity and sociability. PMID:25865798
Density dependent state space model for population abundance data with unequal time intervals
Dennis, Brian; Ponciano, José Miguel
2014-01-01
The Gompertz state-space (GSS) model is a stochastic model for analyzing time series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise and observation error. PMID:25230459
Density-dependent state-space model for population-abundance data with unequal time intervals.
Dennis, Brian; Ponciano, José Miguel
2014-08-01
The Gompertz state-space (GSS) model is a stochastic model for analyzing time-series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise, and observation error. PMID:25230459
DENSITY-DEPENDENT FLOW IN ONE-DIMENSIONAL VARIABLY-SATURATED MEDIA
A one-dimensional finite element is developed to simulate density-dependent flow of saltwater in variably saturated media. The flow and solute equations were solved in a coupled mode (iterative), in a partially coupled mode (non-iterative), and in a completely decoupled mode. P...
A mass-dependent density profile for dark matter haloes including the influence of galaxy formation
NASA Astrophysics Data System (ADS)
Di Cintio, Arianna; Brook, Chris B.; Dutton, Aaron A.; Macciò, Andrea V.; Stinson, Greg S.; Knebe, Alexander
2014-07-01
We introduce a mass-dependent density profile to describe the distribution of dark matter within galaxies, which takes into account the stellar-to-halo mass dependence of the response of dark matter to baryonic processes. The study is based on the analysis of hydrodynamically simulated galaxies from dwarf to Milky Way mass, drawn from the Making Galaxies In a Cosmological Context project, which have been shown to match a wide range of disc scaling relationships. We find that the best-fitting parameters of a generic double power-law density profile vary in a systematic manner that depends on the stellar-to-halo mass ratio of each galaxy. Thus, the quantity M⋆/Mhalo constrains the inner (γ) and outer (β) slopes of dark matter density, and the sharpness of transition between the slopes (α), reducing the number of free parameters of the model to two. Due to the tight relation between stellar mass and halo mass, either of these quantities is sufficient to describe the dark matter halo profile including the effects of baryons. The concentration of the haloes in the hydrodynamical simulations is consistent with N-body expectations up to Milky Way-mass galaxies, at which mass the haloes become twice as concentrated as compared with pure dark matter runs. This mass-dependent density profile can be directly applied to rotation curve data of observed galaxies and to semi-analytic galaxy formation models as a significant improvement over the commonly used NFW profile.
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…
DENSITY-DEPENDENT RESPONSES OF GRAY-TAILED VOLES TO MOWING
Voles (Microtus spp.) commonly inhabit forage crops and may cause excessive damage to these crops. owever, cover removal by mowing or haying may cause vole populations to decline. o determine if gray-tailed voles responded to mowing of alfalfa in a density-dependent manner, the a...
Density dependence of the symmetry energy from neutron skin thickness in finite nuclei
Vinas, X.; Centelles, M.; Roca-Maza, X.; Warda, M.
2012-10-20
The density dependence of the symmetry energy, characterized by the parameter L, is studied using information provided by the neutron skin thickness in finite nuclei. An estimate of L is obtained from experimental data of antiprotonic atoms. We also discuss the ability of parity violating electron scatering to obtain information about the neutron skin thickness in {sup 208}Pb.
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
NASA Astrophysics Data System (ADS)
Yamilov, A.; Petrenko, S.; Sarma, R.; Cao, H.
2016-03-01
The universal bimodal distribution of transmission eigenvalues in lossless diffusive systems underpins such celebrated phenomena as universal conductance fluctuations, quantum shot noise in condensed matter physics, and enhanced transmission in optics and acoustics. Here, we show that in the presence of absorption, the density of the transmission eigenvalues depends on the confinement geometry of the scattering media. Furthermore, in an asymmetric waveguide, the densities of the reflection and absorption eigenvalues also depend on the side from which the waves are incident. With increasing absorption, the density of absorption eigenvalues transforms from a single-peak to a double-peak function. Our findings open an additional avenue for coherent control of wave transmission, reflection, and absorption in random media.
Density-Dependent Selection Incorporating Intraspecific Competition. II. a Diploid Model
Asmussen, Marjorie A.
1983-01-01
A diploid model is introduced and analyzed in which intraspecific competition is incorporated within the context of density-regulated selection. It is assumed that each genotype has a unique carrying capacity corresponding to the equilibrium population size when only that type is present. Each genotypic fitness at a single diallelic autosomal locus is a decreasing function of a distinctive effective population size perceived as a result of intraspecific competition. The resulting fitnesses are both density and frequency dependent with selective advantage determined by a balance between genotypic carrying capacity and sensitivity to intraspecific competition. A major finding is that intergenotypic interactions may allow genetic variation to be more easily maintained than in the corresponding model of purely density-dependent selection. In addition, numerical study confirms the possible existence of multiple interior equilibria and that neither overdominance in fitness nor carrying capacity is necessary for stability. The magnitude of the equilibrium population size and optimization principles are also discussed. PMID:6832584
Alternative approaches to the calculation of nutrient density
Technology Transfer Automated Retrieval System (TEKTRAN)
Over thirty years ago researchers developed a variety of different methods for rating or measuring the nutritional quality of foods. Nutrient density as the initial concept emerged was most commonly defined as the ratio of the amount of nutrients in a food to the energy provided. The nutrient dens...
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...
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state by a time-dependent potential and then allowed to evolve freely in time while statistical data are captured from periodic snapshots of the system. For a variety of systems (e.g., many metals), the electrons reach an effective state of internal equilibrium due to electron-electron interactions on a time scale that is short compared to electron-phonon equilibration. During the initial time-evolution of such systems following electronic excitation, electron-phonon interactions should be negligible, and therefore, TDDFT should successfully capture the internal thermalization of the electrons. However, it is unclear how TDDFT represents the resulting thermal state. In particular, the thermal state is usually represented in quantum statistical mechanics as a mixed state, while the occupations of the TDDFT wave functions are fixed by the initial state in TDDFT. Two key questions involve (1) reformulating quantum statistical mechanics so that thermodynamic expectations can be obtained as an unweighted average over a set of many-body pure states and (2) constructing a family of non-interacting (single determinant) TDDFT states that approximate the required many-body states for the canonical ensemble. In Section II, we will address these questions by first demonstrating that thermodynamic expectations can be evaluated by averaging over certain many-body pure states, which we will call thermal states, and then constructing TDDFT states that approximate these thermal states. In Section III, we will present some numerical tests of the resulting theory, and in Section IV, we will summarize our main results and discuss some possible future directions for this work.
Representing the thermal state in time-dependent density functional theory
Modine, N. A.; Hatcher, R. M.
2015-05-28
Classical molecular dynamics (MD) provides a powerful and widely used approach to determining thermodynamic properties by integrating the classical equations of motion of a system of atoms. Time-Dependent Density Functional Theory (TDDFT) provides a powerful and increasingly useful approach to integrating the quantum equations of motion for a system of electrons. TDDFT efficiently captures the unitary evolution of a many-electron state by mapping the system into a fictitious non-interacting system. In analogy to MD, one could imagine obtaining the thermodynamic properties of an electronic system from a TDDFT simulation in which the electrons are excited from their ground state 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 expectations can be evaluated by averaging over certain many-body pure states, which we will call thermal states, and then constructing TDDFT states that approximate these thermal states. In Section III, we will present some numerical tests of the resulting theory, and in Section IV, we will summarize our main results and discuss some possible future directions for this work.« less
Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout.
Bassar, Ronald D; Letcher, Benjamin H; Nislow, Keith H; Whiteley, Andrew R
2016-02-01
Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) vs. density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type, and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change. PMID:26490737
Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout
Bassar, Ronald D.; Letcher, Benjamin H.; Nislow, Keith H.; Whiteley, Andrew R.
2016-01-01
Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) versus density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change.
UC/MALDI-MS analysis of HDL; evidence for density-dependent post-translational modifications
Johnson, Jeffery D.; Henriquez, Ronald R.; Tichy, Shane E.; Russell, David H.; McNeal, Catherine J.; Macfarlane, Ronald D.
2007-01-01
The purpose of this study is to determine whether the nature of the post-translational modifications of the major apolipoproteins of HDL is different for density-distinct subclasses. These subclasses were separated by ultracentrifugation using a novel density-forming solute to yield a high-resolution separation. The serum of two subjects, a control with a normolipidemic profile and a subject with diagnosed cardiovascular disease, was studied. Aliquots of three HDL subclasses were analyzed by MALDI and considerable differences were seen when comparing density-distinct subclasses and also when comparing the two subjects. A detailed analysis of the post-translational modification pattern of apoA-1 shows evidence of considerable protease activity, particularly in the more dense fractions. We conclude that part of the heterogeneity of the population of HDL particles is due to density-dependent protease activity. PMID:19050741
Dependence of interstellar depletion on hydrogen column density - Possibilities and implications
NASA Technical Reports Server (NTRS)
Tarafdar, S. P.; Prasad, S. S.; Huntress, W. T., Jr.
1983-01-01
A reexamination of the observed column densities of various elements in diffuse clouds suggests that almost all elements including oxygen, nitrogen, sulfur, and argon may be depleted with respect to hydrogen in interstellar clouds with large hydrogen column density. The amount of depletion varies from element to element and increases with increasing column density of hydrogen nuclei. This result is in qualitative agreement with the depletion of oxygen and sulfur independently inferred from the gas phase chemistry of sulfur in dense clouds. The rate of increase of depletion with hydrogen column density implied by the present study is large. It is possible that observational selection effects may have amplified the real dependence on N(H). A broad spectrum of C/O ratios ranging from values greater than unity to values less than unity appears possible for interstellar clouds, which would have the effect of a large variation in chemical composition from cloud to cloud.
Density-dependent productivity in a colonial vulture at two spatial scales.
Fernández-Bellon, Darío; Cortés-Avizanda, Ainara; Arenas, Rafael; Donázar, José Antonio
2016-02-01
Understanding how density dependence modifies demographic parameters in long-lived vertebrates is a challenge for ecologists. Two alternative hypotheses have been used to explain the mechanisms behind density-dependent effects on breeding output: habitat heterogeneity and individual adjustment (also known as interference competition). A number of studies have highlighted the importance of habitat heterogeneity in density dependence in territorial species, but less information exists on demographic processes in colonial species. For these, we expect density-dependent mechanisms to operate at two spatial scales: colony and breeding unit. In this study, we used long-term data from a recovering population of Cinereous Vultures (Aegypius monachus) in southern Spain. We analyzed a long-term data set with information on 2162 breeding attempts at four colonies over a nine-year period (2002-2010) to evaluate environmental and population parameters influencing breeding output. Our results suggest that breeding productivity is subject to density-dependent processes at the colony and the nest site scale and is best explained by interference competition. Factors intrinsic to each colony, as well as environmental constraints linked to physiography and human presence, also play a role in regulatory processes. We detected the existence of a trade-off between the disadvantages of nesting too close to conspecifics and the benefits of coloniality. These could be mediated by the agonistic interactions between breeding pairs and the benefits derived from social sharing of information by breeding individuals. We propose that this trade-off may play a role in defining colony structure and may hold true for other colonial breeding bird species. Our findings also have important management implications for the conservation of this threatened species. PMID:27145615
Density- and Size-Dependent Winter Mortality and Growth of Late Chaoborus flavicans Larvae
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
Progression of Plasmodium berghei through Anopheles stephensi Is Density-Dependent
Sinden, Robert E; Dawes, Emma J; Alavi, Yasmene; Waldock, Joanna; Finney, Olivia; Mendoza, Jacqui; Butcher, Geoff A; Andrews, Laura; Hill, Adrian V; Gilbert, Sarah C; Basez, Mara-Gloria
2007-01-01
It is well documented that the density of Plasmodium in its vertebrate host modulates the physiological response induced; this in turn regulates parasite survival and transmission. It is less clear that parasite density in the mosquito regulates survival and transmission of this important pathogen. Numerous studies have described conversion rates of Plasmodium from one life stage to the next within the mosquito, yet few have considered that these rates might vary with parasite density. Here we establish infections with defined numbers of the rodent malaria parasite Plasmodium berghei to examine how parasite density at each stage of development (gametocytes; ookinetes; oocysts and sporozoites) influences development to the ensuing stage in Anopheles stephensi, and thus the delivery of infectious sporozoites to the vertebrate host. We show that every developmental transition exhibits strong density dependence, with numbers of the ensuing stages saturating at high density. We further show that when fed ookinetes at very low densities, oocyst development is facilitated by increasing ookinete number (i.e., the efficiency of ookineteoocyst transformation follows a sigmoid relationship). We discuss how observations on this model system generate important hypotheses for the understanding of malaria biology, and how these might guide the rational analysis of interventions against the transmission of the malaria parasites of humans by their diverse vector species. PMID:18166078
Peak-shifting in real-time time-dependent density functional theory.
Provorse, Makenzie R; Habenicht, Bradley F; Isborn, Christine M
2015-10-13
In recent years, the development and application of real-time time-dependent density functional theory (RT-TDDFT) has gained momentum as a computationally efficient method for modeling electron dynamics and properties that require going beyond a linear response of the electron density. However, the RT-TDDFT method within the adiabatic approximation can unphysically shift absorption peaks throughout the electron dynamics. Here, we investigate the origin of these time-dependent resonances observed in RT-TDDFT spectra. Using both exact exchange and hybrid exchange-correlation approximate functionals, adiabatic RT-TDDFT gives time-dependent absorption spectra in which the peaks shift in energy as populations of the excited states fluctuate, while exact wave function methods yield peaks that are constant in energy but vary in intensity. The magnitude of the RT-TDDFT peak shift depends on the frequency and intensity of the applied field, in line with previous studies, but it oscillates as a function of time-dependent molecular orbital populations, consistent with a time-dependent superposition electron density. For the first time, we provide a rationale for the direction and magnitude of the time-dependent peak shifts based on the molecular electronic structure. For three small molecules, H2, HeH(+), and LiH, we give contrasting examples of peak-shifting to both higher and lower energies. The shifting is explained as coupled one-electron transitions to a higher and a lower lying state. Whether the peak shifts to higher or lower energies depends on the relative energetics of these one-electron transitions. PMID:26574268
The nutrient density approach to healthy eating: challenges and opportunities.
Nicklas, Theresa A; Drewnowski, Adam; O'Neil, Carol E
2014-12-01
The term 'nutrient density' for foods/beverages has been used loosely to promote the Dietary Guidelines for Americans. The 2010 Dietary Guidelines for Americans defined 'all vegetables, fruits, whole grains, fat-free or low-fat milk and milk products, seafood, lean meats and poultry, eggs, beans and peas (legumes), and nuts and seeds that are prepared without added solid fats, added sugars, and sodium' as nutrient dense. The 2010 Dietary Guidelines for Americans further states that nutrient-dense foods and beverages provide vitamins, minerals and other substances that may have positive health effects with relatively few (kilo)calories or kilojoules. Finally, the definition states nutrients and other beneficial substances have not been 'diluted' by the addition of energy from added solid fats, added sugars or by the solid fats naturally present in the food. However, the Dietary Guidelines Advisory Committee and other scientists have failed to clearly define 'nutrient density' or to provide criteria or indices that specify cut-offs for foods that are nutrient dense. Today, 'nutrient density' is a ubiquitous term used in the scientific literature, policy documents, marketing strategies and consumer messaging. However, the term remains ambiguous without a definitive or universal definition. Classifying or ranking foods according to their nutritional content is known as nutrient profiling. The goal of the present commentary is to address the research gaps that still exist before there can be a consensus on how best to define nutrient density, highlight the situation in the USA and relate this to wider, international efforts in nutrient profiling. PMID:25166614
Tight-binding approach to strain-dependent DNA electronics
NASA Astrophysics Data System (ADS)
Malakooti, Sadeq; Hedin, Eric; Joe, Yong
2013-07-01
Small mechanical strain perturbations are considered in calculations of the poly(G)-poly(C) DNA molecular electronic structure, using a tight-binding framework in conjunction with the theories of Slater-Koster and linear elasticity. Results reveal a strain-induced band gap for DNA which is linearly dependent on the induced strain. Local density of states calculations expose that the contribution of the guanine-cytosine base pairs in the charge transport mechanism is significantly enhanced relative to the backbones when DNA is compressed. Transport investigations also disclose a strain-induced metal-semiconductor transition for the DNA molecule, which suggests possible potential uses for sensing applications.
A coarse-grain force field for RDX: Density dependent and energy conserving.
Moore, Joshua D; Barnes, Brian C; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S; Taylor, DeCarlos E; Brennan, John K
2016-03-14
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions. PMID:26979691
Density-dependent electron transport and precise modeling of GaN high electron mobility transistors
NASA Astrophysics Data System (ADS)
Bajaj, Sanyam; Shoron, Omor F.; Park, Pil Sung; Krishnamoorthy, Sriram; Akyol, Fatih; Hung, Ting-Hsiang; Reza, Shahed; Chumbes, Eduardo M.; Khurgin, Jacob; Rajan, Siddharth
2015-10-01
We report on the direct measurement of two-dimensional sheet charge density dependence of electron transport in AlGaN/GaN high electron mobility transistors (HEMTs). Pulsed IV measurements established increasing electron velocities with decreasing sheet charge densities, resulting in saturation velocity of 1.9 × 107 cm/s at a low sheet charge density of 7.8 × 1011 cm-2. An optical phonon emission-based electron velocity model for GaN is also presented. It accommodates stimulated longitudinal optical (LO) phonon emission which clamps the electron velocity with strong electron-phonon interaction and long LO phonon lifetime in GaN. A comparison with the measured density-dependent saturation velocity shows that it captures the dependence rather well. Finally, the experimental result is applied in TCAD-based device simulator to predict DC and small signal characteristics of a reported GaN HEMT. Good agreement between the simulated and reported experimental results validated the measurement presented in this report and established accurate modeling of GaN HEMTs.
Density-dependent settlement and mortality structure the earliest life phases of a coral population.
Vermeij, Mark J A; Sandin, Stuart A
2008-07-01
The local densities of heterospecifics and conspecifics are known to have profound effects on the dynamics of many benthic species, including rates of settlement and early post-settlement survivorship. We described the early life history of the Caribbean coral, Siderastrea radians by tracking the population dynamics from recently settled planulae to juveniles. Through three years of observation, settlement correlated with the abundance of other benthic organisms, principally turf algae (negatively) and crustose coralline algae (positively). In addition, adult density showed independent effects on coral settlement and early post-settlement survivorship. Settlement rates increased across low levels of adult cover and saturated at a maximum around 10% cover. Early post-settlement survivorship decreased with adult cover, revealing structuring density dependence in coral settlers. The earliest life stages of corals are defined by low survivorship, with survivorship increasing appreciably with colony size. However, recent settlers (one-polyp individuals, < 1-year-old) are more likely to grow into two-polyp juveniles than older single polyps (> 1-year-old) that were delayed in their development. The early benthic phase of corals is defined by a severe demographic bottleneck for S. radians, with appreciable density-dependent and density-independent effects on survivorship. For effective management and restoration of globally imperiled coral reefs, we must focus more attention on this little studied, but dynamic, early life history period of corals. PMID:18705385
Quorum Sensing and Density-Dependent Dispersal in an Aquatic Model System
Fellous, Simon; Duncan, Alison; Coulon, Aurlie; Kaltz, Oliver
2012-01-01
Many organisms use cues to decide whether to disperse or not, especially those related to the composition of their environment. Dispersal hence sometimes depends on population density, which can be important for the dynamics and evolution of sub-divided populations. But very little is known about the factors that organisms use to inform their dispersal decision. We investigated the cues underlying density-dependent dispersal in inter-connected microcosms of the freshwater protozoan Paramecium caudatum. In two experiments, we manipulated (i) the number of cells per microcosm and (ii) the origin of their culture medium (supernatant from high- or low-density populations). We found a negative relationship between population density and rates of dispersal, suggesting the use of physical cues. There was no significant effect of culture medium origin on dispersal and thus no support for chemical cues usage. These results suggest that the perception of density and as a result, the decision to disperse in this organism can be based on physical factors. This type of quorum sensing may be an adaptation optimizing small scale monitoring of the environment and swarm formation in open water. PMID:23144882
Experimental excursions on adaptive landscapes: density-dependent selection on egg size.
Svensson, E; Sinervo, B
2000-08-01
Theories of density-dependent natural selection suggest that intraspecific competition will favor juveniles of high competitive ability. Empirical evidence has been provided from laboratory selection experiments, but field studies are lacking due to the logistical difficulties of experimentally manipulating population densities in natural settings. Here, we present data from a decade-long experimental field study of side-blotched lizards, Uta stansburiana that overcomes these difficulties. We tested the hypothesis that density-dependent natural selection causes egg size to increase from early to late clutches in this and many other species. Using a novel combination of environmental manipulations of hatchling density and phenotypic manipulations of egg size, we demonstrate that the nature of selection on egg size changes dramatically in the absence of older competitors. The strength of selection on egg size among later-clutch hatchlings released in areas without competitors from early clutches became almost doubled in magnitude, compared to that among hatchlings released in the presence of older competitors. These experimental findings demonstrate density-dependent natural selection on egg size; however, they contradict the classical idea that egg size increases during the reproductive season because of competition between early and late hatchlings. The results indicate that competitive age or size asymmetries between early and late hatchlings can override within-cohort asymmetries due to egg size. We suggest that competition could be an important mediator of oscillating selection pressures in this and other systems. Finally, we discuss the utility of "double-level," simultaneous experimental manipulation of both phenotypic traits that are targets of selection (e.g., egg size) as well the environmental agents of selection (e.g., population density). PMID:11005305
Temporal shift in density dependence among North American breeding duck populations.
Murray, Dennis L; Anderson, Michael G; Steury, Todd D
2010-02-01
Environmental perturbation can have a marked influence on abundance and trend in many animal populations, but information is scant on how numerical change relates to variability in density-dependent and density-independent processes acting on populations. Using breeding population estimates for 10 duck species from a survey area of approximately 2.2 million km2 in central North America (1955-2005), we compared population growth models and related parameters among species and across time. All duck species showed evidence of density-dependent growth, and the best-fit relationship between population growth (r(t)) and population size (N(t)) was linear or convex for all species. Density dependence and associated population parameters were not related to an index of species life history strategy. Reanalysis of segmented (1955-1979, 1980-2005) r(t) time series, where the truncation date coincided with a putative decline in wetland availability on breeding grounds, showed that density-dependent forces were weakened during the latter time segment. Additionally, in later years most populations experienced increased first-order autocorrelation in annual counts, decreased intrinsic growth rate, increased nonlinearity in the relationship between r(t) and N(t), increased equilibrium return time, and increased inter-species synchrony in numbers. Such changes were not closely related to species life history strategy or to shifts in mean population size, average trend, and estimated carrying capacity. We speculate that shifts in breeding duck habitat quality altered historical predator-prey dynamics in the system and thereby underlie observed dynamical changes. The paradoxical finding that population abundance and trend do not reveal shifts in population processes highlights the need to go beyond simple numerical assessment when evaluating population responses to environmental perturbation. PMID:20392021
Temperature dependence of seed pulse amplitude and density grating in Brillouin amplification
NASA Astrophysics Data System (ADS)
Lehmann, G.; Spatschek, K. H.
2016-02-01
Seed pulse dynamics as well as plasma response during Brillouin amplification are investigated in the so called strong coupling regime. Due to the finite amplitudes trapping of electrons and ions may become important. These effects are not covered by the commonly used three-wave interaction equations derived from fluid theory. Therefore, here investigations based on a Vlasov model are presented. The kinetic calculations show that the density response is not as predicted by the fluid models. We find a pronounced density grating with significant particle trapping. The influence of the latter on the seed amplitude development is discussed in dependence on the electron and ion temperatures.
NASA Astrophysics Data System (ADS)
Bröker, B.; Hofmann, O. T.; Rangger, G. M.; Frank, P.; Blum, R.-P.; Rieger, R.; Venema, L.; Vollmer, A.; Müllen, K.; Rabe, J. P.; Winkler, A.; Rudolf, P.; Zojer, E.; Koch, N.
2010-06-01
The adsorption of the molecular acceptor hexaazatriphenylene-hexacarbonitrile on Ag(111) was investigated as function of layer density. We find that the orientation of the first molecular layer changes from a face-on to an edge-on conformation depending on layer density, facilitated through specific interactions of the peripheral molecular cyano groups with the metal. This is accompanied by a rehybridization of molecular and metal electronic states, which significantly modifies the interface and surface electronic properties, as rationalized by theoretical modeling.
Quantum Well Width Dependence of Threshold Current Density in InGaN Lasers
Amano, H.; Chow, W.W.; Han, J.; Takeuchi, T.
1999-03-16
The quantum confined Stark effect was found to result in a strong quantum well width dependence of threshold current density in strained group-III nitride quantum well lasers. For an In{sub 0.2}Ga{sub 0.8}N/GaN structure with quantum well width in the neighborhood of 3.5nm, our analysis shows that the reduction in spontaneous emission loss by the electron-hole spatial separation outweighs the corresponding reduction in gain to produce a threshold current density minimum.
NASA Astrophysics Data System (ADS)
Lorenz, Ralph D.; Bridges, Nathan T.; Rosenthal, Alex A.; Donkor, Elise
2014-02-01
We measure the wavelength of aeolian bedforms on the surface of martian volcanoes, spanning a 23 km range in elevation, or nearly an order of magnitude in atmospheric pressure and density. We find that the bedform wavelength (˜1-5 m) varies as the reciprocal of density. The observed wavelengths and wavelength dependence are compared with three recent models of bedform spacing. The results are consistent with the expected increase in threshold friction speed and saturation drag length with elevation. The observations lend support to the expectation that such bedforms on Venus or Titan are too small to be observed in present data.
NASA Astrophysics Data System (ADS)
Rebolini, Elisa; Toulouse, Julien
2016-03-01
We present a range-separated linear-response time-dependent density-functional theory (TDDFT) which combines a density-functional approximation for the short-range response kernel and a frequency-dependent second-order Bethe-Salpeter approximation for the long-range response kernel. This approach goes beyond the adiabatic approximation usually used in linear-response TDDFT and aims at improving the accuracy of calculations of electronic excitation energies of molecular systems. A detailed derivation of the frequency-dependent second-order Bethe-Salpeter correlation kernel is given using many-body Green-function theory. Preliminary tests of this range-separated TDDFT method are presented for the calculation of excitation energies of the He and Be atoms and small molecules (H2, N2, CO2, H2CO, and C2H4). The results suggest that the addition of the long-range second-order Bethe-Salpeter correlation kernel overall slightly improves the excitation energies.
Sum rules and properties in time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Qian, Zhixin; Sahni, Viraht
2001-04-01
Time-dependent quantal density-functional theory (Q-DFT) is a description of the s-system of noninteracting fermions with electronic density equivalent to that of Schrödinger theory, in terms of fields whose sources are quantum-mechanical expectations of Hermitian operators. The theory delineates and defines the contribution of each type of electron correlation to the local electron-interaction potential νee(r,t) of the s system. These correlations are due to the Pauli exclusion principle, Coulomb repulsion, correlation-kinetic, and correlation-current-density effects, the latter two resulting, respectively, from the difference in kinetic energy and current density between the interacting Schrödinger and noninteracting systems. We employ Q-DFT to prove the following sum rules and properties of the s system: (i) the components of the potential due to these correlations separately exert no net force on the system; (ii) the torque of the potential is finite and due solely to correlation-current-density effects; (iii) two sum rules involving the curl of the dynamic electron-interaction kernel defined as the functional derivative of νee(r,t) are derived and shown to depend on the frequency dependent correlation-current-density effect. Furthermore, via adiabatic coupling constant (λ) perturbation theory, we prove: (iv) the exchange potential νx(r,t) is the work done in a conservative field representative of Pauli correlations and lowest-order O(λ) correlation-kinetic and correlation-current-density effects; (v) the correlation potential νc(r,t) commences in O(λ2), and, at each order, it is the work done in a conservative field representative of Coulomb correlations and correlation-kinetic and correlation-current-density effects; (vi) we derive the integral virial theorem relating νee(r,t) to the electron-interaction and correlation-kinetic energy for arbitrary coupling constant strength λ, and show there are no explicit correlation-current-density contributions to the energy. From this integral virial theorem we (vii) obtain the fully interacting (λ=1) and exchange-only (λ=0) integral virial theorems as special cases, the latter showing there is no explicit correlation-kinetic contribution to the exchange energy; and (viii) write expressions for the electron-interaction and correlation-kinetic actions for arbitrary coupling constant λ in terms of the corresponding fields.
A model of activity-dependent changes in dendritic spine density and spine structure.
Crook, S M; Dur-E-Ahmad, M; Baer, S M
2007-10-01
Recent evidence indicates that the morphology and density of dendritic spines are regulated during synaptic plasticity. See, for instance, a review by Hayashi and Majewska [9]. In this work, we extend previous modeling studies [27] by combining a model for activity-dependent spine density with one for calcium-mediated spine stem restructuring. The model is based on the standard dimensionless cable equation, which represents the change in the membrane potential in a passive dendrite. Additional equations characterize the change in spine density along the dendrite, the current balance equation for an individual spine head, the change in calcium concentration in the spine head, and the dynamics of spine stem resistance. We use computational studies to investigate the changes in spine density and structure for differing synaptic inputs and demonstrate the effects of these changes on the input-output properties of the dendritic branch. Moderate amounts of high-frequency synaptic activation to dendritic spines result in an increase in spine stem resistance that is correlated with spine stem elongation. In addition, the spine density increases both inside and outside the input region. The model is formulated so that this long-term potentiation-inducing stimulus eventually leads to structural stability. In contrast, a prolonged low-frequency stimulation paradigm that would typically induce long-term depression results in a decrease in stem resistance (correlated with stem shortening) and an eventual decrease in spine density. PMID:17924715
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.
The local projection in the density functional theory plus U approach: A critical assessment
NASA Astrophysics Data System (ADS)
Wang, Yue-Chao; Chen, Ze-Hua; Jiang, Hong
2016-04-01
Density-functional theory plus the Hubbard U correction (DFT + U) method is widely used in first-principles studies of strongly correlated systems, as it can give qualitatively (and sometimes, semi-quantitatively) correct description of energetic and structural properties of many strongly correlated systems with similar computational cost as local density approximation or generalized gradient approximation. On the other hand, the DFT + U approach is limited both theoretically and practically in several important aspects. In particular, the results of DFT + U often depend on the choice of local orbitals (the local projection) defining the subspace in which the Hubbard U correction is applied. In this work we have systematically investigated the issue of the local projection by considering typical transition metal oxides, β-MnO2 and MnO, and comparing the results obtained from different implementations of DFT + U. We found that the choice of the local projection has significant effects on the DFT + U results, which are more significant for systems with stronger covalent bonding (e.g., MnO2) than those with more ionic bonding (e.g., MnO). These findings can help to clarify some confusion arising from the practical use of DFT + U and may also provide insights for the development of new first-principles approaches beyond DFT + U.
Fischer, Sean A; Cramer, Christopher J; Govind, Niranjan
2016-04-01
Optical-limiting materials are capable of attenuating light to protect delicate equipment from high-intensity light sources. Phthalocyanines have attracted a lot of attention for optical-limiting applications due to their versatility and large nonlinear absorption. With excited-state absorption (ESA) being the primary mechanism for optical limiting behavior in phthalocyanines, the ability to tune the optical absorption of ground and excited states in phthalocyanines would allow for the development of advanced optical limiters. We recently developed a method for the calculation of ESA based on real-time time-dependent density functional theory propagation of an excited-state density. In this work, we apply the approach to zinc phthalocyanine, demonstrating the ability of our method to efficiently identify the optical limiting potential of a molecular complex. PMID:27007445
NASA Astrophysics Data System (ADS)
Badran, R. I.
2007-08-01
The drift mobility for electrons and holes, small-signal mobility lifetime product, trapped-carrier density of states in addition to other correlated physical parameters of microcrystalline silicon sample are estimated from the analysis of field-dependent experimental data using steady-state photocarrier grating technique. The filed-dependent experimental data at room temperature of the sample which was prepared by hot-wire chemical vapor deposition (HWCVD) technique, are analyzed using different approaches based on small-signal photocurrent. The exploitation of the electric-field dependence in these approaches is correlating the photoelectronic properties, which are demonstrated by the transport parameters, to the trapped charge density which is usually not easily accessible. This may also justify the enhanced relationship between the minority carrier mobility-lifetime product and trapped charge density and then the sub-gap absorption in the sample under study.
Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus)
Vas, Judit; Andersen, Inger Lise
2015-01-01
Very little is known about the spacing behaviour in social groups of domestic goats (Capra hircus) in the farm environment. In this experiment, we studied interindividual distances, movement patterns and activity budgets in pregnant goats housed at three different densities. Norwegian dairy goats were kept in stable social groups of six animals throughout pregnancy at 1, 2 or 3 m2 per individual and their spacing behaviours (i.e. distance travelled, nearest and furthest neighbour distance) and activity budgets (e.g. resting, feeding, social activities) were monitored. Observations were made in the first, second and last thirds of pregnancy in the mornings, at noon and in the afternoons of each of these phases (4.5 hours per observation period). The findings show that goats held at animal densities of 2 and 3 m2 moved longer distances when they had more space per animal and kept larger nearest and furthest neighbour distances when compared to the 1 m2 per animal density. Less feeding activity was observed at the high animal density compared to the medium and low density treatments. The phase of gestation also had an impact on almost all behavioural variables. Closer to parturition, animals moved further distances and the increase in nearest and furthest neighbour distance was more pronounced at the lower animal densities. During the last period of gestation, goats spent less time feeding and more on resting, social behaviours and engaging in other various activities. Our data suggest that more space per goat is needed for goats closer to parturition than in the early gestation phase. We concluded that in goats spacing behaviour is density-dependent and changes with stages of pregnancy and activities. Finally, the lower density allowed animals to express individual preferences regarding spacing behaviour which is important in ensuring good welfare in a farming situation. PMID:26657240
Density-Dependent Spacing Behaviour and Activity Budget in Pregnant, Domestic Goats (Capra hircus).
Vas, Judit; Andersen, Inger Lise
2015-01-01
Very little is known about the spacing behaviour in social groups of domestic goats (Capra hircus) in the farm environment. In this experiment, we studied interindividual distances, movement patterns and activity budgets in pregnant goats housed at three different densities. Norwegian dairy goats were kept in stable social groups of six animals throughout pregnancy at 1, 2 or 3 m2 per individual and their spacing behaviours (i.e., distance travelled, nearest and furthest neighbour distance) and activity budgets (e.g., resting, feeding, social activities) were monitored. Observations were made in the first, second and last thirds of pregnancy in the mornings, at noon and in the afternoons of each of these phases (4.5 hours per observation period). The findings show that goats held at animal densities of 2 and 3 m2 moved longer distances when they had more space per animal and kept larger nearest and furthest neighbour distances when compared to the 1 m2 per animal density. Less feeding activity was observed at the high animal density compared to the medium and low density treatments. The phase of gestation also had an impact on almost all behavioural variables. Closer to parturition, animals moved further distances and the increase in nearest and furthest neighbour distance was more pronounced at the lower animal densities. During the last period of gestation, goats spent less time feeding and more on resting, social behaviours and engaging in other various activities. Our data suggest that more space per goat is needed for goats closer to parturition than in the early gestation phase. We concluded that in goats spacing behaviour is density-dependent and changes with stages of pregnancy and activities. Finally, the lower density allowed animals to express individual preferences regarding spacing behaviour which is important in ensuring good welfare in a farming situation. PMID:26657240
Breed, Greg A; Don Bowen, W; Leonard, Marty L
2013-01-01
In populations of colony-breeding marine animals, foraging around colonies can lead to intraspecific competition. This competition affects individual foraging behavior and can cause density-dependent population growth. Where behavioral data are available, it may be possible to infer the mechanism of intraspecific competition. If these mechanics are understood, they can be used to predict the population-level functional response resulting from the competition. Using satellite relocation and dive data, we studied the use of space and foraging behavior of juvenile and adult gray seals (Halichoerus grypus) from a large (over 200,000) and growing population breeding at Sable Island, Nova Scotia (44.0 oN 60.0 oW). These data were first analyzed using a behaviorally switching state-space model to infer foraging areas followed by randomization analysis of foraging region overlap of competing age classes. Patterns of habitat use and behavioral time budgets indicate that young-of-year juveniles (YOY) were likely displaced from foraging areas near (<10 km) the breeding colony by adult females. This displacement was most pronounced in the summer. Additionally, our data suggest that YOY are less capable divers than adults and this limits the habitat available to them. However, other segregating mechanisms cannot be ruled out, and we discuss several alternate hypotheses. Mark–resight data indicate juveniles born between 1998 and 2002 have much reduced survivorship compared with cohorts born in the late 1980s, while adult survivorship has remained steady. Combined with behavioral observations, our data suggest YOY are losing an intraspecific competition between adults and juveniles, resulting in the currently observed decelerating logistic population growth. Competition theory predicts that intraspecific competition resulting in a clear losing competitor should cause compensatory population regulation. This functional response produces a smooth logistic growth curve as carrying capacity is approached, and is consistent with census data collected from this population over the past 50 years. The competitive mechanism causing compensatory regulation likely stems from the capital-breeding life-history strategy employed by gray seals. This strategy decouples reproductive success from resources available around breeding colonies and prevents females from competing with each other while young are dependent. PMID:24198943
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 carrying capacity is approached, and is consistent with census data collected from this population over the past 50 years. The competitive mechanism causing compensatory regulation likely stems from the capital-breeding life-history strategy employed by gray seals. This strategy decouples reproductive success from resources available around breeding colonies and prevents females from competing with each other while young are dependent. PMID:24198943
Minter, Ewan J. A.; Watts, Phillip C.; Lowe, Chris D.; Brockhurst, Michael A.
2015-01-01
Natural populations of free-living protists often exhibit high-levels of intraspecific diversity, yet this is puzzling as classic evolutionary theory predicts dominance by genotypes with high fitness, particularly in large populations where selection is efficient. Here, we test whether negative frequency-dependent selection (NFDS) plays a role in the maintenance of diversity in the marine flagellate Oxyrrhis marina using competition experiments between multiple pairs of strains. We observed strain-specific responses to frequency and density, but an overall signature of NFDS that was intensified at higher population densities. Because our strains were not selected a priori on the basis of particular traits expected to exhibit NFDS, these data represent a relatively unbiased estimate of the role for NFDS in maintaining diversity in protist populations. These findings could help to explain how bloom-forming plankton, which periodically achieve exceptionally high population densities, maintain substantial intraspecific diversity. PMID:26063750
Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation.
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. PMID:25612698
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.
Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation
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.
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.
Minter, Ewan J A; Watts, Phillip C; Lowe, Chris D; Brockhurst, Michael A
2015-06-01
Natural populations of free-living protists often exhibit high-levels of intraspecific diversity, yet this is puzzling as classic evolutionary theory predicts dominance by genotypes with high fitness, particularly in large populations where selection is efficient. Here, we test whether negative frequency-dependent selection (NFDS) plays a role in the maintenance of diversity in the marine flagellate Oxyrrhis marina using competition experiments between multiple pairs of strains. We observed strain-specific responses to frequency and density, but an overall signature of NFDS that was intensified at higher population densities. Because our strains were not selected a priori on the basis of particular traits expected to exhibit NFDS, these data represent a relatively unbiased estimate of the role for NFDS in maintaining diversity in protist populations. These findings could help to explain how bloom-forming plankton, which periodically achieve exceptionally high population densities, maintain substantial intraspecific diversity. PMID:26063750
KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES*
Speyer, Gil; Kiefer, Jeff; Dhruv, Harshil; Berens, Michael; Kim, Seungchan
2015-01-01
We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies. The method constructs gene dependency networks from bootstrapped samples in one condition and computes the divergence between distributions of network likelihood scores from different conditions. It was shown to be capable of sensitive and specific identification of pathways with phenotype-specific dysregulation, i.e., rewiring of dependencies between genes in different conditions. We now present an extension of the method by incorporating prior knowledge into the inference of networks. The degree of prior knowledge incorporation has substantial effect on the sensitivity of the method, as the data is the source of condition specificity while prior knowledge incorporation can provide additional support for dependencies that are only partially supported by the data. Use of prior knowledge also significantly improved the interpretability of the results. Further analysis of topological characteristics of gene differential dependency networks provides a new approach to identify genes that could play important roles in biological signaling in a specific condition, hence, promising targets customized to a specific condition. Through analysis of TCGA glioblastoma multiforme data, we demonstrate the method can identify not only potentially promising targets but also underlying biology for new targets. PMID:26776171
Energy density and stress: A new approach to teaching electromagnetism
NASA Astrophysics Data System (ADS)
Herrmann, F.
1989-08-01
By introducing the electromagnetic field in the customary way, ideas are promoted that do not correspond to those of contemporary physics: on the one hand, ideas that stem from pre-Maxwellian times when interactions were still conceived as actions at a distance and, on the other hand, ideas that can be understood only from the point of view that the electromagnetic field is carried by a medium. A part of a course in electromagnetism is sketched in which, from the beginning, the electromagnetic field is presented as a system in its own right and the local quantities energy density and stress are put into the foreground. In this way, justice is done to the views of modern physics and, moreover, the field becomes conceptually simpler.
Postcatastrophe population dynamics and density dependence of an endemic island duck
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.
Subspace formulation of time-dependent density functional theory for large-scale calculations.
Zhang, Xu; Lu, Gang
2015-08-14
A subspace formulation of time-dependent density functional theory (TDDFT) is proposed for large-scale calculations based on density functional perturbation theory. The formulation is implemented in conjunction with projector augmented-wave method and plane-wave basis set. A key bottleneck of conventional TDDFT method is circumvented by projecting the time-dependent Kohn-Sham eigenvalue equations from a full Hilbert space to a substantially reduced sub-Hilbert space. As a result, both excitation energies and ionic forces can be calculated accurately within the reduced subspace. The method is validated for several model systems and exhibits the similar accuracy as the conventional TDDFT method but at a computational cost of the ground state calculation. The Born-Oppenheimer molecular dynamics can be successfully performed for excited states in C60 and T12 molecules, opening doors for many applications involving excited state dynamics. PMID:26277130
Energy density dependence of hydrogen combustion efficiency in atmospheric pressure microwave plasma
Yoshida, T.; Ezumi, N.; Sawada, K.; Tanaka, Y.; Tanaka, M.; Nishimura, K.
2015-03-15
The recovery of tritium in nuclear fusion plants is a key issue for safety. So far, the oxidation procedure using an atmospheric pressure plasma is expected to be part of the recovery method. In this study, in order to clarify the mechanism of hydrogen oxidation by plasma chemistry, we have investigated the dependence of hydrogen combustion efficiency on gas flow rate and input power in the atmospheric pressure microwave plasma. It has been found that the combustion efficiency depends on energy density of absorbed microwave power. Hence, the energy density is considered as a key parameter for combustion processes. Also neutral gas temperatures inside and outside the plasma were measured by an optical emission spectroscopy method and thermocouple. The result shows that the neutral gas temperature in the plasma is much higher than the outside temperature of plasma. The high neutral gas temperature may affect the combustion reaction. (authors)
NASA Astrophysics Data System (ADS)
Hamid, A. S.; Uedono, A.
2004-11-01
The spin-dependent momentum density and Fermi surface of ferromagnetic Ni have been obtained through positron annihilation experiments. The measurements were carried out through 2D angular correlation of annihilation radiation (ACAR) using longitudinally polarized positrons. The magnetic field direction was reversed in order to study the effect of the spin-dependent positron-electron momentum space density on the Fermi surface of Ni. The results showed that ferromagnetic Ni had different Fermi surfaces for the majority-spin and minority-spin states. The differences due to the spin-states were studied in the momentum space and in the wave vector space. In general, the experimental results showed good agreement with previous theoretical calculations.
Time-dependent Density Functional Results for the Dynamic Hyperpolarizability of C{sub 60}
van Gisbergen, S.; Snijders, J.; Baerends, E.
1997-04-01
The experimental, as well as theoretical, values for the frequency-dependent hyperpolarizability of C{sub 60} differ by orders of magnitude. We present the first density functional calculation of a molecular frequency-dependent hyperpolarizability. Our implementation is very economical, enabling the treatment of molecules of this size, in a potentially much more accurate way than can be obtained with alternative methods. Our results strongly support the recent results by Geng and Wright, who report much lower experimental values than previous authors. {copyright} {ital 1997} {ital The American Physical Society}
Density dependence of electron mobility in the accumulation mode for fully depleted SOI films
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.
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.
An irradiation density dependent energy relaxation in plant photosystem II antenna assembly.
Tian, Wenming; Chen, Jun; Deng, Liezheng; Yao, Mingdong; Yang, Heping; Zheng, Yang; Cui, Rongrong; Sha, Guohe
2015-02-01
Plant photosystem II (PSII) is a multicomponent pigment-protein complex that harvests sunlight via pigments photoexcitation, and converts light energy into chemical energy. Against high light induced photodamage, excess light absorption of antenna pigments triggers the operation of photoprotection mechanism in plant PSII. Non-photochemical energy relaxation as a major photoprotection way is essentially correlated to the excess light absorption. Here we investigate the energy relaxation of plant PSII complexes with varying incident light density, by performing steady-state and transient chlorophyll fluorescence measurements of the grana membranes (called as BBY), functional moiety PSII reaction center and isolated light-harvesting complex LHCII under excess light irradiation. Based on the chlorophyll fluorescence decays of these samples, it is found that an irradiation density dependent energy relaxation occurs in the LHCII assemblies, especially in the antenna assembly of PSII supercomplexes in grana membrane, when irradiation increases to somewhat higher density levels. Correspondingly, the average chlorophyll fluorescence lifetime of the highly isolated BBY fragments gradually decreases from ~1680 to ~1360 ps with increasing the irradiation density from 6.1×10(9) to 5.5×10(10) photon cm(-2) pulse(-1). Analysis of the relation of fluorescence decay change to the aggregation extent of LHCIIs suggests that a dense arrangement of trimeric LHCIIs is likely the structural base for the occurrence of this irradiation density dependent energy relaxation. Once altering the irradiation density, this energy relaxation is quickly reversible, implying that it may play an important role in photoprotection of plant PSII. PMID:25482259
Remarks on time-dependent [current]-density functional theory for open quantum systems.
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. PMID:23787804
Optical properties of Al nanostructures from time dependent density functional theory.
Mokkath, Junais Habeeb; Schwingenschlögl, Udo
2016-04-01
The optical properties of Al nanostructures are investigated by means of time dependent density functional theory, considering chains of varying length and ladders/stripes of varying aspect ratio. The absorption spectra show redshifting for increasing length and aspect ratio. For the chains the absorption is dominated by HOMO → LUMO transitions, whereas ladders and stripes reveal more complex spectra of plasmonic nature above a specific aspect ratio. PMID:27059568
Trenkel, V M; Lorance, P; Fssler, S M M; Hines, S
2015-10-01
Blue whiting Micromesistius poutassou mean total length at age in the north-east Atlantic Ocean was found to vary by around 6% during the period 2004-2011 and mean mass at age by 22% during the years 1981-2013. Linear modelling provided strong evidence that these phenotypic growth variations can be explained by trophic conditions, mainly negative density dependence and also food availability, and a negative long-term temperature effect on asymptotic size. PMID:26376856
Multi-configuration time-dependent density-functional theory based on range separation.
Fromager, Emmanuel; Knecht, Stefan; Jensen, Hans Jrgen Aa
2013-02-28
Multi-configuration range-separated density-functional theory is extended to the time-dependent regime. An exact variational formulation is derived. The approximation, which consists in combining a long-range Multi-Configuration-Self-Consistent Field (MCSCF) treatment with an adiabatic short-range density-functional (DFT) description, is then considered. The resulting time-dependent multi-configuration short-range DFT (TD-MC-srDFT) model is applied to the calculation of singlet excitation energies in H2, Be, and ferrocene, considering both short-range local density (srLDA) and generalized gradient (srGGA) approximations. As expected, when modeling long-range interactions with the MCSCF model instead of the adiabatic Buijse-Baerends density-matrix functional as recently proposed by Pernal [J. Chem. Phys. 136, 184105 (2012)], the description of both the 1(1)D doubly-excited state in Be and the 1(1)?u(+) state in the stretched H2 molecule are improved, although the latter is still significantly underestimated. Exploratory TD-MC-srDFT/GGA calculations for ferrocene yield in general excitation energies at least as good as TD-DFT using the Coulomb attenuated method based on the three-parameter Becke-Lee-Yang-Parr functional (TD-DFT/CAM-B3LYP), and superior to wave-function (TD-MCSCF, symmetry adapted cluster-configuration interaction) and TD-DFT results based on LDA, GGA, and hybrid functionals. PMID:23464134
NASA Astrophysics Data System (ADS)
Cambré, Sofie; Muyshondt, Pieter; Federicci, Remi; Wenseleers, Wim
2015-11-01
Density gradient ultracentrifugation (DGU) becomes increasingly important for the sorting of nanomaterials according to the particles' density, hence structure and dimensions, which determine their unique properties, but the further development of this separation technique is hindered by the limited precision with which the densities could be characterized. In this work, we determine these densities by position-dependent 2D wavelength-dependent IR fluorescence-excitation and resonant Raman spectroscopy measured directly in the density gradient after ultracentrifugation. We apply this method to study the diameter and chirality-dependent sorting of empty and water-filled single-walled carbon nanotubes coated with two different surfactants, sodium cholate (SC) and sodium deoxycholate (DOC). The results elucidate the long standing contradiction that SC would provide better diameter sorting, while DOC is the most efficient surfactant to solubilise the nanotubes. A more predictable separation is obtained for empty DOC-coated nanotubes since their density is found to vary very smoothly with diameter. The accurate and chirality-dependent densities furthermore provide information on the surfactant coating, which is also important for other separation techniques, and allow to determine the mass percentage of water encapsulated inside the nanotubes.Density gradient ultracentrifugation (DGU) becomes increasingly important for the sorting of nanomaterials according to the particles' density, hence structure and dimensions, which determine their unique properties, but the further development of this separation technique is hindered by the limited precision with which the densities could be characterized. In this work, we determine these densities by position-dependent 2D wavelength-dependent IR fluorescence-excitation and resonant Raman spectroscopy measured directly in the density gradient after ultracentrifugation. We apply this method to study the diameter and chirality-dependent sorting of empty and water-filled single-walled carbon nanotubes coated with two different surfactants, sodium cholate (SC) and sodium deoxycholate (DOC). The results elucidate the long standing contradiction that SC would provide better diameter sorting, while DOC is the most efficient surfactant to solubilise the nanotubes. A more predictable separation is obtained for empty DOC-coated nanotubes since their density is found to vary very smoothly with diameter. The accurate and chirality-dependent densities furthermore provide information on the surfactant coating, which is also important for other separation techniques, and allow to determine the mass percentage of water encapsulated inside the nanotubes. Electronic supplementary information (ESI) available: (1) Density calibration, (2) fraction selection and reproducibility, (3) diffusion of the SWCNTs and (4) experimental RRS spectra and fits at various excitation wavelengths. See DOI: 10.1039/c5nr06020f
Density-dependent prey mortality is determined by the spatial scale of predator foraging.
McCarthy, Erin K; White, J Wilson
2016-02-01
Foraging theory predicts which prey patches predators should target. However, in most habitats, what constitutes a 'patch' and how prey density is calculated are subjective concepts and depend on the spatial scale at which the predator (or scientist) is observing. Moreover, the predator's 'foraging scale' affects prey population dynamics: predators should produce directly density-dependent (DDD) prey mortality at the foraging scale, but inversely density-dependent (IDD) mortality (safety-in-numbers) at smaller scales. We performed the first experimental test of these predictions using behavioral assays with guppies (Poecilia reticulata) feeding on bloodworm 'prey' patches. The guppy's foraging scale had already been estimated in a prior study. Our experimental results confirmed theoretical predictions: predation was IDD when prey were aggregated at a scale smaller than the foraging scale, but not when prey were aggregated at larger scales. These results could be used to predict outcomes of predator-prey interactions in continuous, non-discrete habitats in the field. PMID:26116266
De Giovannini, Umberto; Brunetto, Gustavo; Castro, Alberto; Walkenhorst, Jessica; Rubio, Angel
2013-05-10
Molecular absorption and photoelectron spectra can be efficiently predicted with real-time time-dependent density functional theory. We show herein how these techniques can be easily extended to study time-resolved pump-probe experiments, in which a system response (absorption or electron emission) to a probe pulse is measured in an excited state. This simulation tool helps with the interpretation of fast-evolving attosecond time-resolved spectroscopic experiments, in which electronic motion must be followed at its natural timescale. We show how the extra degrees of freedom (pump-pulse duration, intensity, frequency, and time delay), which are absent in a conventional steady-state experiment, provide additional information about electronic structure and dynamics that improve characterization of a system. As an extension of this approach, time-dependent 2D spectroscopy can also be simulated, in principle, for large-scale structures and extended systems. PMID:23520148
The ecological–evolutionary interplay: density-dependent sexual selection in a migratory songbird
Ryder, Thomas B; Fleischer, Robert C; Shriver, W Greg; Marra, Peter P
2012-01-01
Little is understood about how environmental heterogeneity influences the spatial dynamics of sexual selection. Within human-dominated systems, habitat modification creates environmental heterogeneity that could influence the adaptive value of individual phenotypes. Here, we used the gray catbird to examine if the ecological conditions experienced in the suburban matrix (SM) and embedded suburban parks (SP) influence reproductive strategies and the strength of sexual selection. Our results show that these habitats varied in a key ecological factor, breeding density. Moreover, this ecological factor was closely tied to reproductive strategies such that local breeding density predicted the probability that a nest would contain extra-pair offspring. Partitioning reproductive variance showed that while within-pair success was more important in both habitats, extra-pair success increased the opportunity for sexual selection by 39% at higher breeding densities. Body size was a strong predictor of relative reproductive success and was under directional selection in both habitats. Importantly, our results show that the strength of sexual selection did not differ among habitats at the landscape scale but rather that fine-scale variation in an ecological factor, breeding density, influenced sexual selection on male phenotypes. Here, we document density-dependent sexual selection in a migratory bird and hypothesize that coarse-scale environmental heterogeneity, in this case generated by anthropogenic habitat modification, changed the fine-scale ecological conditions that drove the spatial dynamics of sexual selection. PMID:22837842
Density-dependent fitness benefits in quorum-sensing bacterial populations.
Darch, Sophie E; West, Stuart A; Winzer, Klaus; Diggle, Stephen P
2012-05-22
It has been argued that bacteria communicate using small diffusible signal molecules to coordinate, among other things, the production of factors that are secreted outside of the cells in a process known as quorum sensing (QS). The underlying assumption made to explain QS is that the secretion of these extracellular factors is more beneficial at higher cell densities. However, this fundamental assumption has never been tested experimentally. Here, we directly test this by independently manipulating population density and the induction and response to the QS signal, using the opportunistic pathogen Pseudomonas aeruginosa as a model organism. We found that the benefit of QS was relatively greater at higher population densities, and that this was because of more efficient use of QS-dependent extracellular "public goods." In contrast, the benefit of producing "private goods," which are retained within the cell, does not vary with cell density. Overall, these results support the idea that QS is used to coordinate the switching on of social behaviors at high densities when such behaviors are more efficient and will provide the greatest benefit. PMID:22566647
Melzak, Kathryn A; Yu, Kai; Bo, Deng; Kizhakkedathu, Jayachandran N; Toca-Herrera, José L
2015-06-16
Poly(N,N-dimethylacrylamide) (PDMA) brushes with different grafting density and chain length were grown from an ester group-containing initiator using surface-initiated polymerization. Hydrolysis of the PDMA chains from the surface was monitored by measuring thickness of the polymer layer by ellipsometry and extension length by atomic force microscopy. It was found that the initial rate of cleavage of one end-tethered PDMA chains was dependent on the grafting density and chain length; the hydrolysis rate was faster for high grafting density brushes and brushes with higher molecular weights. Additionally, the rate of cleavage of polymer chains during a given experiment changed by up to 1 order of magnitude as the reaction progressed, with a distinct transition to a lower rate as the grafting density decreased. Also, polymer chains undergo selective cleavage, with longer chains in a polydisperse brush being preferentially cleaved at one stage of the hydrolysis reaction. We suggest that the enhanced initial hydrolysis rates seen at high grafting densities and high chain lengths are due to mechanical activation of the ester bond connecting the polymer chains to the surface in association with high lateral pressure within the brush. These results have implications for the preparation of polymers brushes, their stability under harsh conditions, and the analysis of polymer brushes from partial hydrolysates. PMID:26010390
Gotham, Steven; Song, Hojun
2013-11-01
Locusts are well known for exhibiting an extreme form of density-dependent phenotypic plasticity known as locust phase polyphenism. At low density, locust nymphs are cryptically colored and shy, but at high density they transform into conspicuously colored and gregarious individuals. Most of what we know about locust phase polyphenism come from the study of the desert locust Schistocerca gregaria (Forskål), which is a devastating pest species affecting many countries in North Africa and the Middle East. The desert locust belongs to the grasshopper genus Schistocerca Stål, which includes mostly non-swarming, sedentary species. Recent phylogenetic studies suggest that the desert locust is the earliest branching lineage within Schistocerca, which raises a possibility that the presence of density-dependent phenotypic plasticity may be a plesiomorphic trait for the whole genus. In order to test this idea, we have quantified the effect of rearing density in terms of the resulting behavior, color, and morphology in two non-swarming Schistocerca species native to Florida. When reared in both isolated and crowded conditions, the two non-swarming species, Schistocerca americana (Drury) and Schistocerca serialis cubense (Saussure) clearly exhibited plastic reaction norms in all traits measured, which were reminiscent of the desert locust. Specifically, we found that both species were more active and more attracted to each other when reared in a crowded condition than in isolation. They were mainly bright green in color when isolated, but developed strong black patterns and conspicuous background colors when crowded. We found a strong effect of rearing density in terms of size. There were also more mechanoreceptor hairs on the outer face of the hind femora in the crowded nymphs in both species. Although both species responded similarly, there were some clear species-specific differences in terms of color and behavior. Furthermore, we compare and contrast our findings with those on the desert locust and other relevant studies. We attribute the presence of density-dependent phenotypic plasticity in the non-swarming Schistocerca species to phylogenetic conservatism, but there may be a possible role of local adaptation in further shaping the ultimate expressions of plasticity. PMID:24035748
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, Pollard et al.'s, and Dennis and Taper's tests) or lack power (Bulmer's R* test), little justification exists for use of such tests to support or refute the hypothesis of density dependence.
Single-electron approach for time-dependent electron transport
NASA Astrophysics Data System (ADS)
Gurvitz, Shmuel
2015-10-01
We developed a new approach to electron transport in mesoscopic systems by using a particular single-particle basis. Although this basis generates redundant many-particle amplitudes, it greatly simplifies the treatment. By using our method for transport of non-interacting electrons, we generalize the Landauer formula for transient currents and time-dependent potentials. The result has a very simple form and clear physical interpretation. As an example, we apply it to resonant tunneling through a quantum dot where the tunneling barriers are oscillating in time. We obtain an analytical expression for the time-dependent (ac) resonant current. However, in the adiabatic limit this expression displays the dc current for zero bias (electron pumping).
A Dynamic Approach to Modeling Dependence Between Human Failure Events
Boring, Ronald Laurids
2015-09-01
In practice, most HRA methods use direct dependence from 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.
Flockhart, D T Tyler; Martin, Tara G; Norris, D Ryan
2012-01-01
A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism. PMID:22984614
Flockhart, D. T. Tyler; Martin, Tara G.; Norris, D. Ryan
2012-01-01
A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism. PMID:22984614
Time-dependent Kohn-Sham approach to quantum electrodynamics
Ruggenthaler, M.; Mackenroth, F.; Bauer, D.
2011-10-15
We prove a generalization of the van Leeuwen theorem toward quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. We circumvent the symmetry-causality problems associated with the action-functional approach to Kohn-Sham systems. We show that the effective external four-potential and four-current of the Kohn-Sham system are uniquely defined and that the effective four-current takes a very simple form. Further we rederive the Runge-Gross theorem for quantum electrodynamics.
Time-dependent resonant scattering: An analytical approach
NASA Astrophysics Data System (ADS)
Lecomte, J. M.; Kirrander, Adam; Jungen, Ch.
2013-10-01
A time-dependent description is given of a scattering process involving a single resonance embedded in a set of flat continua. An analytical approach is presented which starts from an incident free particle wave packet and yields the Breit-Wigner cross-section formula at infinite times. We show that at intermediate times the so-called Wigner-Weisskopf approximation is equivalent to a scattering process involving a contact potential. Applications in cold-atom scattering and resonance enhanced desorption of molecules are discussed.
Time-dependent, lattice approach to atomic collisions
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.
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.
Resampling Method for Applying Density-Dependent Habitat Selection Theory to Wildlife Surveys
Tardy, Olivia; Massé, Ariane; Pelletier, Fanie; Fortin, Daniel
2015-01-01
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents. PMID:26042998
Resampling method for applying density-dependent habitat selection theory to wildlife surveys.
Tardy, Olivia; Massé, Ariane; Pelletier, Fanie; Fortin, Daniel
2015-01-01
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large geographic extents. PMID:26042998
Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent
Phaiboun, Andy; Zhang, Yiming; Park, Boryung; Kim, Minsu
2015-01-01
In the lifecycle of microorganisms, prolonged starvation is prevalent and sustaining life during starvation periods is a vital task. In the literature, it is commonly assumed that survival kinetics of starving microbes follows exponential decay. This assumption, however, has not been rigorously tested. Currently, it is not clear under what circumstances this assumption is true. Also, it is not known when such survival kinetics deviates from exponential decay and if it deviates, what underlying mechanisms for the deviation are. Here, to address these issues, we quantitatively characterized dynamics of survival and death of starving E. coli cells. The results show that the assumption – starving cells die exponentially – is true only at high cell density. At low density, starving cells persevere for extended periods of time, before dying rapidly exponentially. Detailed analyses show intriguing quantitative characteristics of the density-dependent and biphasic survival kinetics, including that the period of the perseverance is inversely proportional to cell density. These characteristics further lead us to identification of key underlying processes relevant for the perseverance of starving cells. Then, using mathematical modeling, we show how these processes contribute to the density-dependent and biphasic survival kinetics observed. Importantly, our model reveals a thrifty strategy employed by bacteria, by which upon sensing impending depletion of a substrate, the limiting substrate is conserved and utilized later during starvation to delay cell death. These findings advance quantitative understanding of survival of microbes in oligotrophic environments and facilitate quantitative analysis and prediction of microbial dynamics in nature. Furthermore, they prompt revision of previous models used to analyze and predict population dynamics of microbes. PMID:25838110
Adapting approximate-memory potentials for time-dependent density functional theory
NASA Astrophysics Data System (ADS)
Kurzweil, Yair; Baer, Roi
2008-02-01
Frequency dependent exchange-correlation kernels for time-dependent density functional theory can be used to construct approximate exchange-correlation potentials. The resulting potentials are usually not translationally covariant nor do they obey the so-called zero-force condition. These two basic symmetry requirements are essential for using the potentials in actual applications (even in the linear regime). We provide two pragmatic methods for fully imposing these conditions for both linear and nonlinear regimes. As an example, we take the Gross and Kohn frequency dependent XC functional [Phys. Rev. Lett. 55, 2850 (1985)], correct it, and numerically test it on a sodium metal cluster. Violation of the basic symmetries causes instabilities or spurious low frequency modes.
Native defects in oxide semiconductors: a density functional approach
NASA Astrophysics Data System (ADS)
Oba, Fumiyasu; Choi, Minseok; Togo, Atsushi; Seko, Atsuto; Tanaka, Isao
2010-09-01
We report a semilocal and hybrid Hartree-Fock density functional study of native defects in three oxide semiconductors: ZnO, SrTiO3, and SnO. The defect that is responsible for the n-type conductivity of ZnO has been debated, in which the O vacancy, Zn interstitial, their complexes, and residual H impurity are considered candidates. Our results indicate that the O vacancy induces a deep and localized in-gap state, whereas the Zn interstitial is a shallow donor and hence can be a source of the carriers. In view of the formation energies, the O vacancy is likely to form with a substantial concentration under O-poor conditions, but the Zn interstitial is unlikely. We thus propose that the O vacancy is relevant to the nonstoichiometry of ZnO and that a source other than the native defects, such as the H impurity, needs to be considered for the n-type conductivity. For SrTiO3, the O vacancy and its complexes have been regarded as the origins of some of the remarkable electrical and optical properties. We suggest significant roles of the Ti antisite for a new insight into the defect-induced properties. Two types of Ti antisite, both of which are off-centered from the Sr site but toward different directions, exhibit low formation energies under Ti-rich conditions as does the O vacancy. They can explain optical properties such as visible-light emission, deep-level absorption, and the ferroelectricity observed in reduced SrTiO3. As an example of p-type conductors, SnO has been investigated with a focus on the acceptor-like native defects. Under O-rich conditions, the Sn vacancy and O interstitial are found to be energetically favorable. The Sn vacancy induces shallow acceptor levels and can therefore be a source of carriers. The O interstitial shows no in-gap levels and hence it is inactive in terms of the carrier generation and compensation. However, this defect is a key to the understanding of the structures of intermediate compounds between SnO and SnO2.
Rao, Rekha R.; Mondy, Lisa Ann; Noble, David R.; Brunini, Victor; Roberts, Christine Cardinal; Long, Kevin Nicholas; Soehnel, Melissa Marie; Celina, Mathias C.; Wyatt, Nicholas B.; Thompson, Kyle R.; Tinsley, James
2015-09-01
We are studying PMDI polyurethane with a fast catalyst, such that filling and polymerization occur simultaneously. The foam is over-packed to tw ice or more of its free rise density to reach the density of interest. Our approach is to co mbine model development closely with experiments to discover new physics, to parameterize models and to validate the models once they have been developed. The model must be able to repres ent the expansion, filling, curing, and final foam properties. PMDI is chemically blown foam, wh ere carbon dioxide is pr oduced via the reaction of water and isocyanate. The isocyanate also re acts with polyol in a competing reaction, which produces the polymer. A new kinetic model is developed and implemented, which follows a simplified mathematical formalism that decouple s these two reactions. The model predicts the polymerization reaction via condensation chemis try, where vitrification and glass transition temperature evolution must be included to correctly predict this quantity. The foam gas generation kinetics are determined by tracking the molar concentration of both water and carbon dioxide. Understanding the therma l history and loads on the foam due to exothermicity and oven heating is very important to the results, since the kinetics and ma terial properties are all very sensitive to temperature. The conservation eq uations, including the e quations of motion, an energy balance, and thr ee rate equations are solved via a stabilized finite element method. We assume generalized-Newtonian rheology that is dependent on the cure, gas fraction, and temperature. The conservation equations are comb ined with a level set method to determine the location of the free surface over time. Results from the model are compared to experimental flow visualization data and post-te st CT data for the density. Seve ral geometries are investigated including a mock encapsulation part, two configur ations of a mock stru ctural part, and a bar geometry to specifically test the density model. We have found that the model predicts both average density and filling profiles well. However, it under predicts density gradients, especially in the gravity direction. Thoughts on m odel improvements are also discussed.
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 the model results to CHAMP and Streak observations and assess the distinctive features of the observations in terms of the various dependencies involved. Acknowledgements: This research was supported by The Aerospace Corporation's Technical Investment program
Density-dependent reduction and induction of milkweed cardenolides by a sucking insect herbivore.
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. PMID:15139307
Inter-cohort competition drives density dependence and selective mortality in a marine fish.
Samhouri, Jameal F; Steele, Mark A; Forrester, Graham E
2009-04-01
For organisms with complex life cycles, the transition between life stages and between habitats can act as a significant demographic and selective bottleneck. In particular, competition with older and larger conspecifics and heterospecifics may influence the number and characteristics of individuals successfully making the transition. We investigated whether the availability of enemy-free space mediated the interaction between adult goldspot gobies (Gnatholepis thompsoni), a common tropical reef fish, and juvenile conspecifics that had recently settled from the plankton. We added rocks, which provide refuge from predators, to one-half of each of five entire coral reefs in the Bahamas and measured the survival and growth of recent settlers in relation to adult goby densities. We also evaluated whether mortality was selective with respect to three larval traits (age at settlement, size at settlement, and presettlement growth rate) and measured the influence of refuge availability and adult goby density on selection intensity. Selective mortality was measured by comparing larval traits of newly settled gobies (< or = 5 d postsettlement) with those of survivors (2-3 week postsettlement juveniles). We detected a negative relationship between juvenile survival and adult goby density in both low- and high-refuge habitats, though experimental refuge addition reduced the intensity of this density dependence. Juvenile growth also declined with increasing adult goby density, but this effect was similar in both low- and high-refuge habitats. Refuge availability had no consistent effect on selective mortality, but adult goby density was significantly related to the intensity of size-selective mortality: bigger juveniles were favored where adults were abundant, and smaller juveniles were favored where adults were rare. Given the typically large difference in sizes of juveniles and adults, similar stage-structured interactions may be common but underappreciated in many marine species. PMID:19449695
Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems.
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. PMID:27074689
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.
Space-dependent color gamut mapping: a variational approach.
Kimmel, Ron; Shaked, Doron; Elad, Michael; Sobel, Irwin
2005-06-01
Gamut mapping deals with the need to adjust a color image to fit into the constrained color gamut of a given rendering medium. A typical use for this tool is the reproduction of a color image prior to its printing, such that it exploits best the given printer/medium color gamut, namely the colors the printer can produce on the given medium. Most of the classical gamut mapping methods involve a pixel-by-pixel mapping and ignore the spatial color configuration. Recently proposed spatial-dependent approaches for gamut mapping are either based on heuristic assumptions or involve a high computational cost. In this paper, we present a new variational approach for space-dependent gamut mapping. Our treatment starts with the presentation of a new measure for the problem, closely related to a recent measure proposed for Retinex. We also link our method to recent measures that attempt to couple spectral and spatial perceptual measures. It is shown that the gamut mapping problem leads to a quadratic programming formulation, guaranteed to have a unique solution if the gamut of the target device is convex. An efficient numerical solution is proposed with promising results. PMID:15971778
White, J Wilson; Samhouri, Jameal F; Stier, Adrian C; Wormald, Clare L; Hamilton, Scott L; Sandin, Stuart A
2010-07-01
Coral and rocky reef fish populations are widely used as model systems for the experimental exploration of density-dependent vital rates, but patterns of density-dependent mortality in these systems are not yet fully understood. In particular, the paradigm for strong, directly density-dependent (DDD) postsettlement mortality stands in contrast to recent evidence for inversely density-dependent (IDD) mortality. We review the processes responsible for DDD and IDD per capita mortality in reef fishes, noting that the pattern observed depends on predator and prey behavior, the spatial configuration of the reef habitat, and the spatial and temporal scales of observation. Specifically, predators tend to produce DDD prey mortality at their characteristic spatial scale of foraging, but prey mortality is IDD at smaller spatial scales due to attack-abatement effects (e.g., risk dilution). As a result, DDD mortality may be more common than IDD mortality on patch reefs, which tend to constrain predator foraging to the same scale as prey aggregation, eliminating attack-abatement effects. Additionally, adjacent groups of prey on continuous reefs may share a subset of refuges, increasing per capita refuge availability and relaxing DDD mortality relative to prey on patch reefs, where the patch edge could prevent such refuge sharing. These hypotheses lead to a synthetic framework to predict expected mortality patterns for a variety of scenarios. For nonsocial, nonaggregating species and species that aggregate in order to take advantage of spatially clumped refuges, IDD mortality is possible but likely superseded by DDD refuge competition, especially on patch reefs. By contrast, for species that aggregate socially, mortality should be IDD at the scale of individual aggregations but DDD at larger scales. The results of nearly all prior reef fish studies fit within this framework, although additional work is needed to test many of the predicted outcomes. This synthesis reconciles some apparent contradictions in the recent reef fish literature and suggests the importance of accounting for the scale-sensitive details of predator and prey behavior in any study system. PMID:20715614
NASA Astrophysics Data System (ADS)
Puhakka, P. H.; Ylärinne, J. H.; Lammi, M. J.; Saarakkala, S.; Tiitu, V.; Kröger, H.; Virén, T.; Jurvelin, J. S.; Töyräs, J.
2014-11-01
Optical coherence tomography (OCT) has been applied for high resolution imaging of articular cartilage. However, the contribution of individual structural elements of cartilage on OCT signal has not been thoroughly studied. We hypothesize that both collagen and chondrocytes, essential structural components of cartilage, act as important light scatterers and that variation in their concentrations can be detected by OCT through changes in backscattering and attenuation. To evaluate this hypothesis, we established a controlled model system using agarose scaffolds embedded with variable collagen concentrations and chondrocyte densities. Using OCT, we measured the backscattering coefficient (µb) and total attenuation coefficient (µt) in these scaffolds. Along our hypothesis, light backscattering and attenuation in agarose were dependent on collagen concentration and chondrocyte density. Significant correlations were found between µt and chondrocyte density (ρ = 0.853, p < 0.001) and between µt and collagen concentration (ρ = 0.694, p < 0.001). µb correlated significantly with chondrocyte density (ρ = 0.504, p < 0.001) but not with collagen concentration (ρ = 0.103, p = 0.422) of the scaffold. Thus, quantitation of light backscattering and, especially, attenuation could be valuable when evaluating the integrity of soft tissues, such as articular cartilage with OCT.
NASA Astrophysics Data System (ADS)
Farzanehpour, Mehdi; Tokatly, Ilya; Nano-Bio Spectroscopy Group; ETSF Scientific Development Centre Team
2015-03-01
We present a rigorous formulation of the time-dependent density functional theory for interacting lattice electrons strongly coupled to cavity photons. We start with an example of one particle on a Hubbard dimer coupled to a single photonic mode, which is equivalent to the single mode spin-boson model or the quantum Rabi model. For this system we prove that the electron-photon wave function is a unique functional of the electronic density and the expectation value of the photonic coordinate, provided the initial state and the density satisfy a set of well defined conditions. Then we generalize the formalism to many interacting electrons on a lattice coupled to multiple photonic modes and prove the general mapping theorem. We also show that for a system evolving from the ground state of a lattice Hamiltonian any density with a continuous second time derivative is locally v-representable. Spanish Ministry of Economy and Competitiveness (Grant No. FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13), COST Actions CM1204 (XLIC) and MP1306 (EUSpec).
Density-Dependent Effects of an Invasive Ant on a Ground-Dwelling Arthropod Community.
Cooling, M; Sim, D A; Lester, P J
2015-02-01
It is frequently assumed that an invasive species that is ecologically or economically damaging in one region, will typically be so in other environments. The Argentine ant Linepithema humile (Mayr) is listed among the world's worst invaders. It commonly displaces resident ant species where it occurs at high population densities, and may also reduce densities of other ground-dwelling arthropods. We investigated the effect of varying Argentine ant abundance on resident ant and nonant arthropod species richness and abundance in seven cities across its range in New Zealand. Pitfall traps were used to compare an invaded and uninvaded site in each city. Invaded sites were selected based on natural varying abundance of Argentine ant populations. Argentine ant density had a significant negative effect on epigaeic ant abundance and species richness, but hypogaeic ant abundance and species richness was unaffected. We observed a significant decrease in Diplopoda abundance with increasing Argentine ant abundance, while Coleoptera abundance increased. The effect on Amphipoda and Isopoda depended strongly on climate. The severity of the impact on negatively affected taxa was reduced in areas where Argentine ant densities were low. Surprisingly, Argentine ants had no effect on the abundance of the other arthropod taxa examined. Morphospecies richness for all nonant arthropod taxa was unaffected by Argentine ant abundance. Species that are established as invasive in one location therefore cannot be assumed to be invasive in other locations based on presence alone. Appropriate management decisions should reflect this knowledge. PMID:26308805
Albuquerque, Patrícia; Nicola, André M.; Nieves, Edward; Paes, Hugo Costa; Williamson, Peter R.; Silva-Pereira, Ildinete; Casadevall, Arturo
2013-01-01
ABSTRACT Quorum sensing (QS) is a cell density-dependent mechanism of communication between microorganisms, characterized by the release of signaling molecules that affect microbial metabolism and gene expression in a synchronized way. In this study, we investigated cell density-dependent behaviors mediated by conditioned medium (CM) in the pathogenic encapsulated fungus Cryptococcus neoformans. CM produced dose-dependent increases in the growth of planktonic and biofilm cells, glucuronoxylomannan release, and melanin synthesis, important virulence attributes of this organism. Mass spectrometry revealed the presence of pantothenic acid (PA) in our samples, and commercial PA was able to increase growth and melanization, although not to the same extent as CM. Additionally, we found four mutants that were either unable to produce active CM or failed to respond with increased growth in the presence of wild-type CM, providing genetic evidence for the existence of intercellular communication in C. neoformans. C. neoformans CM also increased the growth of Cryptococcus albidus, Candida albicans, and Saccharomyces cerevisiae. Conversely, CM from Cryptococcus albidus, C. albicans, S. cerevisiae, and Sporothrix schenckii increased C. neoformans growth. In summary, we report the existence of a new QS system regulating the growth and virulence factor expression of C. neoformans in vitro and, possibly, also able to regulate growth in other fungi. PMID:24381301
Dependence of the cosmic microwave background lensing power spectrum on the matter density
NASA Astrophysics Data System (ADS)
Pan, Z.; Knox, L.; White, M.
2014-12-01
The anisotropies in the cosmic microwave background (CMB) provide our best laboratory for testing models of the formation and evolution of large-scale structure. The rich features in the CMB anisotropy spectrum, in combination with highly precise observations and theoretical predictions, also allow us to simultaneously constrain a number of cosmological parameters. As observations have progressed, measurements at smaller angular scales have provided increasing leverage. These smaller angular scales provide sensitive measures of the matter density through the effect of gravitational lensing. In this work, we provide an analytic explanation of the manner in which the lensing of CMB anisotropies depends on the matter density, finding that the dominant effect comes from the shape of the matter power spectrum set by the decay of small-scale potentials between horizon crossing and matter-radiation equality.
Guido, Ciro A. Cortona, Pietro; Adamo, Carlo; Institut Universitaire de France, 103 Bd Saint-Michel, F-75005 Paris
2014-03-14
We extend our previous definition of the metric 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.
Verdict: Time-Dependent Density Functional Theory "Not Guilty" of Large Errors for Cyanines.
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. PMID:26596742
Density-dependent cooperation as a mechanism for persistence and coexistence.
Lampert, Adam; Tlusty, Tsvi
2011-10-01
To overcome stress, such as resource limitation, an organism often needs to successfully mediate competition with other members of its own species. This may favor the evolution of defective traits that are harmful to the species population as a whole, and that may lead to its dilution or even to its extinction (the tragedy of the commons). Here, we show that this phenomenon can be circumvented by cooperation plasticity, in which an individual decides, based on environmental conditions, whether to cooperate or to defect. Specifically, we analyze the evolution of density-dependent cooperation. In our model, the population is spatially subdivided, periodically remixed, and comprises several species. We find that evolution pushes individuals to be more cooperative when their own species is at lower densities, and we show that not only could this cooperation prevent the tragedy of the commons, but it could also facilitate coexistence between many species that compete for the same resource. PMID:21967418
Dynamical behaviors for 1D compressible Navier-Stokes equations with density-dependent viscosity
NASA Astrophysics Data System (ADS)
Lian, Ruxu; Guo, Zhenhua; Li, Hai-Liang
The dynamical behaviors of vacuum states for one-dimensional compressible Navier-Stokes equations with density-dependent viscosity coefficient are considered. It is first shown that a unique strong solution to the free boundary value problem exists globally in time, the free boundary expands outwards at an algebraic rate in time, and the density is strictly positive in any finite time but decays pointwise to zero time-asymptotically. Then, it is proved that there exists a unique global weak solution to the initial boundary value problem when the initial data contains discontinuously a piece of continuous vacuum and is regular away from the vacuum. The solution is piecewise regular and contains a piece of continuous vacuum before the time T>0, which is compressed at an algebraic rate and vanishes at the time T, meanwhile the weak solution becomes either a strong solution or a piecewise strong one and tends to the equilibrium state exponentially.
Density-dependent recruitment of the bloater (Coregonus hoyi) in Lake Michigan
Brown, Edward H., Jr.; Eck, Gary W.
1992-01-01
Density-dependent recruitment of the bloater (Coregonus hoyi) in Lake Michigan during and after recovery of the population in about 1977-1983 was best reflected in the fit of the Beverton-Holt recruitment function to age -1 and -2 recruits and estimated eggs of parents surveyed with trawls. A lower growth rate and lower lipid content of bloaters at higher population densities and no evidence of cannibalism supported the conclusion that recruitment is resource limited when alewife (Alosa pseudoharengus) abundance is low. Predation on larvae by alewives was indicated in earlier studies as the probable cause of depressed recruitment of bloaters before their recovery, which coincided with declining alewife abundance. This negative interaction masked any bloater stock-recruitment relation in the earlier period.
Density dependent hadronic models and the relation between neutron stars and neutron skin thickness
Avancini, S. S.; Marinelli, J. R.; Menezes, D. P.; Moraes, M. M. W.; Providencia, C.
2007-05-15
In the present work, we investigate the main differences in the lead neutron skin thickness, binding energy, surface energy, and density profiles obtained with two different density dependent hadron models. Our results are calculated within the Thomas-Fermi approximation with two different numerical prescriptions and compared with results obtained with a common parametrization of the nonlinear Walecka model. The neutron skin thickness is a reflex of the equation of state properties. Hence, a direct correlation is found between the neutron skin thickness and the slope of the symmetry energy. We show that within the present approximations, the asymmetry parameter for low momentum transfer polarized electron scattering is not sensitive to the model differences.
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
Reliable predictions of sediment transport and river morphology in response to driving forces, such as anthropogenic influences, are necessary for river engineering and management. Because engineering and management questions span a wide range of space and time scales, a broad spectrum of modeling approaches has been developed, ranging from sediment transport rating curves to complex three-dimensional, multiple grain-size morphodynamic models. Sediment transport rating curves assume a singular relation between sediment concentration and flow. This approach is attractive for evaluating long-term sediment budgets resulting from changes in flow regimes because it is simple to implement, computationally efficient, and the empirical parameters can be estimated from quantities that are commonly measured in the field (sediment concentration and flow). However, the assumption of a singular relation between sediment concentration and flow contains the following implicit assumptions: 1) that sediment transport is in equilibrium with sediment supply such that the grain-size distribution of the bed sediment is not changing, and 2) that the relation between flow and bed shear stress is constant. These assumptions present limitations that have led to the development of more complex numerical models of flow and morphodynamics. These models rely on momentum and mass conservation for water and sediment and thus have general applicability; however, this comes at a cost in terms of computations as well as the amount of data required for model set-up and testing. We present a hybrid approach that combines aspects of the standard sediment rating curve method and the more complex morphodynamic models. Our approach employs the idea of a shifting rating curve, whereby the relation between sediment concentration and flow changes as a function of the sediment budget in the reach. We have applied this alternative approach to the Colorado River below Glen Canyon Dam. This reach is 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.
Size-dependent error of the density functional theory ionization potential in vacuum and solution
Sosa Vazquez, Xochitl A.; Isborn, Christine M.
2015-12-22
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization 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
Size-dependent error of the density functional theory ionization potential in vacuum and solution
Sosa Vazquez, Xochitl A.; Isborn, Christine M.
2015-12-22
Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potential for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. As a result, in vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.
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.
Density dependence and risk of extinction in a small population of sea otters
Gerber, L.R.; Buenau, K.E.; VanBlaricom, G.
2004-01-01
Sea otters (Enhydra lutris (L.)) were hunted to extinction off the coast of Washington State early in the 20th century. A new population was established by translocations from Alaska in 1969 and 1970. The population, currently numbering at least 550 animals, A major threat to the population is the ongoing risk of majour oil spills in sea otter habitat. We apply population models to census and demographic data in order to evaluate the status of the population. We fit several density dependent models to test for density dependence and determine plausible values for the carrying capacity (K) by comparing model goodness of fit to an exponential model. Model fits were compared using Akaike Information Criterion (AIC). A significant negative relationship was found between the population growth rate and population size (r2=0.27, F=5.57, df=16, p<0.05), suggesting density dependence in Washington state sea otters. Information criterion statistics suggest that the model is the most parsimonious, followed closely by the logistic Beverton-Holt model. Values of K ranged from 612 to 759 with best-fit parameter estimates for the Beverton-Holt model including 0.26 for r and 612 for K. The latest (2001) population index count (555) puts the population at 87-92% of the estimated carrying capacity, above the suggested range for optimum sustainable population (OSP). Elasticity analysis was conducted to examine the effects of proportional changes in vital rates on the population growth rate (??). The elasticity values indicate the population is most sensitive to changes in survival rates (particularly adult survival).
Pressure Dependence of the Charge-Density-Wave Gap in Rare-Earth Tri-Tellurides
Sacchetti, A.; Arcangeletti, E.; Perucchi, A.; Baldassarre, L.; Postorino, P.; Lupi, S.; Ru, N.; Fisher, I.R.; Degiorgi, L.; /Zurich, ETH
2009-12-14
We investigate the pressure dependence of the optical properties of CeTe{sub 3}, which exhibits an incommensurate charge-density-wave (CDW) state already at 300 K. Our data are collected in the mid-infrared spectral range at room temperature and at pressures between 0 and 9 GPa. The energy for the single particle excitation across the CDW gap decreases upon increasing the applied pressure, similarly to the chemical pressure by rare-earth substitution. The broadening of the bands upon lattice compression removes the perfect nesting condition of the Fermi surface and therefore diminishes the impact of the CDW transition on the electronic properties of RTe{sub 3}.
Excitons in Organics Using Time-Dependent Density Functional Theory: PPV, Pentacene, and Picene.
Sharma, S; Dewhurst, J K; Shallcross, S; Madjarova, G K; Gross, E K U
2015-04-14
We apply the bootstrap kernel within time-dependent density functional theory to study the one-dimensional chain of polymer polyphenylenevinylene and molecular crystals of picene and pentacene. The absorption spectra of poly(p-phenylenevinylene) has a bound excitonic peak that is well-reproduced. Pentacene and picene, electronically similar materials, have remarkably different excitonic physics, and this difference is also well captured. We show that the inclusion of local-field effects dramatically changes the spectra of both picene and pentacene but not for poly(p-phenylenevinylene). PMID:26574381
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.
Charge transfer in time-dependent density-functional theory via spin-symmetry breaking
Fuks, Johanna I.; Maitra, Neepa T.
2011-04-15
Long-range charge-transfer excitations pose a major challenge for time-dependent density-functional approximations. We show that spin-symmetry breaking offers a simple solution for molecules composed of open-shell fragments, yielding accurate excitations at large separations when the acceptor effectively contains one active electron. Unrestricted exact-exchange and self-interaction-corrected functionals are performed on one-dimensional models and on the real LiH molecule within the pseudopotential approximation to demonstrate our results.
Barabash, O.M.; Santella, M.; Barabash, R.I.; Ice, G.E.; Tischler, J.
2011-12-14
The indentation-induced elastic-plastic zone in an IN 740 Ni-based superalloy was studied by three-dimensional (3-D) x-ray microdiffraction and electron back scattering diffraction (EBSD). Large lattice reorientations and the formation of geometrically necessary dislocations are observed in the area with a radius of {approx}75 {mu}m. A residual compression zone is found close to the indent edge. An elastic-plastic transition is observed at {approx}20 {mu}m from the indent edge. Depth dependent dislocation densities are determined at different distances from the indent edge.
Density determination of nano-layers depending to the thickness by non-destructive method
Gacem, A.; Doghmane, A.; Hadjoub, Z.
2013-12-16
Non-destructive tests used to characterize and observe the state of the solids near the surface or at depth, without damaging them or damaging them. Density is frequently used to follow the variations of the physical structure of the samples, as well as in the calculation of quantity of material required to fill a given volume, and it is also used to determine the homogeneity of a sample. However, the measurement of the acoustic properties (density, elastic constants,…) of a thin film whose thickness is smaller than several atomic layers is not easy to perform. For that reason, we expose in this work the effects of the thicknesses of thin films on the evolution of the density, where several samples are analyzed. The samples selected structures are thin films deposited on substrates, these coatings have thicknesses varying from a few atomic layers to ten or so micrometers and can change the properties of the substrate on which they are deposited. To do so, we considered a great number of layers (Cr, Al, SiO{sub 2}, ZnO, Cu, AlN, Si{sub 3}N{sub 4}, SiC) deposited on different substrates (Al{sub 2}O{sub 3}, Cu and Quartz). It is first shown that the density exhibits a dispersive behaviour. Such a behaviour is characterized by an initial increase (or decrease) followed by a saturated region. Further investigations of these dependences led to the determination of a semi-empirical universal relations, ρ=f(h/λ{sub T}), for all the investigated layer/substrate combination. Such expression could be of great importance in the density prediction of even layers thicknesses.
Miguel-Hidalgo, Jose J.; Overholser, James C.; Meltzer, Herbert Y.; Stockmeier, Craig A.; Rajkowska, Grazyna
2010-01-01
Background Reduced metabolism, blood flow, and tissue volume have been detected in the dorsolateral prefrontal cortex (dlPFC) of neurologically intact alcoholic subjects and these deficits are accompanied by lower density of neurons and glial cells. Another prefrontal region, the orbitofrontal cortex (ORB), functionally and structurally differentiated from the dlPFC, and heavily involved in decision-making processes, also shows functional alterations in alcoholic subjects. However, it is unknown whether changes in the packing density of neurons or glial cells also occur in the ORB and whether that density may be related to the increased suicide probability of alcoholic subjects or to the duration of alcohol dependence. Methods The present study used a 3-dimensional cell-counting method in postmortem brain tissue to determine the packing density of neurons and glial cells in the ORB (area 47) of 15 subjects with alcohol dependence (8 suicides, 7 nonsuicides) and 8 normal controls and to determine whether cell density is correlated with suicide and duration of alcohol dependence. Results There was a significantly lower density of both neurons (by 27%) and glial cells (by 25%) in the ORB of alcoholic subjects compared with controls. Packing density of either neurons or glial cells was not significantly different in alcoholic suicides compared with alcoholic nonsuicides. Age was not correlated with neuronal or glial density in either group. However, the duration of alcohol dependence and the ratio of that duration to the length of life span were significantly and negatively correlated to the overall density of neurons. Conclusion The present results indicate that alcohol dependence is associated with a decrease in the packing density of neurons and glia in the ORB and that the reduction in neuronal but not glial density progresses with the duration of alcohol dependence. PMID:17067348
NASA Astrophysics Data System (ADS)
Lipatov, A. V.; Zotov, N. P.
2014-11-01
We study the associated production of real (isolated) or virtual photons (with their subsequent leptonic decay) and hadronic jets in proton-proton collisions at the LHC using the kT-factorization approach of QCD. The consideration is based on the off-shell quark-gluon QCD Compton scattering subprocesses. In the case of virtual photon production, the contributions from Z boson exchange as well as ?*-Z interference with the full spin correlations are included. The transversemomentum-dependent (TMD) quark and gluon densities in a proton are determined from the Kimber-Martin-Ryskin prescription or Catani-Ciafoloni-Fiorani-Marchesini (CCFM) equation. In the latter, we restrict to the case where the gluon-to-quark splitting occurs at the last evolution step and calculate the sea quark density as a convolution of the CCFM-evolved gluon distribution and the TMD gluon-to-quark splitting function. Our numerical predictions are compared with the recent experimental data taken by the ATLAS Collaboration. We discuss the theoretical uncertainties of our calculations and argue that further studies are capable of constraining the TMD parton densities in the proton.
NASA Astrophysics Data System (ADS)
Li, Hao; Chen, Guang; Sinha, Shayandev; Das, Siddhartha; Soft Matter, Interfaces,; Energy Laboratory (Smiel) Team
Understanding the electric double layer (EDL) electrostatics of spherical polyelectrolyte (PE) brushes, which are spherical particles grafted with PE layers, is essential for appropriate use of PE-grfated micro-nanoparticles for targeted drug delivery, oil recovery, water harvesting, emulsion stabilization, emulsion breaking, etc. Here we elucidate the EDL electrostatics of spherical PE brushes for the case where the PE exhibits pH-dependent charge density. This pH-dependence necessitates the consideration of explicit hydrogen ion concentration, which in turn dictates the distribution of monomers along the length of the grafted PE. This monomer distribution is shown to be a function of the nature of the sphere (metallic or a charged or uncharged dielectric or a liquid-filled sphere). All the calculations are performed for the case where the PE electrostatics can be decoupled from the PE elastic and excluded volume effects. Initial predictions are also provided for the case where such decoupling is not possible.
Ionic thermal effects on photo-electron emission within time-dependent density-functional theory
NASA Astrophysics Data System (ADS)
Gao, Cong-Zhang; Dinh, Phuong Mai; Reinhard, Paul-Gerhard; Suraud, Eric
2016-02-01
We study the impact of thermal fluctuations of cluster/molecule shape on photo-electron spectra (PES) and photo-electron angular distributions (PAD) using a detailed time-dependent simulation of the emission dynamics and thermal ionic motion. Basis of the description is time-dependent density-functional theory (TDDFT) coupled to molecular dynamics for ionic motion. Test cases are small Na clusters and the C3 molecule. For Na clusters, we find that PES signals are rather robust for one-photon processes while large smearing of the pattern are observed at lower frequencies in multi-photon processes. This effect can be related to the typical spectral response of the metal clusters. PAD are generally much more robust than PES. The C3 molecule produces a greater variety of thermal response. This happens because this molecule has eigenmodes with much different softness.
Field Dependence of the Spin Density Wave Transition Temperature in (TMTSF)_2PF_6
NASA Astrophysics Data System (ADS)
Leone, M. J.; Lee, I. J.; Hope, A. P.; Naughton, M. J.
1997-03-01
The magnetic field dependence of the Spin Density Wave transition in (TMTSF)_2PF6 has been studied at ambient pressure to 17 Tesla using cantilever magnetometry. Simultaneous resistance and torque magnetization measurements have been conducted on a single crystal (Hallelc^*+20^o). Above the spin flop field, we find both measurements yield a linear relationship between T_SDW and the applied field, with slope 0.036 K/T. This appears to be inconsistent with theoretical works by Montambaux(G. Montambaux, Phys. Rev. B 38), 4788 (1988), Bjelis and Maki(A. Bjelis and K. Maki, Phys. Rev. B 45), 12887 (1992), which predict a quadratic dependence at low field followed by saturation at high field. Investigations to higher fields will be reported. ^* Supported by NSF DMR-9258579
Temperature-Dependent Studies of Charge Density Wave States in TbTe3
NASA Astrophysics Data System (ADS)
Boyer, Michael; Kraft, Aaron; Fu, Ling; Sharma, Bishnu; Fisher, Ian
We use temperature-dependent scanning tunneling microscopy (STM) to study charge density wave (CDW) states in TbTe3. TbTe3 undergoes a bulk CDW transition near 335 K, though x-ray data shows evidence for CDW fluctuations up to 363 K. Our STM measurements characterize the well-established, long-range, unidirectional CDW state (qcdw = 0.71 c*) at 300 K. Our temperature-dependent measurements above TCDW show evidence for localized static CDW order which is consistent with x-ray detection of CDW fluctuations above TCDW. Surprisingly, we also find evidence for localized static order associated with a second CDW along the a-axis, a CDW state which never establishes long-range coherence in the bulk of TbTe3 even at low temperatures.
Hone, Jim; Sibly, Richard M
2002-09-29
Identifying the determinants of population growth rate is a central topic in population ecology. Three approaches (demographic, mechanistic and density-dependent) used historically to describe the determinants of population growth rate are here compared and combined for an avian predator, the barn owl (Tyto alba). The owl population remained approximately stable (r approximately 0) throughout the period from 1979 to 1991. There was no evidence of density dependence as assessed by goodness of fit to logistic population growth. The finite (lambda) and instantaneous (r) population growth rates were significantly positively related to food (field vole) availability. The demographic rates, annual adult mortality, juvenile mortality and annual fecundity were reported to be correlated with vole abundance. The best fit (R(2) = 0.82) numerical response of the owl population described a positive effect of food (field voles) and a negative additive effect of owl abundance on r. The numerical response of the barn owl population to food availability was estimated from both census and demographic data, with very similar results. Our analysis shows how the demographic and mechanistic determinants of population growth rate are linked; food availability determines demographic rates, and demographic rates determine population growth rate. The effects of food availability on population growth rate are modified by predator abundance. PMID:12396509
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
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 cocklesCerastoderma edule) across 50 km² of mudflat, and simultaneously, with a novel time-of-arrival methodology, tracked their avian predators (red knotsCalidris 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
Sex modulates approach systems and impulsivity in substance dependence
Perry, Robert I.; Krmpotich, Theodore; Thompson, Laetitia L.; Mikulich-Gilbertson, Susan K.; Banich, Marie T.; Tanabe, Jody
2013-01-01
Background Personality traits such as pathological engagement in approach behaviors, high levels of impulsivity and heightened negative affect are consistently observed in substance dependent individuals (SDI). The clinical course of addiction has been shown to differ between sexes. For example, women increase their rates of consumption of some drugs of abuse more quickly than men. Despite the potential influence of personality and sex on features of addiction, few studies have investigated the interaction of these factors in substance dependence. Methods Fifty-one SDI (26 male, 25 female) and 66 controls (41 male, 25 female) completed the Behavioral Inhibition/Behavioral Activation System (BIS/BAS) Scales, the Barratt Impulsiveness Scale, and the Positive and Negative Affect Schedule (PANAS-X). Data were analyzed with 2×2 ANCOVAs testing for main effects of group, sex and group by sex interactions, adjusting for education level. Results Significant group by sex interactions were observed for BAS scores [F(1,116)=7.03, p<.01] and Barratt Motor Impulsiveness [F(1,116)=6.11, p<.02] with female SDI showing the highest approach tendencies and impulsivity followed by male SDI, male controls, and finally female controls. SDI scored higher on negative affect [F(1,116)=25.23, p<.001] than controls. Behavioral Inhibition System scores were higher in women than men [F(1,116)=14.03, p< .001]. Conclusion Higher BAS and motor impulsivity in SDI women relative to SDI men and control women suggest that personality traits that have been previously associated with drug use may be modulated by sex. These factors may contribute to differences in the disease course observed in male compared to female drug users. PMID:23725607
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.
Antonić, Oleg; Sudarić-Bogojević, Mirta; Lothrop, Hugh; Merdić, Enrih
2014-09-01
The direct inclusion of environmental factors into the empirical model that describes a density-distance relationship (DDR) is demonstrated on dispersal data obtained in a capture-mark-release-recapture experiment (CMRR) with Culex tarsalis conducted around the community of Mecca, CA. Empirical parameters of standard (environmentally independent) DDR were expressed as linear functions of environmental variables: relative orientation (azimuthal deviation of north) of release point (relative to recapture point) and proportions of habitat types surrounding each recapture point. The yielded regression model (R(2) = 0.5373, after optimization on the best subset of linear terms) suggests that spatial density of recaptured individuals after 12 days of a CMRR experiment significantly depended on 1) distance from release point, 2) orientation of recapture points in relation to release point (preferring dispersal toward the south, probably due to wind drift and position of periodically flooded habitats suitable for species egg clutches), and 3) habitat spectrum in surroundings of recapture points (increasing and decreasing population density in desert and urban environment, respectively). PMID:25843098
Density-dependent predation influences the evolution and behavior of masquerading prey
Skelhorn, John; Rowland, Hannah M.; Delf, Jon; Speed, Michael P.; Ruxton, Graeme D.
2011-01-01
Predation is a fundamental process in the interaction between species, and exerts strong selection pressure. Hence, anti-predatory traits have been intensively studied. Although it has long been speculated that individuals of some species gain protection from predators by sometimes almost-uncanny resemblances to uninteresting objects in the local environment (such as twigs or stones), demonstration of antipredatory benefits to such “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
Young-Wolff, Kelly C.; Henriksen, Lisa; Delucchi, Kevin
2014-01-01
Objectives. We examined the density and proximity of tobacco retailers and associations with smoking behavior and mental health in a diverse sample of 1061 smokers with serious mental illness (SMI) residing in the San Francisco Bay Area of California. Methods. Participants’ addresses were geocoded and linked with retailer licensing data to determine the distance between participants’ residence and the nearest retailer (proximity) and the number of retailers within 500-meter and 1-kilometer service areas (density). Results. More than half of the sample lived within 250 meters of a tobacco retailer. A median of 3 retailers were within 500 meters of participants’ residences, and a median of 12 were within 1 kilometer. Among smokers with SMI, tobacco retailer densities were 2-fold greater than for the general population and were associated with poorer mental health, greater nicotine dependence, and lower self-efficacy for quitting. Conclusions. Our findings provide further evidence of the tobacco retail environment as a potential vector contributing to tobacco-related disparities among individuals with SMI and suggest that this group may benefit from progressive environmental protections that restrict tobacco retail licenses and reduce aggressive point-of-sale marketing. PMID:24922145
A DENSITY DEPENDENCE FOR PROTOSTELLAR LUMINOSITY IN CLASS I SOURCES: COLLABORATIVE ACCRETION
Elmegreen, Bruce G.; Hurst, Rachel; Koenig, Xavier
2014-02-10
Class I protostars in three high-mass star-forming regions are found to have correlations among the local projected density of other Class I protostars, the summed flux from these other protostars, and the protostellar luminosity in the WISE 22 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.
Density dependent B parameter of relativistic stars with anisotropy in pseudo-spheroidal space-time
NASA Astrophysics Data System (ADS)
Chattopadhyay, P. K.; Paul, B. C.
2016-04-01
We present a class of relativistic solutions for compact cold stars with strange matter in a pseudo-spheroidal space-time. Considering strange matter equation of state namely, p = 1/3(ρ -4B), where ρ , p and B are energy density, pressure and MIT Bag parameter respectively, stellar models are obtained. In the presence of anisotropy with a pseudo-spheroidal geometry described by Vaidya-Tikekar, metric stellar models are explored where the Bag parameter varies with the energy density (ρ ) inside the compact object. We determine the density dependence of B at different anisotropy. It is noted that although B varies with anisotropy inside the star, finally at the surface it attains a value which is independent of the anisotropy. The Bag parameter B is found to increase with an increase in anisotropy for a given compactness factor (M/b) and spheroidicity λ . It is also noted that for a star with given mass and radius, the parameter B increases with the increase in λ and finally at large λ , it attains a constant. The equation of state (EoS) obtained here from geometrical consideration with allowed `B' value is found same to that one obtains from micro-physics. The stability of the stellar models for compact stars with anisotropy in hydrostatic equilibrium obtained here is also studied.
Mori, Masaki; Triboulet, Robinson; Mohseni, Morvarid; Schlegelmilch, Karin; Shrestha, Kriti; Camargo, Fernando D; Gregory, Richard I
2014-02-27
Global downregulation of microRNAs (miRNAs) is commonly observed in human cancers and can have a causative role in tumorigenesis. The mechanisms responsible for this phenomenon remain poorly understood. Here, we show that YAP, the downstream target of the tumor-suppressive Hippo-signaling pathway regulates miRNA biogenesis in a cell-density-dependent manner. At low cell density, nuclear YAP binds and sequesters p72 (DDX17), a regulatory component of the miRNA-processing machinery. At high cell density, Hippo-mediated cytoplasmic retention of YAP facilitates p72 association with Microprocessor and binding to a specific sequence motif in pri-miRNAs. Inactivation of the Hippo pathway or expression of constitutively active YAP causes widespread miRNA suppression in cells and tumors and a corresponding posttranscriptional induction of MYC expression. Thus, the Hippo pathway links contact-inhibition regulation to miRNA biogenesis and may be responsible for the widespread miRNA repression observed in cancer. PMID:24581491
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. PMID:20528180
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.
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.
Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities
Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz
2005-03-01
Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP.
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.
Density dependence explains tree species abundance and diversity in tropical forests.
Volkov, Igor; Banavar, Jayanth R; He, Fangliang; Hubbell, Stephen P; Maritan, Amos
2005-12-01
The recurrent patterns in the commonness and rarity of species in ecological communities--the relative species abundance--have puzzled ecologists for more than half a century. Here we show that the framework of the current neutral theory in ecology can easily be generalized to incorporate symmetric density dependence. We can calculate precisely the strength of the rare-species advantage that is needed to explain a given RSA distribution. Previously, we demonstrated that a mechanism of dispersal limitation also fits RSA data well. Here we compare fits of the dispersal and density-dependence mechanisms for empirical RSA data on tree species in six New and Old World tropical forests and show that both mechanisms offer sufficient and independent explanations. We suggest that RSA data cannot by themselves be used to discriminate among these explanations of RSA patterns--empirical studies will be required to determine whether RSA patterns are due to one or the other mechanism, or to some combination of both. PMID:16319890
A comprehensive approach to age-dependent dosimetric modeling
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.
Nalmefene: a new approach to the treatment of alcohol dependence
Paille, François; Martini, Hervé
2014-01-01
Reduction of alcohol consumption is not yet a widely accepted treatment objective for alcohol-dependent patients, as abstinence is often considered to be the only possible objective in this situation. However, various studies have demonstrated the value of proposing these two options to such patients. Firstly, reduction of alcohol consumption very significantly reduces the risk of alcohol-related damage, and also modifies the patient’s and the doctor’s perception of the disease, resulting in improved access to care and better patient adherence with the proposed treatment objective and consequently better clinical results. Recent studies have shown that some medicinal products can help patients reduce their alcohol consumption. One such product, nalmefene, has been granted European marketing authorization and is now being released onto the market in various countries. The ESENSE 1 and 2 studies in alcohol-dependent patients showed that, in combination with BRENDA, a psychosocial intervention focusing on reinforcement of motivation and treatment adherence, nalmefene significantly reduced the number of heavy drinking days and mean daily total alcohol consumption versus placebo. This reduction was more marked in the marketing authorization target population, ie, patients with a high or very high drinking risk level according to World Health Organization criteria. Another original feature of this molecule is that it can be used as needed if the patient perceives a risk of drinking, which is a more flexible approach and more likely to ensure the patient’s active involvement in the treatment of his/her disease. This molecule opens up interesting and original therapeutic prospects in the treatment of alcohol dependence. PMID:25187751
Warming and nitrogen affect size structuring and density dependence in a host-parasitoid food web.
de Sassi, Claudio; Staniczenko, Phillip P A; Tylianakis, Jason M
2012-11-01
Body size is a major factor constraining the trophic structure and functioning of ecological communities. Food webs are known to respond to changes in basal resource abundance, and climate change can initiate compounding bottom-up effects on food-web structure through altered resource availability and quality. However, the effects of climate and co-occurring global changes, such as nitrogen deposition, on the density and size relationships between resources and consumers are unknown, particularly in host-parasitoid food webs, where size structuring is less apparent. We use a Bayesian modelling approach to explore the role of consumer and resource density and body size on host-parasitoid food webs assembled from a field experiment with factorial warming and nitrogen treatments. We show that the treatments increased resource (host) availability and quality (size), leading to measureable changes in parasitoid feeding behaviour. Parasitoids interacted less evenly within their host range and increasingly focused on abundant and high-quality (i.e. larger) hosts. In summary, we present evidence that climate-mediated bottom-up effects can significantly alter food-web structure through both density- and trait-mediated effects. PMID:23007092
Herbivore-Specific, Density-Dependent Induction of Plant Volatiles: Honest or Cry Wolf Signals?
Shiojiri, Kaori; Ozawa, Rika; Kugimiya, Soichi; Uefune, Masayoshi; van Wijk, Michiel; Sabelis, Maurice W.; Takabayashi, Junji
2010-01-01
Plants release volatile chemicals upon attack by herbivorous arthropods. They do so commonly in a dose-dependent manner: the more herbivores, the more volatiles released. The volatiles attract predatory arthropods and the amount determines the probability of predator response. We show that seedlings of a cabbage variety (Brassica oleracea var. capitata, cv Shikidori) also show such a response to the density of cabbage white (Pieris rapae) larvae and attract more (naive) parasitoids (Cotesia glomerata) when there are more herbivores on the plant. However, when attacked by diamondback moth (Plutella xylostella) larvae, seedlings of the same variety (cv Shikidori) release volatiles, the total amount of which is high and constant and thus independent of caterpillar density, and naive parasitoids (Cotesia vestalis) of diamondback moth larvae fail to discriminate herbivore-rich from herbivore-poor plants. In contrast, seedlings of another cabbage variety of B. oleracea (var. acephala: kale) respond in a dose-dependent manner to the density of diamondback moth larvae and attract more parasitoids when there are more herbivores. Assuming these responses of the cabbage cultivars reflect behaviour of at least some genotypes of wild plants, we provide arguments why the behaviour of kale (B. oleracea var acephala) is best interpreted as an honest signaling strategy and that of cabbage cv Shikidori (B. oleracea var capitata) as a cry wolf signaling strategy, implying a conflict of interest between the plant and the enemies of its herbivores: the plant profits from being visited by the herbivore's enemies, but the latter would be better off by visiting other plants with more herbivores. If so, evolutionary theory on alarm signaling predicts consequences of major interest to students of plant protection, tritrophic systems and communication alike. PMID:20808961
Time-dependent density functional theory of magneto-optical response of periodic insulators
NASA Astrophysics Data System (ADS)
Rubio, Angel; Tokatly, Ilya V.; Lebedeva, Irina V.
2014-03-01
Though the linear response theory has been successfully used for molecular systems for a long time, the extension of this theory to solids is not straightforward since the position operator is ill defined in extended periodic systems. The theoretical description of homogeneous static magnetic field in periodic systems is particularly challenging as the corresponding vector potential breaks the translational invariance of the Hamiltonian. We present a unified approach to calculation of all-order response to arbitrary electromagnetic fields both for periodic and molecular systems within the formalism of non-equilibrium Green functions. The approach is applied to derive the expression for the magneto-optical response of insulating solids in the approximation of non-interacting electrons. The formula obtained is completely identical to the expression for molecular systems if the proper position and orbital magnetization operators are chosen. The terms corresponding to changes in the optical response due to the orbital magnetization of Bloch states and due to the modified density of Bloch states in the magnetic field are identified. A computational scheme based on the density matrix-perturbation theory is developed for practical calculations of the magneto-optical response. The financial support from the Marie Curie Fellowship PIIF-GA-2012-326435 (RespSpatDisp) is gratefully acknowledged.
Time-dependent density functional theory with twist-averaged boundary conditions
NASA Astrophysics Data System (ADS)
Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.
2016-05-01
Background: Time-dependent density functional theory is widely used to describe excitations of many-fermion systems. In its many applications, three-dimensional (3D) coordinate-space representation is used, and infinite-domain calculations are limited to a finite volume represented by a spatial box. For finite quantum systems (atoms, molecules, nuclei, hadrons), the commonly used periodic or reflecting boundary conditions introduce spurious quantization of the continuum states and artificial reflections from boundary; hence, an incorrect treatment of evaporated particles. Purpose: The finite-volume artifacts for finite systems can be practically cured by invoking an absorbing potential in a certain boundary region sufficiently far from the described system. However, such absorption cannot be applied in the calculations of infinite matter (crystal electrons, quantum fluids, neutron star crust), which suffer from unphysical effects stemming from a finite computational box used. Here, twist-averaged boundary conditions (TABC) have been used successfully to diminish the finite-volume effects. In this work, we extend TABC to time-dependent modes. Method: We use the 3D time-dependent density functional framework with the Skyrme energy density functional. The practical calculations are carried out for small- and large-amplitude electric dipole and quadrupole oscillations of 16O. We apply and compare three kinds of boundary conditions: periodic, absorbing, and twist-averaged. Results: Calculations employing absorbing boundary conditions (ABC) and TABC are superior to those based on periodic boundary conditions. For low-energy excitations, TABC and ABC variants yield very similar results. With only four twist phases per spatial direction in TABC, one obtains an excellent reduction of spurious fluctuations. In the nonlinear regime, one has to deal with evaporated particles. In TABC, the floating nucleon gas remains in the box; the amount of nucleons in the gas is found to be roughly the same as the number of absorbed particles in ABC. Conclusion: We demonstrate that by using TABC, one can reduce finite-volume effects drastically without adding any additional parameters associated with absorption at large distances. Moreover, TABC are an obvious choice for time-dependent calculations for infinite systems. Since TABC calculations for different twists can be performed independently, the method is trivially adapted to parallel computing.
Bouet, Guenaelle; Bouleftour, Wafa; Juignet, Laura; Linossier, Marie-Thrse; Thomas, Mireille; Vanden-Bossche, Arnaud; Aubin, Jane E.; Vico, Laurence; Marchat, David; Malaval, Luc
2015-01-01
Bone sialoprotein (BSP) belongs to the "small integrin-binding ligand N-linked glycoprotein" (SIBLING) family, whose members interact with bone cells and bone mineral. BSP is strongly expressed in bone and we previously showed that BSP knockout (BSP-/-) mice have a higher bone mass than wild type (BSP+/+) littermates, with lower bone remodelling. Because baseline bone formation activity is constitutively lower in BSP-/- mice, we studied the impact of the absence of BSP on in vitro osteogenesis in mouse calvaria cell (MCC) cultures. MCC BSP-/- cultures exhibit fewer fibroblast (CFU-F), preosteoblast (CFU-ALP) and osteoblast colonies (bone nodules) than wild type, indicative of a lower number of osteoprogenitors. No mineralized colonies were observed in BSP-/- cultures, along with little/no expression of either osteogenic markers or SIBLING proteins MEPE or DMP1. Osteopontin (OPN) is the only SIBLING expressed in standard density BSP-/- culture, at higher levels than in wild type in early culture times. At higher plating density, the effects of the absence of BSP were partly rescued, with resumed expression of osteoblast markers and cognate SIBLING proteins, and mineralization of the mutant cultures. OPN expression and amount are further increased in high density BSP-/- cultures, while PHEX and CatB expression are differentiatlly regulated in a manner that may favor mineralization. Altogether, we found that BSP regulates mouse calvaria osteoblast cell clonogenicity, differentiation and activity in vitro in a cell density dependent manner, consistent with the effective skeletogenesis but the low levels of bone formation observed in vivo. The BSP knockout bone microenvironment may alter the proliferation/cell fate of early osteoprogenitors. PMID:25710686
Hazlerigg, Charles R. E.; Lorenzen, Kai; Thorbek, Pernille; Wheeler, James R.; Tyler, Charles R.
2012-01-01
Population regulation is fundamental to the long-term persistence of populations and their responses to harvesting, habitat modification, and exposure to toxic chemicals. In fish and other organisms with complex life histories, regulation may involve density dependence in different life-stages and vital rates. We studied density dependence in body growth and mortality through the life-cycle of laboratory populations of zebrafish Danio rerio. When feed input was held constant at population-level (leading to resource limitation), body growth was strongly density-dependent in the late juvenile and adult phases of the life-cycle. Density dependence in mortality was strong during the early juvenile phase but declined thereafter and virtually ceased prior to maturation. Provision of feed in proportion to individual requirements (easing resource limitation) removed density dependence in growth and substantially reduced density dependence in mortality, thus indicating that ‘bottom-up’ effects act on growth as well as mortality, but most strongly on growth. Both growth and mortality played an important role in population regulation, with density-dependent growth having the greater impact on population biomass while mortality had the greatest impact on numbers. We demonstrate a clear ontogenic pattern of change in density-dependent processes within populations of a very small (maximum length 5 mm) fish, maintained in constant homogeneous laboratory conditions. The patterns are consistent with those distilled from studies on wild fish populations, indicating the presence of broad ontogenic patterns in density-dependent processes that are invariant to maximum body size and hold in homogeneous laboratory, as well as complex natural environments. PMID:22655056
Sharma, A; Kumar, P; Rani, V; Ray, N; Ghosh, S
2016-06-15
We study charge transport in molecular organic semiconductors using two terminal and three terminal field effect transistor devices. Using phthalocyanines as examples, we achieve unification of carrier mobility between the different configurations in a Gaussian density of states. We find that the current density-voltage characteristics for two terminal devices can be understood by introducing a concentration dependence of the carrier mobility, as described by Oelerich et al (2012 Phys. Rev. Lett. 108 226403, 2010 Appl. Phys. Lett. 97 143302). Studying the evolution of the activation energy with the carrier density, we find results consistent with a percolation picture and a density dependent transport energy. PMID:27160656
Cui, Shenghui; Meng, Jianghong; Bhagwat, Arvind A.
2001-01-01
The cell density-dependent acid sensitivity phenotypes of Escherichia coli strains K-12 and O157:H7 were examined with reference to three possible mechanisms of acid resistance. There was no evidence of any diffusible substance released from dead cells which could influence the cell density-dependent acid survival phenotype. Instead, cell density-dependent acid survival phenotype was associated with induction of glutamate- and arginine-decarboxylase acid survival pathways and concomitant availability of glutamate and arginine during acid challenge. PMID:11571202
NASA Astrophysics Data System (ADS)
Inakura, Tsunenori
2014-09-01
Equation of state (EOS) is again shot into the limelight by discovery of the two-solar-mass neutron star. That heavy neutron star eliminates inadequate EOSs which can not support two-solar-mass neutron stars. Now there are several attempts to constrain the neutron matter EOS. In nuclear physics, it is expected to clarify density-dependence of the nuclear symmetry energy, L. We focus our attentions to dipole polarizability of unstable nuclei which has neutron skin. Since the neutron skin is approximately neutron matter, we believe that dynamics of unstable nuclei is affected by the neutron skin and we can extract the properties of neutron matter from it. Although some theoretical calculations using the random-phase approximation demonstrate a strong correlation between L and the dipole polarizability, almost all calculations are performed only for 3 nuclei, 68Ni, 132Sn, and 208Pb with a single interaction. There remains uncertainties on interaction and nuclide dependence. We performed a systematic calculation of the E 1 modes with several interactions. We show that the correlation between L and the dipole polarizability has somewhat depends on interactions and nuclide and that 54Ca, 140Sn are more suitable for extracting constraint on L from the experiments.
Bruggeman, Jason E; Swem, Ted; Andersen, David E; Kennedy, Patricia L; Nigro, Debora
2015-10-01
Intrinsic and extrinsic factors affect vital rates and population-level processes, and understanding these factors is paramount to devising successful management plans for wildlife species. For example, birds time migration in response, in part, to local and broadscale climate fluctuations to initiate breeding upon arrival to nesting territories, and prolonged inclement weather early in the breeding season can inhibit egg-laying and reduce productivity. Also, density-dependent regulation occurs in raptor populations, as territory size is related to resource availability. Arctic Peregrine Falcons (Falco peregrinus tundrius; hereafter Arctic peregrine) have a limited and northern breeding distribution, including the Colville River Special Area (CRSA) in the National Petroleum Reserve-Alaska, USA. We quantified influences of climate, topography, nest productivity, prey habitat, density dependence, and interspecific competition affecting Arctic peregrines in the CRSA by applying the Dail-Madsen model to estimate abundance and vital rates of adults on nesting cliffs from 1981 through 2002. Arctic peregrine abundance increased throughout the 1980s, which spanned the population's recovery from DDT-induced reproductive failure, until exhibiting a stationary trend in the 1990s. Apparent survival rate (i.e., emigration; death) was negatively correlated with the number of adult Arctic peregrines on the cliff the previous year, suggesting effects of density-dependent population regulation. Apparent survival and arrival rates (i.e., immigration; recruitment) were higher during years with earlier snowmelt and milder winters, and apparent survival was positively correlated with nesting season maximum daily temperature. Arrival rate was positively correlated with average Arctic peregrine productivity along a cliff segment from the previous year and initial abundance was positively correlated with cliff height. Higher cliffs with documented higher productivity (presumably indicative of higher-quality habitat), are a priority for continued protection from potential nearby development and disturbance to minimize population-level impacts. Climate change. may affect Arctic peregrines in multiple ways, including through access to more snow-free nest sites and a lengthened breeding season that may increase likelihood of nest success. Our work provides insight into factors affecting a population during and after recovery, and demonstrates how the Dail-Madsen model can be used for any unmarked population with multiple years of abundance data collected through repeated surveys. PMID:26591458
Sofaer, Helen R; Sillett, T Scott; Langin, Kathryn M; Morrison, Scott A; Ghalambor, Cameron K
2014-01-01
Ecological factors often shape demography through multiple mechanisms, making it difficult to identify the sources of demographic variation. In particular, conspecific density can influence both the strength of competition and the predation rate, but density-dependent competition has received more attention, particularly among terrestrial vertebrates and in island populations. A better understanding of how both competition and predation contribute to density-dependent variation in fecundity can be gained by partitioning the effects of density on offspring number from its effects on reproductive failure, while also evaluating how biotic and abiotic factors jointly shape demography. We examined the effects of population density and precipitation on fecundity, nest survival, and adult survival in an insular population of orange-crowned warblers (Oreothlypis celata) that breeds at high densities and exhibits a suite of traits suggesting strong intraspecific competition. Breeding density had a negative influence on fecundity, but it acted by increasing the probability of reproductive failure through nest predation, rather than through competition, which was predicted to reduce the number of offspring produced by successful individuals. Our results demonstrate that density-dependent nest predation can underlie the relationship between population density and fecundity even in a high-density, insular population where intraspecific competition should be strong. PMID:25077023
Debris spatial density dependence on control volume resolution in the geosynchronous environment
NASA Astrophysics Data System (ADS)
Lewis, H. G.; Swinerd, G. G.; Martin, C. E.; Smith, D. A. J.
The debris environment of the Earth can be characterised using spatial density within the cells, or bins, of a spherical control volume, which has dimensions of geocentric radius (altitude), declination and right ascension. The characterisation of the debris environment in this way allows model predictions and measurement data from the USSTRATCOM catalogue, radar and returned surfaces to be compared. In addition, the volume-centred approach enables semi-deterministic models to compute debris fluxes relative to given target spacecraft orbits, provided the volume cells are of sufficiently high resolution. In this way semi-deterministic models employ the spatial density representation of the debris environment to predict future collision events and the future environment. The determination of debris spatial density for discrete sectors of near-Earth space is an integral part of the semi-deterministic models, IDES (Integrated Debris Evolution Suite), LEGEND (LEO-to-GEO Environment Debris model) and DAMAGE (Debris Analysis and Monitoring Architecture for the Geosynchronous Environment). Comparative model studies for the Inter-Agency Space Debris Coordination Committee (IADC) utilise an agreed baseline incorporating the sizes of control volume cells but the sensitivity to the choice of these sizes has not been previously explored due to the computational expense involved. The results of two such sensitivity studies performed using DAMAGE are presented in this paper. DAMAGE characterized the current debris environment by simulating the debris source (launch and fragmentations only) and sink processes for objects larger than 10 cm from the beginning of the space age to May 2001. The simulated environment in the altitude range 35,000 km to 36,800 km was found to be generally consistent with the equivalent historical evolution performed using IDES and the two-line element (TLE) catalogue. Results from the sensitivity studies suggest that computed spatial densities are stable for altitude bin sizes of 25 km or less and for declination bin sizes of 2.5 degrees or less but only outside the declination range [+1, -1] degrees (i.e. close to the Geostationary ring). Within this declination range, spatial density estimates varied by a factor of ten.
Impact of density-dependent migration flows on epidemic outbreaks in heterogeneous metapopulations
NASA Astrophysics Data System (ADS)
Ripoll, J.; Avinyó, A.; Pellicer, M.; Saldaña, J.
2015-08-01
We investigate the role of migration patterns on the spread of epidemics in complex networks. We enhance the SIS-diffusion model on metapopulations to a nonlinear diffusion. Specifically, individuals move randomly over the network but at a rate depending on the population of the departure patch. In the absence of epidemics, the migration-driven equilibrium is described by quantifying the total number of individuals living in heavily or lightly populated areas. Our analytical approach reveals that strengthening the migration from populous areas contains the infection at the early stage of the epidemic. Moreover, depending on the exponent of the nonlinear diffusion rate, epidemic outbreaks do not always occur in the most populated areas as one might expect.
Constraining depth-dependent anisotropy: A new approach
NASA Astrophysics Data System (ADS)
Ishii, M.; Okeler, A.
2014-12-01
Splitting of shear waves is commonly used to infer anisotropy of the Earth's interior. However, most data, such as SKS splitting, provide depth-integrated measure of anisotropy along the ray path, and it is difficult to separate contributions from different layers within the Earth. There have been efforts to focus on specific depth range by analyzing differences in splitting between two ray paths, but these studies only report observed differences or rely upon forward modeling with limited parameter-space search. We have developed a new approach to examine the P-to-S converted phases that allows one to construct depth-dependent multi-layer anisotropy models through combination of inversion and grid search. In addition to the conventional fast splitting direction and delay time, the technique allows one to investigate the tilt of the symmetry axis and dip of the discontinuity associated with the P-to-S conversion. Furthermore, the formulation is such that it naturally extends to include and examine multiple layers with different anisotropic properties. With these flexibilities, we can address anisotropic contributions from different layers in two separate procedures. The first scheme takes advantage of data with similar ray paths (e.g., SKS and SKKS waves recorded at the same station). The rays sample different structure when their ray paths differ (e.g., near the core-mantle boundary), but they sample the same structure when the paths are similar (e.g., in the upper part of the mantle and crust). Using our new approach, we can set up the problem as a two-layer anisotropy model where the layer with ray paths sampling different regions (e.g., lowermost mantle) is allowed to vary laterally. The second type of problem that can be addressed by the new approach is layer-by-layer investigation of anisotropy from top to bottom. This procedure combines the new method with receiver function analysis to obtain anisotropic properties of each layer using P-to-S converted waves from different discontinuities such as the Moho, 410-km and 660-km discontinuities. The application of the methods to real data shows significant lateral variations in anisotropy, both in deep Earth and near the surface.
Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales.
Martínez-García, Ricardo; Murgui, Clara; Hernández-García, Emilio; López, Cristóbal
2015-01-01
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological organisms (like mussels) that tend to cluster at short ranges as a defensive strategy, and strongly disperse if there is a high population pressure at large ranges for optimizing foraging. We perform stochastic simulations of a particle-level model of the system, and derive and analyze a continuous density description (a nonlinear diffusion equation). In both cases we show that this interplay of scale-dependent-behaviors gives rise to a rich formation of spatial patterns ranging from labyrinths to periodic cluster arrangements. In most cases these clusters have the very peculiar appearance of ring-like structures, i.e., organisms arranging in the perimeter of the clusters, which we discuss in detail. PMID:26147351
Thickness dependence of the charge-density-wave transition temperature in VSe{sub 2}
Yang, Jiyong; Liu, Yan; Du, Haifeng; Ning, Wei; Zheng, Guolin; Jin, Chiming; Han, Yuyan; Wang, Ning; Tian, Mingliang Zhang, Yuheng; Wang, Weike; Yang, Zhaorong
2014-08-11
A set of three-dimensional charge-density-wave (3D CDW) VSe{sub 2} nano-flakes with different thicknesses were obtained by the scotch tape-based micro-mechanical exfoliation method. Resistivity measurements showed that the 3D CDW transition temperature T{sub p} decreases systematically from 105 K in bulk to 81.8 K in the 11.6 nm thick flake. The Hall resistivity ρ{sub xy} of all the flakes showed a linear dependent behavior against the magnetic field with a residual electron concentration of the order of ∼10{sup 21} cm{sup −3} at 5 K. The electron concentration n increases slightly as the thickness d decreases, possibly due to the CDW gap is reduced with the decrease of the thickness.
Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales
Martínez-García, Ricardo; Murgui, Clara; Hernández-García, Emilio; López, Cristóbal
2015-01-01
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological organisms (like mussels) that tend to cluster at short ranges as a defensive strategy, and strongly disperse if there is a high population pressure at large ranges for optimizing foraging. We perform stochastic simulations of a particle-level model of the system, and derive and analyze a continuous density description (a nonlinear diffusion equation). In both cases we show that this interplay of scale-dependent-behaviors gives rise to a rich formation of spatial patterns ranging from labyrinths to periodic cluster arrangements. In most cases these clusters have the very peculiar appearance of ring-like structures, i.e., organisms arranging in the perimeter of the clusters, which we discuss in detail. PMID:26147351
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.
Density dependence of the nuclear symmetry energy from measurements of neutron radii in nuclei
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.
Global stability of a delayed SIR epidemic model with density dependent birth and death rates
NASA Astrophysics Data System (ADS)
Yoshida, Naoki; Hara, Tadayuki
2007-04-01
An SIR epidemic model with density dependent birth and death rates is formulated. In our model it is assumed that the total number of the population is governed by logistic equation. The transmission of infection is assumed to be of the standard form, namely proportional to I(t-h)/N(t-h) where N(t) is the total (variable) population size, I(t) is the size of the infective population and a time delay h is a fixed time during which the infectious agents develop in the vector. We consider transmission dynamics for the model. Stability of an endemic equilibrium is investigated. The stability result is stated in terms of a threshold parameter, that is, a basic reproduction number R0.
[A broad educational approach to insulin-dependent diabetics].
de Poret, D; Pouliquen, A; Dejours, C; Assan, R
1985-02-01
Self monitoring of diabetes requires technical knowledge and suitable diabetes oriented behaviour; the latter arises from the patient's psycho-affective functioning, maturity and self sufficiency. A group of 9 insulin dependent ambulatory, adult, diabetics met 15 times over 5 months. The somatic and psycho-affective aspects of the disease were approached by an original methodology. Group animation was focussed on the participants themselves. Dynamic mobilisation of the persons was sought by listening to their explicit and implicit requests, by acting out (case studies and role-playing), by restatement and questioning. Diabetes oriented and psycho-affective behaviours were assessed on the basis of questionnaires and statements. At the end of the study, the psycho-affective attitude of the participants towards their illness was modified. The aggressiveness, mockery and rejection of diabetes and diabetics, initially noted, were progressively replaced by self-awareness and acceptance. As a result, better adjustment of technical behaviour responses was noted. Without precluding any psychodynamic explanation (reunification of the person), this study suggests that the participant's reactions towards their own image can be improved with consequential educational benefit. PMID:3979647
Singh, Raman Preet; Das, Manasmita; Thakare, Vivek; Jain, Sanyog
2012-10-15
The present study investigates the effect of functionalization density on the toxicity and cellular uptake of oxidized multiwalled carbon nanotubes (f-MWCNTs) in vitro. The toxicity of f-MWCNTs at varying degrees of carboxylation was assessed in a murine macrophage RAW 264.7 cell line, a model for liver Kupffer cells. In vitro cytotoxicity of oxidized MWCNTs was directly proportional to their functionalization density. The increased cytotoxicity was associated with a concurrent increase in the number of apoptotic cells and production of reactive nitrogen species (RNS). In contrast, reactive oxygen species (ROS) generation was the highest in the case of pristine MWCNTs and decreased with increased functionalization density. Quantitative cellular uptake studies indicated that endogenous ROS production was independent of the concentration of CNTs internalized by a specific cell population and was directly proportional to their surface hydrophobicity. Mechanistic studies suggested that cellular uptake of CNTs was critically charge-dependent and mediated through scavenger receptors, albeit the involvement of nonscavenger receptor mechanisms at low CNT concentrations and their saturation at the experimental concentration cannot be ruled out. A mathematical model was established to correlate between the cellular uptake of CNTs with their length and zeta potential. In an attempt to correlate the results of in vitro toxicity experiments with those of the in vivo toxicity in the mouse model, we found that the toxicity trends in vitro and in vivo are rather opposing. The apparent anomaly was explained on the basis of different experimental conditions and doses associated with cells under in vivo and in vitro culture conditions. PMID:22994501
Charge density-dependent modifications of hydration shell waters by Hofmeister ions.
Guo, Feng; Friedman, Joel M
2009-08-12
Gadolinium (Gd(3+)) vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe, as a function of added Hofmeister series salts, changes in the OH stretching frequency derived from first-shell waters of aqueous Gd(3+) and of Gd(3+) coordinated to three different types of molecules: (i) a chelate (EDTA), (ii) structured peptides (mSE3/SE2) of the lanthanide-binding tags (LBTs) family with a single high-affinity binding site, and (iii) a calcium-binding protein (calmodulin) with four binding sites. The vibronic sideband (VSB) corresponding to the OH stretching mode of waters coordinated to Gd(3+), whose frequency is inversely correlated with the strength of the hydrogen bonding to neighboring waters, exhibits an increase in frequency when Gd(3+) becomes coordinated to either EDTA, calmodulin, or mSE3 peptide. In all of these cases, the addition of cation chloride or acetate salts to the solution increases the frequency of the vibronic band originating from the OH stretching mode of the coordinated waters in a cation- and concentration-dependent fashion. The cation dependence of the frequency increase scales with charge density of the cations, giving rise to an ordering consistent with the Hofmeister ordering. On the other hand, water Raman spectroscopy shows no significant change upon addition of these salts. Additionally, it is shown that the cation effect is modulated by the specific anion used. The results indicate a mechanism of action for Hofmeister series ions in which hydrogen bonding among hydration shell waters is modulated by several factors. High charge density cations sequester waters in a configuration that precludes strong hydrogen bonding to neighboring waters. Under such conditions, anion effects emerge as anions compete for hydrogen-bonding sites with the remaining free waters on the surface of the hydration shell. The magnitude of the anion effect is both cation and Gd(3+)-binding site specific. PMID:19603752
Exploring Non-Equilibrium Dynamics in Time Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Luo, Kai
Time-dependent density functional theory(TDDFT) is a method of choice for calculations of excitation spectra and response properties in materials science and quantum chemistry. The many-body problem is mapped into a set of one-body Schrodinger equations, called the Kohn-Sham(KS) equations. In principle, the one-body potential can be chosen such that the density of the interacting system is exactly reproduced by the KS system. However, one component of the one-body potential has to be approximated and is typically "diabatic". Though in linear response regime adiabatic approximations give quite good spectra, it is important to explore their performances in non-equilibrium dynamics. In this thesis, I will present the results of the explorations on non-equilibrium dynamics in TDDFT. For the first study, a decomposition of exact exchange-correlation potential into kinetic and interaction components is derived. We compare the components with that of "adiabatic" counterparts in non-perturbative dynamics and find that the interaction component is less poorly approximated adiabatically than the kinetic component. A salient feature is that step structures generically appear, of relevance in the second study. We prove that the step structures only appear in the non-linear response regime. We find an exact condition which is typically violated by the approximations in use today. Spuriously time-dependent spectra in TDDFT can be explained and we find that the more the condition is violated the worse the dynamics is. In last, we envision that orbital functionals are able to incorporate the memory effects and compensate the deficiencies of the "adiabatic" approximations.
Open Quantum Transport and Non-Hermitian Real-Time Time-Dependent Density Functional Theory
NASA Astrophysics Data System (ADS)
Elenewski, Justin; Zhao, Yanxiang; Chen, Hanning
Sub-nanometer electronic devices are notoriously difficult to simulate, with the most widely adopted transport schemes predicting currents that diverge from experiment by several orders of magnitude. This deviation arises from numerous factors, including the inability of these methods to accommodate dynamic processes such as charge reorganization. A promising alternative entails the direct propagation of an electronic structure calculation, as exemplified by real-time time-dependent density functional theory (RT-TDDFT). Unfortunately this framework is inherently that of a closed system, and modifications must be made to handle incoming and outgoing particle fluxes. To this end, we establish a formal correspondence between the quantum master equation for an open, many-particle system and its description in terms of RT-TDDFT and non-Hermitian boundary potentials. By dynamically constraining the particle density within the boundary regions corresponding to the device leads, a simulation may be selectively converged to the non-equilibrium steady state associated with a given electrostatic bias. Our numerical tests demonstrate that this algorithm is both highly stable and readily integrated into existing electronic structure frameworks
Density Dependence of the Exchange Energy in the Bcc Phase of Solid HELIUM-3
NASA Astrophysics Data System (ADS)
Olejniczak, Zbigniew
A high-precision Pulse Fourier-Transform Nuclear -Magnetic-Resonance technique was used to measure the magnetic susceptibility of solid helium-3 in the bcc phase. Several molar volume samples ranging from 19.80 ml/mole to 24.40 ml/mole were studied. The helium-4 impurity level was 27 ppm. The measurements were done between 12 mK and 520 mK in a static magnetic field of 17.1 mT. The density dependence of the Curie-Weiss constant could be described by a power law, with a magnetic Gruneisen constant equal to 12.8 (+OR-) 0.3. The Curie-Weiss constant at a molar volume of 24.2 ml/mole was equal to -1.75 mK, which was nearly a factor of two smaller than previous values. This work resolves a long-standing thermodynamic inconsistency between high-magnetic-field pressure measurements and susceptibility measurements. Additional experiments using an independent thermometer provided an upper limit for a possible systematic error in the data to within (+OR-)0.1 mK. More than a tenfold improvement in the precision of the magnetic susceptibility measurements was achieved. When analysed in terms of a two-parameter model of the exchange interaction, the results imposed more stringent experimental constraints on possible values of exchange integrals at a density near melting.
Wilson, Kenneth; Graham, Robert I
2015-03-01
There is an increasing appreciation of the importance of transgenerational effects on offspring fitness, including in relation to immune function and disease resistance. Here, we assess the impact of parental rearing density on offspring resistance to viral challenge in an insect species expressing density-dependent prophylaxis (DDP); i.e. the adaptive increase in resistance or tolerance to pathogen infection in response to crowding. We quantified survival rates in larvae of the cotton leafworm (Spodoptera littoralis) from either gregarious- or solitary-reared parents following challenge with the baculovirus S. littoralis nucleopolyhedrovirus. Larvae from both the parental and offspring generations exhibited DDP, with gregarious-reared larvae having higher survival rates post-challenge than solitary-reared larvae. Within each of these categories, however, survival following infection was lower in those larvae from gregarious-reared parents than those from solitary-reared, consistent with a transgenerational cost of DDP immune upregulation. This observation demonstrates that crowding influences lepidopteran disease resistance over multiple generations, with potential implications for the dynamics of host-pathogen interactions. PMID:25808002
Wilson, Kenneth; Graham, Robert I.
2015-01-01
There is an increasing appreciation of the importance of transgenerational effects on offspring fitness, including in relation to immune function and disease resistance. Here, we assess the impact of parental rearing density on offspring resistance to viral challenge in an insect species expressing density-dependent prophylaxis (DDP); i.e. the adaptive increase in resistance or tolerance to pathogen infection in response to crowding. We quantified survival rates in larvae of the cotton leafworm (Spodoptera littoralis) from either gregarious- or solitary-reared parents following challenge with the baculovirus S. littoralis nucleopolyhedrovirus. Larvae from both the parental and offspring generations exhibited DDP, with gregarious-reared larvae having higher survival rates post-challenge than solitary-reared larvae. Within each of these categories, however, survival following infection was lower in those larvae from gregarious-reared parents than those from solitary-reared, consistent with a transgenerational cost of DDP immune upregulation. This observation demonstrates that crowding influences lepidopteran disease resistance over multiple generations, with potential implications for the dynamics of host–pathogen interactions. PMID:25808002
A relativistic time-dependent density functional study of the excited states of the mercury dimer
NASA Astrophysics Data System (ADS)
Kullie, Ossama
2014-01-01
In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s2 + 6s6p), (6s2 + 6s7s), and (6s2 + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2.
The phenology of space: Spatial aspects of bison density dependence in Yellowstone National Park
Taper, M.L.; Meagher, M.; Jerde, C.L.
2000-01-01
The Yellowstone bison represent the only bison population in the United States that survived in the wild the near-extermination of the late 1800's. This paper capitalizes on a unique opportunity provided by the record of the bison population of Yellowstone National Park (YNP). This population has been intensely monitored for almost four decades. The analysis of long-term spatio-temporal data from 1970-1997 supports the following conclusions. 1) Even though the Yellowstone bison herd exhibits an extended period of what appears to be linear growth, this pattern can be explained with classical density dependent dynamics if one realizes that perhaps the primary response of the herd to increased density is range expansion. 2) Several spatial aspects of social behavior in the YNP bison may be behavioral adaptations by the bison to environmental changes. These behavioral strategies may buffer, temporarily at least, bison population dynamics from the immediate repercussions of possible environmental stress and habitat deterioration. 3) Bison ecological carrying capacity for YNP is on the order of 2800 to 3200 animals. 4) There do appear to be indications of changes in the bison dynamics that are associated with increasing use of sections of the interior road system in winter. 5) The possibility of habitat degradation is indicated.
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.
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.
A relativistic time-dependent density functional study of the excited states of the mercury dimer.
Kullie, Ossama
2014-01-14
In previous works on Zn2 and Cd2 dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s(2) + 6s6p), (6s(2) + 6s7s), and (6s(2) + 6s7p) atomic asymptotes for the mercury dimer Hg2. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg2 including a comparative analysis with the lighter dimers of the group 12, Cd2, and Zn2, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg2. PMID:24437874
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 ...
Assessment of the ΔSCF density functional theory approach for electronic excitations in organic dyes
Kowalczyk, T.; Yost, S. R.; Van Voorhis, T.
2010-01-01
This paper assesses the accuracy of the ΔSCF method for computing low-lying HOMO→LUMO transitions in organic dye molecules. For a test set of vertical excitation energies of 16 chromophores, surprisingly similar accuracy is observed for time-dependent density functional theory and for ΔSCF density functional theory. In light of this performance, we reconsider the ad hoc ΔSCF prescription and demonstrate that it formally obtains the exact stationary density within the adiabatic approximation, partially justifying its use. The relative merits and future prospects of ΔSCF for simulating individual excited states are discussed.
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.
Modeling solvation effects in real-space and real-time within density functional approaches.
Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea
2015-10-14
The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a dielectric environment, typically liquid solvents. In this contribution, we develop a methodology to account for solvation effects in real-space (and real-time) (TD)DFT calculations. The boundary elements method is used to calculate the solvent reaction potential in terms of the apparent charges that spread over the van der Waals solute surface. In a real-space representation, this potential may exhibit a Coulomb singularity at grid points that are close to the cavity surface. We propose a simple approach to regularize such singularity by using a set of spherical Gaussian functions to distribute the apparent charges. We have implemented the proposed method in the Octopus code and present results for the solvation free energies and solvatochromic shifts for a representative set of organic molecules in water. PMID:26472367
Quantum confined stark effect in wide parabolic quantum wells: real density matrix approach
NASA Astrophysics Data System (ADS)
Zielińska-Raczyńska, Sylwia; Czajkowski, Gerard; Ziemkiewicz, David
2015-12-01
We show how to compute the optical functions of wide parabolic quantum wells (WPQWs) exposed to uniform electric F applied in the growth direction, in the excitonic energy region. The effect of the coherence between the electron-hole pair and the electromagnetic field of the propagating wave including the electron-hole screened Coulomb potential is adopted, and the valence band structure is taken into account in the cylindrical approximation. The role of the interaction potential and of the applied electric field, which mix the energy states according to different quantum numbers and create symmetry forbidden transitions, is stressed. We use the real density matrix approach (RDMA) and an effective e-h potential, which enable to derive analytical expressions for the WPQWs electrooptical functions. Choosing the susceptibility, we performed numerical calculations appropriate to a GaAs/GaAlAs WPQWs. We have obtained a red shift of the absorption maxima (quantum confined Stark effect), asymmetric upon the change of the direction of the applied field ( F → - F), parabolic for the ground state and strongly dependent on the confinement parameters (the QWs sizes), changes in the oscillator strengths, and new peaks related to the states with different parity for electron and hole.
NASA Astrophysics Data System (ADS)
Schrobenhauser, R.; Strzoda, R.; Hartmann, A.; Fleischer, M.; Amann, M.-C.
2014-10-01
We present a miniaturized sensor setup capable of determining the density of airborne particles employing size information provided by an enhanced light-scattering intensity ratio technique and inertia-dependent particle motion. The method is based on the particle density-dependent spatial particle spreading, measured as the time of flight using a divergent laser beam. Measurement results using polystyrene latex and silica particles in a size range of 500-1,600 nm show good agreement with theoretical estimations.
Technology Transfer Automated Retrieval System (TEKTRAN)
Transmission of parasites and pathogens is generally positively density-dependent. Thus, as an insect population's density increases, the risk of an individual becoming attacked or infected increases. In some insect species, individuals experiencing crowded conditions are more resistant to natural e...
NASA Astrophysics Data System (ADS)
Timrov, Iurii; Vast, Nathalie; Gebauer, Ralph; Baroni, Stefano
2013-08-01
The Liouville-Lanczos approach to linear-response time-dependent density-functional theory is generalized so as to encompass electron energy loss and inelastic x-ray scattering spectroscopies in periodic solids. The computation of virtual orbitals and the manipulation of large matrices are avoided by adopting a representation of response orbitals borrowed from (time-independent) density functional perturbation theory and a suitable Lanczos recursion scheme. The latter allows the bulk of the numerical work to be performed at any given transferred momentum only once, for a whole extended frequency range. The numerical complexity of the method is thus greatly reduced, making the computation of the loss function over a wide frequency range at any given transferred momentum only slightly more expensive than a single standard ground-state calculation and opening the way to computations for systems of unprecedented size and complexity. Our method is validated on the paradigmatic examples of bulk silicon and aluminum, for which both experimental and theoretical results already exist in the literature.
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.
Gudur, Madhu Sudhan Reddy; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang
2014-11-01
MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm's accuracy of electron density mapping and its ability to detect bone in the head for eight patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as receiver operating characteristics for bone detection (HU > 200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p = 2 × 10(-4)), 283 for the intensity approach (p = 2 × 10(-6)) and 282 without density correction (p = 5 × 10(-6)). For 90% sensitivity in bone detection, the proposed method achieved a specificity of 86%, compared with 80, 11 and 10% using deformable registration, intensity and without density correction, respectively. Notably, the Bayesian approach was more robust against anatomical differences between patients, with a specificity of 62% in the worst case (patient), compared to 30% specificity in registration-based approach. In conclusion, the proposed unifying Bayesian method provides accurate electron density estimation and bone detection from MRI of the head with highly heterogeneous anatomy. PMID:25321341
NASA Astrophysics Data System (ADS)
Normani, S. D.; Sykes, J. F.; Jensen, M. R.
2009-04-01
A high resolution sub-regional scale (84 km2) density-dependent, fracture zone network groundwater flow model with hydromechanical coupling and pseudo-permafrost, was developed from a larger 5734 km2 regional scale groundwater flow model of a Canadian Shield setting in fractured crystalline rock. The objective of the work is to illustrate aspects of regional and sub-regional groundwater flow that are relevant to the long-term performance of a hypothetical nuclear fuel repository. The discrete fracture dual continuum numerical model FRAC3DVS-OPG was used for all simulations. A discrete fracture zone network model delineated from surface features was superimposed onto an 789887 element flow domain mesh. Orthogonal fracture faces (between adjacent finite element grid blocks) were used to best represent the irregular discrete fracture zone network. The crystalline rock between these structural discontinuities was assigned properties characteristic of those reported for the Canadian Shield at the Underground Research Laboratory at Pinawa, Manitoba. Interconnectivity of permeable fracture features is an important pathway for the possibly relatively rapid migration of average water particles and subsequent reduction in residence times. The multiple 121000 year North American continental scale paleoclimate simulations are provided by W.R. Peltier using the University of Toronto Glacial Systems Model (UofT GSM). Values of ice sheet normal stress, and proglacial lake depth from the UofT GSM are applied to the sub-regional model as surface boundary conditions, using a freshwater head equivalent to the normal stress imposed by the ice sheet at its base. Permafrost depth is applied as a permeability reduction to both three-dimensional grid blocks and fractures that lie within the time varying permafrost zone. Two different paleoclimate simulations are applied to the sub-regional model to investigate the effect on the depth of glacial meltwater migration into the subsurface. In addition, different conceptualizations of fracture permeability with depth, and various hydromechanical loading efficiencies are used to investigate glacial meltwater penetration. The importance of density dependent flow, due to pore waters deep in the Canadian Shield with densities of up to 1200 kg/m3 and total dissolved solids concentrations in excess of 300 g/L, is also illustrated. Performance measures used in the assessment include depth of glacial meltwater penetration using a tracer, and mean life expectancy. Consistent with the findings from isotope and geochemical assessments, the analyses support the conclusion that for the discrete fracture zone and matrix properties simulated in this study, glacial meltwaters would not likely impact a deep geologic repository in a crystalline rock setting.
Direct microscopic calculation of nuclear level densities in the shell model Monte Carlo approach
NASA Astrophysics Data System (ADS)
Alhassid, Y.; Bonett-Matiz, M.; Liu, S.; Nakada, H.
2015-08-01
Nuclear level densities are required for estimating statistical nuclear reaction rates. The shell model Monte Carlo method is a powerful approach for microscopic calculation of state densities in very large model spaces. However, these state densities include the spin degeneracy of each energy level, whereas experiments often measure level densities, in which each level is counted only once. To enable the direct comparison of theory with experiments, we introduce a method to calculate directly the level density in the shell model Monte Carlo approach. The method employs a projection on the minimal absolute value of the magnetic quantum number. We apply the method to nuclei in the iron region and to the strongly deformed rare-earth nucleus 162Dy . We find very good agreement with experimental data obtained by various methods, including level counting at low energies, charged particle spectra and Oslo method data at intermediate energies, neutron and proton resonance data, and Ericson's fluctuation analysis at higher excitation energies. We also extract a thermal moment of inertia from the ratio between the state density and the level density, and observe that in even-even nuclei it exhibits a signature of a phase transition to a superconducting phase below a certain excitation energy.
NASA Astrophysics Data System (ADS)
Aban, C. J. G.; Bacolod, R. O.; Confesor, M. N. P.
2015-06-01
A The White Noise Path Integral Approach is used in evaluating the B-cell density or the number of B-cell per unit volume for a basic type of immune system response based on the modeling done by Perelson and Wiegel. From the scaling principles of Perelson [1], the B- cell density is obtained where antigens and antibodies mutates and activation function f(|S-SA|) is defined describing the interaction between a specific antigen and a B-cell. If the activation function f(|S-SA|) is held constant, the major form of the B-cell density evaluated using white noise analysis is similar to the form of the B-cell density obtained by Perelson and Wiegel using a differential approach.A piecewise linear functionis also used to describe the activation f(|S-SA|). If f(|S-SA|) is zero, the density decreases exponentially. If f(|S-SA|) = S-SA-SB, the B- cell density increases exponentially until it reaches a certain maximum value. For f(|S-SA|) = 2SA-SB-S, the behavior of B-cell density is oscillating and remains to be in small values.
Leventhal, Gabriel E.; Günthard, Huldrych F.; Bonhoeffer, Sebastian; Stadler, Tanja
2014-01-01
The control, prediction, and understanding of epidemiological processes require insight into how infectious pathogens transmit in a population. The chain of transmission can in principle be reconstructed with phylogenetic methods which analyze the evolutionary history using pathogen sequence data. The quality of the reconstruction, however, crucially depends on the underlying epidemiological model used in phylogenetic inference. Until now, only simple epidemiological models have been used, which make limiting assumptions such as constant rate parameters, infinite total population size, or deterministically changing population size of infected individuals. Here, we present a novel phylogenetic method to infer parameters based on a classical stochastic epidemiological model. Specifically, we use the susceptible-infected-susceptible model, which accounts for density-dependent transmission rates and finite total population size, leading to a stochastically changing infected population size. We first validate our method by estimating epidemic parameters for simulated data and then apply it to transmission clusters from the Swiss HIV epidemic. Our estimates of the basic reproductive number R0 for the considered Swiss HIV transmission clusters are significantly higher than previous estimates, which were derived assuming infinite population size. This difference in key parameter estimates highlights the importance of careful model choice when doing phylogenetic inference. In summary, this article presents the first fully stochastic implementation of a classical epidemiological model for phylogenetic inference and thereby addresses a key aspect in ongoing efforts to merge phylogenetics and epidemiology. PMID:24085839
Phase interpretation for polarization-dependent near-field images of high-density gratings
NASA Astrophysics Data System (ADS)
Zheng, Jiangjun; Zhou, Changhe; Wang, Bo
2008-06-01
It has been described that the near-field images of a high-density grating at the half self-imaging distance could be different for TE and TM polarization states. We propose that the phases of the diffraction orders play an important role in such polarization dependence. The view is verified through the coincidence of the numerical result of finite-difference time-domain method and the reconstructed results from the rigorous coupled-wave analysis. Field distributions of TE and TM polarizations are given numerically for a grating with period d = 2.3 λ, which are verified through experiments with the scanning near-field optical microscopy technique. The concept of phase interpretation not only explains the polarization dependence at the half self-imaging distance of gratings with a physical view, but also, it could be widely used to describe the near-field diffraction of a variety of periodic diffractive optical elements whose feature size comparable to the wavelength.
High current density PQQ-dependent alcohol and aldehyde dehydrogenase bioanodes.
Aquino Neto, Sidney; Hickey, David P; Milton, Ross D; De Andrade, Adalgisa R; Minteer, Shelley D
2015-10-15
In this paper, we explore the bioelectrooxidation of ethanol using pyrroloquinoline quinone (PQQ)-dependent alcohol and aldehyde dehydrogenase (ADH and AldDH) enzymes for biofuel cell applications. The bioanode architectures were designed with both direct electron transfer (DET) and mediated electron transfer (MET) mechanisms employing high surface area materials such as multi-walled carbon nanotubes (MWCNTs) and MWCNT-decorated gold nanoparticles, along with different immobilization techniques. Three different polymeric matrices were tested (tetrabutyl ammonium bromide (TBAB)-modified Nafion; octyl-modified linear polyethyleneimine (C8-LPEI); and cellulose) in the DET studies. The modified Nafion membrane provided the best electrical communication between enzymes and the electrode surface, with catalytic currents as high as 16.8 ± 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. PMID:25988787
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.
Spillmann, Frank; Trimpert, Christiane; Peng, Jun; Eckerle, Lars G; Staudt, Alexander; Warstat, Katrin; Felix, Stephan B; Pieske, Burkert; Tschpe, Carsten; Van Linthout, Sophie
2015-10-16
Palmitate has been implicated in the induction of cardiomyocyte apoptosis via reducing the activity of 5' AMP-activated protein kinase (AMPK). We sought to evaluate whether high-density lipoproteins (HDLs), known for their cardioprotective features and their potential to increase AMPK activity, can reduce palmitate-induced cardiomyocyte apoptosis and whether this effect is AMPK-dependent. Therefore, cardiomyocytes were isolated from adult Wistar rat hearts via perfusion on a Langendorff-apparatus and cultured in free fatty acid-free BSA control medium or 0.5mM palmitate medium in the presence or absence of HDL (5?g protein/ml) with or without 0.1?M of the AMPK-inhibitor compound S for the analysis of Annexin V/propidium, genes involved in apoptosis and fatty acid oxidation, and cardiomyocyte contractility. We found that HDLs decreased palmitate-induced cardiomyocyte apoptosis as indicated by a reduction in Annexin V-positive cardiomyocytes and an increase in Bcl-2 versus Bax ratio. Concomitantly, HDLs increased the palmitate-impaired expression of genes involved in fatty acid oxidation. Furthermore, HDLs improved the palmitate-impaired cardiomyocyte contractility. All effects were mediated in an AMPK-dependent manner, concluding that HDLs reduce palmitate-induced cardiomyocyte apoptosis, resulting in improved cardiomyocyte contractility through a mechanism involving AMPK. PMID:26362182
A density-dependant finite element model for analysis of saltwater intrusion in coastal aquifers
NASA Astrophysics Data System (ADS)
Abd-Elhamid, H. F.; Javadi, A. A.
2011-05-01
SummarySaltwater intrusion is a serious problem in coastal regions all over the world. It is one of the processes that degrade water-quality by raising salinity to levels exceeding acceptable drinking water standards. It may occur due to human activities and/or by natural events. Over-abstraction is considered the main cause of saltwater intrusion. Moreover, climate change and sea level rise speed up saltwater intrusion. This paper presents the development and validation of a coupled transient finite element model for simulation of fluid flow and solute transport in saturate and unsaturated soils with application to study saltwater intrusion in coastal aquifers. The model includes coupling of water flow, air flow, heat flow and solute transport. Furthermore, transient density-dependent flow is included in the model and the dependency of dispersion on velocity is considered. Different mechanisms that govern solute transport in porous media including, advection, diffusion, dispersion, adsorption, chemical reactions and biological degradation are included in the model. The governing equation of the solute transport is solved together with three balance equations for water flow, air flow and heat transfer. The nonlinear system of governing differential equations is solved using the finite element method in the space domain and a finite difference scheme in the time domain. The model is validated by application to a standard case study from the literature (Henry's problem) and then applied to predict saltwater intrusion in a coastal aquifer. The results of the model predictions are presented and discussed.
2007 Time_Dependent Density-Functional Therory (July 15-20, 2007 Colby College, Maine)
Ullrich Carsten Nancy Ryan Gray
2008-09-19
Time-dependent density-functional theory (TDDFT) provides an efficient, elegant, and formally exact way of describing the dynamics of interacting many-body quantum systems, circumventing the need for solving the full time-dependent Schroedinger equation. In the 20 years since it was first rigorously established in 1984, the field of TDDFT has made rapid and significant advances both formally as well as in terms of successful applications in chemistry, physics and materials science. Today, TDDFT has become the method of choice for calculating excitation energies of complex molecules, and is becoming increasingly popular for describing optical and spectroscopic properties of a variety of materials such as bulk solids, clusters and nanostructures. Other growing areas of applications of TDDFT are nonlinear dynamics of strongly excited electronic systems and molecular electronics. The purpose and scope of this Gordon Research Conference is to provide a platform for discussing the current state of the art of the rapidly progressing, highly interdisciplinary field of TDDFT, to identify and debate open questions, and to point out new promising research directions. The conference will bring together experts with a diverse background in chemistry, physics, and materials science.
Habershon, Scott
2013-09-14
We introduce a new approach for calculating quantum time-correlation functions and time-dependent expectation values in many-body thermal systems; both electronically adiabatic and non-adiabatic cases can be treated. Our approach uses a path integral simulation to sample an initial thermal density matrix; subsequent evolution of this density matrix is equivalent to solution of the time-dependent Schrödinger equation, which we perform using a linear expansion of Gaussian wavepacket basis functions which evolve according to simple classical-like trajectories. Overall, this methodology represents a formally exact approach for calculating time-dependent quantum properties; by introducing approximations into both the imaginary-time and real-time propagations, this approach can be adapted for complex many-particle systems interacting through arbitrary potentials. We demonstrate this method for the spin Boson model, where we find good agreement with numerically exact calculations. We also discuss future directions of improvement for our approach with a view to improving accuracy and efficiency.
Reconstructive approaches to one- and two-electron density matrix theory
NASA Astrophysics Data System (ADS)
Herbert, John Michael
Novel computational methods for electronic structure theory are explored, in which the fundamental variable is either the one- or the two-electron reduced density matrix (1- or 2-RDM), rather than the electronic wavefunction. A unifying theme among these methods is density matrix reconstruction, that is, decoupling approximations that express higher-order density matrices as functionals of lower-order ones. On the 2-RDM side, a connected (extensive) version of the Contracted Schrodinger Equation (CSE) is developed, in which the basic unknowns are the RDM cumulants through order four. Reconstruction functionals that neglect the 3- and 4-RDM cumulants are examined and revealed to be significantly less accurate than suggested by previous minimal-basis results. Exact 3-RDM cumulants for some four-electron systems are calculated and found to be comparable in importance to unconnected products of lower-order cumulants. Decoupling approximations for the 3- and 4-RDM cumulants are developed based upon a renormalized, diagrammatic perturbation theory for the three- and four-particle Green's functions, in which the effective, pairwise interaction is extracted from the two-particle cumulant. Diagram rules suitable for both the time-dependent and time-independent versions of this perturbation theory are derived. Reconstructive approaches to natural orbital (1-RDM) functional theory are also examined, wherein the 2-RDM is parametrized in terms of the natural orbitals and their (generally fractional) occupancies. It is demonstrated, at the theorem level, that proposed "corrected Hartree" and "corrected Hartree-Fock" natural orbital functionals necessarily violate positivity of the 2-RDM, which is closely related to their failure to respect antisymmetry. Calculations demonstrate that negative eigenvalues of the 2-RDM are associated with a large, stabilizing (but ultimately spurious) contribution to the energy. Nevertheless, a partially self-interaction-corrected version of the corrected Hartree functional is shown to yield high-quality potential energy curves---comparable to multireference configuration interaction---for the strongly-correlated diatomic molecules HF and C2. A new class of functionals that preserve both anti-symmetry and positivity are proposed and subjected to some preliminary tests.
Normal mode analysis of single bunch, charge density dependent behavior in electron/positron beams
NASA Astrophysics Data System (ADS)
Ehrlichman, Michael
Accelerator science in coming years will be increasingly dependent upon high single-bunch charges and/or small emittances. Under these conditions, single-particle dynamics are not a sufficient description of beam behavior and interactions between the beam particles must be taken into account. One such interaction is when collisions between the particles that compose a bunch perturb the motion of the colliding particles significantly and frequently enough to impact the beam dynamics. Multiple, small-angle, collisions blow up the emittance of the bunch and are referred to as intrabeam scattering (IBS). Here are documented the theoretical and experimental studies of IBS in storage rings undertaken as part of the CesrTA program. Under the conditions where IBS becomes dominant, other multi-particle effects can also appear. The additional effects we investigate include potential well distortion, coherent current-dependent tune shift, and direct space charge. CesrTA design and analysis is conducted in a normal mode coordinates environment which allows for natural handling of coupling. To that end, we develop a 6D normal modes decomposition of the linear beam optics. Multi-particle effects are also important for Energy Recovery Linear Accelerators (ERLs). Because the beam circulates for only a short period of time in an ERL, the beam lifetime imposed by Touschek scattering is not significant. However, the particles scattered out of the bunch can generate a radiation hazard where they collide with the beam pipe. We re-derive Piwinski's original Touschek scattering equation to check its validity when applied to ERL beams, then repurpose the formula to generate a profile of where scattered particles are generated and where they are lost. The results presented here advance our understanding of charge-dependent behavior in the sorts of high charge-density accelerators that will be implemented in coming years.
Momentum-dependent band spin splitting in semiconducting MnO2: a density functional calculation.
Noda, Yusuke; Ohno, Kaoru; Nakamura, Shinichiro
2016-05-11
Recently, manganese-oxide compounds have attracted considerable attention, in particular, as candidate materials for photochemical water-splitting reactions. Here, we investigate electronic states of pristine manganese dioxides (MnO2) in different crystal phases using spin-polarized density functional theory (DFT) with Hubbard U correction. Geometrical structures and band dispersions of α-, β-, δ-, and λ-MnO2 crystals with collinear magnetic [ferromagnetic (FM) and antiferromagnetic (AFM)] orders are discussed in detail. We reveal that penalty energies that arise by violating the Goodenough-Kanamori rule are important and the origin of the magnetic interactions of the MnO2 crystals is governed by the superexchange interactions of Mn-O-Mn groups. In addition, it is found that momentum-dependent band spin splitting occurs in the AFM α-, β-, and δ-MnO2 crystals while no spin splitting occurs in the AFM λ-MnO2 crystal. Our results show that spin-split band dispersions stem from the different orientations of Mn-centred oxygen octahedra. Such interesting electronic states of the MnO2 crystals are unraveled by our discussion on the relationship between the effective (spin-dependent) single-electron potentials and the space-group symmetry operations that map up-spin Mn atoms onto down-spin Mn atoms. This work provides a basis to understand the relationship between the spin-dependent electronic states and the crystallography of manganese oxides. Another relationship to the recent experimental observations of the photochemical oxygen evolution of MnO2 crystals is also discussed. PMID:27119122
NASA Astrophysics Data System (ADS)
Zelovich, Tamar; Kronik, Leeor; Hod, Oded
2014-03-01
A new method for simulating electron dynamics in open quantum systems out of equilibrium, motivated by the intuitive and practical nature of the damped Liouville von-Neumann equation approach of Sánchez et al. [J. Chem Phys, 124, 214708 (2006)], is presented. The new approach is based on a transformation of the Hamiltonian matrix from an atomistic to a state representation of the molecular junction. This allows us to define the bias voltage across the system uniquely while maintaining a proper thermal distribution within the lead models. Furthermore, it allows us to investigate time-dependent effects in non-linear and multi-lead configurations. We investigate the degree of conservation of exact conditions such as the N-representability of the density matrix and suggest ways to remedy the violation of Pauli's exclusion principle. We believe that the new approach offers a practical and physically sound route for performing atomistic time-dependent transport calculations in realistic models of molecular electronics junctions.
Liu, Yu
2016-05-11
I developed a novel time-dependent density functional theory (TDDFT) and applied it to complicated 3-dimensional systems for the first time. Superior to conventional TDDFT, the diffusion coefficient is modeled as a function of density profile, which is self-determined by the entropy scaling rule instead using an input parameter. The theory was employed to mimic gas diffusion in a nanoporous material. The TDDFT prediction on the transport diffusivity was reasonable compared to simulations. Moreover, the time-dependent density profiles gave an insight into the microscopic mechanism of the diffusion process. PMID:27121986
NASA Astrophysics Data System (ADS)
Castro, Alberto; Rubio, Angel; Gross, Eberhard K. U.
2015-08-01
High harmonic generation (HHG) provides a flexible framework for the development of coherent light sources in the extreme-ultraviolet and soft X-ray regimes. However it suffers from low conversion efficiencies as the control of the HHG spectral and temporal characteristics requires manipulating electron trajectories on attosecond time scale. The phase matching mechanism has been employed to selectively enhance specific quantum paths leading to HHG. A few important fundamental questions remain open, among those how much of the enhancement can be achieved by the single-emitter and what is the role of correlations (or the electronic structure) in the selectivity and control of HHG generation. Here we address those questions by examining computationally the possibility of optimizing the HHG spectrum of isolated hydrogen and helium atoms by shaping the slowly varying envelope of a 800 nm, 200-cycles long laser pulse. The spectra are computed with a fully quantum mechanical description, by explicitly computing the time-dependent dipole moment of the systems using a time-dependent density-functional approach (or the single-electron Schrdinger equation for the case of H), on top of a one-dimensional model. The sought optimization corresponds to the selective enhancement of single harmonics, which we find to be significant. This selectivity is entirely due to the single atom response, and not to any propagation or phase-matching effect. Moreover, we see that the electronic correlation plays a role in the determining the degree of optimization that can be obtained.
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 quality of the estimations and facilitate further arrangements of this approach.
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.
Hu, Zhongwei; Autschbach, Jochen; Jensen, Lasse
2016-03-01
A general implementation for damped cubic response properties is presented using time-dependent density functional theory (TDDFT) and Slater-type orbital basis sets. To directly calculate two-photon absorption (TPA) cross sections, we also present an implementation of a reduced damped cubic response approach. Validation of the implementations includes a detailed comparison between response theory and the sum-over-states approach for calculating the nonlinear optical properties of LiH, as well as a comparison between the simulated and experimental TPA and third-harmonic generation (THG) spectra for the dimethylamino-nitrostilbene (DANS) molecule. The study of LiH demonstrates the incorrect pole structure obtained in response theory due to the adiabatic approximation typically employed for the exchange-correlation kernel. For DANS, we find reasonable agreement between simulated and experimental TPA and THG spectra. Overall, this work shows that care must be taken when calculating higher-order response functions in the vicinity of one-photon poles due to the approximate kernels typically used in the simulations. PMID:26841327
Factors Influencing Density-Dependent Groundwater Flow in the Michigan Basin
NASA Astrophysics Data System (ADS)
Sykes, J. F.; Normani, S. D.; Yin, Y.
2010-12-01
Regional-scale density-dependent groundwater flow is analyzed in an approximately 18000 sq km domain of the Michigan basin centered on a site at Tiverton Ontario near the shore of Lake Huron for a proposed deep geologic repository (DGR) for low and intermediate level nuclear waste. Flow was also analyzed in an approximately 600 km west-to-east cross-section through the center of the basin. Both domains extend from the Precambrian basement to the surface and include minimal upscaling of the complex stratigraphy in the basin. The model FRAC3DVS-OPG was used for all analyses. The hydraulic gradients across the basin are small as both Lake Huron and Lake Michigan have the same water surface elevation. As a result, groundwater flow in the basin is expected to be stagnant. Hydrogeologic parameters for the models were developed from borehole and petrophysics data from the DGR site for units from the Cambrian sandstone to the Devonian. Literature data were used for the shallower units in Michigan. Excluding the surficial drift, the hydraulic conductivity in the basin ranges from 3x10e-6 m/s in the Cambrian to less than 10e-14 m/s in the Ordovician sediments. Groundwater flow is sensitive to the distribution of total dissolved solids concentration with concentrations ranging up to 384 g/L in the Guelph formation in the Silurian. Both TDS data from porewater and groundwater at the DGR site and literature data for TDS versus depth were assigned to the sedimentary rock. The TDS distribution with depth for the Precambrian rock was assigned using both data for the Canadian Shield and a literature based model. Data at the DGR site indicates that the Cambrian is overpressured with respect to the surface while the Ordovician sediments are underpressured. It is hypothesized that the underpressures are the result of the presence of a gas phase in the units. The steps in determining a converged solution for saturated density-dependent flow were as follows: (1) solve steady state density-independent flow, (2) assign a TDS concentration distribution and allow the initial equivalent freshwater heads to equilibrate to the fixed TDS distribution, (3) allow the resulting heads to equilibrate to the TDS concentration with solute transport enabled. Convergence of a solution for the regional-scale model was not achieved without the middle step. For the Michigan Basin cross-section, the 3rd step would not yield a converged solution using FRAC3DVS-OPG. Flow in both analyses is sensitive to surface topography and the TDS distribution. The overpressure in the Cambrian could be described by density differences across the basin and surface topography differences. The underpressures can be described with a gas water analysis using TOUGH2-MP. Paleoclimate analyses that included mechanical loading could not describe the underpressures. Flow in the intracratonic Michigan Basin is complex and dynamic as a result of glaciation. Converged solutions are difficult to achieve. Flow in the low permeability units such as those of the Ordovician and Silurian is negligible with solute transport being diffusion dominant. The analyses provide a bench mark for evaluating the upscaling of stratigraphic units required in continental-scale simulations.
ERIC Educational Resources Information Center
Ipek, Ismail
2011-01-01
The purpose of this study was to investigate the effects of variations in text density levels and the cognitive style of field dependence on learning from a CBI tutorial, based on the dependent measures of achievement, reading comprehension, and reading rate, and of lesson completion time. Eighty college undergraduate students were randomly…
A relativistic time-dependent density functional study of the excited states of the mercury dimer
Kullie, Ossama E-mail: ossama.kullie@unistra.fr
2014-01-14
In previous works on Zn{sub 2} and Cd{sub 2} dimers we found that the long-range corrected CAMB3LYP gives better results than other density functional approximations for the excited states, especially in the asymptotic region. In this paper, we use it to present a time-dependent density functional (TDDFT) study for the ground-state as well as the excited states corresponding to the (6s{sup 2} + 6s6p), (6s{sup 2} + 6s7s), and (6s{sup 2} + 6s7p) atomic asymptotes for the mercury dimer Hg{sub 2}. We analyze its spectrum obtained from all-electron calculations performed with the relativistic Dirac-Coulomb and relativistic spinfree Hamiltonian as implemented in DIRAC-PACKAGE. A comparison with the literature is given as far as available. Our result is excellent for the most of the lower excited states and very encouraging for the higher excited states, it shows generally good agreements with experimental results and outperforms other theoretical results. This enables us to give a detailed analysis of the spectrum of the Hg{sub 2} including a comparative analysis with the lighter dimers of the group 12, Cd{sub 2}, and Zn{sub 2}, especially for the relativistic effects, the spin-orbit interaction, and the performance of CAMB3LYP and is enlightened for similar systems. The result shows, as expected, that spinfree Hamiltonian is less efficient than Dirac-Coulomb Hamiltonian for systems containing heavy elements such as Hg{sub 2}.
Treatment for tobacco dependence: effect on brain nicotinic acetylcholine receptor density.
Brody, Arthur L; Mukhin, Alexey G; Stephanie Shulenberger; Mamoun, Michael S; Kozman, Maggie; Phuong, Jonathan; Neary, Meaghan; Luu, Trinh; Mandelkern, Mark A
2013-07-01
Cigarette smoking leads to upregulation of brain nicotinic acetylcholine receptors (nAChRs), including the common α4β2* nAChR subtype. Although a substantial percentage of smokers receive treatment for tobacco dependence with counseling and/or medication, the effect of a standard course of these treatments on nAChR upregulation has not yet been reported. In the present study, 48 otherwise healthy smokers underwent positron emission tomography (PET) scanning with the radiotracer 2-FA (for labeling α4β2* nAChRs) before and after treatment with either cognitive-behavioral therapy, bupropion HCl, or pill placebo. Specific binding volume of distribution (VS/fP), a measure proportional to α4β2* nAChR density, was determined for regions known to have nAChR upregulation with smoking (prefrontal cortex, brainstem, and cerebellum). In the overall study sample, significant decreases in VS/fP were found for the prefrontal cortex, brainstem, and cerebellum of -20 (±35), -25 (±36), and -25 (±31)%, respectively, which represented movement of VS/fP values toward values found in non-smokers (mean 58.2% normalization of receptor levels). Participants who quit smoking had significantly greater reductions in VS/fP across regions than non-quitters, and correlations were found between reductions in cigarettes per day and decreases in VS/fP for brainstem and cerebellum, but there was no between-group effect of treatment type. Thus, smoking reduction and cessation with commonly used treatments (and pill placebo) lead to decreased α4β2* nAChR densities across brain regions. Study findings could prove useful in the treatment of smokers by providing encouragement with the knowledge that decreased smoking leads to normalization of specific brain receptors. PMID:23429692
A constant-density approach for incompressible multi-phase SPH
NASA Astrophysics Data System (ADS)
Hu, X. Y.; Adams, N. A.
2009-04-01
A constant-density approach, which corrects intermediate density errors by adjusting the half-time-step velocity with exact projection, is proposed for the multi-phase SPH method developed in our previous work [X.Y. Hu, N.A. Adams, An incompressible multi-phase SPH method, J. Comput. Phys. 227 (2007) 264-278]. As no prescribed reference pressure is required, the present approach introduces smaller numerical viscosity and allows to simulate flows with unprecedentedly high density ratios by the projection SPH method. Numerical examples for Taylor-Green flow, capillary waves and for Rayleigh-Taylor instability are presented and compared to theoretical solutions or references from the literature.
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, the higher was the error of estimated crown bottom height. Finally, the spatial distribution of points inside the tree crown was analyzed, by creating a normalized tree crown. It confirms a high concentration of LiDAR points inside the central part of a tree.
NASA Astrophysics Data System (ADS)
Podlipskas, Ž.; Aleksiejūnas, R.; Kadys, A.; Mickevičius, J.; Jurkevičius, J.; Tamulaitis, G.; Shur, M.; Shatalov, M.; Yang, J.; Gaska, R.
2016-04-01
Dynamics of radiative and nonradiative recombination of non-equilibrium carriers is investigated in thick AlGaN epitaxial layers with Al content ranging from 0.11 to 0.71. The internal quantum efficiency (IQE) in the epilayers was obtained using two approaches: either estimated from PL measurements or calculated using the recombination coefficients of a simple ABC model, retrieved by fitting the kinetics of light induced transient gratings (LITG). At photoexcited carrier densities below ~1019 cm-3, both approaches provided similar IQE values indicating that the simple ABC model is applicable to analyze carrier recombination at such carrier densities. The increase in IQE at higher carrier densities slowed down for the values extracted from PL considerably faster than for those obtained from LITG transients. This discrepancy is explained in terms of the mixed nature of the rate coefficient B caused by the onset of the density-activated nonradiative recombination at high carrier densities.
Hansen, M.J.; Beard, T.D., Jr.; 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.
THE COLUMN DENSITY VARIANCE IN TURBULENT INTERSTELLAR MEDIA: A FRACTAL MODEL APPROACH
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.
Two-electron Rabi oscillations in real-time time-dependent density-functional theory
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 S{sub 0} state and the doubly-excited S{sub 2} 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.
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.
Huntsman, Brock M.; Petty, J. Todd
2014-01-01
Spatial population models predict strong density-dependence and relatively stable population dynamics near the core of a species' distribution with increasing variance and importance of density-independent processes operating towards the population periphery. Using a 10-year data set and an information-theoretic approach, we tested a series of candidate models considering density-dependent and density-independent controls on brook trout population dynamics across a core-periphery distribution gradient within a central Appalachian watershed. We sampled seven sub-populations with study sites ranging in drainage area from 1.3–60 km2 and long-term average densities ranging from 0.335–0.006 trout/m. Modeled response variables included per capita population growth rate of young-of-the-year, adult, and total brook trout. We also quantified a stock-recruitment relationship for the headwater population and coefficients of variability in mean trout density for all sub-populations over time. Density-dependent regulation was prevalent throughout the study area regardless of stream size. However, density-independent temperature models carried substantial weight and likely reflect the effect of year-to-year variability in water temperature on trout dispersal between cold tributaries and warm main stems. Estimated adult carrying capacities decreased exponentially with increasing stream size from 0.24 trout/m in headwaters to 0.005 trout/m in the main stem. Finally, temporal variance in brook trout population size was lowest in the high-density headwater population, tended to peak in mid-sized streams and declined slightly in the largest streams with the lowest densities. Our results provide support for the hypothesis that local density-dependent processes have a strong control on brook trout dynamics across the entire distribution gradient. However, the mechanisms of regulation likely shift from competition for limited food and space in headwater streams to competition for thermal refugia in larger main stems. It also is likely that source-sink dynamics and dispersal from small headwater habitats may partially influence brook trout population dynamics in the main stem. PMID:24618602
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.
Size dependence of the surface charge density in EDL-MF
NASA Astrophysics Data System (ADS)
Tourinho, F. A.; Campos, A. F. C.; Aquino, R.; Lara, M. C. F. L.; Depeyrot, J.
2002-11-01
We determine the surface charge density of electric double layered magnetic fluids based on manganese ferrite nanoparticles of two different sizes using simultaneous potentiometric-conductimetric titrations. The saturation superficial density of charge is reduced for smaller particles.
The Dependency Structure of Coordinate Phrases: A Corpus Approach
ERIC Educational Resources Information Center
Temperley, David
2005-01-01
Hudson (1990) proposes that each conjunct in a coordinate phrase forms dependency relations with heads or dependents outside the coordinate phrase (the "multi-head" view). This proposal is tested through corpus analysis of Wall Street Journal text. For right-branching constituents (such as direct-object NPs), a short-long preference for conjunct…
Satija, Sushil K.; Mendez, Sergio; Balamurugan, Sreelatha S.; Balamurugan, Subramanian; Kent, Michael Stuart; Yim, Hyun; Lopez, Gabriel P.
2003-07-01
Poly(N-isopropylacrylamide) (PNIPAM) exhibits a lower critical solution temperature (LCST) of {approx}30 C in water that is attributed to alterations in the hydrogen-bonding interactions of the amide group. PNIPAM in various forms has been explored for a variety of applications including controlled drug delivery, solute separation, tissue culture substrates, and controlling the adsorption of proteins, blood cells, and bacteria. Grafting PNIPAM onto surfaces is a promising strategy for creating responsive surfaces, since the physical properties of PNIPAM are readily controlled by changing the temperature. Considerable effort has been devoted to studying variations in chain conformations with temperature (T) in PNIPAM-based materials. Kubota et al. studied conformational changes of PNIPAM free chains with temperature for molecular weights ranging from 1.63 x 10{sup 6} to 2.52 x 10{sup 7} g/mol (M{sub w}/M{sub n} > 1.3) in water using laser light scattering. They reported a decrease in the radius of gyration (R{sub g}) as the solution temperature increased above the LCST. The magnitude of the effect was more pronounced with increasing molecular weight, ranging up to a factor of two for the highest molecular weight sample. In a similar study, Wu et al. observed a decrease in R{sub g} of a factor of seven for a high molecular weight PNIPAM sample with very low polydispersity (M{sub w} = 1.3 x 10{sup 7} g/mol, M{sub w}/M{sub n} < 1.05). Regarding grafted PNIPAM chains, Kidoaki et al. recently employed an iniferter-based graft polymerization method to generate a dense, high molecular weight brush and reported changes in the thickness measured by AFM. The thickness of the grafted layer was obtained from AFM images of the boundary between grafted and nongrafted (ablated by laser light) regions. They found that the swollen film thickness decreased by a factor of {approx}2 with increasing temperature from 25 to 40 C for samples with a range of dry film thickness from 250 to 1500 {angstrom}. More recently, Balamurugan et al. used surface plasmon resonance (SPR) to probe conformational changes in a PNIPAM brush grafted onto a gold layer by atom transfer radical polymerization (ATRP). For a sample with a dry film thickness of 517 {angstrom}, the SPR measurements indicated a significant contraction (extension of the layer with increasing/decreasing) temperature through the transition. Quantification of the change in profile characteristics was not reported, but it was noted that the change in the SPR signal occurred over a much broader range of temperature (15-35 C) than is typical of the transition for free chains in bulk solution. No systematic study of detailed PNIPAM chain conformations has yet been reported as a function of the two critical brush parameters, the surface density and molecular weight. A recent theoretical analysis by Baulin and Halperin has identified the surface density as a critical parameter demarcating different regimes of behavior. This arises from the concentration dependence of the Flory {chi} parameter as obtained from a recent phase behavior study of free chains in solution. Little attention has been paid to the surface density in previous experimental studies of grafted PNIPAM chains. We have begun a systematic study of the temperature-dependent conformational changes of PNIPAM grafted chains in water as a function of surface density and molecular weight using neutron reflection (NR). In previous work, we investigated the conformational changes of PNIPAM chains tethered to silicon oxide using two methods. The first was the 'grafting from' method in which N-isopropylacrylamide monomers were polymerized from the silicon surface with a chain transfer, free-radical technique. In the second method, preformed PNIPAM chains with carboxylic acid end groups associated with terminal hydroxyl groups of a mixed self-assembling monolayer. Detailed concentration profiles of the PNIPAM brushes were determined in D{sub 2}O as a function of temperature and also in d-acetone at room temperature. Profiles were obtained in the two solvents in order to investigate the role of the solvent in mediating interactions. The profiles in D{sub 2}O were bilayers, composed of a very thin layer with higher concentration at the surface and a low concentration layer extending well into the subphase. The very thin, higher concentration surface layer was attributed to attractive segment-surface interactions. The profiles in acetone were smoothly decaying single-layer profiles. The low segment concentration at the surface in acetone indicated that the surface density of these brushes was rather low. The dry film thicknesses were less than 40 {angstrom}, much lower than in the study of Kidoaki et al. On the basis of the molecular weights and dry film thicknesses, the surface density ({sigma}, chains/{angstrom}{sup 2}) ranged from 1 x 10{sup -4} to 2 x 10{sup -4} for those samples.
NASA Astrophysics Data System (ADS)
Horie, Masanobu; Sakurai, Tatsunari; Kitahata, Hiroyuki
2016-01-01
We investigated the phase-response curve of a coupled system of density oscillators with an analytical approach. The behaviors of two-, three-, and four-coupled systems seen in the experiments were reproduced by the model considering the phase-response curve. Especially in a four-coupled system, the clustering state and its incidence rate as functions of the coupling strength are well reproduced with this approach. Moreover, we confirmed that the shape of the phase-response curve we obtained analytically was close to that observed in the experiment where a perturbation is added to a single-density oscillator. We expect that this approach to obtaining the phase-response curve is general in the sense that it could be applied to coupled systems of other oscillators such as electrical-circuit oscillators, metronomes, and so on.
Optical Rotation Calculated with Time-Dependent Density Functional Theory: The OR45 Benchmark
Srebro, Monika; Govind, Niranjan; De Jong, Wibe A.; Autschbach, Jochen
2011-10-13
Time-dependent density functional theory (TDDFT) computations are performed for 42 organic molecules and 3 transition metal complexes, with experimental molar optical rotations ranging from 2 to 2 x 10{sup 4} deg cm{sup 2} dmol{sup -1}. The performance of the global hybrid functionals B3LYP, PBE0, and BHLYP, and of the range-separated functionals CAM-B3LYP and LR-PBE0 (the latter being fully long-range corrected), are investigated. The performance of different basis sets is studied. When compared to liquid-phase experimental data, the range-separated functionals do, on average, not perform better than B3LYP and PBE0. Median relative deviations between calculations and experiment range from 25 to 29%. A basis set recently proposed for optical rotation calculations (LPol-ds) on average does not give improved results compared to aug-cc-pVDZ in TDDFT calculations with B3LYP. Individual cases are discussed in some detail, among them norbornenone for which the LR-PBE0 functional produced an optical rotation that is close to available data from coupled-cluster calculations, but significantly smaller in magnitude than the liquid-phase experimental value. Range-separated functionals and BHLYP perform well for helicenes and helicene derivatives. Metal complexes pose a challenge to first-principles calculations of optical rotation.
Krawczyk, Przemysław
2015-05-01
The absorption and emission spectra of three azo sulfonamide compounds in different solvents were investigated theoretically by using response functions combined with density functional theory (DFT), while the solvent effect on the structure and the electronic transitions was determined using the integral equation formalism for the polarizable continuum model (IEF-PCM). The results show that the applied different exchange-correlation functionals can reproduce the experimental values well. DFT calculations of the title compounds showed that the H-bond formed between the solute and solvent molecules is one of the major causes of the reversible solvatochromism observed in measured spectra. This is due to a better stabilization of the neutral form than the zwitterionic form in the polar protic solvents, which is characteristic of the hypsochromic shift. On the other hand, the molecules considered exhibit a monotonic behavior regarding the polarity of the low-lying excited state (Δμg-CT) as a function of the solvent polarity. This dependence occurs in the case of the positive solvatochromism and confirms the thesis regarding the H-bond solute-solvent interactions. Theoretically determined values of the two-photon cross section revealed that the (σOF(2)) shows similar trends with changes in λabs, in contrast to <δ(OF)> values. In conclusion, the results demonstrate that the investigated molecules can be used successfully as fluorochromes in bioimaging. PMID:25877526
Delineating effects of tensor force on the density dependence of nuclear symmetry energy
NASA Astrophysics Data System (ADS)
Xu, Chang; Li, Ang; Li, Bao-An
2013-03-01
In this talk, we report results of our recent studies to delineate effects of the tensor force on the density dependence of nuclear symmetry energy within phenomenological models. The tensor force active in the isosinglet neutron roton interaction channel leads to appreciable depletion/population of nucleons below/above the Fermi surface in the single-nucleon momentum distribution in cold symmetric nuclear matter (SNM). We found that as a consequence of the high momentum tail in SNM the kinetic part of the symmetry energy Ekinsym(ρ) is significantly below the well-known Fermi gas model prediction of approximately 125(ρ/ρ0)2/3. With about 15% nucleons in the high momentum tail as indicated by the recent experiments at J-Lab by the CLAS Collaboration, the Ekinsym(ρ) is negligibly small. It even becomes negative when more nucleons are in the high momentum tail in SNM. These features have recently been confirmed by three independent studies based on the state-of-the-art microscopic nuclear many-body theories. In addition, we also estimate the second-order tensor force contribution to the potential part of the symmetry energy. Implications of these findings in extracting information about nuclear symmetry energy from nuclear reactions are discussed briefly.
Stenseth, N. C.; rnstad, O. N. Bj; Falck, W.; Fromentin, J.-M.; ter, J. Gj s; Gray, J. S.
1999-01-01
Skagerrak populations of Atlantic cod (Gadus morhua L.) have been surveyed at several fixed stations since 1919. These coastal populations consist of local stocks with a low age of maturity and a short life span. We investigated 60 time-series of 0-group juveniles (i.e. young of the year) sampled annually from 1945 to 1994. An age-structured model was developed which incorporates asymmetrical interactions between the juvenile cohorts (0-group and 1-group; i.e. one-year-old juveniles) and stochastic reproduction. The model was expressed in delay coordinates in order to estimate model parameters directly from the time-series and thereby test the model predictions. The autocovariance structure of the time-series was consistent with the delay coordinates model superimposed upon a long-term trend. The model illustrates how both regulatory (density-dependent) and disruptive (stochastic) forces are crucial in shaping the dynamics of the coastal cod populations. The age-structured life cycle acts to resonance the stochasticity inherent in the recruitment process.
Optical rotation calculated with time-dependent density functional theory: the OR45 benchmark.
Srebro, Monika; Govind, Niranjan; de Jong, Wibe A; Autschbach, Jochen
2011-10-13
Time-dependent density functional theory (TDDFT) computations are performed for 42 organic molecules and three transition metal complexes, with experimental molar optical rotations ranging from 2 to 2 × 10(4) deg cm(2) dmol(-1). The performances of the global hybrid functionals B3LYP, PBE0, and BHLYP, and of the range-separated functionals CAM-B3LYP and LC-PBE0 (the latter being fully long-range corrected), are investigated. The performance of different basis sets is studied. When compared to liquid-phase experimental data, the range-separated functionals do, on average, not perform better than B3LYP and PBE0. Median relative deviations between calculations and experiment range from 25 to 29%. A basis set recently proposed for optical rotation calculations (LPol-ds) on average does not give improved results compared to aug-cc-pVDZ in TDDFT calculations with B3LYP. Individual cases are discussed in some detail, among them norbornenone for which the LC-PBE0 functional produced an optical rotation that is close to available data from coupled-cluster calculations, but significantly smaller in magnitude than the liquid-phase experimental value. Range-separated functionals and BHLYP perform well for helicenes and helicene derivatives. Metal complexes pose a challenge to first-principles calculations of optical rotation. PMID:21827151
Density Dependent Strong Coupling Constant of QCD Derived from Compact Star Data
NASA Astrophysics Data System (ADS)
Ray, Subharthi; Dey, Jishnu; Dey, Mira
Since 1996 there is major influx of X-ray and ?-ray data from binary stars, one or both of which are compact objects that are difficult to explain as neutron stars since they contain a mass M in too small a radius R. The suggestion has been put forward that these are strange quark stars (SS) explainable in a simple model with chiral symmetry restoration (CSR) for the quarks and the M, R and other properties like QPOs (quasi-periodic oscillations) in their X-ray power spectrum. It would be nice if this astrophysical data could shed some light on fundamental properties of quarks obeying QCD. One can relate the strong coupling constant of QCD, ?s to the quark mass through the Dyson-Schwinger gap equation using the real time formalism of Dolan and Jackiw. This enables us to obtain the density dependence of ?s from the simple CSR referred to above. This way fundamental physics, difficult to extract from other models like for example lattice QCD, can be constrained from present-day compact star data and may be put back to modeling the dense quark phase of early universe.
Shell structure and {rho}-tensor correlations in density dependent relativistic Hartree-Fock theory
Long Wenhui; Sagawa, Hiroyuki; Giai, Nguyen Van; Meng Jie
2007-09-15
A new effective interaction PKA1 with {rho}-tensor couplings for the density dependent relativistic Hartree-Fock (DDRHF) theory is presented. It is obtained by fitting selected empirical ground state and shell structure properties. It provides satisfactory descriptions of nuclear matter and the ground state properties of finite nuclei at the same quantitative level as recent DDRHF and relativistic mean field (RMF) models. Significant improvement in the single-particle spectra is also found due to the inclusion of {rho}-tensor couplings. As a result, PKA1 cures a common disease of the existing DDRHF and RMF Lagrangians, namely, the artificial shells at 58 and 92, and recovers the realistic subshell closure at 64. Moreover, the proper spin-orbit splittings and well-conserved pseudospin symmetry are obtained with the new effective interaction PKA1. Due to the extra binding introduced by the {rho}-tensor correlations, the balance between the nuclear attractions and the repulsions is changed, and this constitutes the physical reason for the improvement of the nuclear shell structure.
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.
Trajectory-based nonadiabatic dynamics with time-dependent density functional theory.
Curchod, Basile F E; Rothlisberger, Ursula; Tavernelli, Ivano
2013-05-10
Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecular machines, the control of photochemical reactions, and the possibility of capturing sunlight energy. However, many challenging conceptual and technical problems are involved in the description of these phenomena such as 1) the failure of the well-known Born-Oppenheimer approximation; 2) the need for accurate electronic properties such as potential energy surfaces, excited nuclear forces, or nonadiabatic coupling terms; and 3) the necessity of describing the dynamics of the photoexcited nuclear wavepacket. This review provides an overview of the current methods to address points 1) and 3) and shows how time-dependent density functional theory (TDDFT) and its linear-response extension can be used for point 2). First, the derivation of Ehrenfest dynamics and nonadiabatic Bohmian dynamics is discussed and linked to Tully's trajectory surface hopping. Second, the coupling of these trajectory-based nonadiabatic schemes with TDDFT is described in detail with special emphasis on the derivation of the required electronic structure properties. PMID:23